ORCID Profile
0000-0001-5188-7957
Current Organisations
Università Cattolica del Sacro Cuore
,
University of Adelaide
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Publications
Alloreactive T‐cell recognition of bovine major histocompatibility complex class II products defined by one‐dimensional isoelectric focusing
Publisher: Wiley
Date: 04-1992
Sequence variation in the bovine and ovine PRNP genes
Publisher: Wiley
Date: 19-05-2003
DOI: 10.1046/J.1365-2052.2003.00977.X
Abstract: A resequencing approach was adopted to identify sequence variants in the PRNP gene that may affect susceptibility or resistance to bovine spongiform encephalopathy. The entire PRNP gene (>21 kb) was sequenced from 26 chromosomes from a group of Holstein-Friesian cows, as well as exon 3 of PRNP (>4 kb) from a further 24 chromosomes from six erse breeds. We identified 51 variant sequences of which 42 were single nucleotide polymorphisms and nine were insertion/deletion (indel) events. The study was extended to exon 3 of the sheep PRNP gene where 23 sequence variants were observed, four of which were indels. The level of nucleotide ersity in the complete bovine PRNP gene was pi = 0.00079, which is similar to that found at the bovine T-cell receptor alpha delta joining region (pi = 0.00077), but somewhat less than that observed for the bovine leptin (pi = 0.00265). Sequence variation within exon 3 of PRNP in both cattle (pi = 0.00102) and sheep (pi = 0.00171) was greater than that for the complete PRNP gene, with sheep showing greater sequence variation in exon 3 than cattle. The level of sequence variation reported here is greater than previously thought for the bovine PRNP gene in cattle. This study highlights the contribution that recombination plays in increasing allelic ersity in this species.
Genetic Control of Meat Quality Traits
Publisher: Springer New York
Date: 2008
New insights into mammalian sex chromosome structure and evolution using high-quality sequences from bovine X and Y chromosomes
Publisher: Springer Science and Business Media LLC
Date: 12-2019
DOI: 10.1186/S12864-019-6364-Z
Abstract: Mammalian X chromosomes are mainly euchromatic with a similar size and structure among species whereas Y chromosomes are smaller, have undergone substantial evolutionary changes and accumulated male specific genes and genes involved in sex determination. The pseudoautosomal region (PAR) is conserved on the X and Y and pair during meiosis. The structure, evolution and function of mammalian sex chromosomes, particularly the Y chromsome, is still poorly understood because few species have high quality sex chromosome assemblies. Here we report the first bovine sex chromosome assemblies that include the complete PAR spanning 6.84 Mb and three Y chromosome X-degenerate (X-d) regions. The PAR comprises 31 genes, including genes that are missing from the X chromosome in current cattle, sheep and goat reference genomes. Twenty-nine PAR genes are single-copy genes and two are multi-copy gene families, OBP, which has 3 copies and BDA20, which has 4 copies. The Y chromosome X-d1, 2a and 2b regions contain 11, 2 and 2 gametologs, respectively. The ruminant PAR comprises 31 genes and is similar to the PAR of pig and dog but extends further than those of human and horse. Differences in the pseudoautosomal boundaries are consistent with evolutionary ergence times. A bovidae-specific expansion of members of the lipocalin gene family in the PAR reported here, may affect immune-modulation and anti-inflammatory responses in ruminants. Comparison of the X-d regions of Y chromosomes across species revealed that five of the X-Y gametologs, which are known to be global regulators of gene activity and candidate sexual dimorphism genes, are conserved.
Polymorphisms within the Toll-Like Receptor (TLR)-2, -4, and -6 Genes in Cattle
Publisher: MDPI AG
Date: 30-07-2009
DOI: 10.3390/D1010007
Meta-analysis of two genome-wide association studies of bovine paratuberculosis.
Publisher: Public Library of Science (PLoS)
Date: 02-03-2012
Relationship between collagen characteristics, lipid content and raw and cooked texture of meat from young bulls of fifteen European breeds
Publisher: Elsevier BV
Date: 2011
DOI: 10.1016/J.MEATSCI.2010.09.003
Abstract: Variations in texture were determined for 10 day aged raw and cooked Longissimus thoracis (LT) muscle from 436 bulls of 15 European cattle breeds slaughtered at an age of 13-16 months. Variations in texture were related to differences in pH 24 h post-mortem, sarcomere length, collagen characteristics and lipid content. The shear force of cooked meat s les varied from 43.8 to 67.4 N/cm². Simmental, Highland and Marchigiana cattle had the highest shear force values and Avileña-Negra Ibérica, Charolais, Casina and Pirenaica cattle had the lowest values. Cooked meat toughness showed a weak negative correlation to lipid content (P<0.001) but no correlation to collagen characteristics. Raw meat texture measured by compression correlated positively (P<0.001) with total and insoluble collagen. In conclusion, collagen characteristics showed correlation to raw meat texture but not to cooked meat toughness of LT muscle in European young bulls.
Johne's disease in cattle: an in vitro model to study early response to infection of Mycobacterium avium subsp. paratuberculosis using RNA-seq.
Publisher: Elsevier BV
Date: 11-2017
DOI: 10.1016/J.MOLIMM.2017.08.017
Abstract: Johne's disease is a chronic granulomatous enteritis caused by Mycobacterium avium subsp. paratubercolosis (MAP) which affects ruminants worldwide and has a significant economic impact. MAP has also been associated with human Crohn's disease, although this connection is not well established. MAP is highly adapted for survival within host macrophages and prevents macrophage activation, blocks phagosome acidification and maturation, and attenuates presentation of antigens to the immune system. The consequence is a very long silent infection before clinical signs are observed. The present work examined the transcriptome of bovine monocyte-derived macrophages (MDM) infected with the L1 strain of MAP at 2h, 6h and 24h post infection using RNA-seq. Pathway over-representation analysis of genes differentially expressed between infected vs. control MDM identified that immune related pathways were affected. Genes belonging to the cytokine-cytokine receptor interaction pathway and members of the JAK-STAT pathway, which is involved in the regulation of immune response, were up-regulated. However, in parallel inhibitors of immune functions were activated, including suppressor of cytokine signaling (SOCS) and cytokine-inducible SH2-containing protein (CISH), which most likely suppresses IFNγ and the JAK/STAT signaling cascade in infected MDM, which may favour MAP survival. After exposure, macrophages phagocytise pathogens, activate the complement cascade and the adaptive immune system through the antigen presentation process. However, data presented here suggest that genes related to phagocytosis and lysosome function are down regulated in MAP infected MDM. Genes of MHC class II and complement pathway were also down-regulated. This study therefore shows that MAP infection is associated with changes in expression of genes related to the host immune response that may affect its ability to survive and multiply inside the host cell.
The other side of comparative genomics: genes with no orthologs between the cow and other mammalian species
Publisher: Springer Science and Business Media LLC
Date: 2009
1D‐IEF analysis of BoLA class I expression using allo‐antisera reveals additional complexity
Publisher: Wiley
Date: 12-1993
DOI: 10.1111/J.1365-2052.1993.TB00356.X
Abstract: The use of the bovine allo-antisera in lymphocyte microcytotoxicity assays suggests that there is a single highly polymorphic class I product expressed by the BoLA system encoded by one locus. In contrast, biochemical techniques, such as 1D-IEF, reveal a complex pattern of bands for BoLA class I molecules from each animal. In order to understand the origins of this heterogeneity bovine allo-antisera were used in the immunoprecipitation step of 1D-IEF and the results compared with those from immunoprecipitation using the monoclonal antibody W6/32. By modifying existing protocols to include Gammabind G a range of bovine allo-antisera were used successfully to immunoprecipitate bovine MHC class I molecules. The results indicate that the bovine allo-antisera do not recognize all molecules previously assigned to BoLA class I serotypes by 1D-IEF. Furthermore, some of the allo-antisera immunoprecipitated molecules are not recognized by W6/32 and vice versa. This suggests that more than one polymorphic locus is expressed from the bovine MHC and that each allo-antiserum recognizes molecules encoded by different loci. Examination of the results also suggests the existence of linkage disequilibrium in the BoLA class I region.
Physical and linkage mapping of mammary-derived expressed sequence tags in cattle.
Publisher: Elsevier BV
Date: 2004
DOI: 10.1016/S0888-7543(03)00218-0
Abstract: This study describes the physical and linkage mapping of 42 gene-associated markers developed from mammary gland-derived expressed sequence tags to the cattle genome. Of the markers, 25 were placed on the USDA reference linkage map and 37 were positioned on the Roslin 3000-rad radiation hybrid (RH) map, with 20 assignments shared between the maps. Although no novel regions of conserved synteny between the cattle and the human genomes were identified, the coverage was extended for bovine chromosomes 3, 7, 15, and 29 compared with previously published comparative maps between human and bovine genomes. Overall, these data improve the resolution of the human-bovine comparative maps and will assist future efforts to integrate bovine RH and linkage map data.
Identification of a female-sterile mutation affecting yolk protein 2 in Drosophila melanogaster
Publisher: Springer Science and Business Media LLC
Date: 09-1987
DOI: 10.1007/BF00329666
Associations between the 11‐bp deletion in the myostatin gene and carcass quality in Angus‐sired cattle
Publisher: Wiley
Date: 19-01-2009
DOI: 10.1111/J.1365-2052.2008.01790.X
Abstract: An 11-bp deletion in the bovine myostatin (MSTN) gene was identified as the causative mutation for the double-muscling phenotype in Belgian Blue and Asturiana cattle. More recently, this mutation was also identified in the South Devon breed of cattle, in which it has been found to be associated with a general increase in muscle mass. The present study found that the mutant allele was also segregating in a commercial population of Scottish Aberdeen Angus beef cattle. The mutation was found at a low frequency (0.04) with no animals homozygous for the mutation in the s le population (536 animals). The effects of this mutation on various carcass traits of economic interest were then tested. We found that the mutation significantly increased carcass weight, sirloin weight, hindquarter weight, muscle conformation score and eye muscle area, but had no effect on the fat traits.
Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C
Publisher: Springer Science and Business Media LLC
Date: 28-04-2021
DOI: 10.1038/S41467-020-20536-Y
Abstract: Haplotype-resolved genome assemblies are important for understanding how combinations of variants impact phenotypes. To date, these assemblies have been best created with complex protocols, such as cultured cells that contain a single-haplotype (haploid) genome, single cells where haplotypes are separated, or co-sequencing of parental genomes in a trio-based approach. These approaches are impractical in most situations. To address this issue, we present FALCON-Phase, a phasing tool that uses ultra-long-range Hi-C chromatin interaction data to extend phase blocks of partially-phased diploid assembles to chromosome or scaffold scale. FALCON-Phase uses the inherent phasing information in Hi-C reads, skipping variant calling, and reduces the computational complexity of phasing. Our method is validated on three benchmark datasets generated as part of the Vertebrate Genomes Project (VGP), including human, cow, and zebra finch, for which high-quality, fully haplotype-resolved assemblies are available using the trio-based approach. FALCON-Phase is accurate without having parental data and performance is better in s les with higher heterozygosity. For cow and zebra finch the accuracy is 97% compared to 80–91% for human. FALCON-Phase is applicable to any draft assembly that contains long primary contigs and phased associate contigs.
Genome-wide analysis of DNA methylation in hypothalamus and ovary of Capra hircus
Publisher: Springer Science and Business Media LLC
Date: 23-06-2017
Cloning and radiation hybrid mapping of bovine toll-like receptor-4 (TLR-4) signaling molecules
Publisher: Elsevier BV
Date: 08-2006
DOI: 10.1016/J.VETIMM.2006.03.003
Abstract: Toll-like receptor (TLR)-4 is a transmembrane receptor for lipopolysaccharide, a highly pro-inflammatory component of the outer membrane of Gram-negative bacteria. To date, molecules of the TLR-4 signaling pathway have not been well characterized in cattle. The goal of this study was to clone and sequence the full-length coding regions of bovine genes involved in TLR-4 signaling including CASP8, IRAK1, LY96 (MD-2), TICAM2, TIRAP, TOLLIP and TRAF 6 and to position these genes, as well as MyD88 and TICAM1, on the bovine genome using radiation hybrid mapping. Results of this work indicate differences with a previously published bovine sequence for LY96 and a predicted sequence in the GenBank database for TIRAP based on the most recent assembly of the bovine genome. In addition, discrepancies between actual and predicted chromosomal map positions based on the Btau_2.0 genome assembly release were identified, although map positions were consistent with predicted locations based on the current bovine-human comparative map. Alignment of the bovine amino acid sequences with human and murine sequences showed a broad range in conservation, from 52 to 93%. Overall, this work should assist in the assembly and annotation of the bovine genome sequence, the identification of variations in genes critically involved in host innate immunity, and facilitate the study of TLR-4 signaling pathways in cattle.
Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity
Publisher: Springer Science and Business Media LLC
Date: 16-01-2019
DOI: 10.1038/S41467-018-08260-0
Abstract: Rapid innovation in sequencing technologies and improvement in assembly algorithms have enabled the creation of highly contiguous mammalian genomes. Here we report a chromosome-level assembly of the water buffalo ( Bubalus bubalis ) genome using single-molecule sequencing and chromatin conformation capture data. PacBio Sequel reads, with a mean length of 11.5 kb, helped to resolve repetitive elements and generate sequence contiguity. All five B. bubalis sub-metacentric chromosomes were correctly scaffolded with centromeres spanned. Although the index animal was partly inbred, 58% of the genome was haplotype-phased by FALCON-Unzip. This new reference genome improves the contig N50 of the previous short-read based buffalo assembly more than a thousand-fold and contains only 383 gaps. It surpasses the human and goat references in sequence contiguity and facilitates the annotation of hard to assemble gene clusters such as the major histocompatibility complex (MHC).
Responses of Bovine Innate Immunity to Mycobacterium avium subsp. paratuberculosis Infection Revealed by Changes in Gene Expression and Levels of MicroRNA
Publisher: Public Library of Science (PLoS)
Date: 19-10-2016
Assignment of the PRPH gene to bovine chromosome 5q1.4 by FISH and confirmation by RH mapping
Publisher: Wiley
Date: 29-10-2004
Assignment of the <i>MRPS35</i> gene to bovine chromosome 5q3.2→q3.4 by fluorescence in situ hybridization and confirmation by radiation hybrid mapping
Publisher: S. Karger AG
Date: 2005
DOI: 10.1159/000084215
A gene expression atlas of the domestic water buffalo (Bubalus bubalis)
Publisher: Frontiers Media SA
Date: 24-07-2019
A physical map of the bovine genome
Publisher: Springer Science and Business Media LLC
Date: 2007
Comparative mapping of the POLG gene to cattle chromosome 21q17→q22 by FISH and confirmation by RH mapping
Publisher: S. Karger AG
Date: 2002
DOI: 10.1159/000066595
Genetics of transmissible spongiform encephalopathy susceptibility and the search for surrogate markers for infection
Publisher: CSIRO Publishing
Date: 2004
DOI: 10.1071/EA03235
Abstract: The transmissible spongiform encephalopathy diseases are unusual in that they can be sporadic or infectious, and that the infectious agent does not contain nucleic acids. Instead, infectivity is associated with a modified host-encoded protein referred to as a prion. During the course of disease, host encoded prion protein (PrP) is converted from the normal cellular form, PrPC, to a disease form, PrPSC/BSE, which is highly resistant to degradation by heat or proteinases. The occurrence of the sporadic form of transmissible spongiform encephalopathy disease in humans, as well as susceptibility to infection in humans and some animal species has been correlated with particular alleles of the host PrP gene. Scrapie has been endemic in sheep populations in many countries for over 100 years, with no apparent adverse effects on human health, however the occurrence of bovine spongiform encephalopathy in the mid 1980s in the United Kingdom and subsequently other countries has stimulated interest in the transmissible spongiform encephalopathy diseases. Bovine spongiform encephalopathy seems to have arisen from the recycling of ruminant offals, although it is not clear whether bovine spongiform encephalopathy was already endemic in the cattle population and this practice simply increased the incidence, or if the disease was newly introduced to cattle by transmission of scrapie from sheep. A new form of Creutzfeldt-Jacob disease that bares all the hallmarks of bovine spongiform encephalopathy was recently described in humans, suggesting that it arose from consumption of bovine spongiform encephalopathy-infected beef. Subsequent studies have demonstrated that transmissible spongiform encephalopathy disease can be experimentally transmitted between species and has alerted us to the potential risk of allowing scrapie to remain in the sheep population. In the United Kingdom, the sheep population is being PrP-genotyped and breeding stock selected from animals with genotypes that have been shown to be more resistant to scrapie. However, the resistant sheep genotypes may still harbour disease. There is no convincing evidence for PrP genotypes in cattle that are resistant to bovine spongiform encephalopathy. Work in cattle and mice has shown that there are loci other than PrP that influence the host response to a transmissible spongiform encephalopathy challenge. In order to monitor, and ultimately control, transmissible spongiform encephalopathy diseases in livestock it is important to identify markers for infection that are robust, appear early in infection and can be measured in an easily obtained s le, such as blood. We have developed a bovine ‘non-redundant’ cDNA set from brain to allow expression profiling using macro- and micro array technology. The identities of genes represented the in the non-redundant cDNAs set were assigned by oligo-nucleotide fingerprinting and have been confirmed by sequencing. This non-redundant cDNA set has been used to create a bovine array that is being used to examine expression in tissues from cattle during a time course of experimental bovine spongiform encephalopathy infection in order to identify genes with expression profiles that are altered following infection. Such genes may provide surrogate markers to detect transmissible spongiform encephalopathy infection during the early stages of disease. Ultimately knowledge of such genes may suggest targets for pharmacological intervention to arrest the disease process before the onset of the major neurological damage associated with the terminal stage of the disease.
Genome-wide search for markers associated with bovine spongiform encephalopathy
Publisher: Springer Science and Business Media LLC
Date: 03-2002
A new mutation in the coding region of the bovine leptin gene associated with feed intake
Publisher: Wiley
Date: 18-09-2003
DOI: 10.1046/J.1365-2052.2003.01028.X
Abstract: An experimental cattle population was screened for polymorphisms in the leptin gene and five SNPs were found in the regions containing the coding sequences. The association of these polymorphisms with feed intake and fat-related traits was evaluated. The results suggest an association between a polymorphism in exon 2, described here for the first time, and feed intake. In iduals with genotype A/T at this position had 19% greater mean feed intake than in iduals with genotype A/A. There was also evidence for a link between leptin haplotypes and some fat-related traits.
Genomic structural differences between cattle and River Buffalo identified through comparative genomic and transcriptomic analysis
Publisher: Elsevier BV
Date: 08-2018
Predicting colostrum and calf blood components based on refractometry
Publisher: Cambridge University Press (CUP)
Date: 30-04-2021
DOI: 10.1017/S0022029921000340
Abstract: Provision of good quality colostrum is essential for the passive immunity and nutrition of newborn calves. In order to better predict the quality of colostrum and the transfer of passive immunity, the relationships between colostrum components and between calf serum components were examined in this study. S les of bulk tank milk, colostrum pooled from several cows 0–4 d postpartum, and colostrum collected from in idual cows twice daily for 3 d post-partum were compared. With the exception of fat percentage, there were strong correlations between the levels of the components in the pooled colostrum and in the in idual cow colostrum collected 0–1 d postpartum. The correlations between total solids as measured by Brix refractometry and total protein, immunoglobulin G (IgG), lactose % and protein % in colostrum within 1 d postpartum and pooled colostrum were 0.92, 0.90, −0.88 and 0.98, respectively. These high correlations enabled these colostrum components to be accurately predicted from Brix % and therefore, the volume of colostrum required to feed neonate calves can be optimised based on Brix refractometry to avoid failure of passive immunity transfer. To assess whether the components obtained from colostrum were correlated in calf blood, newborn calves were separated from their dams before suckling and blood s led before feeding (day 0), and on days 1 and 7, after receiving colostrum or milk twice a day. The correlations between glucose, total protein, IgG, and gamma-glutamyl transferase (GGT) levels in the calf blood were lower than the correlations observed between the colostrum components. The highest correlation was between serum protein measured by refractometer and serum IgG within one week postpartum. GGT activity was not a good indicator of serum IgG levels. However, serum protein refractometer measurements predicted serum IgG level with high accuracy, providing an on-farm test to determine that calves have received sufficient passive immunity and colostrum components.
Genetic Regulation of Biomarkers as Stress Proxies in Dairy Cows
Publisher: MDPI AG
Date: 06-04-2021
Abstract: Stress in livestock reduces productivity and is a welfare concern. At a physiological level, stress is associated with the activation of inflammatory responses and increased levels of harmful reactive oxygen species. Biomarkers that are indicative of stress could facilitate the identification of more stress-resilient animals. We examined twenty-one metabolic, immune response, and liver function biomarkers that have been associated with stress in 416 Italian Simmental and 436 Italian Holstein cows which were genotyped for 150K SNPs. Single-SNP and haplotype-based genome-wide association studies were carried out to assess whether the variation in the levels in these biomarkers is under genetic control and to identify the genomic loci involved. Significant associations were found for the plasma levels of ceruloplasmin (Bos taurus chromosome 1—BTA1), paraoxonase (BTA4) and γ-glutamyl transferase (BTA17) in the in idual breed analysis that coincided with the position of the genes coding for these proteins, suggesting that their expression is under cis-regulation. A meta-analysis of both breeds identified additional significant associations with paraoxonase on BTA 16 and 26. Finding genetic associations with variations in the levels of these biomarkers suggests that the selection for high or low levels of expression could be achieved rapidly. Whether the level of expression of the biomarkers correlates with the response to stressful situations has yet to be determined.
Landscape of copy number variations in Bos taurus: Individual - and inter-breed variability
Publisher: Springer Science and Business Media LLC
Date: 29-05-2018
Extended haplotype phasing of de novo genome assemblies with FALCON-Phase
Publisher: Cold Spring Harbor Laboratory
Date: 21-05-2018
DOI: 10.1101/327064
Abstract: Haplotype-resolved genome assemblies are important for understanding how combinations of variants impact phenotypes. These assemblies can be created in various ways, such as use of tissues that contain single-haplotype (haploid) genomes, or by co-sequencing of parental genomes, but these approaches can be impractical in many situations. We present FALCON-Phase, which integrates long-read sequencing data and ultra-long-range Hi-C chromatin interaction data of a diploid in idual to create high-quality, phased diploid genome assemblies. The method was evaluated by application to three datasets, including human, cattle, and zebra finch, for which high-quality, fully haplotype resolved assemblies were available for benchmarking. Phasing algorithm accuracy was affected by heterozygosity of the in idual sequenced, with higher accuracy for cattle and zebra finch ( %) compared to human (82%). In addition, scaffolding with the same Hi-C chromatin contact data resulted in phased chromosome-scale scaffolds.
