ORCID Profile
0000-0003-3165-4579
Current Organisation
Università Cattolica del Sacro Cuore Sede di Piacenza e Cremona
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Publications
Genome wide analysis of fertility and production traits in Italian Holstein cattle.
Publisher: Public Library of Science (PLoS)
Date: 12-11-2013
A genome wide survey of SNP variation reveals the genetic structure of sheep breeds
Publisher: Public Library of Science (PLoS)
Date: 03-03-2009
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.
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.
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.
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.
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
Genome wide scan for somatic cell counts in holstein bulls
Publisher: Springer Science and Business Media LLC
Date: 03-06-2011
Low levels of taurine introgression in the current Brazilian Nelore and Gir indicine cattle populations
Publisher: Springer Science and Business Media LLC
Date: 17-04-2015
A PLAG1 mutation contributed to stature recovery in modern cattle
Publisher: Springer Science and Business Media LLC
Date: 07-12-2017
DOI: 10.1038/S41598-017-17127-1
Abstract: The recent evolution of cattle is marked by fluctuations in body size. Height in the Bos taurus lineage was reduced by a factor of ~1.5 from the Neolithic to the Middle Ages, and increased again only during the Early Modern Ages. Using haplotype analysis, we found evidence that the bovine PLAG1 mutation ( Q ) with major effects on body size, weight and reproduction is a ,000 years old derived allele that increased rapidly in frequency in Northwestern European B. taurus between the 16 th and 18 th centuries. Towards the 19 th and 20 th centuries, Q was introgressed into non-European B. taurus and Bos indicus breeds. These data implicate a major role of Q in recent changes in body size in modern cattle, and represent one of the first ex les of a genomic sweep in livestock that was driven by selection on a complex trait.
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.
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.
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
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.
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.
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.
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
Distribution of ncRNAs expression across hypothalamic-pituitary-gonadal axis in Capra hircus
Publisher: Springer Science and Business Media LLC
Date: 30-05-2018
Synergies between assisted reproduction technologies and functional genomics
Publisher: Springer Science and Business Media LLC
Date: 08-2016
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).
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
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.
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
Gene co-expression networks in liver and muscle transcriptome reveal sex-specific gene expression in lambs fed with a mix of essential oils
Publisher: Springer Science and Business Media LLC
Date: 04-04-2018
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.
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.
Genome-wide epigenetic characterization of tissues from three germ layers isolated from sheep fetuses
Publisher: Frontiers Media SA
Date: 04-09-2017
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.
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
Revealing misassembled segments in the bovine reference genome by high resolution linkage disequilibrium scan
Publisher: Springer Science and Business Media LLC
Date: 05-09-2016
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.
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
Pleiotropic Genes Affecting Carcass Traits in Bos indicus (Nellore) Cattle Are Modulators of Growth
Publisher: Public Library of Science (PLoS)
Date: 13-07-2016
Revealing the history of sheep domestication using retrovirus integrations
Publisher: American Association for the Advancement of Science (AAAS)
Date: 24-04-2009
Abstract: Sheep retroviruses can be used to map the selective preferences of early farmers and trace livestock movements across Europe.
Related Organisations
Università Cattolica Del Sacro Cuore Sede Di Piacenza E Cremona
Location: Italy
Related Funding Activities
No related grants have been discovered for Paolo AJMONE MARSAN.