Dataset Information

Genome-wide association analysis for quantitative trait loci influencing Warner-Bratzler shear force in five taurine cattle breeds.

ABSTRACT: We performed a genome-wide association study for Warner-Bratzler shear force (WBSF), a measure of meat tenderness, by genotyping 3360 animals from five breeds with 54 790 BovineSNP50 and 96 putative single-nucleotide polymorphisms (SNPs) within ?-calpain [HUGO nomenclature calpain 1, (mu/I) large subunit; CAPN1] and calpastatin (CAST). Within- and across-breed analyses estimated SNP allele substitution effects (ASEs) by genomic best linear unbiased prediction (GBLUP) and variance components by restricted maximum likelihood under an animal model incorporating a genomic relationship matrix. GBLUP estimates of ASEs from the across-breed analysis were moderately correlated (0.31-0.66) with those from the individual within-breed analyses, indicating that prediction equations for molecular estimates of breeding value developed from across-breed analyses should be effective for genomic selection within breeds. We identified 79 genomic regions associated with WBSF in at least three breeds, but only eight were detected in all five breeds, suggesting that the within-breed analyses were underpowered, that different quantitative trait loci (QTL) underlie variation between breeds or that the BovineSNP50 SNP density is insufficient to detect common QTL among breeds. In the across-breed analysis, CAPN1 was followed by CAST as the most strongly associated WBSF QTL genome-wide, and associations with both were detected in all five breeds. We show that none of the four commercialized CAST and CAPN1 SNP diagnostics are causal for associations with WBSF, and we putatively fine-map the CAPN1 causal mutation to a 4581-bp region. We estimate that variation in CAST and CAPN1 explains 1.02 and 1.85% of the phenotypic variation in WBSF respectively.

SUBMITTER: McClure MC

PROVIDER: S-EPMC3506923 | biostudies-literature | 2012 Dec

REPOSITORIES: biostudies-literature

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Genome-wide association analysis for quantitative trait loci influencing Warner-Bratzler shear force in five taurine cattle breeds.

McClure M C MC Ramey H R HR Rolf M M MM McKay S D SD Decker J E JE Chapple R H RH Kim J W JW Taxis T M TM Weaber R L RL Schnabel R D RD Taylor J F JF

Animal genetics 20120227 6

We performed a genome-wide association study for Warner-Bratzler shear force (WBSF), a measure of meat tenderness, by genotyping 3360 animals from five breeds with 54 790 BovineSNP50 and 96 putative single-nucleotide polymorphisms (SNPs) within μ-calpain [HUGO nomenclature calpain 1, (mu/I) large subunit; CAPN1] and calpastatin (CAST). Within- and across-breed analyses estimated SNP allele substitution effects (ASEs) by genomic best linear unbiased prediction (GBLUP) and variance components by r ...[more]

PMID: 22497286

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Project description:BackgroundAnimal African Trypanosomosis particularly affects cattle and dramatically impairs livestock development in sub-Saharan Africa. African Zebu (AFZ) or European taurine breeds usually die of the disease in the absence of treatment, whereas West African taurine breeds (AFT), considered trypanotolerant, are able to control the pathogenic effects of trypanosomosis. Up to now, only one AFT breed, the longhorn N'Dama (NDA), has been largely studied and is considered as the reference trypanotolerant breed. Shorthorn taurine trypanotolerance has never been properly assessed and compared to NDA and AFZ breeds.Methodology/principal findingsThis study compared the trypanotolerant/susceptible phenotype of five West African local breeds that differ in their demographic history. Thirty-six individuals belonging to the longhorn taurine NDA breed, two shorthorn taurine Lagune (LAG) and Baoulé (BAO) breeds, the Zebu Fulani (ZFU) and the Borgou (BOR), an admixed breed between AFT and AFZ, were infected by Trypanosoma congolense IL1180. All the cattle were genetically characterized using dense SNP markers, and parameters linked to parasitaemia, anaemia and leukocytes were analysed using synthetic variables and mixed models. We showed that LAG, followed by NDA and BAO, displayed the best control of anaemia. ZFU showed the greatest anaemia and the BOR breed had an intermediate value, as expected from its admixed origin. Large differences in leukocyte counts were also observed, with higher leukocytosis for AFT. Nevertheless, no differences in parasitaemia were found, except a tendency to take longer to display detectable parasites in ZFU.ConclusionsWe demonstrated that LAG and BAO are as trypanotolerant as NDA. This study highlights the value of shorthorn taurine breeds, which display strong local adaptation to trypanosomosis. Thanks to further analyses based on comparisons of the genome or transcriptome of the breeds, these results open up the way for better knowledge of host-pathogen interactions and, furthermore, for identifying key biological pathways.