On the Breeds of Cattle—Historic and Current Classifications
Publisher: MDPI AG
Date: 09-11-2011
DOI: 10.3390/D3040660
Abstract: Classification of cattle breeds contributes to our understanding of the history of cattle and is essential for an effective conservation of genetic ersity. Here we review the various classifications over the last two centuries and compare the most recent classifications with genetic data. The classifications devised during the 19th to the late 20th century were in line with the Linnaean taxonomy and emphasized cranial or horn morphology. Subsequent classifications were based on coat color, geographic origin or molecular markers. Several theories were developed that linked breed characteristics either to a supposed ancestral aurochs subspecies or to a presumed ethnic origin. Most of the older classifications have now been discarded, but have introduced several Latin terms that are still in use. The most consistent classification was proposed in 1995 by Felius and emphasizes the geographic origin of breeds. This is largely in agreement with the breed clusters indicated by a biochemical and molecular genetic analysis, which reflect either groups of breeds with a common geographic origin or single breeds that have expanded by export and/or crossbreeding. We propose that this information is also relevant for managing the genetic ersity of cattle.
Mapping and transcription profiling of CASP1, 3, 6, 7 and 8 in relation to caspase activity in the bovine cumulus-oocyte complex
Publisher: Wiley
Date: 16-04-2004
Near-Infrared Reflectance Spectroscopy for Predicting the Phospholipid Fraction and the Total Fatty Acid Composition of Freeze-Dried Beef
Publisher: MDPI AG
Date: 20-06-2021
DOI: 10.3390/S21124230
Abstract: Research on fatty acids (FA) is important because their intake is related to human health. NIRS can be a useful tool to estimate the FA of beef but due to the high moisture and the high absorbance of water makes it difficult to calibrate the analyses. This work evaluated near-infrared reflectance spectroscopy as a tool to assess the total fatty acid composition and the phospholipid fraction of fatty acids of beef using freeze-dried meat. An average of 22 unrelated pure breed young bulls from 15 European breeds were reared on a common concentrate-based diet. A total of 332 longissimus thoracis steaks were analysed for fatty acid composition and a freeze-dried s le was subjected to near-infrared spectral analysis. 220 s les (67%) were used as a calibration set with the remaining 110 (33%) being used for validation of the models obtained. There was a large variation in the total FA concentration across the animals giving a good data set for the analysis and whilst the coefficient of variation was nearly 68% for the monounsaturated FA it was only 27% for the polyunsaturated fatty acids (PUFA). PLS method was used to develop the prediction models. The models for the phospholipid fraction had a low R2p and high standard error, while models for neutral lipid had the best performance, in general. It was not possible to obtain a good prediction of many in idual PUFA concentrations being present at low concentrations and less variable than other FA. The best models were developed for Total FA, saturated FA, 9c18:1 and 16:1 with R2p greater than 0.76. This study indicates that NIRS is a feasible and useful tool for screening purposes and it has the potential to predict most of the FA of freeze-dried beef.
Genomic organization, comparative analysis, and genetic polymorphisms of the bovine and ovine prion Doppel genes (PRND)
Publisher: Springer Science and Business Media LLC
Date: 09-2001
DOI: 10.1007/S00335-001-2064-4
Abstract: The doppel protein (Dpl) is a prion-like protein encoded by the gene PRND, which has been found downstream of the prion gene, PRNP, in human and mouse. This paper describes the isolation and structural organization of the bovine and ovine PRND genes, which are composed of two exons compared with the three of human and mouse. Intergenic distances between PRNP and PRND were covered by means of long-range PCR and found to be 16.8 and 20 kb, in cattle and sheep respectively. The 5' and 3' untranslated regions (UTR) were analyzed to identify transcription regulatory sequences and compared with those from the PRND and PRNP sequences published for other species. Three polymorphisms (R50H, N110H, and R132Q) were revealed in the cattle coding region two synonymous substitutions (I12I, A26A) were found in sheep. None of the polymorphisms was significantly associated with either Bovine Spongiform Encephalopathy (BSE) in cattle or scrapie in sheep.
Simultaneous analysis of conformation and transcription of A and B groups of vitellogenin genes in male and female Xenopus daring primary and secondary activation by estrogen
Publisher: Oxford University Press (OUP)
Date: 1983
Abstract: In male Xenopus, primary estradiol administration results in noncoordinate activation in the liver of the A and B groups of vitellogenin genes, both as judged by transcription and DNase I sensitivity in isolated nuclei, B group genes being activated preferentially in the first 20 hr. Secondary induction in males or "primary" induction in females results in a coordinate and equal transcription of these two groups of genes. The elevated transcriptional activity following primary estrogen stimulation returns to low levels rapidly but the high DNase I sensitivity of these genes persists for 2-3 months. A non-coordinate activation of the A and B groups of vitellogenin genes is however re-established in response to a second administration of estradiol 8 months after primary stimulation of male Xenopus.
A genetically unique Chinese cattle population shows evidence of common ancestry with wild species when analysed with a reduced ascertainment bias SNP panel
Publisher: Public Library of Science (PLoS)
Date: 09-04-2020
Distinctive gene expression patterns and imprinting signatures revealed in reciprocal crosses between cattle sub-species
Publisher: Springer Science and Business Media LLC
Date: 03-06-2021
DOI: 10.1186/S12864-021-07667-2
Abstract: There are two genetically distinct subspecies of cattle, Bos taurus taurus and Bos taurus indicus, which arose from independent domestication events. The two types of cattle show substantial phenotypic differences, some of which emerge during fetal development and are reflected in birth outcomes, including birth weight. We explored gene expression profiles in the placenta and four fetal tissues at mid-gestation from one taurine ( Bos taurus taurus Angus) and one indicine ( Bos taurus indicus Brahman) breed and their reciprocal crosses. In total 120 s les were analysed from a pure taurine breed, an indicine breed and their reciprocal cross fetuses, which identified 6456 differentially expressed genes (DEGs) between the two pure breeds in at least one fetal tissue of which 110 genes were differentially expressed in all five tissues examined. DEGs shared across tissues were enriched for pathways related to immune and stress response functions. Only the liver had a substantial number of DEGs when reciprocal crossed were compared among which 310 DEGs were found to be in common with DEGs identified between purebred livers these DEGs were significantly enriched for metabolic process GO terms. Analysis of DEGs across purebred and crossbred tissues suggested an additive expression pattern for most genes, where both paternal and maternal alleles contributed to variation in gene expression levels. However, expression of 5% of DEGs in each tissue was consistent with parent of origin effects, with both paternal and maternal dominance effects identified. These data identify candidate genes potentially driving the tissue-specific differences between these taurine and indicine breeds and provide a biological insight into parental genome effects underlying phenotypic differences in bovine fetal development.
Assessing SNP markers for assigning individuals to cattle populations
Publisher: Wiley
Date: 19-01-2009
DOI: 10.1111/J.1365-2052.2008.01800.X
Abstract: The effectiveness of single nucleotide polymorphisms (SNPs) for the assignment of cattle to their source breeds was investigated by analysing a panel of 90 SNPs assayed on 24 European breeds. Breed assignment was performed by comparing the Bayesian and frequentist methods implemented in the STRUCTURE 2.2 and GENECLASS 2 software programs. The use of SNPs for the reallocation of known in iduals to their breeds of origin and the assignment of unknown in iduals was tested. In the reallocation tests, the methods implemented in STRUCTURE 2.2 performed better than those in GENECLASS 2, with 96% vs. 85% correct assignments respectively. In contrast, the methods implemented in GENECLASS 2 showed a greater correct assignment rate in allocating animals treated as unknowns to a reference dataset (62% vs. 51% and 80% vs. 65% in field tests 1 and 2 respectively). These results demonstrate that SNPs are suitable for the assignment of in iduals to reference breeds. The results also indicate that STRUCTURE 2.2 and GENECLASS 2 can be complementary tools to assess breed integrity and assignment. Our findings also stress the importance of a high-quality reference dataset in allocation studies.
Distribution of ncRNAs expression across hypothalamic-pituitary-gonadal axis in Capra hircus
Publisher: Springer Science and Business Media LLC
Date: 30-05-2018
Implications of miRNA expression pattern in bovine oocytes and follicular fluids for developmental competence
Publisher: Elsevier BV
Date: 03-2020
Microsatellite genotyping of medieval cattle from central italy suggests an old origin of chianina and romagnola cattle
Publisher: Frontiers Media SA
Date: 04-03-2015
Transfection, expression, and DNA sequence of a gene encoding a BoLA-A11 antigen
Publisher: Springer Science and Business Media LLC
Date: 02-1995
DOI: 10.1007/BF00172066
Differentiation of European cattle by AFLP fingerprinting
Publisher: Wiley
Date: 25-01-2007
DOI: 10.1111/J.1365-2052.2007.01554.X
Abstract: The Neolithic introduction of domestic cattle into Europe was followed by differential adaptation, selection, migration and genetic isolation, leading ultimately to the emergence of specialized breeds. We have studied the differentiation of European cattle by lified fragment length polymorphism (AFLP) fingerprinting. Combining AFLP data sets from two laboratories yielded 81 biallelic polymorphic markers scored in 19-22 in idual animals from 51 breeds. Model-based clustering differentiated Podolian cattle as well as French and Alpine breeds from other European cattle. AFLP genetic distances correlated well with microsatellite-based genetic distances calculated for the same breeds. However, the AFLP data emphasized the ergence of taurine and indicine cattle relative to the variation among European breeds and indicated an Eastern influence on Italian and Hungarian Podolian breeds. This probably reflects import from the East after the original introduction of domestic cattle into Europe. Our data suggest that Italian cattle breeds are relatively erse at the DNA sequence level.
Identification of additional loci associated with antibody response to Mycobacterium avium ssp. Paratuberculosis in cattle by GSEA–SNP analysis
Publisher: Springer Science and Business Media LLC
Date: 09-2017
DOI: 10.1007/S00335-017-9714-7
Abstract: Mycobacterium avium subsp. paratuberculosis: (MAP) causes a contagious chronic infection results in Johne's disease in a wide range of animal species, including cattle. Several genome-wide association studies (GWAS) have been carried out to identify loci putatively associated with MAP susceptibility by testing each marker separately and identifying SNPs that show a significant association with the phenotype, while SNP with modest effects are usually ignored. The objective of this study was to identify modest-effect genes associated with MAP susceptibility using a pathway-based approach. The Illumina BovineSNP50 BeadChip was used to genotype 966 Holstein cows, 483 positive and 483 negative for antibody response to MAP, data were then analyzed using novel SNP-based Gene Set Enrichment Analysis (GSEA-SNP) and validated with Adaptive Rank Truncated Product methodology. An allele-based test was carried out to estimate the statistical association for each marker with the phenotype, subsequently SNPs were mapped to the closest genes, considering for each gene the single variant with the highest value within a window of 50 kb, then pathway-statistics were tested using the GSEA-SNP method. The GO biological process "embryogenesis and morphogenesis" was most highly associated with antibody response to MAP. Within this pathway, five genes code for proteins which play a role in the immune defense relevant to response to bacterial infection. The immune response genes identified would not have been considered using a standard GWAS, thus demonstrating that the pathway approach can extend the interpretation of genome-wide association analyses and identify additional candidate genes for target traits.
Marker‐assisted conservation of European cattle breeds: an evaluation
Publisher: Wiley
Date: 18-09-2006
DOI: 10.1111/J.1365-2052.2006.01511.X
Abstract: Two methods have been developed for the assessment of conservation priorities on the basis of molecular markers. According to the Weitzman approach, contributions to genetic ersity are derived from genetic distances between populations. Alternatively, ersity within and across populations is optimized by minimizing marker-estimated kinships. We have applied, for the first time, both methods to a comprehensive data set of 69 European cattle breeds, including all cosmopolitan breeds and several local breeds, for which genotypes of 30 microsatellite markers in 25-50 animals per breed have been obtained. Both methods were used to calculate the gain in ersity if a breed was added to a set of nine non-endangered breeds. Weitzman-derived ersities were confounded by genetic drift in isolated populations, which dominates the genetic distances but does not necessarily increase the conservation value of a breed. Marker-estimated kinships across populations were less disturbed by genetic drift than the Weitzman ersities and assigned high conservation values to Mediterranean breeds, which indeed have genetic histories that differ from the non-endangered breeds. Prospects and limitations of marker-assisted decisions on conservation priorities are discussed.
A medium-density genetic linkage map of the bovine genome
Publisher: Springer Science and Business Media LLC
Date: 1997
Abstract: A cattle genetic linkage map was constructed which covers more than 95 percent of the bovine genome at medium density. Seven hundred and forty six DNA polymorphisms were genotyped in cattle families which comprise 347 in iduals in full sibling pedigrees. Seven hundred and three of the loci are linked to at least one other locus. All linkage groups are assigned to chromosomes, and all are orientated with regards to the centromere. There is little overall difference in the lengths of the bull and cow linkage maps although there are in idual differences between maps of chromosomes. One hundred and sixty polymorphisms are in or near genes, and the resultant genome-wide comparative analyses indicate that while there is greater conservation of synteny between cattle and humans compared with mice, the conservation of gene order between cattle and humans is much less than would be expected from the conservation of synteny. This map provides a basis for high-resolution mapping of the bovine genome with physical resources such as Yeast and Bacterial Artificial Chromosomes as well as providing the underpinning for the interpolation of information from the Human Genome Project.
Cosmid-derived markers anchoring the bovine genetic map to the physical map
Publisher: Springer Science and Business Media LLC
Date: 1997
Abstract: The mapping strategy for the bovine genome described in this paper uses large insert clones as a tool for physical mapping and as a source of highly polymorphic microsatellites for genetic typing, and was one objective of the BovMap Project funded by the European Union (UE). Eight-three cosmid and phage clones were characterized and used to physically anchor the linkage groups defining all the bovine autosomes and the X Chromosome (Chr). By combining physical and genetic mapping, clones described in this paper have led to the identification of the linkage groups corresponding to Chr 9, 12, 16, and 25. In addition, anchored loci from this study were used to orient the linkage groups corresponding to Chr 3, 7, 8, 9, 13, 16, 18, 19, and 28 as identified in previously published maps. Comparison of the estimated size of the physical and linkage maps suggests that the genetic length of the bovine genome may be around 4000 cM.
Mapping of Multiple Quantitative Trait Loci Affecting Bovine Spongiform Encephalopathy
Publisher: Oxford University Press (OUP)
Date: 08-2004
DOI: 10.1534/GENETICS.104.026401
Abstract: A whole-genome scan was conducted to map quantitative trait loci (QTL) for BSE resistance or susceptibility. Cows from four half-sib families were included and 173 microsatellite markers were used to construct a 2835-cM (Kosambi) linkage map covering 29 autosomes and the pseudoautosomal region of the sex chromosome. Interval mapping by linear regression was applied and extended to a multiple-QTL analysis approach that used identified QTL on other chromosomes as cofactors to increase mapping power. In the multiple-QTL analysis, two genome-wide significant QTL (BTA17 and X/Yps) and four genome-wide suggestive QTL (BTA1, 6, 13, and 19) were revealed. The QTL identified here using linkage analysis do not overlap with regions previously identified using TDT analysis. One factor that may explain the disparity between the results is that a more extensive data set was used in the present study. Furthermore, methodological differences between TDT and linkage analyses may affect the power of these approaches.
A comparative map of bovine chromosome 19 based on a combination of mapping on a bacterial artificial chromosome scaffold map, a whole genome radiation hybrid panel and the human draft sequence
Publisher: S. Karger AG
Date: 2003
DOI: 10.1159/000075721
Abstract: We have constructed a medium density physical map of bovine chromosome 19 using a combination of mapping loci on both a bovine bacterial artificial chromosome (BAC) scaffold map and a whole genome radiation hybrid (WGRH) panel. The resulting map contains 70 loci spanning the length of bovine chromosome 19. Three contiguous groups of BACs were identified on the basis of multiple loci mapping to in idual BAC clones. Bovine chromosome 19 was found in this study to be comprised almost entirely from regions of human chromosome 17, with a small region putatively assigned to human chromosome 10. Fourteen breakpoints between the bovine and human chromosomes were detected, with a possibility of five more based on ordering of the WGRH map.
Deinduction of transcription of Xenopus 74‐kDa albumin genes and destabilization of mRNA by estrogen in vivo and in hepatocyte cultures
Publisher: Wiley
Date: 02-1985
DOI: 10.1111/J.1432-1033.1985.TB08678.X
Abstract: The goal of this study is to explain the molecular basis of the marked deinduction of Xenopus albumin synthesis and secretion accompanying the activation of vitellogenin genes by estrogen. We have characterized by restriction analysis, DNA sequencing and hybrid-selected translation of mRNA, a cloned cDNA specifying the two 74-kDa albumins which constitute the predominant circulating form of albumin in Xenopus laevis. Using this recombinant DNA plasmid as a hybridization probe, we have determined the steady-state levels of albumin mRNA, the rate of transcription of the two 74-kDa albumin genes and the stability of the mRNA in male and female Xenopus hepatocytes in vivo and in primary cell cultures following estrogen treatment. In both whole liver and cultured hepatocytes estradiol caused a rapid drop in the steady-state levels of 74-kDa albumin mRNAs, which was reversed spontaneously in the continued presence of the hormone. The concentration of albumin mRNA was substantially higher in male than in female hepatocytes, the hormonal effect being more marked in male than in female hepatocytes. The decrease in steady-state levels of mRNA was anticipated in male hepatocytes by a 70% inhibition of rate of transcription of albumin genes within 2 h of exposure to estradiol, as measured by run-off transcription in liver nuclei isolated from animals treated in vivo or by determining the absolute transcription rate in cell cultures. In the latter the diminished transcription rate returned to normal within 12 h in the continued presence of the hormone. Estradiol caused a threefold destabilization of albumin mRNA in both male and female hepatocyte cultures to t 1/2 = 3 h and 2 h respectively. The combined effects on rate of or transcription and mRNA stability largely explain the changes in the steady-state levels of mRNA caused by hormone administration. Comparison of the kinetics of transcription rates of vitellogenin and albumin genes in vivo and in vitro reveals a striking reciprocity in the selective activation of the inducible genes and deinduction of the constitutively expressed genes at the early stages of response of Xenopus hepatocytes to estrogen.
Investigation of the genetic architecture of a bone carcass weight QTL on BTA6
Publisher: Wiley
Date: 27-02-2012
DOI: 10.1111/J.1365-2052.2012.02322.X
Abstract: A previous analysis of an F(2) /Backcross Charolais × Holstein cross population identified the presence of a highly significant QTL on chromosome 6 (BTA6) affecting the proportion of bone in the carcass. Two closely linked QTL affected birth weight (BW) and body length at birth (BBL). In this report, the marker density around the QTL on BTA6 was increased, adding four additional microsatellite markers across the chromosome and 46 SNPs within the target QTL confidence interval. Of the SNPs, 26 were in positional candidate genes and the remaining 20 provided an even distribution of markers in the target QTL region. As a bone-related trait, the sum of the bone weight for all the left fore- and hindquarter joints of the carcass was analysed. We also studied the BW and BBL. Analyses of the data substantially reduced the QTL confidence interval. No strong evidence was found that the QTL for the three traits studied are different, and we conclude that the results are consistent with a single pleiotropic QTL influencing the three traits, with the largest effects on the proportion of bone in the carcass. The analyses also suggest that none of the SNPs tested is the sole causative variant of the QTL effects. Specifically, the SNP in the NCAPG gene previously reported as a causal mutation for foetal growth and carcass traits in other cattle populations was excluded as the causal mutation for the QTL reported here. Polymorphisms located in other previously identified candidate genes including SPP1, ABCG2, IBSP, MEPE and PPARGC1A were also excluded. The results suggest that SNP51_BTA-119876 is the polymorphism in strongest linkage disequilibrium with the causal mutation(s). Further research is required to identify the causal variant(s) associated with this bone-related QTL.
Differential transcription of the bovine AMPD3 gene in single blastocysts cultured under various oxygen tensions
Publisher: Wiley
Date: 13-09-2004
Marker-assisted introgression of the Compact mutant myostatin allele Mstn Cmpt-dl1Abc into a mouse line with extreme growth effects on body composition and muscularity
Publisher: Hindawi Limited
Date: 12-2004
DOI: 10.1017/S0016672304007165
Abstract: Myostatin is a negative regulator of muscle growth and mutations in its gene lead to muscular hypertrophy and reduced fat. In cattle, this is seen in ‘double muscled’ breeds. We have used marker-assisted introgression to introduce a murine myostatin mutation, Mstn Cmpt-dl1Abc [ Compact ( C )], into an inbred line of mice (DUHi) that had been selected on body weight and had exceptional growth. Compared with homozygous wild-type mice, homozygous ( C / C ) mice of this line were ~4–5% lighter, had ~7–8% shorter tails, substantially increased muscle weights (e.g. quadriceps muscle in males was 59% heavier) and an increased ‘dressing percentage’ (~49% vs 39%), an indicator of overall muscularity. The weights of several organs (e.g. liver, kidney, heart and digestive tract) were significantly reduced, by 12–20%. Myostatin deficiency also resulted in drastic reductions of total body fat and of various fat depots, total body fat proportion falling from ~17·5% in wild-type animals of both sexes to 9·5% and 11·6% in homozygous ( C / C ) females and males, respectively. Males with a deficiency in myostatin had higher gains in muscle traits than females. Additionally, there was a strong distortion of the segregation ratio on the DUHi background. Of 838 genotyped pups from inter se matings 29%, 63% and 8% were homozygous wild type (+/+), heterozygous ( C /+) and homozygous ( C / C ), respectively, showing that Mstn Cmpt-dl1Abc has lower fitness on this background. This line, when congenic, will be a useful resource in gene expression studies and for finding modifying genes.
