ORCID Profile
0000-0003-0666-656X
Current Organisation
Michigan State University
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In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Turbulent Flows | Quantum Chemistry | Genetics | Animal Breeding | Interdisciplinary Engineering | Neural, Evolutionary and Fuzzy Computation | Nanophotonics | Quantitative Genetics (incl. Disease and Trait Mapping Genetics)
Education and Training not elsewhere classified | Beef Cattle | Sheep - Meat | Information and Communication Services not elsewhere classified | Expanding Knowledge in the Information and Computing Sciences | Expanding Knowledge in the Biological Sciences |
Publisher: IGI Global
Date: 2012
Publisher: Public Library of Science (PLoS)
Date: 07-10-2013
Publisher: Humana Press
Date: 2013
Publisher: Springer Science and Business Media LLC
Date: 18-02-2012
Publisher: Springer Science and Business Media LLC
Date: 24-11-2015
Publisher: Public Library of Science (PLoS)
Date: 29-03-2016
Publisher: Springer Science and Business Media LLC
Date: 12-2011
Abstract: In livestock populations the genetic contribution to muscling is intensively monitored in the progeny of industry sires and used as a tool in selective breeding programs. The genes and pathways conferring this genetic merit are largely undefined. Genetic variation within a population has potential, amongst other mechanisms, to alter gene expression via cis- or trans-acting mechanisms in a manner that impacts the functional activities of specific pathways that contribute to muscling traits. By integrating sire-based genetic merit information for a muscling trait with progeny-based gene expression data we directly tested the hypothesis that there is genetic structure in the gene expression program in ovine skeletal muscle. The genetic performance of six sires for a well defined muscling trait, longissimus lumborum muscle depth, was measured using extensive progeny testing and expressed as an Estimated Breeding Value by comparison with contemporary sires. Microarray gene expression data were obtained for longissimus lumborum s les taken from forty progeny of the six sires (4-8 progeny/sire). Initial unsupervised hierarchical clustering analysis revealed strong genetic architecture to the gene expression data, which also discriminated the sire-based Estimated Breeding Value for the trait. An integrated systems biology approach was then used to identify the major functional pathways contributing to the genetics of enhanced muscling by using both Estimated Breeding Value weighted gene co-expression network analysis and a differential gene co-expression network analysis. The modules of genes revealed by these analyses were enriched for a number of functional terms summarised as muscle sarcomere organisation and development, protein catabolism (proteosome), RNA processing, mitochondrial function and transcriptional regulation. This study has revealed strong genetic structure in the gene expression program within ovine longissimus lumborum muscle. The balance between muscle protein synthesis, at the levels of both transcription and translation control, and protein catabolism mediated by regulated proteolysis is likely to be the primary determinant of the genetic merit for the muscling trait in this sheep population. There is also evidence that high genetic merit for muscling is associated with a fibre type shift toward fast glycolytic fibres. This study provides insight into mechanisms, presumably subject to strong artificial selection, that underpin enhanced muscling in sheep populations.
Publisher: Springer Science and Business Media LLC
Date: 26-07-2016
Publisher: CSIRO Publishing
Date: 2014
DOI: 10.1071/AN12398
Abstract: Hormonal growth promotants (HGP) have been used to improve feed conversion ratio (FCR) and growth rates of cattle by modifying protein turnover rates. Residual feed intake (RFI) is correlated with FCR and has been adopted in Australia as a measure of feed efficiency in cattle for the purpose of genetic improvement. Eight genes (AHSG, GHR, GSTM1, INHBA, PCDH19, S100A10, SERPINI2 and SOD3) have been previously reported to be highly associated with RFI and could potentially be used to predict RFI in bulls and steers. In this study, expression levels of these genes in liver tissue of 46 cattle were measured by quantitative real-time PCR. These cattle were part of a larger tenderness gene marker experiment consisting of two breeds (Angus and Brahman) two sexes (steers and heifers) and HGP treatments (implanted vs control). Cattle were measured for growth, feed efficiency, body composition and carcass traits. Results showed the expression of these eight genes was significantly correlated with RFI. However, HGP treatment did not affect RFI or the expression of the RFI-associated genes. HGP treatment increased average daily gain by 20%, improved FCR by 18%, and increased rib eye-muscle area by 7.5%. HGP treatment was effective in improving growth rate, presumably by its known action in the protein turnover mechanism. This mechanism has been hypothesised as one of the regulators of RFI. Lack of effect of HGP treatment on RFI does not support this hypothesis.
Publisher: Springer Science and Business Media LLC
Date: 12-2015
DOI: 10.1186/S12862-015-0563-2
Abstract: The main cattle breed in Korea is the brown Hanwoo, which has been under artificial selection within a national breeding program for several decades. Varieties of the Hanwoo known as Jeju Black and Chikso were not included in the breeding program and remained isolated from the effects of recent artificial selection advancements. We analysed the Jeju Black and Chikso populations in regards to their genetic variability, state of inbreeding, as well as level of differentiation from the mainland Hanwoo population. Jeju Black and Chikso were found to have small estimated effective population sizes ( N e ) of only 11 and 7, respectively. Despite a small N e , higher than expected heterozygosity levels were observed (0.303 and 0.306), however, lower allelic richness was found for the two island populations (1.76 and 1.77) compared to the mainland population (1.81). The increase in heterozygosity could be due to environmental disease challenges that promoted maintenance of higher genetic variability however, no direct proof exists. Increased heterozygosity due to a first generation crossing of genetically different populations is not recorded. The differentiation between the Korean populations had F ST values between 0.014 and 0.036 which is not as high as the differentiation within European beef or dairy cattle breeds (0.047–0.111). This suggests that the three populations have not separated into independent breeds. Results agree with an island model of speciation where the brown Hanwoo represents the ancestral breed, whilst the Jeju Black and Chikso erge from this common ancestor, following different evolutionary trajectories. Nevertheless, differences are minor and whether Jeju Black and Chikso cattle will develop into discrete breeds or reintegrate with the main population has to be seen in the future and will largely depend on human management decisions. This offers a rare opportunity to accompany the development of new breeds but also poses challenges on how to preserve these incipient breeds and ensure their long term viability.
Publisher: Springer Science and Business Media LLC
Date: 2013
Publisher: Elsevier BV
Date: 04-2014
DOI: 10.1016/J.MEATSCI.2013.11.026
Abstract: The objective of this study was to evaluate the effects of seven single nucleotide polymorphisms (SNPs) in Calpain 1 and Calpastatin genes previously associated with meat tenderness attributes in other cattle breeds in Korean Hanwoo cattle. The Hanwoo resource population was used to study association of 7 SNPs with beef tenderness, flavor, juiciness, intramuscular fat and shear force. In this association study, CAST:c.182A>G (+0.14, P=0.04) and CAST:c.1985G>C (-0.12, P=0.02) had significant effects on juiciness, but no effects on other traits. In contrast, CAPN1:c.1589G>A was associated with meat tenderness (P=0.01) and juiciness (P=0.04). The CAPN1:c.1589G>A (Val530Ile) SNP marker displayed significant effect on the meat tenderness score which is strongly supported by molecular modeling of the CAPN1:c.1589G>A (Val530Ile) variant that inhibits CAST protein from binding more strongly than the wild-type protein, which may explain its effect on meat tenderness.
Publisher: Humana Press
Date: 2013
DOI: 10.1007/978-1-62703-447-0_19
Abstract: Natural selection has molded the evolution of species across all taxa. Much more recently, on an evolutionary scale, human-oriented selection started to play an important role in shaping organisms, markedly so after the domestication of animals and plants. These selection processes have left traceable marks in the genome. Following from the recent advances in molecular genetics technologies, a number of methods have been developed to detect such signals, termed genomic signatures of selection. In this chapter we discuss a straightforward protocol based on the F ST statistic to identify genomic regions that exhibit high variation in allelic frequency between groups, which is a characteristic of genomic regions that have gone through differential selection. How to define the borders of these regions and further explore its genetic content is then discussed.