Assessment of AFLP® marker behaviour in enriching STS radiation hybrid maps
Publisher: Wiley
Date: 11-07-2008
DOI: 10.1111/J.1365-2052.2008.01747.X
Abstract: Radiation hybrid (RH) mapping provides a powerful tool to build high-resolution maps of genomes. Here, we demonstrate the use of the AFLP technique for high-throughput typing of RH cell lines. Cattle were used as the model species because an RH panel was available to investigate the behaviour of AFLP markers within the microsatellite- and STS-based maps of this species. A total of 747 AFLP markers were typed on the TM112 RH radiation panel and 651 of these were assigned by two-point analysis to the 29 bovine autosomes and sex chromosomes. AFLP markers were added to the 1222 microsatellite and STS markers that were included in earlier RH maps. Multipoint maps were constructed for seven ex le chromosomes, which retained 248 microsatellite and STS markers, and added 123 AFLP markers at LOD 4. The addition of the AFLP markers increased the number of markers by 42.1% and the map length by 10.4%. The AFLP markers showed lower retention frequency (RF) values than the STS markers. The comparison of RF values in AFLP markers and their corresponding AFLP-derived STSs demonstrated that the lower RF values were due to the lower detection sensitivity of the AFLP technique. Despite these differences, AFLP and AFLP-derived STS markers mapped to identical or similar positions. These results demonstrate that it is possible to merge AFLP and microsatellite markers in the same map. The application of AFLP technology could permit the rapid construction of RH maps in species for which extensive genome information and large numbers of SNP and microsatellite markers are not available.
Genome-Wide Scan Identifies Loci Associated with Classical BSE Occurrence
Publisher: Public Library of Science (PLoS)
Date: 04-11-2011
Genome assembly and transcriptome resource for river buffalo, Bubalus bubalis (2n = 50)
Publisher: No publisher found
Date: 2017
Elucidating the genetic basis of an oligogenic birth defect using whole genome sequence data in a non-model organism, Bubalus bubalis
Publisher: Springer Science and Business Media LLC
Date: 03-01-2017
DOI: 10.1038/SREP39719
Abstract: Recent strong selection for dairy traits in water buffalo has been associated with higher levels of inbreeding, leading to an increase in the prevalence of genetic diseases such as transverse hemimelia (TH), a congenital developmental abnormality characterized by absence of a variable distal portion of the hindlimbs. Limited genomic resources available for water buffalo required an original approach to identify genetic variants associated with the disease. The genomes of 4 bilateral and 7 unilateral affected cases and 14 controls were sequenced. A concordance analysis of SNPs and INDELs requiring homozygosity unique to all unilateral and bilateral cases revealed two genes, WNT7A and SMARCA4 , known to play a role in embryonic hindlimb development. Additionally, SNP alleles in NOTCH1 and RARB were homozygous exclusively in the bilateral cases, suggesting an oligogenic mode of inheritance. Homozygosity mapping by whole genome de novo assembly also supported oligogenic inheritance implicating 13 genes involved in hindlimb development in bilateral cases and 11 in unilateral cases. A genome-wide association study (GWAS) predicted additional modifier genes. Although our data show a complex inheritance of TH, we predict that homozygous variants in WNT7A and SMARCA4 are necessary for expression of TH and selection against these variants should eradicate TH.
Construction of bovine whole‐genome radiation hybrid and linkage maps using high‐throughput genotyping
Publisher: Wiley
Date: 15-02-2007
Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle
Publisher: Springer Science and Business Media LLC
Date: 29-04-2020
DOI: 10.1038/S41467-020-15848-Y
Abstract: Inbred animals were historically chosen for genome analysis to circumvent assembly issues caused by haplotype variation but this resulted in a composite of the two genomes. Here we report a haplotype-aware scaffolding and polishing pipeline which was used to create haplotype-resolved, chromosome-level genome assemblies of Angus (taurine) and Brahman (indicine) cattle subspecies from contigs generated by the trio binning method. These assemblies reveal structural and copy number variants that differentiate the subspecies and that variant detection is sensitive to the specific reference genome chosen. Six genes with immune related functions have additional copies in the indicine compared with taurine lineage and an indicus-specific extra copy of fatty acid desaturase is under positive selection. The haplotyped genomes also enable transcripts to be phased to detect allele-specific expression. This work exemplifies the value of haplotype-resolved genomes to better explore evolutionary and functional variations.
Expression of genes involved in the T cell signalling pathway in circulating immune cells of cattle 24months following oral challenge with Bovine Amyloidotic Spongiform Encephalopathy (BASE)
Publisher: Springer Science and Business Media LLC
Date: 09-05-2015
Dual Origins of Dairy Cattle Farming – Evidence from a Comprehensive Survey of European Y-Chromosomal Variation
Publisher: Public Library of Science (PLoS)
Date: 06-01-2011
Computational detection and experimental validation of segmental duplications and associated copy number variations in water buffalo (Bubalus bubalis)
Publisher: Springer Science and Business Media LLC
Date: 07-02-2019
DOI: 10.1007/S10142-019-00657-4
Abstract: Duplicated sequences are an important source of gene evolution and structural variation within mammalian genomes. Using a read depth approach based on next-generation sequencing, we performed a genome-wide analysis of segmental duplications (SDs) and associated copy number variations (CNVs) in the water buffalo (Bubalus bubalis). By aligning short reads of Olimpia (the reference water buffalo) to the UMD3.1 cattle genome, we identified 1,038 segmental duplications comprising 44.6 Mb (equivalent to ~1.73% of the cattle genome) of the autosomal and X chromosomal sequence in the buffalo genome. We experimentally validated 70.3% (71/101) of these duplications using fluorescent in situ hybridization. We also detected a total of 1,344 CNV regions across 14 additional water buffaloes, amounting to 59.8 Mb of variable sequence or the equivalent of 2.2% of the cattle genome. The CNV regions overlap 1,245 genes that are significantly enriched for specific biological functions including immune response, oxygen transport, sensory system and signal transduction. Additionally, we performed array Comparative Genomic Hybridization (aCGH) experiments using the 14 water buffaloes as test s les and Olimpia as the reference. Using a linear regression model, a high Pearson correlation (r = 0.781) was observed between the log
Integrative analysis of methylomic and transcriptomic data in fetal sheep muscle tissues in response to maternal diet during pregnancy
Publisher: Springer Science and Business Media LLC
Date: 06-02-2018
The distribution of runs of homozygosity in the genome of river and swamp buffaloes reveals a history of adaptation, migration and crossbred events
Publisher: Springer Science and Business Media LLC
Date: 27-02-2021
DOI: 10.1186/S12711-021-00616-3
Abstract: Water buffalo is one of the most important livestock species in the world. Two types of water buffalo exist: river buffalo ( Bubalus bubalis bubalis ) and sw buffalo ( Bubalus bubalis carabanensis ). The buffalo genome has been recently sequenced, and thus a new 90 K single nucleotide polymorphism (SNP) bead chip has been developed. In this study, we investigated the genomic population structure and the level of inbreeding of 185 river and 153 sw buffaloes using runs of homozygosity (ROH). Analyses were carried out jointly and separately for the two buffalo types. The SNP bead chip detected in sw about one-third of the SNPs identified in the river type. In total, 18,116 ROH were detected in the combined data set (17,784 SNPs), and 16,251 of these were unique. ROH were present in both buffalo types mostly detected (~ 59%) in sw buffalo. The number of ROH per animal was larger and genomic inbreeding was higher in sw than river buffalo. In the separated datasets (46,891 and 17,690 SNPs for river and sw type, respectively), 19,760 and 10,581 ROH were found in river and sw , respectively. The genes that map to the ROH islands are associated with the adaptation to the environment, fitness traits and reproduction. Analysis of ROH features in the genome of the two water buffalo types allowed their genomic characterization and highlighted differences between buffalo types and between breeds. A large ROH island on chromosome 2 was shared between river and sw buffaloes and contained genes that are involved in environmental adaptation and reproduction.
Genetic variation in the bovine myostatin gene in UK beef cattle: Allele frequencies and haplotype analysis in the South Devon
Publisher: Wiley
Date: 10-2000
DOI: 10.1046/J.1365-2052.2000.00521.X
Abstract: Work on Belgian Blue cattle revealed that an 11 base pair (bp) deletion within the bovine myostatin gene (GDF8) is associated with the double-muscled phenotype seen in this breed. Investigations focusing on other European breeds known to show double-muscling identified several mutations within the coding region of the gene associated with the double-muscled phenotype in different breeds. The number of mutations found suggest that myostatin is highly variable within beef cattle. Variations that alter the structure of the gene product such that the protein is inactivated are associated with the most pronounced form of double-muscling as seen in the Belgian Blue. However, other mutations may have a less extreme affect on muscle development. While overt double-muscling gives rise to a high incidence of dystocia (calving difficulty), it is possible that some variants may give enhanced muscling, but with limited calving problems. We describe sequence analysis of the myostatin gene in ten beef breeds commonly used in the UK and show that the 11-bp deletion responsible for double-muscling in the Belgian Blue is also present in the South Devon cattle population. Allele frequencies and haplotypes in the South Devon and a polymerase chain reaction (PCR) based test for the deletion are described. PCR lification across the deleted region provides a quick and effective test with clear identification of heterozygous in iduals. We discuss our results with regard to the effect of genotype on phenotype and differences observed between the Belgian Blue and the South Devon.
Chromosomal localization and molecular characterization of 53 cosmid-derived bovine microsatellites
Publisher: Springer Science and Business Media LLC
Date: 09-1995
DOI: 10.1007/BF00352370
Effects of the Compact Mutant Myostatin Allele Mstn Cmpt-dl1Abc Introgressed into a High Growth Mouse Line on Skeletal Muscle Cellularity
Publisher: Springer Science and Business Media LLC
Date: 04-2005
DOI: 10.1007/S10974-005-1099-7
Abstract: The murine myostatin mutation Mstn(Cmpt-dl1Abc) (Compact C) was introduced into an inbred mouse line with extreme growth (DUHi) by marker-assisted introgression. To study the allelic effects on muscle fibre hyperplasia and hypertrophy, myonuclear proliferation, protein accretion, capillary density, and muscle fibre metabolism, s les from M. rectus femoris (RF) and M. longissimus dorsi (LD) muscles of animals wild-type (+/+), heterozygous (C/+), and homozygous (C/C) for the Mstn(Cmpt-dl1Abc) allele were examined by histological and biochemical analyses. Homozygous C/C mice exhibited lower body (-12%) but higher muscle weights (+38%) than ++ mice. Total muscle fibre number was increased (+24%), whereas fibre size was not significantly affected. Protein and DNA concentrations and DNA:protein ratios as well as specific CK activity remained unchanged for higher mass muscle implying increases in the total contents of DNA and muscle specific protein. Fibre type distribution was markedly shifted to the white glycolytic muscle fibres (+16-17% units) at the expense of red oxidative fibres. Capillary density was substantially lower in C/C than in ++ mice as seen by lower number of capillaries per fibre (-35%) and larger fibre area per capillary (+77%). However, the Mstn(Cmpt-dl1Abc) allele was partially recessive in heterozygous C/+ mice for both fibre type frequencies and capillary density. The results show that hypermuscularity caused by mutations in the myostatin gene results from muscle fibre hyperplasia rather than hypertrophy, and from balanced increases in myonuclear proliferation and protein accretion. However, capillary supply is adversely affected and muscle metabolism shifted towards glycolysis, which could have negative consequences for physical fitness.
Phenotypic and genotypic background underlying variations in fatty acid composition and sensory parameters in European bovine breeds
Publisher: Springer Science and Business Media LLC
Date: 15-04-2014
Fine mapping1 of the bovine solute carrier family 25, member 4 (SLC25A4) gene to BTA27q14-q15 by fluorescence in situ hybridization and radiation hybrid mapping
Publisher: Wiley
Date: 08-2002
Discriminating among cattle breeds using genetic markers.
Publisher: Springer Science and Business Media LLC
Date: 06-1999
DOI: 10.1046/J.1365-2540.1999.00521.X
Abstract: Genetic markers provide a potentially powerful means of identifying the breed of in idual animals. In this study diallelic and microsatellite loci were compared for their efficiency in discriminating among cattle breeds. Data were simulated for seven European cattle breeds using allele frequencies estimated at 20 microsatellite and 30 diallelic markers. Animals were assigned to the breed for which their genotype had the highest probability, and the power of the method assessed by estimating the error rate or proportion of animals misclassified. The number of markers required for discriminating among pure, or both pure and crossbreed, animals was investigated using either randomly s led markers or markers selected on in idual error rate. The relationship between in idual marker variability and discriminatory power was also investigated. Microsatellite markers were found to be more powerful than diallelic markers for distinguishing among the breeds. The most discriminatory markers were those with the highest average heterozygosity and observed number of alleles. The number of markers needed to achieve a particular error rate could be reduced by selecting markers with the lowest in idual error rates. Discrimination among both crossbreeds and pure breeds required approximately three times as many markers as discrimination among pure breeds alone.
Sequencing, chromosomal mapping, and functional characterization of bovine FLICE-Like Inhibitory Protein <i>(FLIP)</i>
Publisher: S. Karger AG
Date: 03-11-2005
DOI: 10.1159/000087518
Abstract: FLICE-like inhibitory protein (FLIP) has been shown in both humans and mice to inhibit apoptosis and NF-ĸB activation induced by pro-inflammatory mediators. The activation of NF-ĸB and the induction of apoptosis are critical events in the pathogenesis of a variety of disease states in cattle, including mastitis. Since FLIP is known to moderate these events in other species, we mapped the bovine FLIP gene, sequenced bovine i FLIP /i cDNA, and characterized its expression in cultured primary bovine endothelial cells. Sequencing of bovine i FLIP /i revealed approximately 83, 74, and 68% amino acid sequence identity to its porcine, human, and murine orthologs, respectively. Bovine i FLIP /i was mapped to chromosome 2 by radiation hybrid mapping. Interestingly the region to which bovine i FLIP /i maps contains a putative quantitative trait locus for functional herd life which is an indicator of a cow’s ability to survive involuntary culling due primarily to mastitis and infertility. In addition to sequencing and mapping, the function of bovine FLIP was studied. Over-expression of bovine FLIP protected against bacterial lipopolysaccharide (LPS)- and TNF-α-induced apoptosis in bovine endothelial cells consistent with previous studies of human FLIP. In addition, elevated expression of bovine FLIP blocked LPS- and TNF-α-induced upregulation of NF-ĸB-dependent gene products as assayed by E-selectin expression. Only the full-length bovine FLIP protein could inhibit NF-ĸB activation induced by LPS, whereas the death effector domain region alone was able to inhibit TNF-α-induced NF-ĸB activation. Together, these data demonstrate the conservation of FLIP’s ability to inhibit apoptosis and to downregulate NF-ĸB activation across species.
Assignment of the bovine TYK2 and PDE4A genes to bovine chromosome 7q15 by fluorescence in situ hybridization and radiation hybrid mapping
Publisher: S. Karger AG
Date: 13-12-2005
DOI: 10.1159/000081540
Comparative mapping of bovine chromosome 27 with human chromosome 8 near a dairy form QTL in cattle
Publisher: S. Karger AG
Date: 03-11-2005
DOI: 10.1159/000087519
Abstract: In the absence of a complete and annotated bovine genome sequence, detailed human-bovine comparative maps are one of the most effective tools for identification of positional candidate genes contributing to quantitative trait loci (QTL) in cattle. In the present study, eight genes from human chromosome 8 were selected for mapping in cattle to improve breakpoint resolution and confirm gene order on the comparative map near the 40 cM region of the BTA27 linkage map where a QTL affecting dairy form had previously been identified. The resulting map identified i ADRB3 /i as a positional candidate gene for the QTL contributing to the dairy form trait based on its estimated position between 40 and 45 cM on the linkage map. It is also a functional candidate gene due to its role in fat metabolism, and polymorphisms in the i ADRB3 /i gene associated with obesity and metabolic disease in humans, as well as, carcass fat in sheep. Further studies are underway to investigate the existence of polymorphisms in the bovine i ADRB3 /i gene and their association with traits related to fat deposition in cattle.
Joint Analysis of Quantitative Trait Loci for Clinical Mastitis and Somatic Cell Score on Five Chromosomes in Three Nordic Dairy Cattle Breeds
Publisher: American Dairy Science Association
Date: 11-2007
Abstract: Five chromosomes were selected for joint quantitative trait loci (QTL) analyses for clinical mastitis (CM) and somatic cell score (SCS) in 3 breeds: Finnish Ayrshire (FA), Swedish Red and White (SRB), and Danish Red (DR). In total, 19 grandsires and 672 sons in FA, 19 grandsires and 499 sons in SRB, and 8 grandsires and 258 sons in DR were used in the study. These in iduals were genotyped with the 61 microsatellite markers used in any of the previous QTL scans on the selected chromosomes. Within-family QTL analyses based on linear regression models were carried out for CM and SCS to identify the segregating sires for each region. On the segregating families, joint single-trait and 2-trait analyses were performed using variance components models. The analyses confirmed that QTL affecting CM or SCS, or both, segregate on Bos taurus autosomes (BTA) 9, 11, 14, and 18, whereas a QTL on BTA29 could not be confirmed. Our results indicate that there may be at least 2 linked QTL on BTA9, one that primarily affects CM and a second that primarily affects SCS. On chromosomes BTA11, 14, and 18, the joint analyses were only significant for SCS.
Haplotype-Resolved cattle genomes provide insights into structural variation and adaptation
Publisher: Cold Spring Harbor Laboratory
Date: 08-2019
DOI: 10.1101/720797
Abstract: We present high quality, phased genome assemblies representative of taurine and indicine cattle, subspecies that differ markedly in productivity-related traits and environmental adaptation. We report a new haplotype-aware scaffolding and polishing pipeline using contigs generated by the trio binning method to produce haplotype-resolved, chromosome-level genome assemblies of Angus (taurine) and Brahman (indicine) cattle breeds. These assemblies were used to identify structural and copy number variants that differentiate the subspecies and we found variant detection was sensitive to the specific reference genome chosen. Six gene families with immune related functions are expanded in the indicine lineage. Assembly of the genomes of both subspecies from a single in idual enabled transcripts to be phased to detect allele-specific expression, and to study genome-wide selective sweeps. An indicus-specific extra copy of fatty acid desaturase is under positive selection and may contribute to indicine adaptation to heat and drought.
Synchronous diversification of Sulawesi’s iconic artiodactyls driven by recent geological events
Publisher: Cold Spring Harbor Laboratory
Date: 04-01-2018
DOI: 10.1101/241448
Abstract: The high degree of endemism on Sulawesi has previously been suggested to have vicariant origins, dating back 40 Myr ago. Recent studies, however, suggest that much of Sulawesi’s fauna assembled over the last 15 Myr. Here, we test the hypothesis that recent uplift of previously submerged portions of land on Sulawesi promoted ersification, and that much of the its faunal assemblage is much younger than the island itself. To do so, we combined palaeogeographical reconstructions with genetic and morphometric data sets derived from Sulawesi’s three largest mammals: the Babirusa, Anoa, and Sulawesi warty pig. Our results indicate that although these species most likely colonized the area that is now Sulawesi at different times (14 Myr ago to 2-3 Myr ago), they experienced an almost synchronous expansion from the central part of the island. Geological reconstructions indicate that this area was above sea level for most of the last 4 Myr, unlike most parts of the island. We conclude that recent emergence of land on Sulawesi (~1–2 Myr) may have allowed species to expand synchronously. Altogether, our results indicates that the establishment of the highly endemic faunal assemblage on Sulawesi was driven by geological events over the last few million years.
Association of genes involved in carcass and meat quality traits in 15 European bovine breeds
Publisher: Elsevier BV
Date: 06-2013
Muscle lipid composition in bulls from 15 European breeds
Publisher: Elsevier BV
Date: 02-2014
Searching new signals for production traits through gene-based association analysis in three Italian cattle breeds.
Publisher: Wiley
Date: 22-05-2015
DOI: 10.1111/AGE.12303
Abstract: Genome-wide association studies (GWAS) have been widely applied to disentangle the genetic basis of complex traits. In cattle breeds, classical GWAS approaches with medium-density marker panels are far from conclusive, especially for complex traits. This is due to the intrinsic limitations of GWAS and the assumptions that are made to step from the association signals to the functional variations. Here, we applied a gene-based strategy to prioritize genotype-phenotype associations found for milk production and quality traits with classical approaches in three Italian dairy cattle breeds with different s le sizes (Italian Brown n = 745 Italian Holstein n = 2058 Italian Simmental n = 477). Although classical regression on single markers revealed only a single genome-wide significant genotype-phenotype association, for Italian Holstein, the gene-based approach identified specific genes in each breed that are associated with milk physiology and mammary gland development. As no standard method has yet been established to step from variation to functional units (i.e., genes), the strategy proposed here may contribute to revealing new genes that play significant roles in complex traits, such as those investigated here, lifying low association signals using a gene-centric approach.
Mapping the bovine factor H gene to chromosome 16 by SSCP analysis
Publisher: Springer Science and Business Media LLC
Date: 1997
A second generation radiation hybrid map to aid the assembly of the bovine genome sequence
Publisher: Springer Science and Business Media LLC
Date: 06-11-2006
Characterization and mapping of bovine dopamine receptors 1 and 5
Publisher: Wiley
Date: 22-07-2003
DOI: 10.1046/J.1365-2052.2003.00994.X
Abstract: A cDNA encoding the bovine dopamine receptor 1 (DRD1) was isolated from a bovine cDNA library, cloned and completely sequenced. The coding region showed 93 and 91% sequence identity on DNA level and 96 and 94% on protein level with its respective porcine and human orthologs. The bovine DRD1 and dopamine receptor 5 (DRD5) were mapped, respectively, to BTA10 and 6 by radiation hybrid mapping. One SNP was found in DRD1 and four in DRD5. Using polymerase chain reaction-restriction fragment length polymorphism, 11 different European cattle breeds were screened for the presence of the DRD1 and DRD5 substitutions. Allele frequencies for DRD1 and DRD5 alleles were very similar across all the breeds examined. Allele frequency discrepancies were found between Belgian Blue beef breed and the other breeds.
Profiling bovine blastocyst microRNAs using deep sequencing
Publisher: CSIRO Publishing
Date: 2017
DOI: 10.1071/RD16110
Abstract: MicroRNAs (miRNAs) are known to control several reproductive functions, including oocyte maturation, implantation and early embryonic development. Recent advances in deep sequencing have allowed the analysis of all miRNAs of a s le. However, when working with embryos, due to the low RNA content, miRNA profiling is challenging because of the relatively large amount of total RNA required for library preparation protocols. In the present study we compared three different procedures for RNA extraction and prepared libraries using pools of 30 bovine blastocysts. In total, 14 of the 15 most abundantly expressed miRNAs were common to all three procedures. Furthermore, using miRDeep discovery and annotation software (Max Delbrück Center), we identified 1363 miRNA sequences, of which bta-miR-10b and bta-miR-378 were the most abundant. Most of the 179 genes identified as experimentally validated (86.6%) or predicted targets (13.4%) were associated with cancer canonical pathways. We conclude that reliable analysis of bovine blastocyst miRNAs can be achieved using the procedures described herein. The repeatability of the results across different procedures and independent replicates, as well as their consistency with results obtained in other species, support the biological relevance of these miRNAs and of the gene pathways they modulate in early embryogenesis.