Publisher: Wiley
Date: 04-02-2014
DOI: 10.1111/AGE.12119
Abstract: The Korean Hanwoo cattle have been intensively selected for production traits, especially high intramuscular fat content. It is believed that ancient crossings between different breeds contributed to forming the Hanwoo, but little is known about the genomic differences and similarities between other cattle breeds and the Hanwoo. In this work, cattle breeds were grouped by origin into four types and used for comparisons: the Europeans (represented by six breeds), zebu (Nelore), African taurine (N'Dama) and Hanwoo. All animals had genotypes for around 680 000 SNPs after quality control of genotypes. Average heterozygosity was lower in Nelore and N'Dama (0.22 and 0.21 respectively) than in Europeans (0.26-0.31, with Shorthorn as outlier at 0.24) and Hanwoo (0.29). Pairwise FST analyses demonstrated that Hanwoo are more related to European cattle than to Nelore, with N'Dama in an intermediate position. This finding was corroborated by principal components and unsupervised hierarchical clustering. Using genome-wide smoothed FST , 55 genomic regions potentially under positive selection in Hanwoo were identified. Among these, 29 were regions also detected in previous studies. Twenty-four regions were exclusive to Hanwoo, and a number of other regions were shared with one or two of the other groups. These regions overlap a number of genes that are related to immune, reproduction and fatty acid metabolism pathways. Further analyses are needed to better characterize the ancestry of the Hanwoo cattle and to define the genes responsible to the identified selection peaks.
Publisher: Elsevier BV
Date: 07-2014
Publisher: Springer Science and Business Media LLC
Date: 09-06-2010
Abstract: Whole genome association studies using highly dense single nucleotide polymorphisms (SNPs) are a set of methods to identify DNA markers associated with variation in a particular complex trait of interest. One of the main outcomes from these studies is a subset of statistically significant SNPs. Finding the potential biological functions of such SNPs can be an important step towards further use in human and agricultural populations (e.g., for identifying genes related to susceptibility to complex diseases or genes playing key roles in development or performance). The current challenge is that the information holding the clues to SNP functions is distributed across many different databases. Efficient bioinformatics tools are therefore needed to seamlessly integrate up-to-date functional information on SNPs. Many web services have arisen to meet the challenge but most work only within the framework of human medical research. Although we acknowledge the importance of human research, we identify there is a need for SNP annotation tools for other organisms. We introduce an R package called FunctSNP, which is the user interface to custom built species-specific databases. The local relational databases contain SNP data together with functional annotations extracted from online resources. FunctSNP provides a unified bioinformatics resource to link SNPs with functional knowledge (e.g., genes, pathways, ontologies). We also introduce dbAutoMaker, a suite of Perl scripts, which can be scheduled to run periodically to automatically create/update the customised SNP databases. We illustrate the use of FunctSNP with a livestock ex le, but the approach and software tools presented here can be applied also to human and other organisms. Finding the potential functional significance of SNPs is important when further using the outcomes from whole genome association studies. FunctSNP is unique in that it is the only R package that links SNPs to functional annotation. FunctSNP interfaces to local SNP customised databases which can be built for any species contained in the National Center for Biotechnology Information dbSNP database.
Publisher: Asian Australasian Association of Animal Production Societies
Date: 15-12-2016
DOI: 10.5713/AJAS.15.0605
Publisher: Elsevier BV
Date: 08-2014
DOI: 10.1016/J.BIOCEL.2014.04.025
Abstract: Molecular mechanisms that are associated with age-related denervation and loss of skeletal muscle mass and function (sarcopenia) are described for female C57Bl/6J mice aged 3, 15, 24, 27 and 29 months (m). Changes in mRNAs and proteins associated with myofibre denervation and protein metabolism in ageing muscles are reported, across the transition from healthy adult myofibres to sarcopenia that occurs between 15 and 24 m. This onset of sarcopenia at 24 m, corresponded with increased expression of genes associated with neuromuscular junction denervation including Chnrg, Chrnd, Ncam1, Runx1, Gadd45a and Myog. Sarcopenia in quadriceps muscles also coincided with increased protein levels for Igf1 receptor, Akt and ribosomal protein S6 (Rps6) with increased phosphorylation of Rps6 (Ser235/236) and elevated Murf1 mRNA and protein, but not Fbxo32: many of these changes are also linked to denervation. Global transcription profiling via microarray analysis confirmed these functional themes and highlighted additional themes that may be a consequence of pathology associated with sarcopenia, including changes in fatty acid metabolism, extracellular matrix structure and protein catabolism. Ageing was also associated with increased global gene expression variance, consistent with decreased control of gene regulation.
Publisher: Springer Science and Business Media LLC
Date: 09-11-2010
Publisher: Wiley
Date: 02-08-2015
DOI: 10.1111/JBG.12179
Abstract: Reliability of parentage test panels is usually based on its power to exclude wrong parentage assignments based on allele frequencies. We evaluated the rates of false exclusions and inclusions in parentage assignments, and how these results are affected by allele frequencies, panel sizes and the number of allowed mismatches. We also evaluated the reliability of parentage testing by comparing populations with distinct genetic backgrounds using pure and composite families of cattle and sheep. Allowing for 1% genotype mismatches in true parent-offspring relations provided the best compromise between false-positive and false-negative assignments. Pure breeds needed at least 200-210 single-nucleotide polymorphism (SNP) markers to correctly assign relations, but between 700 and 890 markers to avoid assigning incorrect relationships. Composite breeds needed between 220 (sheep) and 500 (cattle) markers for correct assignment 680 (cattle) to 4400 (sheep) SNPs were needed to eliminate false-positive assignments. Allowing 0% genotype mismatches decreased false-positive but increased false-negative assignments, whilst a higher threshold of 2% showed the opposite effects. Panels with high minor allele frequencies (0.35-0.45) provided the best chance for correct parentage resolutions requiring fewer markers. Further, we propose that a dynamic threshold would allow adapting to population specific error rates. A comparison to the performance of the official International Society for Animal Genetics SNP panel for cattle and a recently published SNP panel for sheep showed that randomly selected markers performed only slightly worse for the applied parentage test based on opposing homozygotes. This suggests that even with carefully selected panels, only marginal assignment improvements are obtainable for a particular number of SNPs. The main point for improvement is the number of markers used. We recommend using at least 200 SNP markers for parentage testing if the aim is to reduce false-negative results. To fully exclude false positives at least 700 markers are required.
Publisher: Wiley
Date: 18-07-2014
DOI: 10.1111/AGE.12198
Abstract: In genome-wide association studies, quality control (QC) of genotypes is important to avoid spurious results. It is also important to maintain long-term data integrity, particularly in settings with ongoing genotyping (e.g. estimation of genomic breeding values). Here we discuss SNPQc, a fully automated pipeline to perform QC analyses of Illumina SNP array data. It applies a wide range of common quality metrics with user-defined filtering thresholds to generate a comprehensive QC report and a filtered dataset, including a genomic relationship matrix, ready for further downstream analyses which make it amenable for integration in high-throughput environments. SNPQC also builds a database to store genotypic, phenotypic and quality metrics to ensure data integrity and the option of integrating more s les from subsequent runs. The program is generic across species and array designs, providing a convenient interface between the genotyping laboratory and downstream genome-wide association study or genomic prediction.
Publisher: Asian Australasian Association of Animal Production Societies
Date: 05-2013
Publisher: Korean Society of Animal Science and Technology
Date: 05-2021
Publisher: American Society for Microbiology
Date: 07-2009
DOI: 10.1128/CVI.00157-09
Abstract: The cattle tick, Rhipicephalus ( Boophilus ) microplus , is a major threat to the improvement of cattle production in tropical and subtropical countries worldwide. Bos indicus cattle are naturally more resistant to infestation with the cattle tick than are Bos taurus breeds, although considerable variation in resistance occurs within and between breeds. It is not known which genes contribute to the resistant phenotype, nor have immune parameters involved in resistance to R. microplus been fully described for the bovine host. This study was undertaken to determine whether selected cellular and antibody parameters of the peripheral circulation differed between tick-resistant Bos indicus and tick-susceptible Bos taurus cattle following a period of tick infestations. This study demonstrated significant differences between the two breeds with respect to the percentage of cellular subsets comprising the peripheral blood mononuclear cell population, cytokine expression by peripheral blood leukocytes, and levels of tick-specific immunoglobulin G1 (IgG1) antibodies measured in the peripheral circulation. In addition to these parameters, the Affymetrix bovine genome microarray was used to analyze gene expression by peripheral blood leukocytes of these animals. The results demonstrate that the Bos indicus cattle developed a stabilized T-cell-mediated response to tick infestation evidenced by their cellular profile and leukocyte cytokine spectrum. The Bos taurus cattle demonstrated cellular and gene expression profiles consistent with a sustained innate, inflammatory response to infestation, although high tick-specific IgG1 titers suggest that these animals have also developed a T-cell response to infestation.