Polymorphisms of the prion gene coding region in born-after-the-reinforced-ban (BARB) bovine spongiform encephalopathy cattle in Great Britain
Publisher: Microbiology Society
Date: 04-2007
Abstract: Polymorphisms of the prion protein gene are associated with differing susceptibilities to transmissible spongiform encephalopathy diseases, as shown for variant Creutzfeldt–Jakob disease in humans and scrapie in sheep, but not yet in cattle. Imposition of control measures in the UK, including a reinforced ruminant feed ban in 1996, has led to a reduction in the incidence of bovine spongiform encephalopathy (BSE). BSE-affected cattle born after 1996 in Great Britain have been termed born-after-the-reinforced-ban (BARB) cases. In this study, the PrP gene coding region from 100 BARB BSE cases and 66 matched healthy-control cattle was sequenced to investigate whether this would reveal a genetic basis to their origin. Polymorphisms identified were not found to be associated with increased susceptibility to BSE in the BARB cases. Analysis of BARB cases grouped either by clinical status or by whether they formed an isolated or clustered case was also undertaken, but differences were not found to be significant.
Dwarfism in Dexter cattle is not caused by the mutations in FGFR3 responsible for achondroplasia in humans
Publisher: Wiley
Date: 02-1997
DOI: 10.1111/J.1365-2052.1997.00068.X
Abstract: Dexter cattle carry a genetic defect causing a dwarf phenotype in the heterozygotes (Dx+/-), while homozygotes (Dx+/+) are stillborn with extreme shortening of limbs and gross craniofacial defects and are described as 'bulldog' calves. The heterozygous phenotype has been likened to achondroplastic dwarfism in humans (ACH), which has recently been shown to be the result of mutations in the transmembrane region of the fibroblast growth factor receptor 3 (FGFR3) gene. We have sequenced the transmembrane region of bovine FGFR3 from normal Dexter cattle (Dx-/-) and bulldog calves (Dx+/+). The sequence from both is identical and therefore excludes mutations in the trans-membrane region of FGFR3 as the cause of Dexter dwarfism.
A major genetic component of BSE susceptibility
Publisher: Springer Science and Business Media LLC
Date: 02-10-2006
Genetic relationships among European cattle breeds
Publisher: Wiley
Date: 08-1998
DOI: 10.1046/J.1365-2052.1998.00327.X
Abstract: Genetic relationships among 37 European cattle breeds were investigated using blood group and serum protein polymorphisms. The 18,859 animals included in the study represented a random s le from pedigree populations in the UK. Within-breed variation was estimated by average heterozygosity and number of alleles observed, and breed relationships were evaluated by genetic distance. Standard errors of the heterozygosity, number of alleles and genetic distance were obtained by bootstrapping. The significance of breed differences was tested using an exact test of differentiation. French, Italian and Channel Island breeds were found to have generally higher heterozygosities and a greater number of alleles than breeds from mainland Britain and North Europe. Genetic distances ranged between 0.011 (+/- 0.005) and 0.309 (+/- 0.071). Two major breed groups were identified a group of French, Italian and Channel Island breeds together with the Simmental and Gelbvieh, and a second group consisting of the mainland British and North European breeds. The exact test of breed differentiation showed all breeds to be significantly different from one another (P < 0.0001). Overall relationships among breeds reflected their geographical origin and common ancestry rather than the agricultural use for which the breeds have been selected.
Polymorphism analysis of the prion gene in BSE‐affected and unaffected cattle
Publisher: Wiley
Date: 10-1994
DOI: 10.1111/J.1365-2052.1994.TB00364.X
Abstract: Polymerase chain reaction (PCR) primers designed to lify the octapeptide repeat region of the bovine prion gene were used to test the association of genotypes with bovine spongiform encephalitis (BSE) in 56 BSE-affected and 177 unaffected animals. Three alleles (A,B,C) were detected as single-strand conformation polymorphisms (SSCPs) and two alleles (1,2--representing six or five copies of the octapeptide repeat respectively) were detected as lified double-strand fragment length polymorphisms (AMFLPs). Observed genotypes of SSCPs and AMFLPs were analysed by chi-square. The SSCP genotypes of nuclear family members of animals with BSE and BSE-affected animals were different (P < 0.001, P 0.469). No AMFLP genotypic differences were detected between BSE-affected animals, their relatives, unrelated animals of the same breed or animals of different breeds (P > 0.05). These data suggest that BSE-affected animals and their relatives are more likely to have the AA SSCP genotype than unrelated animals of the same breed or animals of different breeds.
Comparative sequence alignment reveals River Buffalo genomic structural differences compared with cattle
Publisher: Elsevier BV
Date: 05-2019
DOI: 10.1016/J.YGENO.2018.02.018
Abstract: This study sought to characterize differences in gene content, regulation and structure between taurine cattle and river buffalo (one subspecies of domestic water buffalo) using the extensively annotated UMD3.1 cattle reference genome as a basis for comparisons. We identified 127 deletion CNV regions in river buffalo representing 5 annotated cattle genes. We also characterized 583 merged mobile element insertion (MEI) events within the upstream regions of annotated cattle genes. Transcriptome analysis in various tissue types on river buffalo confirmed the absence of four cattle genes. Four genes which may be related to phenotypic differences in meat quality and color, had upstream MEI predictions and were found to have significantly elevated expression in river buffalo compared with cattle. Our comparative alignment approach and gene expression analyses suggested a functional role for many genomic structural variations, which may contribute to the unique phenotypes of river buffalo.
Physical mapping of <i>CHX10</i>, <i>ALDH6A1</i>, and <i>ABCD4</i> on bovine chromosome 10q34
Publisher: S. Karger AG
Date: 2005
DOI: 10.1159/000084217
RNA-sequence analysis of gene expression from honeybees (Apis mellifera) infected with Nosema ceranae
Publisher: Public Library of Science (PLoS)
Date: 28-03-2017
Colostrum source and passive immunity transfer in dairy bull calves
Publisher: American Dairy Science Association
Date: 07-2021
Abstract: Colostrum is essential for good neonate health however, it is not known whether different calves absorb the nutrients from colostrum equally well. In this study, the absorption of protein, IgG, and γ-glutamyl transferase was compared in newborn dairy bull calves for 1 wk after feeding colostrum from different sources. Thirty-five Holstein-Friesian bull calves were randomly allocated into 3 groups and fed colostrum within 4 h after birth. Group A calves (n = 12) were bottle fed colostrum from their own dam for 3 d. Colostrum from these group A cows was also used as foster cow colostrum for the group B calves (n = 12), such that each group A and B calf pair received identical colostrum from each milking of the respective group A dam (10% of birth weight per day). The group C calves (n = 11) were fed 1 bottle (2 L) of pooled colostrum and transition milk (referred to as pooled colostrum), as was the standard practice on the dairy farm. The pooled colostrum was collected from the other dairy cows on the farm 0 to 4 d postpartum and stored at 4°C for less than 12 h. Blood was s led from calves before the first feeding and at 1, 2, 3, and 7 d after birth. Levels of total solids, total protein, and IgG were higher in the dam colostrum than in the pooled colostrum. At birth, there were no differences between the calf groups for any measurements, and all calves had very low IgG levels. After receiving colostrum, the glucose, plasma γ-glutamyl transferase, serum total protein, and IgG concentrations increased significantly in all calves. There were no differences in any blood measurements at any time point between the pairs of group A and group B calves that received colostrum from the same cow except for the IgG concentration 2 d after birth. However, the group A calves had a higher total serum protein level and IgG concentration than the group C calves for all the time points after the first feeding. The group B calves had a higher IgG concentration than the group C calves on d 1, 2, and 7 after birth. Compared with groups A and B, there was no difference in the proportion of calves in group C that failed to have passive immunity transferred adequately based on the IgG threshold (<10 g/L). Thus, the calves receiving identical colostrum from the same cow had the same levels of IgG, and even the pooled colostrum provided sufficient transfer of IgG as the calves were fed within 4 h after birth.
Application of AFLP® technology to radiation hybrid mapping
Publisher: Springer Science and Business Media LLC
Date: 2004
DOI: 10.1023/B:CHRO.0000021912.22552.FF
Abstract: We have investigated the use of AFLP technology as a tool for the high throughput enrichment of Radiation Hybrid (RH) maps. The 3000 rad TM112 bovine RH panel was assayed with 37 EcoRI/TaqI AFLP primer combinations. The number of selective nucleotides used during PCR was increased to seven, to reduce the complexity of the AFLP profile and minimise the overlap between hamster and bovine bands co- lified from hybrid cell clones. Seven-hundred-forty-seven bovine AFLP bands were lified that could be distinguished following electrophoresis. Repeatability was tested within and between laboratories on independent template preparations and an error rate of 1.3% found. Two-point linkage analysis clustered 428 AFLP fragments in 39 linkage groups of at least 4 markers. Multi-point maps were constructed for 5 s le linkage groups. The study demonstrated that the AFLP approach could be used to rapidly screen for the most informative clones during panel construction and to increase the number of markers on RH maps, which could be useful for joining linkage groups formed by other markers. The use of AFLP markers as anchor points between existing RH maps and other physical maps, such as BAC contigs, is also discussed.
A bovine YAC library containing four- to five-fold genome equivalents
Publisher: Springer Science and Business Media LLC
Date: 08-1999
Production of alloantisera against class II bovine lymphocyte antigens (BoLA) by cross‐immunization between class I matched cattle
Publisher: Wiley
Date: 10-1991
DOI: 10.1111/J.1365-2052.1991.TB00700.X
Abstract: This paper describes the production of alloantisera directed against bovine major histocompatibility complex (MHC) (BoLA) class II antigens in animals whose MHC phenotypes had been defined by one dimensional isoelectric focusing. Animals of closely matched BoLA class I types were selected by serology and subsequently typed for class I and class II by 1D-IEF of immunoprecipitated antigens. Those with similar class I type by both methods, but differing at the class II locus, were chosen for reciprocal immunization. Cross-immunization was by two skin implantations 6 weeks apart. The resulting antisera showed low titre after the first immunization and elevated titre 3 weeks after the second immunization. The sera reacted strongly with cells expressing specific BoLA class II antigens. The pattern of reactivity correlated well with IEF class II typing on a panel of animals representing all of the class II IEF types present in the Friesian population.
Intragenic haplotypes at the bovine CSN1S1 locus
Publisher: Copernicus GmbH
Date: 10-10-2002
Abstract: Abstract. A new alternative genotyping method based on PCR-SSCP was developed for direct differentiation of the CSN1S1 alleles B and C in the coding region. In addition a PCR-RFLP test based on a MaeIII restriction site in the promoter region of CSN1S1, reported in the literature as an alternative test for the differentiation of CSN1S1*B and C was used and the alleles named b and c. Genotyping of 649 animals belonging to 17 European and Turkish cattle breeds showed differences in occurrence and frequency of the alleles. CSN1S1*B occurred in all breeds with frequencies varying from 0.50 in Anatolian Blackup to 1.0 in e.g. Ayrshire. CSN1S1*b on the other hand varied from 0.63 in Jersey, 0.97 in Ayrshire to 1.0 in e.g. Angler. Comparison of the results from both typing methods and positions in the gene showed that both mutations do not always occur together. From the resulting four intragenic haplotypes (B-b, B-c, C-c and C-b) B-b is predominant in all breeds with frequencies varying from 0.3450 in Anatolian Black to 1.0 in Angler and Scottish Highland. The number of haplotypes varied from only one in Angler and Scottish Highland, two in Ayrshire, three in Asturian Valley and Turkish Grey Steppe to all four in the other 12 breeds. Correlation between allele frequencies and the geographic origin of the breeds was significant for the MaeIII promoter polymorphism.
Analysis of immune-related microRNAs in cows and newborn calves
Publisher: American Dairy Science Association
Date: 04-2023
A 2cM genome-wide scan of European Holstein cattle affected by classical BSE
Publisher: Springer Science and Business Media LLC
Date: 29-03-2010
Abstract: Classical bovine spongiform encephalopathy (BSE) is an acquired prion disease that is invariably fatal in cattle and has been implicated as a significant human health risk. Polymorphisms that alter the prion protein of sheep or humans have been associated with variations in transmissible spongiform encephalopathy susceptibility or resistance. In contrast, there is no strong evidence that non-synonymous mutations in the bovine prion gene ( PRNP ) are associated with classical BSE disease susceptibility. However, two bovine PRNP insertion/deletion polymorphisms, one within the promoter region and the other in intron 1, have been associated with susceptibility to classical BSE. These associations do not explain the full extent of BSE susceptibility, and loci outside of PRNP appear to be associated with disease incidence in some cattle populations. To test for associations with BSE susceptibility, we conducted a genome wide scan using a panel of 3,072 single nucleotide polymorphism (SNP) markers on 814 animals representing cases and control Holstein cattle from the United Kingdom BSE epidemic. Two sets of BSE affected Holstein cattle were analyzed in this study, one set with known family relationships and the second set of paired cases with controls. The family set comprises half-sibling progeny from six sires. The progeny from four of these sires had previously been scanned with microsatellite markers. The results obtained from the current analysis of the family set yielded both some supporting and new results compared with those obtained in the earlier study. The results revealed 27 SNPs representing 18 chromosomes associated with incidence of BSE disease. These results confirm a region previously reported on chromosome 20, and identify additional regions on chromosomes 2, 14, 16, 21 and 28. This study did not identify a significant association near the PRNP in the family s le set. The only association found in the PRNP region was in the case-control s le set and this was not significant after multiple test correction. The genome scan of the case-control animals did not identify any associations that passed a stringent genome-wide significance threshold. Several regions of the genome are statistically associated with the incidence of classical BSE in European Holstein cattle. Further investigation of loci on chromosomes 2, 14, 16, 20, 21 and 28 will be required to uncover any biological significance underlying these marker associations.
A bovine whole-genome radiation hybrid panel and outline map
Publisher: Springer Science and Business Media LLC
Date: 08-2002
DOI: 10.1007/S00335-002-3001-X
Abstract: A 3000-rad radiation hybrid panel was constructed for cattle and used to build outline RH maps for all 29 autosomes and the X and Y chromosomes. These outline maps contain about 1200 markers, most of which are anonymous microsatellite loci. Comparisons between the RH chromosome maps, other published RH maps, and linkage maps allow regions of chromosomes that are poorly mapped or that have sparse marker coverage to be identified. In some cases, mapping ambiguities can be resolved. The RH maps presented here are the starting point for mapping additional loci, in particular genes and ESTs that will allow detailed comparative maps between cattle and other species to be constructed. Radiation hybrid cell panels allow high-density genetic maps to be constructed, with the advantage over linkage mapping that markers do not need to be polymorphic. A large quantity of DNA has been prepared from the cells forming the RH panel reported here and is publicly available for mapping large numbers of loci.
The efficacy of a secondary reinforcer (clicker) during acquisition and extinction of an operant task in horses
Publisher: Elsevier BV
Date: 10-2004
Identification of quantitative trait loci affecting cattle temperament.
Publisher: Oxford University Press (OUP)
Date: 19-05-2008
Abstract: In addition to its potential contribution to improving animal welfare, the study of the genetics of cattle behavior may provide more general insights into the genetic control of such complex traits. We carried out a genome scan in a Holstein x Charolais cross cattle population to identify quantitative trait loci (QTL) influencing temperament-related traits. In iduals belonging to the second-generation of this population (F(2) and backcross in iduals) were subjected to 2 behavioral tests. The flight from feeder (FF) test measured the distance at which the animal moved away from an approaching human observer, whereas the social separation (SS) test categorized different activities which the animal engaged in when removed from its penmates. The entire population was genotyped with 165 microsatellite markers. A regression interval mapping analysis identified 29 regions exceeding the 5% chromosome-wide significance level, which in idually explained a relatively small fraction of the phenotypic variance of the traits (from 3.8% to 8.4%). One of the significant associations influencing an FF test trait on chromosome 29 reached the 5% genome-wide significance level. Eight other QTL, all associated with an SS test trait, reached the 1% chromosome-wide significance level. The location of some QTL coincided with other previously reported temperament QTL in cattle, whereas those that are reported for the first time here may represent general loci controlling temperament differences between cattle breeds. No overlapping QTL were identified for the traits measured by the 2 different tests, supporting the hypothesis that different genetic factors influence behavioral responses to different situations.
The effects of a mutation in the myostatin gene on meat and carcass quality
Publisher: Elsevier BV
Date: 09-2009
DOI: 10.1016/J.MEATSCI.2009.04.010
Abstract: This study examined the effects of a mutation that inactivates the myostatin gene on calving, growth, carcass and meat quality traits in South Devon cattle. This breed carries at intermediate frequency an 11-bp deletion (MH) in the myostatin gene, known to be associated with the double-muscling phenotype, thus allowing a comparison of three genotype classes. The MH allele was associated with increased calving difficulty, carcass weight, muscle conformation and ratio of polyunsaturated to saturated fatty acids, as well as with reduced growth rate, carcass and meat fatness, and desirable flavour. However, the nature of the genetic effects differed between traits: in some cases the heterozygote MH carriers were more similar to the non-carriers than to homozygote carriers and in some cases, intermediate between the two homozygotes. The direction of these genetic effects has implications for the management of this genetic variation in the South Devon and other breeds.
PRNP haplotype associated with classical BSE incidence in European Holstein cattle
Publisher: Public Library of Science (PLoS)
Date: 16-09-2010
Genome-wide epigenetic characterization of tissues from three germ layers isolated from sheep fetuses
Publisher: Frontiers Media SA
Date: 04-09-2017
Has breed any effect on beef sensory quality?
Publisher: Elsevier BV
Date: 08-2021
Signatures of selection? Patterns of microsatellite diversity on a chromosome containing a selected locus
Publisher: Springer Science and Business Media LLC
Date: 25-04-2202
Estimation of breed and heterosis effects for growth and carcass traits in cattle using published crossbreeding studies
Publisher: Oxford University Press (OUP)
Date: 02-2010
Abstract: Current genetic evaluations are performed separately for each breed. Multiple breed genetic evaluations, however, assume a common base among breeds, enabling producers to compare cattle of different breed makeup. Breed and heterosis effects are needed in a multibreed evaluation because databases maintained by breed associations include few crossbred animals, which may not be enough to accurately estimate these effects. The objective of this study was to infer breed effects, maternal effects, direct heterosis effects, and maternal heterosis effects for growth and carcass traits using least squares means estimates from crossbreeding studies published in the literature from 1976 to 1996. The data set was formed by recording each least squares mean along with the breed composition, maternal breed composition, and direct and maternal heterozygosity. Each trait was analyzed using a single trait fixed effect model, which included study as a fixed effect and breed composition and heterozygosity as covariates. Breed solutions for each trait were expressed relative to the Angus breed. Direct breed effects for weaning weight ranged from -7.0 +/- 0.67 kg (British Dairy) to 29.3 +/- 0.74 kg (Simmental), and maternal effects ranged from -11.7 +/- 0.24 kg (Hereford) to 31.1 +/- 2.22 kg (Gelbvieh). Direct breed effects for birth weight ranged from -0.5 +/- 0.14 kg (British Dairy) to 10.1 +/- 0.46 kg (Continental Beef), and maternal effects ranged from -7.2 +/- 0.13 kg (Brahman) to 6.0 +/- 1.07 kg (Continental Beef). Direct breed effects ranged from -17.9 +/- 1.64 kg (Brahman) to 21.6 +/- 1.95 kg (Charolais), from -6.5 +/- 1.29 kg (Brahman) to 55.8 +/- 1.47 kg (Continental Beef), from -8.1 +/- 0.48 cm(2) (Shorthorn) to 21.0 +/- 0.48 cm(2) (Continental Beef), and from -1.1 +/- 0.02 cm (Continental Beef) to 0 +/- 0.00 cm (Angus) for postweaning BW gain, carcass weight, LM area, and fat thickness, respectively. The use of literature estimates to predict direct and maternal breed and heterosis effects may supplement their direct prediction in a multibreed evaluation.
Chromosomal mapping and quantitative analysis of estrogen-related receptor alpha-1, estrogen receptors alpha and beta and progesterone receptor in the bovine mammary gland
Publisher: Bioscientifica
Date: 06-2005
DOI: 10.1677/JOE.1.06139
Abstract: Steroid receptors are key transcriptional regulators of mammary growth, development and lactation. Expression of estrogen receptors alpha (ERα) and beta (ERβ), progesterone receptor (PR), and estrogen-related receptor alpha-1 (ERRβ) have been evaluated in bovine mammary gland. The ERRα is an orphan receptor that, in other species and tissues, appears to function in the regulation of estrogen-response genes including lactoferrin and medium chain acyl-CoA dehydrogenase and in mitochondrial biogenesis. Expression of ERα, ERβ, PR and ERRα was characterized in mammary tissue obtained from multiple stages of bovine mammary gland development using quantitative real-time RT-PCR. Expression was evaluated in prepubertal heifers, primigravid cows, lactating non-pregnant cows, lactating pregnant cows and non-lactating pregnant cows ( n =4 to 9 animals/stage). In addition, ERα, ERβ, PR and ERRα were mapped to chromosomes 9, 10, 15 and 29 respectively, by linkage and radiation hybrid mapping. Results indicated that expression of ERα, PR and ERRα was largely coordinately regulated and they were present in significant quantity during all physiological stages evaluated. In contrast, ERβ transcripts were present at a very low concentration during all stages. Furthermore, no ERβ protein could be detected in bovine mammary tissue by immunohistochemistry. The ERα and PR proteins were detected during all physiological states, including lactation. Our results demonstrate the presence of ERα, PR and ERRα during all physiological stages, and suggest a functional role for ERRα and a relative lack of a role for ERβ in bovine mammary gland development and lactation.
Identification of polymorphisms in the malic enzyme 1, NADP(+)-dependent, cytosolic and nuclear receptor subfamily 0, group B, member 2 genes and their associations with meat and carcass quality traits in commercial Angus cattle.