Publisher: American Physiological Society
Date: 07-2013
DOI: 10.1152/AJPCELL.00027.2013
Abstract: Circadian rhythms and metabolism are tightly integrated, and rhythmic expression of metabolic factors is common in homeostatic processes. We measured the temporal changes in the expression of myogenic regulatory factors and expression and activity level of molecules involved in protein metabolism in skeletal muscles and livers in mice and examined the impact of fasting. Tissues were collected over 24 h (at zeitgeber times ZT1, ZT5, ZT9, ZT13, ZT17, ZT21, and ZT1 the following day) from adult male C57Bl/6J mice that had been either freely fed or fasted for 24 h. In skeletal muscle, there was a robust rise in the mRNA expression of the myogenic regulatory factors MyoD and myogenin during dark hours which was strongly suppressed by fasting. Circadian pattern was observed for mRNA of MuRF1, Akt1, and ribosomal protein S6 in muscles in fed and fasted mice and for Fbxo32 in fed mice. Activity (phosphorylation) levels of Akt(Ser473) displayed temporal regulation in fasted (but not fed) mice and were high at ZT9. Fasting caused significant reductions in phosphorylation for both Akt and S6 in muscles, indicative of inactivation. Hepatic phosphorylated Akt(Ser473) and S6(Ser235/236) proteins did not exhibit daily rhythms. Fasting significantly reduced hepatic Akt(473) phosphorylation compared with fed levels, although (unlike in muscle) it did not affect S6(Ser235/236) phosphorylation. This in vivo circadian study addresses for the first time the signaling activities of key molecules related to protein turnover and their possible cross-regulation of expression of genes related to protein degradation.
Publisher: Springer Science and Business Media LLC
Date: 12-09-2017
Publisher: Humana Press
Date: 2013
DOI: 10.1007/978-1-62703-447-0_1
Abstract: In recent years R has become de facto statistical programming language of choice for statisticians and it is also arguably the most widely used generic environment for analysis of high-throughput genomic data. In this chapter we discuss some approaches to improve performance of R when working with large SNP datasets.
Publisher: Wiley
Date: 18-10-2014
DOI: 10.1111/AGE.12092
Abstract: Residual feed intake (RFI) has been adopted in Australia for the purpose of genetic improvement in feed efficiency in beef cattle. RFI is the difference between the observed feed intake of an animal and the predicted feed intake based on its size and growth rate over a test period. Gene expression of eight candidate genes (AHSG, GHR, GSTM1, INHBA, PCDH19, S100A10, SERPINI2 and SOD3), previously identified as differentially expressed between ergent lines of high- and low-RFI animals, was measured in an unselected population of 60 steers from the Angus Society Elite Progeny Test Program using quantitative real-time PCR. Results showed that the levels of gene expression were significantly correlated with RFI. The genes explain around 33.2% of the phenotypic variance in RFI, and prediction equations using the expression data are reasonably accurate estimators of RFI. The association of these genes with economically important traits, such as other feed efficiency-related traits and fat, growth and carcass traits, was investigated as well. The expression of these candidate genes was significantly correlated with feed conversion ratio and daily feed intake, which are highly associated with RFI, suggesting a functional role for these genes in modulating feed utilisation. The expression of these genes did not show any association with average daily gain, eye muscle area and carcass composition.
Publisher: Humana Press
Date: 2013
DOI: 10.1007/978-1-62703-447-0_5
Abstract: This chapter overviews the quality control (QC) issues for SNP-based genotyping methods used in genome-wide association studies. The main metrics for evaluating the quality of the genotypes are discussed followed by a worked out ex le of QC pipeline starting with raw data and finishing with a fully filtered dataset ready for downstream analysis. The emphasis is on automation of data storage, filtering, and manipulation to ensure data integrity throughput the process and on how to extract a global summary from these high dimensional datasets to allow better-informed downstream analytical decisions. All ex les will be run using the R statistical programming language followed by a practical ex le using a fully automated QC pipeline for the Illumina platform.
Publisher: Wiley
Date: 2017
DOI: 10.1111/PIM.12402
Abstract: Resistance to cattle tick infestation in single-host ticks is primarily manifested against the larval stage and results in the immature tick failing to attach successfully and obtain a meal. This study was conducted to identify immune responses that characterize the tick-resistant phenotype in cattle. Thirty-five tick-naïve Santa Gertrudis heifers were used in this study, thirty of which were artificially infested for thirteen weeks with tick larvae while five animals remained at a tick-free quarantine property to serve as a control group. Following thirteen weeks of tick infestation, the animals in this trial exhibited highly ergent tick-resistant phenotypes. Blood s les collected throughout the trial were used to measure peripheral immune parameters: haematology, the percentage of cellular subsets comprising the peripheral blood mononuclear cell (PBMC) population, tick-specific IgG
Publisher: Springer Science and Business Media LLC
Date: 31-01-2012
Publisher: Elsevier BV
Date: 03-2010
DOI: 10.1016/J.IJPARA.2009.09.009
Abstract: Cattle demonstrate ergent and heritable phenotypes of resistance and susceptibility to infestation with the cattle tick Rhipicephalus (Boophilus) microplus. Bos indicus cattle are generally more resistant to tick infestation than Bos taurus breeds although large variations in resistance can occur within subspecies and within breed. Increased tick resistance has been previously associated with an intense hypersensitivity response in B. taurus breeds however, the mechanism by which highly resistant B. indicus cattle acquire and sustain high levels of tick resistance remains to be elucidated. Using the commercially available Affymetrix microarray gene expression platform, together with histological examination of the larval attachment site, this study aimed to describe those processes responsible for high levels of tick resistance in Brahman (B. indicus) cattle that differ from those in low-resistance Holstein-Friesian (B. taurus) cattle. We found that genes involved in inflammatory processes and immune responsiveness to infestation by ticks, although up-regulated in tick-infested Holstein-Friesian cattle, were not up-regulated in Brahman cattle. In contrast, genes encoding constituents of the extracellular matrix were up-regulated in Brahmans. Furthermore, the susceptible Holstein-Friesian animals displayed a much greater cellular inflammatory response at the site of larval R. microplus attachment compared with the tick-resistant Brahman cattle.
Publisher: F1000 Research Ltd
Date: 04-03-2013
DOI: 10.12688/F1000RESEARCH.2-72.V1
Abstract: The Aspergillus nidulans xprG gene encodes a putative transcriptional activator that is a member of the Ndt80 family in the p53-like superfamily of proteins. Previous studies have shown that XprG controls the production of extracellular proteases in response to starvation. We undertook transcriptional profiling to investigate whether XprG has a wider role as a global regulator of the carbon nutrient stress response. Our microarray data showed that the expression of a large number of genes, including genes involved in secondary metabolism, development, high-affinity glucose uptake and autolysis, were altered in an xprG Δ null mutant. Many of these genes are known to be regulated in response to carbon starvation. We confirmed that sterigmatocystin and penicillin production is reduced in xprG - mutants. The loss of fungal mass and secretion of pigments that accompanies fungal autolysis in response to nutrient depletion was accelerated in an xprG1 gain-of-function mutant and decreased or absent in an xprG - mutant. The results support the hypothesis that XprG plays a major role in the response to carbon limitation and that nutrient sensing may represent one of the ancestral roles for the p53-like superfamily. Disruption of the AN6015 gene, which encodes a second Ndt80-like protein, showed that it is required for sexual reproduction in A. nidulans .
Publisher: Elsevier BV
Date: 08-2011
DOI: 10.1016/J.IJPARA.2011.05.003
Abstract: Knowledge of cattle tick (Rhipicephalus (Boophilus) microplus Acari: Ixodidae) molecular and cellular pathways has been h ered by the lack of an annotated genome. In addition, most of the tick expressed sequence tags (ESTs) available to date consist of ∼50% unassigned sequences without predicted functions. The most common approach to address this has been the application of RNA interference (RNAi) methods to investigate genes and their pathways. This approach has been widely adopted in tick research despite minimal knowledge of the tick RNAi pathway and double-stranded RNA (dsRNA) uptake mechanisms. A strong knockdown phenotype of adult female ticks had previously been observed using a 594 bp dsRNA targeting the cattle tick homologue for the Drosophila Ubiquitin-63E gene leading to nil or deformed eggs. A NimbleGen cattle tick custom microarray based on the BmiGI.V2 database of R. microplus ESTs was used to evaluate the expression of mRNAs harvested from ticks treated with the tick Ubiquitin-63E 594 bp dsRNA compared with controls. A total of 144 ESTs including TC6372 (Ubiquitin-63E) were down-regulated with 136 ESTs up-regulated following treatment. The results obtained substantiated the knockdown phenotype with ESTs identified as being associated with ubiquitin proteolysis as well as oogenesis, embryogenesis, fatty acid synthesis and stress responses. A bioinformatics analysis was undertaken to predict off-target effects (OTE) resulting from the in silico dicing of the 594 bp Ubiquitin-63E dsRNA which identified 10 down-regulated ESTs (including TC6372) within the list of differentially expressed probes on the microarrays. Subsequent knockdown experiments utilising 196 and 109 bp dsRNAs, and a cocktail of short hairpin RNAs (shRNA) targeting Ubiquitin-63E, demonstrated similar phenotypes for the dsRNAs but nil effect following shRNA treatment. Quantitative reverse transcriptase PCR analysis confirmed differential expression of TC6372 and selected ESTs. Our study demonstrated the minimisation of predicted OTEs in the shorter dsRNA treatments (∼100-200 bp) and the usefulness of microarrays to study knockdown phenotypes.