Publisher: Wiley
Date: 07-06-2012
DOI: 10.1111/J.1365-2052.2011.02216.X
Abstract: Genes involved in the physiological control of energy and triglyceride synthesis, such as malic enzyme 1, NADP(+)-dependent, cytosolic (ME1) and nuclear receptor subfamily 0, group B, member 2 (NR0B2), are key candidates that may have effects on meat and carcass quality traits. These genes were sequenced in Aberdeen Angus beef cattle, and the possibility of associations between SNPs and economically important carcass and meat quality traits was tested. Six novel SNPs, five in ME1 and one in NR0B2, were identified. A SNP in exon eight of ME1 resulted in a non-synonymous amino acid change from valine to isoleucine. Phenotypic data were recorded on 536 commercial Aberdeen Angus-cross beef cattle, which comprised 28 carcass quality, tenderness and sensory traits. The majority of the SNPs were associated with at least one of these traits, including an association between the NR0B2 SNP and fat class, and associations between at least one of the ME1 SNPs and eye muscle area, sirloin weight before maturation, sirloin steak tail length, and juiciness.
Polymorphisms in twelve candidate genes are associated with growth, muscle lipid profile and meat quality traits in eleven European cattle breeds
Publisher: Springer Science and Business Media LLC
Date: 10-04-2014
DOI: 10.1007/S11033-014-3343-Y
Abstract: Current customers' demands focus on the nutritional and sensory quality of cattle meat. Candidate gene approach allows identification of genetic polymorphisms that have a measurable effect on traits of interest. The aim of this work is to identify new molecular markers for beef production through an association study using 27 candidate genes and 314 purebred bulls from 11 European cattle breeds. Twelve genes were found associated with different lipid and meat quality traits, and among these stand out the considerable effect of CAST on fatness score, CGGBP1 on growth traits, HSPB1 on the percentage of lauric acid (12:0) and phospholipid docosahexaenoic acid (DHA 22:6 n - 3), RORA on the ratio of light absorption (K) to light scattering (S) (K/S), and TNFA on lightness (L*). Most of these traits are related to post-mortem muscle biochemical changes, which are key factors controlling meat quality and consumers' acceptance. Also, the variations produced on muscle fatty acid profiles, such as those of AANAT, CRH, CSN3, HSPB1, and TNFA, give insights into the genetic networks controlling these complex traits and the possibility of future improvement of meat nutritional quality.
Detection of quantitative trait loci for meat quality traits in cattle.
Publisher: Wiley
Date: 30-01-2008
DOI: 10.1111/J.1365-2052.2007.01682.X
Abstract: A whole-genome scan was carried out to detect quantitative trait loci (QTL) affecting sensory, organoleptic, physical and chemical properties of meat. The study used phenotypic data from 235 second-generation cross-bred bull calves of a Charolais x Holstein experimental population. Loin muscle s les were evaluated for yield force, intramuscular fat and nitrogen contents, myofibrillar fragmentation index, haem pigment concentration, moisture content and pH at 24 h postmortem. A sensory assessment was performed on grilled loin and roasted silverside joints by trained panellists. A linear regression analysis based on 165 markers revealed 35 QTL at the 5% chromosome-wide significance level (20 for sensory traits and 15 for physical and chemical traits), five of which were highly significant (F-value: > or =9). The most significant QTL was located on chromosome 6 (with the best likely position at 39 cM) and affected haem pigment concentration. The Holstein allele for this QTL was associated with an increase of 0.53 SD in the haem scores. A QTL for pH(24h) was identified on chromosome 14 (at 40 cM) and a QTL for moisture content was identified on chromosome 22 (at 21 cM). Two highly significant QTL were identified for sensory panel-assessed traits: beef odour intensity (grilled s le) on chromosome 10 (at 119 cM), and juiciness (roast s le) on chromosome 16 (at 70 cM). The proportion of phenotypic variance explained by the significant QTL ranged from 3.6% (for nitrogen content on chromosome 10) to 9.5% (for juiciness, roast s le on chromosome 16).
Mapping and SNP analysis of bovine candidate genes for meat and carcass quality
Publisher: Wiley
Date: 18-09-2003
DOI: 10.1046/J.1365-2052.2003.01008.X
Abstract: The chromosomal localization of 13 bovine genes was determined using radiation hybrid (RH) mapping. The RH mapping data were in agreement with published data using either linkage, somatic cell hybrids or in situ hybridization. Mutation analysis using single-stranded conformational polymorphism, restriction fragment length polymorphism (RFLP) and sequencing revealed 13 SNPs in four different genes, namely carboxypeptidase E (CPE), uncoupling protein 2 (UCP2), single-minded (Drosophila) homologue 1 (SIM1) and methallothionein IIa (MT2A). With the exception of one mutation in CPE, all other mutations are either silent or are situated in an intron. The polymerase chain reaction RFLP was used on unrelated animals from different cattle breeds for determing allelic distribution.
Microarray Analysis of Differentially Expressed Genes from Peyer's Patches of Cattle Orally Challenged with Bovine Spongiform Encephalopathy
Publisher: Informa UK Limited
Date: 31-07-2009
DOI: 10.1080/15287390903084199
Abstract: The most likely route of entry of infection following oral exposure to transmissible spongiform encephalopathies (TSE) is via the immunologically active Peyer's patches (PP). These secondary lymphoid organs appear to be the potential route for prion neuroinvasion. However, the molecular mechanisms involved in the uptake of the infectious prion agent and progression of disease remain still unclear. This investigation examined the changes in gene expression in PP following oral exposure of cattle to bovine spongiform encephalopathy (BSE) agents. The gene expression patterns in PP from cows 12 mo after BSE challenge were compared with controls using a microarray platform containing 24,000 oligonucleotides representing 16,846 unique gene loci and 5943 Expressed Sequence Tag (EST) from bovine genome. Between the challanged and control animals, 90 genes and 16 EST were identified as significantly differentially, expressed (>2.0-fold change): 36 were upregulated and 70 were downregulated. Of these genes, five were found to be related to immune function. Major histocompatibility complex (MHC) class II, MHC class II DQ alpha, L-RAP, and two hypothetical proteins. Differentially expressed genes related to cellular and metabolic processes including development and maturation of cells in the PP were also identified. In this context, the potential impacts of these gene expression changes in PP on BSE development are discussed.
Microarray analysis in caudal medulla of cattle orally challenged with bovine spongiform encephalopathy
Publisher: Genetics and Molecular Research
Date: 2011
Association of selected SNP with carcass and taste panel assessed meat quality traits in a commercial population of Aberdeen Angus-sired beef cattle
Publisher: Springer Science and Business Media LLC
Date: 25-06-2200
Understanding the effects of the bovine POLLED variants
Publisher: Wiley
Date: 30-01-2020
DOI: 10.1111/AGE.12915
Abstract: Horns are paired appendages on the head of bovine species, comprising an inner bony core and outer keratin sheath. The horn bud forms during early fetal development but ossification of the developing horn does not occur until approximately 1 month after birth. Little is known about the genetic pathways that lead to horn growth. Hornless, or polled, animals are found in all domestic bovids. Histological studies of bovine fetuses have shown that the horn bud does not form in polled in iduals. There are currently four known genetic variants for polledness in cattle on BTA1. All of the variants are intergenic, but probably affect regulation of nearby genes or long non-coding RNAs. Transcriptomic studies suggest that the expression of two nearby long non-coding RNAs are affected by the Celtic POLLED variant, but further studies are required to confirm these data. Candidate genes located elsewhere in the genome are involved in regulating bone formation and epithelial-to-mesenchymal transition. Expression of one of these candidate genes, RXFP2, appears to be reduced in the fetal horn bud of polled animals carrying the Celtic variant compared with horned in iduals. Investigating horn ontogenesis and the genetic pathway by which the POLLED variants prevent horn development has implications for cattle breeding. If the genetic basis of horn bud formation and polledness is better understood, then new targets may be identified for precision genome editing to create polled in iduals.
Search for quantitative trait loci affecting growth and carcass traits in a cross population of beef and dairy cattle
Publisher: Oxford University Press (OUP)
Date: 2009
Abstract: A genome scan to detect QTL influencing growth and carcass-related traits was conducted in a Charolais x Holstein crossbred cattle population. Phenotypic measurements related to growth and carcass traits were made on the 235 second-generation crossbred males of this herd (F2 and reciprocal backcrosses), which were born in 4 consecutive annual cohorts. Traits measured in vivo were related to birth dimensions, growth rates, and ultrasound measurements of fat and muscle depth. The animals were slaughtered near a target BW of 550 kg, and a wide range of postmortem traits were measured: visual assessment of carcass conformation and carcass fatness, estimated subcutaneous fat percentage, weights of kidney knob and channel fat, and weights of carcass components after commercial and full-tissue dissections. The whole population, including grandparents, parents, and the crossbred bulls, was genotyped initially for 139 genome-wide microsatellite markers. Twenty-six additional markers were subsequently analyzed to increase marker density on some of the chromosomes where QTL had been initially identified. The linear regression analyses based on the 165 markers revealed a total of 51 significant QTL at the suggestive level, 21 of which were highly significant (F-value >or=9 based on the genome-wide thresholds obtained in the initial scan). A large proportion of the highly significant associations were found on chromosomes 5 and 6. The most highly significant QTL was localized between markers DIK1054 and DIK082 on chromosome 6 and explained about 20% of the phenotypic variance for the total bone proportion estimated after the commercial dissection. In the adjacent marker interval on this chromosome, 2 other highly significant QTL were found that explain about 30% of the phenotypic variance for birth dimension traits (BW and body length at birth). On chromosome 5, the most significant association influenced the lean:bone ratio at the forerib joint and was flanked by markers DIK4782 and BR2936. Other highly significant associations were detected on chromosomes 10 (estimated subcutaneous fat percentage), 11 (total saleable meat proportion), 16 (prehousing growth rate), and 22 (bone proportion at the leg joint). These results provide a useful starting point for the identification of the genes associated with traits of direct interest to the beef industry, using fine mapping or positional candidate gene approaches.
The bovine cocaine and amphetamine-regulated transcript locus: Gene characterization and SNP discovery
Publisher: Wiley
Date: 21-12-2005
The genetic background of clinical mastitis in Holstein-Friesian cattle
Publisher: Elsevier BV
Date: 2019
Topologically associating domains in the POLLED region are the same for Angus‐ and Brahman‐specific Hi‐C reads from F1 hybrid fetal tissue
Publisher: Wiley
Date: 29-03-2023
DOI: 10.1111/AGE.13322
Abstract: Horns, a form of headgear carried by Bovidae, have ethical and economic implications for ruminant production species such as cattle and goats. Hornless (polled) in iduals are preferred. In cattle, four genetic variants (Celtic, Friesian, Mongolian and Guarani) are associated with the polled phenotype, which are clustered in a 300‐kb region on chromosome 1. As the variants are intergenic, the functional effect is unknown. The aim of this study was to determine if the POLLED variants affect chromatin structure or disrupt enhancers using publicly available data. Topologically associating domains (TADs) were analyzed using Angus‐ and Brahman‐specific Hi‐C reads from lung tissue of an Angus (Celtic allele) cross Brahman (horned) fetus. Predicted bovine enhancers and chromatin immunoprecipitation sequencing peaks for histone modifications associated with enhancers (H3K27ac and H3K4me1) were mapped to the POLLED region. TADs analyzed from Angus‐ and Brahman‐specific Hi‐C reads were the same, therefore, the Celtic variant does not appear to affect this level of chromatin structure. The Celtic variant is located in a different TAD from the Friesian, Mongolian, and Guarani variants. Predicted enhancers and histone modifications overlapped with the Guarani and Friesian variants but not the Celtic or Mongolian variants. This study provides insight into the mechanisms of the POLLED variants for disrupting horn development. These results should be validated using data produced from the horn bud region of horned and polled bovine fetuses.
Synergies between assisted reproduction technologies and functional genomics
Publisher: Springer Science and Business Media LLC
Date: 08-2016
SNPchiMp v.3: integrating and standardizing single nucleotide polymorphism data for livestock species
Publisher: Springer Science and Business Media LLC
Date: 10-04-2015
Gene Expression in the Medulla Following Oral Infection of Cattle with Bovine Spongiform Encephalopathy
Publisher: Informa UK Limited
Date: 06-01-2011
DOI: 10.1080/15287394.2011.529061
Abstract: The identification of variations in gene expression in response to bovine spongiform encephalopathy (BSE) may help to elucidate the mechanisms of neuropathology and prion replication and discover biomarkers for disease. In this study, genes that are differentially expressed in the caudal medulla tissues of animals infected with different doses of PrP(BSE) at 12 and 45 mo post infection were compared using array containing 24,000 oligonucleotide probes. Data analysis identified 966 differentially expressed (DE) genes between control and infected animals. Genes identified in at least two of four experiments (control versus 1-g infected animals at 12 and 45-mo control versus 100-g infected animals at 12 and 45 mo) were considered to be the genes that may be associated with BSE disease. From the 176 DE genes associated with BSE, 84 had functions described in the Gene Ontology (GO) database. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of 14 genes revealed that prion infection may cause dysfunction of several different networks, including extracellular matrix (ECM), cell adhesion, neuroactive ligand-receptor interaction, complement and coagulation cascades, MAPK signaling, neurodegenerative disorder, SNARE interactions in vesicular transport, and the transforming growth factor (TGF) beta signaling pathways. The identification of DE genes will contribute to a better understanding of the molecular mechanisms of neuropathology in bovine species. Additional studies on larger number of animals are in progress in our laboratory to investigate the roles of these DE genes in pathogenesis of BSE.
De novo assembly of haplotype-resolved genomes with trio binning
Publisher: Springer Science and Business Media LLC
Date: 22-10-2018
DOI: 10.1038/NBT.4277
Transcriptome Analysis of the Medulla Tissue from Cattle in Response to Bovine Spongiform Encephalopathy using Digital Gene Expression Tag Profiling
Publisher: Informa UK Limited
Date: 06-01-2011
DOI: 10.1080/15287394.2011.529062
Abstract: Bovine spongiform encephalopathy (BSE) is a transmissible, fatal neurodegenerative disorder of cattle produced by prions. The use of excessive parallel sequencing for comparison of gene expression in bovine control and infected tissues may help to elucidate the molecular mechanisms associated with this disease. In this study, tag profiling Solexa sequencing was used for transcriptome analysis of bovine brain tissues. Replicate libraries were prepared from mRNA isolated from control and infected (challenged with 100 g of BSE-infected brain) medulla tissues 45 mo after infection. For each library, 5-6 million sequence reads were generated and approximately 67-70% of the reads were mapped against the Bovine Genome database to approximately 13,700-14,120 transcripts (each having at least one read). About 42-47% of the total reads mapped uniquely. Using the GeneSifter software package, 190 differentially expressed (DE) genes were identified (>2.0-fold change, p < .01): 73 upregulated and 117 downregulated. Seventy-nine DE genes had functions described in the Gene Ontology (GO) database and 16 DE genes were involved in 38 different pathways described in the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Digital analysis expression by tag profiling may be a powerful approach to comprehensive transcriptome analysis to identify changes associated with disease progression, leading to a better understanding of the underlying mechanism of pathogenesis of BSE.
Mining the bovine genome with the Bovine SNP Retriever
Publisher: Oxford University Press (OUP)
Date: 2008
Abstract: Online resources for the bovine genome analysis are provided at the most important Web sites. Nonetheless, retrieval of single-nucleotide polymorphism (SNP)-related information is not always easy when searches must focus on complementary features. In this work, we present the Bovine SNP Retriever: a user-friendly tool for bovine SNP retrieval that also facilities the retrieval of SNP-related information within user-selected quantitative traits loci regions and reverse electronic polymerase chain reaction analysis on the bovine genome. The Bovine SNP Retriever is available at www.itb.cnr.it tp/bovine_snp_retriever/.
Revisiting AFLP fingerprinting for an unbiased assessment of genetic structure and differentiation of taurine and zebu cattle.
Publisher: Springer Science and Business Media LLC
Date: 17-04-2014
Assessment of MDA efficiency for genotyping using cloned embryo biopsies.
Publisher: Elsevier BV
Date: 2013
DOI: 10.1016/J.YGENO.2012.09.002
Abstract: The possibility to genotype embryos prior to implantation would have advantages for increasing the speed of selection of cattle. Reliable genotyping requires more DNA than can be obtained from biopsies of embryos, if they are to remain viable. Multiple displacement lification (MDA) is a whole genome lification technique used to increase the amount of DNA from biopsies for analysis. Reduced genome coverage resulting in Allele Drop Out (ADO) at heterozygous loci or missing genotypes are drawbacks of MDA. The present article describes the correlation between the input DNA quantity or embryo biopsy size and MDA success. Missing genotypes and ADO drastically increased when fewer than 30-40 cells or the genomic equivalents were used. However, embryo viability was found to be reduced if biopsied with more than 10 cells. Therefore, in vitro cell culture was investigated as a means to increase the number of cells available and the genotyping reliability.
Susceptibility of different chicken lines to H7N1 highly pathogenic avian influenza virus and the role of Mx gene polymorphism coding amino acid position 631
Publisher: Elsevier BV
Date: 10-2008
DOI: 10.1016/J.VIROL.2008.07.022
Abstract: Five chicken lines were experimentally infected with a HPAI H7N1 virus, to examine the variation in susceptibility to infection. Three lines showed high susceptibility to the virus, while two showed some resistance, with 7 out of 20, and 11 out of 15 birds, respectively, remaining healthy and surviving the experimental infection. Genotyping for the G/A polymorphism at position 2032 of Mx cDNA showed that one line was fixed for the G allele, and two were segregating for A and G alleles. Birds in the other two lines were selected to be fixed for the A allele. Statistical analyses indicated that the Mx genotype did not affect the clinical status or the time course of infection after viral inoculation.
Assignment of the bovine C10orf2 gene to bovine 26q13→q21 by fluorescence in situ hybridization and confirmation by radiation hybrid mapping
Publisher: S. Karger AG
Date: 2002
DOI: 10.1159/000066600
Genomic study of the response of chicken to highly pathogenic avian influenza virus
Publisher: Springer Science and Business Media LLC
Date: 03-06-2011
DOI: 10.1186/1753-6561-5-S4-S25
Abstract: The host mounts an immune response to pathogens, but few data are currently available on the role of host genetics in variation in response to avian influenza (AI). The study presented here investigated the role of the host genetic background in response to in vivo infection with AI virus (AIV). Experimental lines of chicken and commercial crosses were experimentally infected intratracheally with 10 3 EID 50 /bird of A/Chicken/Italy/13474/99 H7N1 highly pathogenic avian influenza virus (HPAIV). Chickens were genotyped for the Mx polymorphism causing the S631N mutation, and for the Major Histocompatibility Complex (MHC). Whole-genome genotyping was carried out using 60 k Single Nucleotide Polymorphism (SNP) array developed by the poultry Genome-Wide Marker-Assisted Selection Consortium (GWMASC). Variability in response of different chicken lines to the HPAIV infections and some degree of resistance to AI were observed: a statistically significant effect of chicken line on the response to infection was found. There was no association between survival in healthy conditions and polymorphisms at the Mx gene and the MHC- B region. The analysis based on the 60 k SNPs provided a good clustering of the chicken lines, but no specific genetic cluster associated with response to AIV was identified. Neither the genotype at the Mx gene or MHC- B locus, nor for SNP spanning the whole-genome identified loci involved in variations to response to AIV infection. These results point towards the possibility that either the genetic factors affecting the response of chickens to the H7N1 HPAIV are weak, or relevant alleles were not segregating in the studied populations.
Biochemically defined polymorphism of bovine MHC class II antigens
Publisher: Springer Science and Business Media LLC
Date: 03-1989
DOI: 10.1007/BF00373649
Abstract: To test the hypothesis that diffusion-weighted (DW)-PROPELLER (periodically rotated overlapping parallel lines with enhanced reconstruction) MRI provides more accurate liver tumor necrotic fraction (NF) and viable tumor volume (VTV) measurements than conventional DW-SE-EPI (spin echo echo-planar imaging) methods. Our institutional Animal Care and Use Committee approved all experiments. In six rabbits implanted with 10 VX2 liver tumors, DW-PROPELLER and DW-SE-EPI scans were performed at contiguous axial slice positions covering each tumor volume. Apparent diffusion coefficient maps of each tumor were used to generate spatially resolved tumor viability maps for NF and VTV measurements. We compared NF, whole tumor volume (WTV), and VTV measurements to corresponding reference standard histological measurements based on correlation and concordance coefficients and the Bland-Altman analysis. DW-PROPELLER generally improved image quality with less distortion compared to DW-SE-EPI. DW-PROPELLER NF, WTV, and VTV measurements were strongly correlated and satisfactorily concordant with histological measurements. DW-SE-EPI NF measurements were weakly correlated and poorly concordant with histological measurements. Bland-Altman analysis demonstrated that DW-PROPELLER WTV and VTV measurements were less biased from histological measurements than the corresponding DW-SE-EPI measurements. DW-PROPELLER MRI can provide spatially resolved liver tumor viability maps for accurate NF and VTV measurements, superior to DW-SE-EPI approaches. DW-PROPELLER measurements may serve as a noninvasive surrogate for pathology, offering the potential for more accurate assessments of therapy response than conventional anatomic size measurements.
Variation in the early host-pathogen interaction of bovine macrophages with divergent Mycobacterium bovis strains in the United Kingdom
Publisher: American Society for Microbiology
Date: 03-2018
DOI: 10.1128/IAI.00385-17
Abstract: Bovine tuberculosis has been an escalating animal health issue in the United Kingdom since the 1980s, even though control policies have been in place for over 60 years. The importance of the genetics of the etiological agent, Mycobacterium bovis , in the reemergence of the disease has been largely overlooked. We compared the interaction between bovine monocyte-derived macrophages (bMDM) and two M. bovis strains, AF2122/97 and G18, representing distinct genotypes currently circulating in the United Kingdom. These M. bovis strains exhibited differences in survival and growth in bMDM. Although uptake was similar, the number of viable intracellular AF2122/97 organisms increased rapidly, while G18 growth was constrained for the first 24 h. AF2122/97 infection induced a greater transcriptional response by bMDM than G18 infection with respect to the number of differentially expressed genes and the fold changes measured. AF2122/97 infection induced more bMDM cell death, with characteristics of necrosis and apoptosis, more inflammasome activation, and a greater type I interferon response than G18. In conclusion, the two investigated M. bovis strains interact in significantly different ways with the host macrophage. In contrast to the relatively silent infection by G18, AF2122/97 induces greater signaling to attract other immune cells and induces host cell death, which may promote secondary infections of naive macrophages. These differences may affect early events in the host-pathogen interaction, including granuloma development, which could in turn alter the progression of the disease. Therefore, the potential involvement of M. bovis genotypes in the reemergence of bovine tuberculosis in the United Kingdom warrants further investigation.
Characterization of class I bovine lymphocyte antigens (BoLA) by one‐dimensional isoelectricfocusing
Publisher: Wiley
Date: 04-1988
DOI: 10.1111/J.1365-2052.1988.TB00796.X
Abstract: BoLA class I antigens were characterized in a group of British and Dutch Friesian cattle by one-dimensional isoelectric focusing (1D-IEF) and the results compared with serology using alloantisera and microcytotoxicity. For IEF analysis, non-stimulated peripheral blood mononuclear cells (PBM) were metabolically labelled with 35S methionine, detergent lysates were prepared and MHC molecules precipitated with the monoclonal antibodies (mAbs) W6/32 or B1.1G6. Staphylococcus protein A precipitated antigens were separated on a vertical slab gel under denaturing conditions. The banding patterns seen for the W6/32 precipitated molecules obtained by 1D-IEF were compared with the serological specificities. Characteristic banding patterns were observed for most serological specificities as well as workshop undefined haplotypes. These patterns were seen both in families and the outbred population. In families IEF haplotypes segregated with serotypes. Additional MHC class I products were suggested by variable banding patterns for different w10 haplotypes and when using the different mAbs. A pulse chase experiment with a w12 animal also suggested more than one expressed product. The w2 and w5 specificities were not precipitated by either W6/32 or B1.1G6 and w6.2 and w6.4 were precipitated by W6/32 but not by B1.1G6. These results show that 1D-IEF is useful for BoLA typing. For the characterization of class I antigens, however, much depends on the mAbs used.
Genetic Loci Involved in Antibody Response to Mycobacterium avium ssp. paratuberculosis in Cattle
Publisher: Public Library of Science (PLoS)
Date: 15-06-2010
Analysis of Gene Expression in White Blood Cells of Cattle Orally Challenged with Bovine Amyloidotic Spongiform Encephalopathy
Publisher: Informa UK Limited
Date: 06-01-2011
DOI: 10.1080/15287394.2011.529059
Abstract: Bovine amyloidotic spongiform encephalopathy (BASE) is one of the recently discovered atypical forms of BSE, which is transmissible to primates, and may be the bovine equivalent of sporadic Creutzfeldt-Jacob disease (CJD) in humans. Although it is transmissible, it is unknown whether BASE is acquired through infection or arises spontaneously. In the present study, the gene expression of white blood cells (WBCs) from 5 cattle at 1 yr after oral BASE challenge was compared with negative controls using a custom microarray containing 43,768 unique gene probes. In total, 56 genes were found to be differentially expressed between BASE and control animals with a log fold change of 2 or greater. Of these, 39 were upregulated in BASE animals, while 17 were downregulated. The majority of these genes are related to immune function. In particular, BASE animals appeared to have significantly modified expression of genes linked to T- and B-cell development and activation, and to inflammatory responses. The potential impacts of these gene expression changes are described.
Accuracy of imputation of single-nucleotide polymorphism marker genotypes for water buffaloes (Bubalus bubalis) using different reference population sizes and imputation tools
Publisher: Elsevier BV
Date: 10-2018
Fine-mapping QTL for mastitis resistance on BTA9 in three Nordic red cattle breeds.
Publisher: Wiley
Date: 11-07-2008
Genome-Wide Survey of SNP Variation Uncovers the Genetic Structure of Cattle Breeds
Publisher: American Association for the Advancement of Science (AAAS)
Date: 24-04-2009
Abstract: A survey of genetic ersity of cattle suggests two domestication events in Asia and selection by husbandry.
Genotype by region and season interactions on weaning weight in United States angus cattle
Publisher: Oxford University Press (OUP)
Date: 10-2012
Abstract: The objective of this study was to determine if weaning weight performance is genetically consistent across different environments in the United States. The American Angus Association provided weight and pedigree data. Weaning weights observed in the Southeast (SoE) and Northwest (NW) were the focus of this study, as these regions are perceived as opposite extremes in climate. The 2 most represented calving seasons in each region were fall and winter in the SoE and winter and spring in the NW. The original data were edited to remove weaning weight records outside of 3 SD from the respective region-season mean, contemporary groups smaller than 20, and single-sire contemporary groups. The final dataset included 884,465 weaning weight records with 64,907 from fall-born calves in the SoE, 74,820 from winter-born calves in the SoE, 346,724 from winter-born calves in the NW and 398,014 from spring-born calves in the NW. Weaning weights of calves born in different region-season classes adjusted to 205 d of age were considered different but genetically correlated traits in a multivariate analysis. The sole fixed effect was weaning contemporary group and random effects included direct, maternal, maternal permanent environment, and a residual. Direct heritability estimates differed little across environments: 0.31 and 0.35 for weight in fall- and winter-born calves in the SoE, and 0.29 and 0.32 for winter- and spring-born calves in NW. Maternal heritability estimates ranged from 0.12 in the NW to 0.16 the SoE. Genetic correlations spanned from 0.69 to 0.93 among direct effects and from 0.65 to 0.95 among maternal effects. All heritability estimates had small (0.01 to 0.04) SE. The most distinct environments appeared to be winter in SoE and spring in NW (correlations of 0.69 and 0.65 for the direct and maternal effects). Different choices of sires for different environments might be justified to achieve the growth performance expected.
RNA sequencing-based analysis of the spleen transcriptome following infectious bronchitis virus infection of chickens selected for different mannose-binding lectin serum concentrations
Publisher: Springer Science and Business Media LLC
Date: 27-01-2016
Testing for the presence of previously identified QTL for milk production traits in new populations.
Publisher: Wiley
Date: 12-2000
DOI: 10.1046/J.1365-2052.2000.00689.X
Abstract: Five chromosomal regions previously associated with milk production traits were tested in 16 families of Black and White cattle from the UK. The traits were also linearly transformed into genetically and phenotypically independent variables normalized by phenotypic variances ('canonical traits'). Significant associations with the untransformed and canonical traits were found for bovine chromosome 6. There was also evidence that chromosome 9 influenced these traits. The linear transformation clarified the effects of chromosomal regions regions with effects on all three untransformed traits (milk, fat and protein yields) were generally condensed into an effect on a single canonical trait. Comparison of our results with those reported previously for American Holstein cattle suggested that the QTL may not be the same.
PCR-RFLP genotyping protocol for chicken Mx gene G/A polymorphism associated with the S631N mutation
Publisher: Genetics and Molecular Research
Date: 2010
DOI: 10.4238/VOL9-2GMR811
Abstract: The Mx (myxovirus resistance) gene codes for a protein with antiviral activity. Non-synonymous G/A polymorphism at position 2032 of chicken Mx cDNA results in a change at amino acid 631 of the Mx protein. This mutation has been shown to affect the antiviral activity of the Mx molecule, although recent studies have not confirmed this effect in response to some influenza strains. Nevertheless, the G/A polymorphism could be important for the chicken's response to other viruses. A robust PCR-RFLP protocol for genotyping chicken Mx gene polymorphism associated with the S631N mutation was developed. The F primer anneals to the last intron of the Mx gene, and the R primer anneals to the last exon of the gene, with an expected PCR product of 299 bp. PCR products were digested with Hpy8I. This enzyme cuts the sequence 5'-GTN|NAC-3', 2 bp downstream of the Mx polymorphism for the G allele, whereas the fragment containing the A allele is not cleaved. One hundred and twenty-seven chickens (commercial broilers, White Leghorn and New H shire) were genotyped using this protocol, and genotyping data were validated by sequencing. Full identity of results between the two genotyping methods was observed for all 127 s les, proving the reliability and robustness of this PCR-RFLP protocol.
Analysis of runs of homozygosity and their relationship with inbreeding in five cattle breeds farmed in Italy.
Publisher: Wiley
Date: 22-12-2015
DOI: 10.1111/AGE.12259
Abstract: Increased inbreeding is an inevitable consequence of selection in livestock populations. The analysis of high-density single nucleotide polymorphisms (SNPs) facilitates the identification of long and uninterrupted runs of homozygosity (ROH) that can be used to identify chromosomal regions that are identical by descent. In this work, the distribution of ROH of different lengths in five Italian cattle breeds is described. A total of 4095 bulls from five cattle breeds (2093 Italian Holstein, 749 Italian Brown, 364 Piedmontese, 410 Marchigiana and 479 Italian Simmental) were genotyped at 54K SNP loci. ROH were identified and used to estimate molecular inbreeding coefficients (FROH ), which were compared with inbreeding coefficients estimated from pedigree information (FPED ) and using the genomic relationship matrix (FGRM ). The average number of ROH per animal ranged from 54 ± 7.2 in Piedmontese to 94.6 ± 11.6 in Italian Brown. The highest number of short ROH (related to ancient consanguinity) was found in Piedmontese, followed by Simmental. The Italian Brown and Holstein had a higher proportion of longer ROH distributed across the whole genome, revealing recent inbreeding. The FPED were moderately correlated with FROH > 1 Mb (0.662, 0.700 and 0.669 in Italian Brown, Italian Holstein and Italian Simmental respectively) but poorly correlated with FGRM (0.134, 0.128 and 0.448 for Italian Brown, Italian Holstein and Italian Simmental respectively). The inclusion of ROH > 8 Mb in the inbreeding calculation improved the correlation of FROH with FPED and FGRM . ROH are a direct measure of autozygosity at the DNA level and can overcome approximations and errors resulting from incomplete pedigree data. In populations with high linkage disequilibrium (LD) and recent inbreeding (e.g. Italian Holstein and Italian Brown), a medium-density marker panel, such as the one used here, may provide a good estimate of inbreeding. However, in populations with low LD and ancient inbreeding, marker density would have to be increased to identify short ROH that are identical by descent more precisely.
Complete genomic sequence of the bovine prion gene (PRNP) and polymorphism in its promoter region
Publisher: Wiley
Date: 07-08-2001
Inbreeding and purging at the genomic Level: The Chillingham cattle reveal extensive, non-random SNP heterozygosity
Publisher: Wiley
Date: 11-11-2016
DOI: 10.1111/AGE.12376
Abstract: Local breeds of livestock are of conservation significance as components of global bio ersity and as reservoirs of genetic variation relevant to the future sustainability of agriculture. One such rare historic breed, the Chillingham cattle of northern England, has a 350-year history of isolation and inbreeding yet shows no diminution of viability or fertility. The Chillingham cattle have not been subjected to selective breeding. It has been suggested previously that the herd has minimal genetic variation. In this study, high-density SNP genotyping with the 777K SNP chip showed that 9.1% of loci on the chip are polymorphic in the herd, compared with 62-90% seen in commercial cattle breeds. Instead of being homogeneously distributed along the genome, these loci are clustered at specific chromosomal locations. A high proportion of the Chillingham in iduals examined were heterozygous at many of these polymorphic loci, suggesting that some loci are under balancing selection. Some of these frequently heterozygous loci have been implicated as sites of recessive lethal mutations in cattle. Linkage disequilibrium equal or close to 100% was found to span up to 1350 kb, and LD was above r(2) = 0.25 up to more than 5000 kb. This strong LD is consistent with the lack of polymorphic loci in the herd. The heterozygous regions in the Chillingham cattle may be the locations of genes relevant to fitness or survival, which may help elucidate the biology of local adaptation in traditional breeds and facilitate selection for such traits in commercial cattle.
A luteinizing hormone receptor intronic variant is significantly associated with decreased risk of Alzheimer's disease in males carrying an apolipoprotein E ε4 allele
Publisher: Springer Science and Business Media LLC
Date: 25-04-2008
Abstract: Genetic and biochemical studies support the apolipoprotein E ( APOE ) ε4 allele as a major risk factor for late-onset Alzheimer's disease (AD), though ~50% of AD patients do not carry the allele. APOE transports cholesterol for luteinizing hormone (LH)-regulated steroidogenesis, and both LH and neurosteroids have been implicated in the etiology of AD. Since polymorphisms of LH beta-subunit ( LHB ) and its receptor ( LHCGR ) have not been tested for their association with AD, we scored AD and age-matched control s les for APOE genotype and 14 polymorphisms of LHB and LHCGR . Thirteen gene-gene interactions between the loci of LHB , LHCGR , and APOE were associated with AD. The most strongly supported of these interactions was between an LHCGR intronic polymorphism (rs4073366 lhcgr2) and APOE in males, which was detected using all three interaction analyses: linkage disequilibrium, multi-dimensionality reduction, and logistic regression. While the APOE ε4 allele carried significant risk of AD in males [p = 0.007, odds ratio (OR) = 3.08(95%confidence interval: 1.37, 6.91)], ε4-positive males carrying 1 or 2 C-alleles at lhcgr2 exhibited significantly decreased risk of AD [OR = 0.06(0.01, 0.38) p = 0.003]. This suggests that the lhcgr2 C-allele or a closely linked locus greatly reduces the risk of AD in males carrying an APOE ε4 allele. The reversal of risk embodied in this interaction powerfully supports the importance of considering the role gene-gene interactions play in the etiology of complex biological diseases and demonstrates the importance of using multiple analytic methods to detect well-supported gene-gene interactions.
A heritable subset of the core rumen microbiome dictates dairy cow productivity and emissions
Publisher: American Association for the Advancement of Science (AAAS)
Date: 05-07-2019
Abstract: Cow genes dictate environmentally friendly microbiomes: a step towards reducing greenhouse gas emissions.
Adaptive selection signatures in river buffalo with emphasis on immune and major histocompatibility complex genes
Publisher: Elsevier BV
Date: 11-2021
DOI: 10.1016/J.YGENO.2021.08.021
Abstract: River buffalo is an agriculturally important species with many traits, such as disease tolerance, which promote its use worldwide. Highly contiguous genome assemblies of the river buffalo, goat, pig, human and two cattle subspecies were aligned to study gene gains and losses and signs of positive selection. The gene families that have changed significantly in river buffalo since ergence from cattle play important roles in protein degradation, the olfactory receptor system, detoxification and the immune system. We used the branch site model in PAML to analyse single-copy orthologs to identify positively selected genes that may be involved in skin differentiation, mammary development and bone formation in the river buffalo branch. The high contiguity of the genomes enabled evaluation of differences among species in the major histocompatibility complex. We identified a Babesia-like L1 LINE insertion in the DRB1-like gene in the river buffalo and discuss the implication of this finding.
Analysis of copy number variations in Holstein-Friesian cow genomes based on whole-genome sequence data
Publisher: American Dairy Science Association
Date: 07-2017
Abstract: Thirty-two whole genome DNA sequences of cows were analyzed to evaluate inter-in idual variability in the distribution and length of copy number variations (CNV) and to functionally annotate CNV breakpoints. The total number of deletions per in idual varied between 9,731 and 15,051, whereas the number of duplications was between 1,694 and 5,187. Most of the deletions (81%) and duplications (86%) were unique to a single cow. No relation between the pattern of variant sharing and a family relationship or disease status was found. The animal-averaged length of deletions was from 5,234 to 9,145 bp and the average length of duplications was between 7,254 and 8,843 bp. Highly significant inter-in idual variation in length and number of CNV was detected for both deletions and duplications. The majority of deletion and duplication breakpoints were located in intergenic regions and introns, whereas fewer were identified in noncoding transcripts and splice regions. Only 1.35 and 0.79% of the deletion and duplication breakpoints were observed within coding regions. A gene with the highest number of deletion breakpoints codes for protein kinase cGMP-dependent type I, whereas the T-cell receptor α constant gene had the most duplication breakpoints. The functional annotation of genes with the largest incidence of deletion/duplication breakpoints identified 87/112 Kyoto Encyclopedia of Genes and Genomes pathways, but none of the pathways were significantly enriched or depleted with breakpoints. The analysis of Gene Ontology (GO) terms revealed that a cluster with the highest enrichment score among genes with many deletion breakpoints was represented by GO terms related to ion transport, whereas the GO term cluster mostly enriched among the genes with many duplication breakpoints was related to binding of macromolecules. Furthermore, when considering the number of deletion breakpoints per gene functional category, no significant differences were observed between the "housekeeping" and "strong selection" categories, but genes representing the "low selection pressure" group showed a significantly higher number of breakpoints.
A high proportion of bovine blastocysts produced in vitro are mixoploid
Publisher: Oxford University Press (OUP)
Date: 06-1999
DOI: 10.1095/BIOLREPROD60.6.1273
Abstract: Fluorescence in situ hybridization with chromosome 6- and chromosome 7-specific probes was used to assess the extent of chromosome abnormalities in developing bovine blastocysts at 7-8 days after insemination in vivo or in vitro. Interphase nuclei (N = 10 946) were analyzed from 151 blastocysts produced in vitro and from 28 blastocysts recovered from superovulated animals. This revealed that 72% (109 of 151) of the in vitro-produced blastocysts were mixoploid, i.e., were a mixture of normal, diploid, and polyploid cells. However, only a small fraction of the total number of cells were chromosomally abnormal. Of the mixoploid blastocysts, 83% (91 of 109) contained less than 10% polyploid cells, 13% (14 of 109) contained 11-25% polyploid cells, and only 4% (4 of 109) of the blastocysts had more than 25% polyploid cells per blastocyst. In contrast, a significantly lower proportion (25%) of mixoploidy was found in 28 bovine blastocysts developed in vivo (p < 0.0001). All of the mixoploid blastocysts that had developed in vivo contained less than 10% polyploid cells. No entirely aneuploid blastocysts, i. e., blastocysts in which all cells had the same type of chromosome abnormality, were found in either of the groups. Taken together, the most common chromosome abnormalities observed were diploid-triploid mixoploidies and diploid-tetraploid mixoploidies. Thus, our results confirm earlier reports that morphologically normal bovine blastocysts developed in vivo are often mixoploids. We further show that in vitro-produced bovine blastocysts have a high rate of mixoploidy. Although the difference in mixoploidy rate detected in this study may not be general, it is an interesting phenomenon for further studies.
Live weight, body size and carcass characteristics of young bulls of fifteen European breeds
Publisher: Elsevier BV
Date: 03-2008
Characterization of bovine FAS-associated death domain gene
Publisher: Wiley
Date: 16-12-2005
DOI: 10.1111/J.1365-2052.2004.01207.X
Abstract: The FAS-associated death domain (FADD) protein is an adapter/signaling molecule that has been shown to function in human cells to promote apoptosis and to inhibit NF-kappaB activation. Because of the critical role that apoptosis and NF-kappaB play in a variety of disease states, we mapped the bovine FADD gene, sequenced bovine FADD cDNA, and characterized its expression in endothelial cells (EC). Sequencing of bovine FADD revealed approximately 65 and 58% amino acid sequence identity to its human and murine homologues, respectively. Bovine FADD was mapped to chromosome 29 by radiation hybrid mapping. In addition, the functionality of bovine FADD was studied. Expression of a bovine FADD dominant-negative construct blocked bacterial lipopolysaccharide (LPS)- and TNF-alpha-induced apoptosis in bovine EC consistent with previous studies of human FADD. In contrast to human FADD, elevated expression of bovine FADD had no effect on LPS- or TNF-alpha-induced upregulation of NF-kappaB-dependent gene products as assayed by E-selectin expression. Thus, while the role of FADD in mediating apoptosis is conserved across species, its role in regulating NF-kappaB-dependent gene expression is not.
AffyPipe: an open-source pipeline for Affymetrix Axiom genotyping workflow.
Publisher: Oxford University Press (OUP)
Date: 15-07-2014
DOI: 10.1093/BIOINFORMATICS/BTU486
Abstract: The Affymetrix Axiom genotyping standard and ‘best practice’ workflow for Linux and Mac users consists of three stand-alone executable programs (Affymetrix Power Tools) and an R package (SNPolisher). Currently, SNP analysis has to be performed in a step-by-step procedure. Manual intervention and/or programming skills by the user is required at each intermediate point, as Affymetrix Power Tools programs do not produce input files for the program next-in-line. An additional problem is that the output format of genotypes is not compatible with most analysis software currently available. AffyPipe solves all the above problems, by automating both standard and ‘best practice’ workflows for any species genotyped with the Axiom technology. AffyPipe does not require programming skills and performs all the steps necessary to obtain a final genotype file. Furthermore, users can directly edit SNP probes and export genotypes in PLINK format. Availability and implementation: icolazzie/AffyPipe.git . Contact: ezequiel.nicolazzi@tecnoparco.org
Consistency statistics and genetic parameters for taste panel assessed meat quality traits and their relationship with carcass quality traits in a commercial population of Angus-sired beef cattle
Publisher: Elsevier BV
Date: 2010
Comparison of the response of mammary gland tissue from two divergent lines of goat with high and low milk somatic cell scores to an experimental Staphylococcus aureus infection
Publisher: Elsevier BV
Date: 04-2021
Genome wide analysis of fertility and production traits in Italian Holstein cattle.
Publisher: Public Library of Science (PLoS)
Date: 12-11-2013
Discovery, characterization and validation of single nucleotide polymorphisms within 206 bovine genes that may be considered as candidate genes for beef production and quality
Publisher: Wiley
Date: 14-11-2009
DOI: 10.1111/J.1365-2052.2009.01874.X
Abstract: A large number of putative single nucleotide polymorphisms (SNPs) have been identified from the bovine genome-sequencing project. However, few of these have been validated and many will turn out to be sequencing artefacts or have low minor allele frequencies. In addition, there is little information available on SNPs within coding regions, which are likely to be responsible for phenotypic variation. Therefore, additional SNP discovery is necessary to identify and validate polymorphisms both in specific genes and genome-wide. Sequence-tagged sites within 286 genes were resequenced from a panel of animals representing a wide range of European cattle breeds. For 80 genes, no polymorphisms were identified, and 672 putative SNPs were identified within 206 genes. Fifteen European cattle breeds (436 in iduals plus available parents) were genotyped with these putative SNPs, and 389 SNPs were confirmed to have minor allele frequencies above 10%. The genes containing SNPs were localized on chromosomes by radiation hybrid mapping and on the bovine genome sequence by Blast. Flanking microsatellite loci were identified, to facilitate the alignment of the genes containing the SNPs in relation to mapped quantitative trait loci. Of the 672 putative SNPs discovered in this work, only 11 were found among the validated SNPs and 100 were found among the approximately 2.3 million putative SNPs currently in dbSNP. The genes studied in this work could be considered as candidates for traits associated with beef production and the SNPs reported will help to assess the role of the genes in the genetic control of muscle development and meat quality. The allele frequency data presented allows the general utility of the SNPs to be assessed.