Publisher: Wiley
Date: 31-03-2011
DOI: 10.1111/J.1365-2052.2011.02182.X
Abstract: Feed efficiency is an economically important trait in beef production. It can be measured as residual feed intake. This is the difference between actual feed intake recorded over a test period and the expected feed intake of an animal based on its size and growth rate. DNA-based marker-assisted selection would help beef breeders to accelerate genetic improvement for feed efficiency by reducing the generation interval and would obviate the high cost of measuring residual feed intake. Although numbers of quantitative trait loci and candidate genes have been identified with the advance of molecular genetics, our understanding of the physiological mechanisms and the nature of genes underlying residual feed intake is limited. The aim of the study was to use global gene expression profiling by microarray to identify genes that are differentially expressed in cattle, using lines genetically selected for low and high residual feed intake, and to uncover candidate genes for residual feed intake. A long-oligo microarray with 24 000 probes was used to profile the liver transcriptome of 44 cattle selected for high or low residual feed intake. One hundred and sixty-one unique genes were identified as being differentially expressed between animals with high and low residual feed intake. These genes were involved in seven gene networks affecting cellular growth and proliferation, cellular assembly and organization, cell signalling, drug metabolism, protein synthesis, lipid metabolism, and carbohydrate metabolism. Analysis of functional data using a transcriptional approach allows a better understanding of the underlying biological processes involved in residual feed intake and also allows the identification of candidate genes for marker-assisted selection.
Publisher: Korean Society for Biochemistry and Molecular Biology - BMB Reports
Date: 30-09-2016
DOI: 10.5483/BMBREP.2016.49.9.074
Abstract: Korean cattle (Hanwoo) are categorized into three breeds based on color: brown, brindle, and black. Among these breeds, brown Hanwoo has been subjected to intensive selection to improve meat traits. To identify genetic traces driven by recent selection in brown Hanwoo, we scanned the genomes of brown and brindle Hanwoo using a bovine SNP chip. We identified 17 candidate selection signatures in brown Hanwoo and sequenced four candidate regions from 10 in iduals each of brown and brindle Hanwoo. In particular, non-synonymous SNPs in the ADSL gene (K88M, L189H, and R302Q) might have had mutational effects on protein structure as a result of altering the purine pathway during nucleotide breakdown. The ADSL gene was previously reported to affect meat quality and yield in livestock. Meat quality and yield are main breeding goals for brown Hanwoo, and our results support a potential causal influence of non-synonymous SNPs in the ADSL gene. [BMB Reports 2016 49(9): 514-519].
Publisher: Springer Science and Business Media LLC
Date: 30-07-2011
DOI: 10.1007/S00335-011-9331-9
Abstract: Causal mutations affecting quantitative trait variation can be good targets for marker-assisted selection for carcass traits in beef cattle. In this study, linkage and linkage disequilibrium analysis (LDLA) for four carcass traits was undertaken using 19 markers on bovine chromosome 14. The LDLA analysis detected quantitative trait loci (QTL) for carcass weight (CWT) and eye muscle area (EMA) at the same position at around 50 cM and surrounded by the markers FABP4SNP2774C>G and FABP4_μsat3237. The QTL for marbling (MAR) was identified at the midpoint of markers BMS4513 and RM137 in a 3.5-cM marker interval. The most likely position for a second QTL for CWT was found at the midpoint of tenth marker bracket (FABP4SNP2774C>G and FABP4_μsat3237). For this marker bracket, the total number of haplotypes was 34 with a most common frequency of 0.118. Effects of haplotypes on CWT varied from a -5-kg deviation for haplotype 6 to +8 kg for haplotype 23. To determine which genes contribute to the QTL effect, gene expression analysis was performed in muscle for a wide range of phenotypes. The results demonstrate that two genes, LOC781182 (p = 0.002) and TRPS1 (p = 0.006) were upregulated with increasing CWT and EMA, whereas only LOC614744 (p = 0.04) has a significant effect on intramuscular fat (IMF) content. Two genetic markers detected in FABP4 were the most likely QTL position in this QTL study, but FABP4 did not show a significant effect on both traits (CWT and EMA) in gene expression analysis. We conclude that three genes could be potential causal genes affecting carcass traits CWT, EMA, and IMF in Hanwoo.