Evaluation of responses to vaccination of angus cattle for four viruses that contribute to bovine respiratory disease complex
Publisher: Oxford University Press (OUP)
Date: 11-2017
DOI: 10.2527/JAS2017.1793
Bovine microsatellite loci are highly conserved in red deer (Cervus elaphus), sika deer (Cervus nippon) and Soay sheep (Ovis aries)
Publisher: Wiley
Date: 08-1998
DOI: 10.1046/J.1365-2052.1998.00347.X
Abstract: We tested 174 bovine microsatellite primer pairs for use in a primitive breed of sheep and two species of deer. Of 173 markers, 127 (73.4%) gave a product in Soay sheep (Ovis aries) of which 54 (42.5%) were polymorphic. One hundred and twenty-nine of 174 (74.1%) markers gave a product in red deer (Cervus elaphus) of which 72 (55.8%) were polymorphic. In sika deer (Cervus nippon) 126 of 171 (73.7%) microsatellite primers gave a product with 47 (37.3%) polymorphic. The proportion of bovine microsatellite loci conserved across artiodactyl species was significantly greater in this study than previously reported. Reasons for this high degree of microsatellite conservation are discussed. We suggest that a high resolution comparative map of the artiodactyls can be constructed using microsatellites.
Characterization of a 320-kb region containing the HEXA gene on bovine chromosome 10 and analysis of its association with BSE susceptibility
Publisher: Wiley
Date: 11-07-2008
DOI: 10.1111/J.1365-2052.2008.01743.X
Abstract: Bovine spongiform encephalopathy (BSE) belongs to a group of neurodegenerative diseases known as transmissible prion diseases. Recently, variants in the promoter region of the prion protein (PRNP) gene have been shown to have a considerable effect on the susceptibility to BSE. However, a previous genome scan revealed other putative BSE-susceptibility loci. Here, we analysed such a region on BTA10, which contains the functional candidate gene HEXA. Three hundred and twenty kilobases that, besides HEXA, also contain ARIH1, BRUNOL6 and PARP6 were characterized and screened for polymorphisms. Genotyping of 38 SNPs in Holstein-Friesian animals from the UK (350 diseased and 270 controls) revealed two intronic SNPs that were associated with BSE incidence, with experiment-wise P-values of 3.5 x 10(-3) and 7.7 x 10(-3) respectively. Both SNPs were in strong linkage disequilibrium and the rare alleles had a protective effect. These alleles were contained in a haplotype dubbed 'UK-protective' that was significantly overrepresented in the controls with a permuted P-value of 2 x 10(-3). An association study in German Holstein animals (73 diseased and 627 controls) revealed an opposite effect of the 'UK-protective' haplotype in this population, i.e. it was overrepresented in the diseased animals, although not significant after correction for multiple testing. These findings indicate a causal variant for BSE susceptibility on BTA10 in linkage disequilibrium with the markers studied. Candidate gene analyses of the surrounding region and additional association studies will help to clarify the origin of the protective effects and to identify causal variants for BSE susceptibility on BTA10.
Demystifying the Clinical Diagnosis of Greater Trochanteric Pain Syndrome in Women
Publisher: Mary Ann Liebert Inc
Date: 06-2017
Abstract: To evaluate the diagnostic accuracy of 10 clinical tests that can be used in the diagnosis of greater trochanteric pain syndrome (GTPS) in women, and to compare these clinical tests to magnetic resonance imaging (MRI) findings. Twenty-eight participants with GTPS (49.5 ± 22.0 years) and 18 asymptomatic participants (mean age ± standard deviation [SD], 52.5 ± 22.8 years) were included. A blinded physiotherapist performed 10 pain provocation tests potentially diagnostic for GTPS-palpation of the greater trochanter, resisted external derotation test, modified resisted external derotation test, standard and modified Ober's tests, Patrick's or FABER test, resisted hip abduction, single-leg stance test, and the resisted hip internal rotation test. A s le of 16 symptomatic and 17 asymptomatic women undertook a hip MRI scan. Gluteal tendons were evaluated and categorized as no pathology, mild tendinosis, moderate tendinosis artial tear, or full-thickness tear. Clinical test analyses show high specificity, high positive predictive value, low to moderate sensitivity, and negative predictive value for most clinical tests. All symptomatic and 88% of asymptomatic participants had pathological gluteal tendon changes on MRI, from mild tendinosis to full-thickness tear. The study found the Patrick's or FABER test, palpation of the greater trochanter, resisted hip abduction, and the resisted external derotation test to have the highest diagnostic test accuracy for GTPS. Tendon pathology on MRI is seen in both symptomatic and asymptomatic women.
Breed relationships and definition in British cattle: a genetic analysis.
Publisher: Springer Science and Business Media LLC
Date: 25-08-2004
Synchronous diversification of sulawesi’s iconic artiodactyls driven by recent geological events
Publisher: The Royal Society
Date: 11-04-2018
Abstract: The high degree of endemism on Sulawesi has previously been suggested to have vicariant origins, dating back to 40 Ma. Recent studies, however, suggest that much of Sulawesi's fauna assembled over the last 15 Myr. Here, we test the hypothesis that more recent uplift of previously submerged portions of land on Sulawesi promoted ersification and that much of its faunal assemblage is much younger than the island itself. To do so, we combined palaeogeographical reconstructions with genetic and morphometric datasets derived from Sulawesi's three largest mammals: the babirusa, anoa and Sulawesi warty pig. Our results indicate that although these species most likely colonized the area that is now Sulawesi at different times (14 Ma to 2–3 Ma), they experienced an almost synchronous expansion from the central part of the island. Geological reconstructions indicate that this area was above sea level for most of the last 4 Myr, unlike most parts of the island. We conclude that emergence of land on Sulawesi (approx. 1–2 Myr) may have allowed species to expand synchronously. Altogether, our results indicate that the establishment of the highly endemic faunal assemblage on Sulawesi was driven by geological events over the last few million years.
A genome-wide scan for signatures of selection in Azeri and Khuzestani buffalo breeds
Publisher: Springer Science and Business Media LLC
Date: 11-06-2018
Verification of the identity of bovine semen using DNA microsatellite markers
Publisher: Wiley
Date: 04-1997
Abstract: Over the past 30 years cattle have been identified by blood typing, but recently the use of DNA markers has provided a more precise method of identifying in iduals and verifying their parentage. This article describes the use of microsatellite-based DNA markers for confirming the identity of semen, as part of the evidence presented in a legal dispute. Two panels of markers and two methods for identifying allelic variation are compared for both approaches the likelihood of finding two Charolais in iduals with the same genotype was less than one in a million. Animals can therefore be identified conclusively from DNA s les, a technique which could be of use when their identity is in dispute.
New Insights into Mammalian Sex Chromosome Structure and Evolution from High-quality Bovine X and Y Chromosome Sequences
Publisher: Research Square Platform LLC
Date: 20-11-2019
Abstract: Background Mammalian X chromosomes are mainly euchromatic with a similar size and structure among species whereas Y chromosomes are smaller, have undergone substantial evolutionary changes and accumulated male specific genes and genes involved in sex determination. The PAR is conserved on the X and Y and pair during meiosis. The structure, evolution and function of mammalian sex chromosomes is still poorly understood because few species have high quality sex chromosome assemblies. Results Here we report the first bovine sex chromosome assemblies that include the complete pseudoautosomal region (PAR) spanning 6.84 Mb and three Y chromosome X-degenerate (X-d) regions. We show that the ruminant PAR comprises 31 genes and is similar to the PAR of pig and dog but extends further than those of human and horse. Differences in the pseudoautosomal boundaries are consistent with evolutionary ergence times. Conclusions A bovidae-specific expansion of members of the lipocalin gene family in the PAR may reflect immune-modulation and anti-inflammatory responses that contribute to parasite resistance in ruminants. Comparison of the X-d regions of Y chromosomes across species reveal five conserved X-Y gametologs, which are global regulators of gene activity, and may have a fundamental role in mammalian sexual dimorphism.
New Insights into Mammalian Sex Chromosome Structure and Evolution from High-quality Bovine X and Y Chromosome Sequences
Publisher: Research Square Platform LLC
Date: 30-08-2019
Abstract: Background Mammalian X chromosomes are mainly euchromatic with a similar size and structure among species whereas Y chromosomes are smaller, have undergone substantial evolutionary changes and accumulated male specific genes and genes involved in sex determination. The PAR is conserved on the X and Y and pair during meiosis. The structure, evolution and function of mammalian sex chromosomes is still poorly understood because few species have high quality sex chromosome assemblies. Results Here we report the first bovine sex chromosome assemblies that include the complete pseudoautosomal region (PAR) spanning 6.84 Mb and three Y chromosome X-degenerate (X-d) regions. We show that the ruminant PAR comprises 31 genes and is similar to the PAR of pig and dog but extends further than those of human and horse. Differences in the pseudoautosomal boundaries are consistent with evolutionary ergence times. Conclusions A bovidae-specific expansion of members of the lipocalin gene family in the PAR may reflect immune-modulation and anti-inflammatory responses that contribute to parasite resistance in ruminants. Comparison of the X-d regions of Y chromosomes across species reveal five conserved X-Y gametologs, which are global regulators of gene activity, and may have a fundamental role in mammalian sexual dimorphism.
New Insights into Mammalian Sex Chromosome Structure and Evolution from High-quality Bovine X and Y Chromosome Sequences
Publisher: Research Square Platform LLC
Date: 07-10-2019
Abstract: Background Mammalian X chromosomes are mainly euchromatic with a similar size and structure among species whereas Y chromosomes are smaller, have undergone substantial evolutionary changes and accumulated male specific genes and genes involved in sex determination. The PAR is conserved on the X and Y and pair during meiosis. The structure, evolution and function of mammalian sex chromosomes is still poorly understood because few species have high quality sex chromosome assemblies. Results Here we report the first bovine sex chromosome assemblies that include the complete pseudoautosomal region (PAR) spanning 6.84 Mb and three Y chromosome X-degenerate (X-d) regions. We show that the ruminant PAR comprises 31 genes and is similar to the PAR of pig and dog but extends further than those of human and horse. Differences in the pseudoautosomal boundaries are consistent with evolutionary ergence times. Conclusions A bovidae-specific expansion of members of the lipocalin gene family in the PAR may reflect immune-modulation and anti-inflammatory responses that contribute to parasite resistance in ruminants. Comparison of the X-d regions of Y chromosomes across species reveal five conserved X-Y gametologs, which are global regulators of gene activity, and may have a fundamental role in mammalian sexual dimorphism.
Design and validation of a 90K SNP genotyping assay for the water buffalo (Bubalus bubalis)
Publisher: Public Library of Science (PLoS)
Date: 05-10-2017
Associations between single nucleotide polymorphisms in multiple candidate genes and carcass and meat quality traits in a commercial Angus-cross population
Publisher: Elsevier BV
Date: 12-2010
DOI: 10.1016/J.MEATSCI.2010.08.005
Abstract: The aim of this study was to evaluate the effects of 28 single nucleotide polymorphisms (SNP) in 10 candidate genes previously shown to be associated with quality traits in pigs and cattle. The data set comprised 28 traits recorded on a commercial population of 536 Aberdeen Angus-cross beef cattle. Among the traits, 20 were carcass and sirloin quality related, one mechanical measure of tenderness, and the remaining seven were taste panel assessed sensory traits. The candidate genes studied included growth hormone (GH) and pro-opiomelanocortin (POMC). Association analysis showed that 13 of the 28 SNPs were significantly associated with at least one of the traits. Some of these were novel (POMC and mechanical tenderness), whilst others confirmed previous results (GH and eye muscle length). Following validation in other populations and breeds, these markers could be incorporated into breeding programs to increase the rate of improvement in carcass and meat quality traits.
The subtle effects of sea water acidification on the amphipod <i>Gammarus locusta</i>
Publisher: Copernicus GmbH
Date: 07-08-2009
Abstract: Abstract. We report an investigation of the effects of increases in pCO2 on the survival, growth and molecular physiology of the neritic hipod Gammarus locusta which has a cosmopolitan distribution in estuaries. Amphipods were reared from juvenile to mature adult in laboratory microcosms at three different levels of pH in nominal range 8.1–7.6. Growth rate was estimated from weekly measures of body length. At sexual maturity the hipods were sacrificed and assayed for changes in the expression of genes coding for a heat shock protein (hsp70 gene) and the metabolic enzyme glyceraldehyde-3-phosphate dehydrogenase (gapdh gene). The data show that the growth and survival of this species is not significantly impacted by a decrease in sea water pH of up to 0.5 units. Quantitative real-time PCR analysis indicated that there was no significant effect of growth in acidified sea water on the sustained expression of the hsp70 gene. There was a consistent and significant increase in the expression of the gapdh gene at a pH of ~7.5 which, when combined with observations from other workers, suggests that metabolic changes may occur in response to acidification. It is concluded that sensitive assays of tissue physiology and molecular biology should be routinely employed in future studies of the impacts of sea water acidification as subtle effects on the physiology and metabolism of coastal marine species may be overlooked in conventional gross "end-point" studies of organism growth or mortality.
Mapping of the bovine homologue of the human chromosome 14 open reading frame 4 (C14orf4) gene to BTA10q36
Publisher: Wiley
Date: 29-11-2004
Relationships between Podolic cattle breeds assessed by single nucleotide polymorphisms (SNPs) genotyping
Publisher: Wiley
Date: 28-10-2010
DOI: 10.1111/J.1439-0388.2010.00868.X
Abstract: Italian Maremmana, Turkish Grey and Hungarian Grey breeds belong to the same Podolic group of cattle, have a similar conformation and recently experienced a similar demographic reduction. The aim of this study was to assess the relationship among the analysed Podolic breeds and to verify whether their genetic state reflects their history. To do so, approximately 100 single nucleotide polymorphisms (SNPs) were genotyped on in iduals belonging to these breeds and compared to genotypes of in iduals of two Italian beef breeds, Marchigiana and Piemontese, which underwent different selection and migration histories. Population genetic parameters such as allelic frequencies and heterozygosity values were assessed, genetic distances calculated and assignment test performed to evaluate the possibility of recent admixture between the populations. The data show that the physical similarity among the Podolic breeds examined, and particularly between Hungarian Grey and Maremmana cattle that experienced admixture in the recent past, is mainly morphological. The assignment of in iduals from genotype data was achieved using Bayesian inference, confirming that the set of chosen SNPs is able to distinguish among the breeds and that the breeds are genetically distinct. In iduals of Turkish Grey breed were clearly assigned to their breed of origin for all clustering alternatives, showing that this breed can be differentiated from the others on the basis of the allelic frequencies. Remarkably, in the Turkish Grey there were differences observed between the population of Enez district, where in situ conservation studies are practised, and that of Bandirma district of Balikesir, where ex situ conservation studies are practised out of the original raising area. In conclusion, this study demonstrates that molecular data could be used to reveal an unbiased view of past events and provide the basis for a rational exploitation of livestock, suggesting appropriate cross-breeding plans based on genetic distance or breeding strategies that include the population structure.
Identification of QTL with effects on fatty acid composition of meat in a Charolais×Holstein cross population
Publisher: Elsevier BV
Date: 08-2010
DOI: 10.1016/J.MEATSCI.2010.03.031
Abstract: A whole-genome scan was carried out to detect quantitative trait loci (QTL) influencing beef fatty acid composition using a CharolaisxHolstein population established using a balanced F2 and Backcross breeding design. The phenotypes considered in this study included a total of 24 fatty acid related traits determined in loin muscle s les of the 235 second-generation cross-bred bull calves of the herd. The QTL regression analysis performed, based on 165 microsatellite markers distributed across the 29 bovine autosomes, identified 34 QTL with F-ratios exceeding the 5% chromosome-wide significance threshold. Three of these QTL, one located on chromosome 1 (for the content on linoleic acid, C18:2n-6) and two on chromosome 10 (for the content of gamma-linoleic DPA-docosapentaenoic and DPA-docosapentaenoic, C20:3n-6 and C22:5n-3), also exceeded the 5% genome-wide significance level. A follow-up analysis correcting for intramuscular fat content showed that some of the QTL detected initially (e.g. those localised on chromosome 22) were influenced by fat deposition differences between the founder breeds. The coincident location of some of the linkage associations identified and QTL previously reported for beef fatty acid composition and other meat quality traits, in the same or other cattle populations, provides supporting evidence for the results reported here.
Information content in genome-wide scans: concordance between patterns of genetic differentiation and linkage mapping associations
Publisher: Springer Science and Business Media LLC
Date: 26-01-2011
Whole genome linkage disequilibrium maps in cattle
Publisher: Springer Science and Business Media LLC
Date: 25-10-2007
Abstract: Bovine whole genome linkage disequilibrium maps were constructed for eight breeds of cattle. These data provide fundamental information concerning bovine genome organization which will allow the design of studies to associate genetic variation with economically important traits and also provides background information concerning the extent of long range linkage disequilibrium in cattle. Linkage disequilibrium was assessed using r 2 among all pairs of syntenic markers within eight breeds of cattle from the Bos taurus and Bos indicus subspecies. Bos taurus breeds included Angus, Charolais, Dutch Black and White Dairy, Holstein, Japanese Black and Limousin while Bos indicus breeds included Brahman and Nelore. Approximately 2670 markers spanning the entire bovine autosomal genome were used to estimate pairwise r 2 values. We found that the extent of linkage disequilibrium is no more than 0.5 Mb in these eight breeds of cattle. Linkage disequilibrium in cattle has previously been reported to extend several tens of centimorgans. Our results, based on a much larger s le of marker loci and across eight breeds of cattle indicate that in cattle linkage disequilibrium persists over much more limited distances. Our findings suggest that 30,000–50,000 loci will be needed to conduct whole genome association studies in cattle.
An expanded comparative map of bovine chromosome 27 targeting dairy form QTL regions
Publisher: Wiley
Date: 08-06-2004
An alternative experimental case-control design for genetic association studies on bovine mastitis
Publisher: Elsevier BV
Date: 2017
The quest for genes involved in adaptation to climate change in ruminant livestock
Publisher: MDPI AG
Date: 28-09-2021
DOI: 10.3390/ANI11102833
Abstract: Livestock radiated out from domestication centres to most regions of the world, gradually adapting to erse environments, from very hot to sub-zero temperatures and from wet and humid conditions to deserts. The climate is changing generally global temperature is increasing, although there are also more extreme cold periods, storms, and higher solar radiation. These changes impact livestock welfare and productivity. This review describes advances in the methodology for studying livestock genomes and the impact of the environment on animal production, giving ex les of discoveries made. Sequencing livestock genomes has facilitated genome-wide association studies to localize genes controlling many traits, and population genetics has identified genomic regions under selection or introgressed from one breed into another to improve production or facilitate adaptation. Landscape genomics, which combines global positioning and genomics, has identified genomic features that enable animals to adapt to local environments. Combining the advances in genomics and methods for predicting changes in climate is generating an explosion of data which calls for innovations in the way big data sets are treated. Artificial intelligence and machine learning are now being used to study the interactions between the genome and the environment to identify historic effects on the genome and to model future scenarios.
A viable herd of genetically uniform cattle
Publisher: Springer Science and Business Media LLC
Date: 18-01-2001
DOI: 10.1038/35053160
Colour variability of beef in young bulls from fifteen European breeds
Publisher: Wiley
Date: 27-07-2018
DOI: 10.1111/IJFS.13890
Altered expression of class I major histocompatibility antigens on bovine cells infected with the protozoan parasite Theileria annulata
Publisher: Elsevier BV
Date: 03-1996
DOI: 10.1016/0165-2427(95)05487-1
Abstract: Theileria annulata infection is controlled by MHC class I restricted cytotoxic T cell killing of infected cells. The long term persistence of parasite suggests that it employs a mechanism to avoid immune surveillance. In this paper we describe the modification of BoLA class I antigens on the surface of Theileria annulata transformed lymphoblastoid cells. The extent of modification is different between in iduals varying from extensive to undetectable.
Elucidating the genetic basis of an oligogenic birth defect using whole genome sequence data in a non-model organism,Bubalus bubalis
Publisher: Cold Spring Harbor Laboratory
Date: 29-06-2016
DOI: 10.1101/060996
Abstract: Recent strong selection for dairy traits in water buffalo has been associated with higher levels of inbreeding, leading to an increase in the prevalence of genetic diseases such as transverse hemimelia (TH), a congenital developmental abnormality characterized by the absence of a variable distal portion of the hindlimbs. The limited genomic resources available for water buffalo, in conjunction with an unconfirmed inheritance pattern, required an original approach to identify genetic variants associated with this disease. The genomes of 4 bilaterally affected cases, 7 unilaterally affected cases, and 14 controls were sequenced. Variant calling identified 19.8 million high confidence single nucleotide polymorphisms (SNPs) and 2.8 million insertions/deletions (INDELs). A concordance analysis of SNPs and INDELs requiring all unilateral and bilateral cases and none of the controls to be homozygous for the same allele, revealed two genes, WNT7A and SMARCA4 , known to play a role in embryonic hindlimb development. Additionally, SNP alleles in NOTCH1 and RARB were homozygous exclusively in the bilaterally affected cases, suggesting an oligogenic mode of inheritance. Homozygosity mapping by whole genome de novo assembly was then used to identify large contigs representing regions of homozygosity in the cases. This also supported an oligogenic mode of inheritance implicating 13 genes involved in aberrant hindlimb development in the bilateral cases and 11 in the unilateral cases. A genome-wide association study (GWAS) predicted additional modifier genes. Results from these analyses suggest that mutations in SMARCA4 and WNT7A are required for expression of TH, while several other loci including NOTCH1 act as modifiers and increase the severity of the disease phenotype. Although our data show that the inheritance of TH is complex, we predict that homozygous variants in WNT7A and SMARCA4 are necessary for the expression of TH and selection against these variants and avoidance of carrier-to-carrier matings should eradicate TH. Genetic diseases often occur and are spread through small populations under strong selection where rates of inbreeding can be significant. The use of a limited number of water buffalo males via artificial insemination for genetic improvement of milk and milk composition has increased the frequency of the genetic disease, transverse hemimelia (TH). Transverse hemimelia affected calves are normally developed except for malformation of one or both hindlimbs or both hindlimbs and one or both forelimbs. Little is known about the inheritance pattern of TH. We discovered genetic variants present in cases where both hindlimbs and one forelimb were affected, cases were both hindlimbs were affected, cases where only one hindlimb was affected, and in non-affected water buffalo that predict TH to be inherited as an oligogenic disease with two driver loci necessary for disease expression and several additional modifier genes that are responsible for the severity of the disease phenotype. We predict that selection against mutations in the two major loci and the avoidance of mating animals that are heterozygous for these mutations will eliminate TH from water buffalo.