Publisher: Public Library of Science (PLoS)
Date: 10-10-2012
Publisher: Springer Science and Business Media LLC
Date: 15-06-2010
Abstract: The developmental transition between the late fetus and a newborn animal is associated with profound changes in skeletal muscle function as it adapts to the new physiological demands of locomotion and postural support against gravity. The mechanisms underpinning this adaption process are unclear but are likely to be initiated by changes in hormone levels. We tested the hypothesis that this developmental transition is associated with large coordinated changes in the transcription of skeletal muscle genes. Using an ovine model, transcriptional profiling was performed on Longissimus dorsi skeletal muscle taken at three fetal developmental time points (80, 100 and 120 d of fetal development) and two postnatal time points, one approximately 3 days postpartum and a second at 3 months of age. The developmental time course was dominated by large changes in expression of 2,471 genes during the interval between late fetal development (120 d fetal development) and 1-3 days postpartum. Analysis of the functions of genes that were uniquely up-regulated in this interval showed strong enrichment for oxidative metabolism and the tricarboxylic acid cycle indicating enhanced mitochondrial activity. Histological examination of tissues from these developmental time points directly confirmed a marked increase in mitochondrial activity between the late fetal and early postnatal s les. The promoters of genes that were up-regulated during this fetal to neonatal transition were enriched for estrogen receptor 1 and estrogen related receptor alpha cis-regulatory motifs. The genes down-regulated during this interval highlighted de-emphasis of an array of functions including Wnt signaling, cell adhesion and differentiation. There were also changes in gene expression prior to this late fetal - postnatal transition and between the two postnatal time points. The former genes were enriched for functions involving the extracellular matrix and immune response while the latter principally involved functions associated with transcriptional regulation of metabolic processes. It is concluded that during late skeletal muscle development there are substantial and coordinated changes in the transcription of a large number of genes many of which are probably triggered by increased estrogen levels. These changes probably underpin the adaption of muscle to new physiological demands in the postnatal environment.
Publisher: Wiley
Date: 06-2009
DOI: 10.1111/J.1365-2052.2008.01836.X
Abstract: This paper presents results from a mapping experiment to detect quantitative trait loci (QTL) for resistance to Haemonchus contortus infestation in merino sheep. The primary trait analysed was faecal worm egg count in response to artificial challenge at 6 months of age. In the first stage of the experiment, whole genome linkage analysis was used for broad-scale mapping. The animal resource used was a designed flock comprising 571 in iduals from four half-sib families. The average marker spacing was about 20 cM. For the primary trait, 11 QTL (as chromosomal/family combinations) were significant at the 5% chromosome-wide level, with allelic substitution effects of between 0.19 and 0.38 phenotypic standard deviation units. In general, these QTL did not have a significant effect on faecal worm egg count recorded at 13 months of age. In the second stage of the experiment, three promising regions (located on chromosomes 1, 3 and 4) were fine-mapped. This involved typing more closely spaced markers on in iduals from the designed flock as well as an additional 495 in iduals selected from a related population with a deeper pedigree. Analysis was performed using a linkage disequilibrium-linkage approach, under additive, dominant and multiple QTL models. Of these, the multiple QTL model resulted in the most refined QTL positions, with resolutions of <10 cM achieved for two regions. Because of the moderate size of effect of the QTL, and the apparent age and/or immune status specificity of the QTL, it is suggested that a panel of QTL will be required for significant genetic gains to be achieved within industry via marker-assisted selection.
Publisher: Springer Science and Business Media LLC
Date: 2010
Publisher: Wiley
Date: 27-03-2014
DOI: 10.1111/AGE.12145
Start Date: 2013
End Date: 03-2017
Amount: $246,000.00
Funder: Australian Research Council
View Funded ActivityStart Date: 2014
End Date: 12-2016
Amount: $1,025,000.00
Funder: Australian Research Council
View Funded Activity