Study of whole genome linkage disequilibrium patterns of Iranian water buffalo breeds using the Axiom Buffalo Genotyping 90K Array
Publisher: Public Library of Science (PLoS)
Date: 31-05-2019
Genome‐wide association study for antibody response to Mycobacterium avium ssp. paratubeculosis in goats
Publisher: Wiley
Date: 02-11-2023
DOI: 10.1111/AGE.13271
Abstract: Mycobacterium avium ssp. paratuberculosis (MAP), causes Johne's disease (JD), or paratuberculosis, a chronic enteritis of ruminants, which in goats is characterized by ileal lesions. The work described here is a case–control association study using the Illumina Caprine SNP50 BeadChip to unravel the genes involved in susceptibility of goats to JD. Goats in herds with a high occurrence of Johne's disease were classified as healthy or infected based on the level of serum antibodies against MAP, and 331 animals were selected for the association study. Goats belonged to the Jonica (157) and Siriana breeds (174). Whole‐genome association analysis identified one region suggestive of significance associated with an antibody response to MAP on chromosome 7 ( p ‐value = 1.23 × 10 −5 ). These results provide evidence for genetic loci involved in the antibody response to MAP in goats.
Natural killer cell receptors in cattle: a bovine killer cell immunoglobulin-like receptor multigene family contains members with divergent signaling motifs
Publisher: Wiley
Date: 04-2003
Abstract: Natural killer (NK) cells recognize and kill certain tumor cells, virally infected cells and MHC class I-disparate normal hematopoietic cells. NK cell cytotoxicity is regulated by a multitude of receptors with either activating or inhibitory signaling function. We here report the molecular cloning of bovine CD94 [killer cell lectin-like receptor (KLR)-D1] and NKp46 orthologues, four members of a bovine CD158 [killer cell immunoglobulin-like receptor (KIR)] family, and a novel KLR. This novel receptor was termed KLRJ1 and is most similar to Ly-49 (KLRA). The KLRD1 and KLRJ1 loci were mapped to a bovine NK gene complex on chromosome 5 by radiation hybrid mapping, whereas KIR2DL1 and NKP46 were localized to chromosome 18. Two of the bovine KIR(KIR2DL1 and KIR3DL1) contain immunoreceptor tyrosine-based inhibition motifs (ITIM), suggesting an inhibitory function. Bovine KIR2DS1 and KIR3DS1 lack ITIM but have an arginine-containing motif in their transmembrane domain, similar to primate KIR2DL4. Thus, KIR multigene families with ergent signaling motifs do not only exist in primates. Based on sequence comparison, it appears that the primate and bovine KIR multigene families may have evolved independently.
Genome-wide search for markers associated with bovine spongiform encephalopathy
Publisher: Springer Science and Business Media LLC
Date: 03-2002
DOI: 10.1007/BF02684022
Molecular cloning, expression and radiation hybrid mapping of the bovine deiodinase type II (DIO2) and deiodinase type III (DIO3) genes
Publisher: Wiley
Date: 06-2005
DOI: 10.1111/J.1365-2052.2005.01282.X
Abstract: Thyroid hormones play a critical role in mammalian development and metabolism. Their activity is regulated in a complex, tissue-specific manner by three isoforms of deiodinases. The goal of this study was to sequence the full-length bovine type II deiodinase (DIO2) and type III deiodinase (DIO3) cDNAs and characterize mRNA expression levels of each of the three deiodinase isoforms in several bovine tissues. Sequencing of bovine DIO2 and DIO3 cDNAs revealed a high degree of predicted amino acid sequence identity with their orthologs in other mammalian species and demonstrated the conservation of selenocysteine residues within the catalytic domains of both bovine proteins. Bovine DIO2 and DIO3 were positioned on chromosomes 10 and 21, respectively, by radiation hybrid mapping. Expression patterns of the three deiodinase isoforms were similar for deiodinase type I (DIO1) and DIO2 to those observed in other species. Expression level of DIO3 transcripts was greatest in mammary gland and kidney, although low-level expression was detected in most tissues s led. Results of this work will aid in the study of deiodinase gene expression and thyroid hormone regulation in cattle.
SNP included in candidate genes involved in muscle, lipid and energy metabolism behave like neutral markers
Publisher: CSIRO Publishing
Date: 2015
DOI: 10.1071/AN14605
Abstract: Studies of population structure and ersity in cattle have provided insights into the origins of breeds, their history and evolution, and allow the identification of global livestock ersity hotspots, which is important for conservation of ersity. Genetic ersity, genetic relationship, population structure, and the presence of hotspots of genetic ersity among 15 European bovine breeds from five countries were assessed using 435 single nucleotide polymorphisms (SNP) markers identified in candidate genes for muscle, lipid and energy metabolism, thus providing the opportunity to compare the breed relationships obtained using putatively functional markers with previous data using neutral loci. In iduals belonging to 11 breeds tended to be clearly assigned to a single cluster when the number of pre-defined populations reached a maximum in the likelihood of the data at K = 12, whereas Asturiana de los Valles, Danish Red, Simmental, and Avileña-Negra Ibérica displayed a greater degree of admixture, which may be explained by their erse ancestry. Although overall results were in agreement with those reported by studies based on neutral genetic variations, some additional breed relationship information emerged using markers in candidate functional loci, including the relationship between the Asturiana de los Valles and Piedmontese, and Danish Red and Charolais breeds. This study indicates that the analysed loci have not been main targets for selection or for adaptation processes, but also that SNP within candidate genes related with beef characteristics and performance may provide a slightly new perspective on past breeding and may also help in the development of strategies for the rational conservation of livestock ersity.
Genome wide scan for somatic cell counts in holstein bulls
Publisher: Springer Science and Business Media LLC
Date: 03-06-2011
The effects of early training sessions on the reactions of foals at 1, 2, and 3 months of age
Publisher: Elsevier BV
Date: 05-2002
An assessment of population structure in eight breeds of cattle using a whole genome SNP panel
Publisher: Springer Science and Business Media LLC
Date: 20-05-0051
Abstract: Analyses of population structure and breed ersity have provided insight into the origin and evolution of cattle. Previously, these studies have used a low density of microsatellite markers, however, with the large number of single nucleotide polymorphism markers that are now available, it is possible to perform genome wide population genetic analyses in cattle. In this study, we used a high-density panel of SNP markers to examine population structure and ersity among eight cattle breeds s led from Bos indicus and Bos taurus . Two thousand six hundred and forty one single nucleotide polymorphisms (SNPs) spanning all of the bovine autosomal genome were genotyped in Angus, Brahman, Charolais, Dutch Black and White Dairy, Holstein, Japanese Black, Limousin and Nelore cattle. Population structure was examined using the linkage model in the program STRUCTURE and Fst estimates were used to construct a neighbor-joining tree to represent the phylogenetic relationship among these breeds. The whole-genome SNP panel identified several levels of population substructure in the set of examined cattle breeds. The greatest level of genetic differentiation was detected between the Bos taurus and Bos indicus breeds. When the Bos indicus breeds were excluded from the analysis, genetic differences among beef versus dairy and European versus Asian breeds were detected among the Bos taurus breeds. Exploration of the number of SNP loci required to differentiate between breeds showed that for 100 SNP loci, in iduals could only be correctly clustered into breeds 50% of the time, thus a large number of SNP markers are required to replace the 30 microsatellite markers that are currently commonly used in genetic ersity studies.
New insights on water buffalo genomic diversity and post-domestication migration routes from medium density SNP chip data
Publisher: Frontiers Media SA
Date: 02-03-2018
Combinatorial discriminant analysis applied to RNAseq data reveals a set of 10 transcripts as signatures of exposure of cattle to mycobacterium avium subsp. Paratuberculosis
Publisher: MDPI AG
Date: 05-02-2020
DOI: 10.3390/ANI10020253
Abstract: Paratuberculosis or Johne’s disease in cattle is a chronic granulomatous gastroenteritis caused by infection with Mycobacterium avium subspecies paratuberculosis (MAP). Paratuberculosis is not treatable therefore, the early identification and isolation of infected animals is a key point to reduce its incidence. In this paper, we analyse RNAseq experimental data of 5 ELISA-negative cattle exposed to MAP in a positive herd, compared to 5 negative-unexposed controls. The purpose was to find a small set of differentially expressed genes able to discriminate between exposed animals in a preclinical phase from non-exposed controls. Our results identified 10 transcripts that differentiate between ELISA-negative, clinically healthy, and exposed animals belonging to paratuberculosis-positive herds and negative-unexposed animals. Of the 10 transcripts, five (TRPV4, RIC8B, IL5RA, ERF, CDC40) showed significant differential expression between the three groups while the remaining 5 (RDM1, EPHX1, STAU1, TLE1, ASB8) did not show a significant difference in at least one of the pairwise comparisons. When tested in a larger cohort, these findings may contribute to the development of a new diagnostic test for paratuberculosis based on a gene expression signature. Such a diagnostic tool could allow early interventions to reduce the risk of the infection spreading.
Transcriptional analysis of liver from chickens with fast (meat bird), moderate (F1 layer x meat bird cross) and low (layer bird) growth potential
Publisher: Springer Science and Business Media LLC
Date: 02-05-2018
Whole genome analysis of water buffalo and global cattle breeds highlights convergent signatures of domestication
Publisher: Springer Science and Business Media LLC
Date: 21-09-2020
DOI: 10.1038/S41467-020-18550-1
Abstract: More people globally depend on the water buffalo than any other domesticated species, and as the most closely related domesticated species to cattle they can provide important insights into the shared evolutionary basis of domestication. Here, we sequence the genomes of 79 water buffalo across seven breeds and compare patterns of between breed selective sweeps with those seen for 294 cattle genomes representing 13 global breeds. The genomic regions under selection between cattle breeds significantly overlap regions linked to stature in human genetic studies, with a disproportionate number of these loci also shown to be under selection between water buffalo breeds. Investigation of potential functional variants in the water buffalo genome identifies a rare ex le of convergent domestication down to the same mutation having independently occurred and been selected for across domesticated species. Cross-species comparisons of recent selective sweeps can consequently help identify and refine important loci linked to domestication.
Reduced stability of RNA coding for yolk polypeptide 3 in Drosophila melanogaster ovary
Publisher: Wiley
Date: 11-1986
DOI: 10.1111/J.1432-1033.1986.TB10128.X
Abstract: In Drosophila three yolk polypeptides (YP1, YP2 and YP3) are synthesized at two sites in the adult female: in the fat body tissue, from which they are transported via the haemolymph to the ovary, and in the ovarian follicle cells which surround the developing oocytes. All three yolk polypeptides are synthesized at equal levels in the fat body. In this paper we show that the steady-state level of YP3 RNA is significantly reduced in the ovary in comparison with the fat body, and that none of the yolk protein genes is lified either in the fat body or the follicle cells. In order to determine the basis of the reduced level of YP3 RNA in the ovary, which could result from a lower rate of transcription or through a decreased stability of the RNA, we have devised an in vivo method of determining relative rates of gene transcription. In both the fat body and the ovary all three yolk proteins are transcribed at similar rates. Thus we infer that YP3 RNA is destabilised in the ovary, accounting for the reduction in its steady-state level.
Response of the goat mammary gland to infection with Staphylococcus aureus revealed by gene expression profiling in milk somatic and white blood cells
Publisher: Springer Science and Business Media LLC
Date: 09-10-2012
Abstract: S. aureus is one of the main pathogens responsible for the intra-mammary infection in dairy ruminants. Although much work has been carried out to understand the complex physiological and cellular events that occur in the mammary gland in response to S. aureus , the protective mechanisms are still poorly understood. The objectives of the present study were to investigate gene expression during the early response of the goat mammary gland to an experimental challenge with S. aureus, in order to better understand the local and systemic response and to compare them in two ergent lines of goat selected for high and low milk somatic cell scores. No differences in gene expression were found between high and low SCS (Somatic Cells Score) selection lines. Analysing the two groups together, an expression of 300 genes were found to change from T0 before infection, and T4 at 24 hours and T5 at 30 hours following challenge. In blood derived white blood cells 8 genes showed increased expression between T0 and T5 and 1 gene has reduced expression. The genes showing the greatest increase in expression following challenge (5.65 to 3.16 fold change) play an important role in (i) immune and inflammatory response ( NFKB1 , TNFAIP6 , BASP1 , IRF1 , PLEK , BATF3 ) (ii) the regulation of innate resistance to pathogens ( PTX3 ) and (iii) the regulation of cell metabolism ( CYTH4 , SLC2A6 , ARG2 ). The genes with reduced expression (−1.5 to −2.5 fold) included genes involved in (i) lipid metabolism ( ABCG2 , FASN ), (ii) chemokine, cytokine and intracellular signalling ( SPPI ), and (iii) cell cytoskeleton and extracellular matrix ( KRT19 ). Analysis of genes with differential expression following infection showed an inverse relationship between immune response and lipid metabolism in the early response of the mammary gland to the S. aureus challenge. PTX3 showed a large change in expression in both milk and blood, and is therefore a candidate for further studies on immune response associated with mastitis.
Three bovine chromosome 15 microsatellite markers
Publisher: Wiley
Date: 04-1995
Traceability of four European Protected Geographic Indication (PGI) beef products using Single Nucleotide Polymorphisms (SNP) and Bayesian statistics
Publisher: Elsevier BV
Date: 12-2008
DOI: 10.1016/J.MEATSCI.2008.05.021
Abstract: The use of SNPs in combination with Bayesian statistics for the geographic traceability of cattle was evaluated using a dataset comprising 24 breeds from Italy, France, Spain, Denmark, the Netherlands, Switzerland and UK genotyped with 90 polymorphic markers. The percentage of correct assignment of the in iduals to their Country of origin was 90%, with an average assignment probability of 93% and an average specificity of 92%. The higher value was observed for UK breeds (97% of correct assignment) while Swiss animals were the most difficult to allocate (77% of correct assignment). Tracing of Protected Geographic Indication (PGI) products, the approach correctly assigned 100% of Guaranteed Pure Highland Beef 97% of "Vitellone dell'Appennino Centrale" breeds 84% of Ternera de Navarra, and 80% of Boeuf de Chalosse. Methods to verify Products of Designated Origin (PDO) and Protected Geographic Indication (PGI) products will help to protect regional foods and promote the economic growth of marginal rural areas by encouraging the production of high quality niche market foods.
Complete assembly of parental haplotypes with trio binning
Publisher: Cold Spring Harbor Laboratory
Date: 26-02-2018
DOI: 10.1101/271486
Abstract: Reference genome projects have historically selected inbred in iduals to minimize heterozygosity and simplify assembly. We challenge this dogma and present a new approach designed specifically for heterozygous genomes. “Trio binning” uses short reads from two parental genomes to partition long reads from an offspring into haplotype-specific sets prior to assembly. Each haplotype is then assembled independently, resulting in a complete diploid reconstruction. On a benchmark human trio, this method achieved high accuracy and recovered complex structural variants missed by alternative approaches. To demonstrate its effectiveness on a heterozygous genome, we sequenced an F1 cross between cattle subspecies Bos taurus taurus and Bos taurus indicus , and completely assembled both parental haplotypes with NG50 haplotig sizes Mbp and 99.998% accuracy, surpassing the quality of current cattle reference genomes. We propose trio binning as a new best practice for diploid genome assembly that will enable new studies of haplotype variation and inheritance.
Mapping of the ATP11B gene and refined localization of the SOX2a and FXR1b genes to BTA1q33
Publisher: Wiley
Date: 29-11-2004
Physical mapping of the KCNJ8 gene to bovine chromosome 5q3.2-q3.4
Publisher: Wiley
Date: 29-10-2004
SLCO1B1 variants and statin-induced myopathy - A genomewide study
Publisher: Massachusetts Medical Society
Date: 21-08-2008
Annotation of 390 bovine miRNA genes by sequence similarity with other species
Publisher: Wiley
Date: 19-01-2009
Genetic effects on coat colour in cattle: dilution of eumelanin and phaeomelanin pigments in an F2-Backcross Charolais × Holstein population
Publisher: Springer Science and Business Media LLC
Date: 16-08-2007
A 5× genome coverage bovine BAC library: production, characterization, and distribution
Publisher: Springer Science and Business Media LLC
Date: 07-1999
Abstract: A bovine large-insert DNA library has been constructed in a Bacterial Artificial Chromosome (BAC) vector. The source DNA was derived from lymphocytes of a Jersey male. High-molecular-weight DNA fragments were produced by treatment with EcoRI/EcoRI methylase and cloned into the EcoRI site of pBACe3.6. In total, 157,240 in idual BACs have been picked into 384-well plates. Approximately 190 randomly chosen clones have been characterized by Pulsed Field Gel Electrophoresis (PFGE) and have an average insert size of 105 kb, suggesting library coverage representing 5-6 genome equivalents. The frequency of clones without inserts is 4%. The chromosomal location of 51 BACs was studied by FISH 3 showed more than one signal, indicating a chimerism frequency of roughly 6%. Approximately 50% of the clones in the library contain Simple Repeat Sequences (microsatellites), and 4% of the clones contain centromeric repeats. Insert stability was assessed by restriction digestion of DNA prepared from 20 clones after serial culture for one and three nights. Only one clone showed any evidence of an altered restriction pattern. Clones from 360 x 384-well plates (138,240 colonies) were gridded onto high-density membranes, and PCR superpools were produced from the same set of clones. Both membranes and superpools are available from the RZPD, Berlin (www.rzpd.de). PCR 4-D superpools have been prepared from an additional 23,000 clones. The library has been screened for a total of 24 single-copy sequences positive clones have been obtained in all cases.
Using Omics Approaches in the Discovery of Biomarkers for Early Diagnosis of Johne’s Disease in Sheep and Goats
Publisher: MDPI AG
Date: 27-06-2021
DOI: 10.3390/ANI11071912
Abstract: Johne’s disease (JD) is caused by Mycobacterium avium subsp. paratuberculosis (MAP) and is an important and emerging problem in livestock therefore, its control and prevention is a priority to reduce economic losses and health risks. Most JD research has been carried out on cattle, but interest in the pathogenesis and diagnosis of this disease in sheep and goats is greatest in developing countries. Sheep and goats are also a relevant part of livestock production in Europe and Australia, and these species provide an excellent resource to study and better understand the mechanism of survival of MAP and gain insights into possible approaches to control this disease. This review gives an overview of the literature on paratuberculosis in sheep and goats, highlighting the immunological aspects and the potential for “omics” approaches to identify effective biomarkers for the early detection of infection. As JD has a long incubation period before the disease becomes evident, early diagnosis is important to control the spread of the disease.
Maternal peri-conceptional undernourishment perturbs offspring sperm methylome
Publisher: Bioscientifica
Date: 05-2020
DOI: 10.1530/REP-19-0549
Abstract: The genotype of an organism is stable throughout its life however, its epigenome is dynamic and can be altered in response to environmental factors, such as diet. Inheritance of acquired epigenetic modifications by the next generation occurs through the germline, although the precise mechanisms remain to be elucidated. Here, we used a sheep model to evaluate if modification of the maternal diet (CTR control, UND: undernutrition FA: undernutrition and folic acid supplementation) during the peri-conceptional period affects the genome-wide methylation status of the gametes of male offspring. Sperm DNA methylation, measured by Reduced Representation Bisulfite Sequencing (RRBS), identified Differentially Methylated Regions (DMR) in offspring that experienced in utero undernutrition, both in UND (244) and FA (240), compared with CTR. Gene ontology (GO) analysis identified DMRs in categories related to sperm function, therefore we investigated whether the fertilizing capacity of the semen from the three groups differed in an in vitro fertilization assay. Spermatozoa from the undernourished groups showed lower motility and sperm chromatin structure abnormalities, represented by a higher percentage of DNA fragmentation and an increased number of immature cells, compared with CTR. While good quality blastocysts were obtained from all three groups, the proportion of embryos reaching the blastocyst stage was reduced in the UND vs CTR, an effect partially rescued by the FA treatment. The data reported here show that nutritional stress during early pregnancy leads to epigenetic modifications in the semen of the resulting offspring, the effects of which in next generation remain to be elucidated.
Genes involved in muscle lipid composition in 15 European Bos taurus breeds
Publisher: Wiley
Date: 23-04-2013
DOI: 10.1111/AGE.12044
Abstract: Consumers demand healthy and palatable meat, both factors being affected by fat composition. However, red meat has relatively high concentration of saturated fatty acids and low concentration of the beneficial polyunsaturated fatty acids. To select animals prone to produce particular fat types, it is necessary to identify the genes influencing muscle lipid composition. This paper describes an association study in which a large panel of candidate genes involved in adipogenesis, lipid metabolism and energy homoeostasis was tested for effects on fat composition in 15 European cattle breeds. Sixteen genes were found to have significant effects on different lipid traits, and among these, CFL1 and MYOZ1 were found to have large effects on the ratio of 18:2/18:3, CRI1 on the amount of neutral adrenic acid (22:4 n-6), MMP1 on docosahexaenoic acid (22:6 n-3) and conjugated linoleic acid, PLTP on the ratio of n-6:n-3 and IGF2R on flavour. Several genes - ALDH2, CHRNE, CRHR2, DGAT1, IGFBP3, NEB, SOCS2, SUSP1, TCF12 and FOXO1 - also were found to be associated with both lipid and organoleptic traits although with smaller effect. The results presented here help in understanding the genetic and biochemical background underlying variations in fatty acid composition and flavour in beef.
Related Organisations
The University Of Edinburgh The Roslin Institute
Location: United Kingdom of Great Britain and Northern Ireland
King's College London
Location: United Kingdom of Great Britain and Northern Ireland
The University Of Edinburgh
Location: United Kingdom of Great Britain and Northern Ireland
National Institute For Medical Research
Location: United Kingdom of Great Britain and Northern Ireland
AFRC, The Animal Breeding Research Organisation
Location: United Kingdom of Great Britain and Northern Ireland
Related Funding Activities
No related grants have been discovered for John Williams.