Project description:BACKGROUND:Linear type traits, which reflect the muscular characteristics of an animal, could provide insight into how, in some cases, morphologically very different animals can yield the same carcass weight. Such variability may contribute to differences in the overall value of the carcass since primal cuts vary greatly in price; such variability may also hinder successful genome-based association studies. Therefore, the objective of our study was to identify genomic regions that are associated with five muscularity linear type traits and to determine if these significant regions are common across five different breeds. Analyses were carried out using linear mixed models on imputed whole-genome sequence data in each of the five breeds, separately. Then, the results of the within-breed analyses were used to conduct an across-breed meta-analysis per trait. RESULTS:We identified many quantitative trait loci (QTL) that are located across the whole genome and associated with each trait in each breed. The only commonality among the breeds and traits was a large-effect pleiotropic QTL on BTA2 that contained the MSTN gene, which was associated with all traits in the Charolais and Limousin breeds. Other plausible candidate genes were identified for muscularity traits including PDE1A, PPP1R1C and multiple collagen and HOXD genes. In addition, associated (gene ontology) GO terms and KEGG pathways tended to differ between breeds and between traits especially in the numerically smaller populations of Angus, Hereford, and Simmental breeds. Most of the SNPs that were associated with any of the traits were intergenic or intronic SNPs located within regulatory regions of the genome. CONCLUSIONS:The commonality between the Charolais and Limousin breeds indicates that the genetic architecture of the muscularity traits may be similar in these breeds due to their similar origins. Conversely, there were vast differences in the QTL associated with muscularity in Angus, Hereford, and Simmental. Knowledge of these differences in genetic architecture between breeds is useful to develop accurate genomic prediction equations that can operate effectively across breeds. Overall, the associated QTL differed according to trait, which suggests that breeding for a morphologically different (e.g. longer and wider versus shorter and smaller) more efficient animal may become possible in the future.

Project description:ObjectiveThe objective of this study was to identify genes associated with 305-day milk yield (MY) and fat yield (FY) that also influence the adaptability of the Thai multibreed dairy cattle population to tropical conditions.MethodsA total of 75,776 imputed and actual single nucleotide polymorphisms (SNPs) from 2,661 animals were used to identify genomic regions associated with MY and FY using the single-step genomic best linear unbiased predictions. Fixed effects included herd-yearseason, breed regression, heterosis regression and calving age regression effects. Random effects were animal additive genetic and residual. Individual SNPs with a p-value smaller than 0.05 were selected for gene mapping, function analysis, and quantitative trait loci (QTL) annotation analysis.ResultsA substantial number of QTLs associated with MY (9,334) and FY (8,977) were identified by integrating SNP genotypes and QTL annotations. Notably, we discovered 17 annotated QTLs within the health and exterior QTL classes, corresponding to nine unique genes. Among these genes, Rho GTPase activating protein 15 (ARHGAP15) and catenin alpha 2 (CTNNA2) have previously been linked to physiological traits associated with tropical adaptation in various cattle breeds. Interestingly, these two genes also showed signs of positive selection, indicating their potential role in conferring tolerance to trypanosomiasis, a prevalent tropical disease.ConclusionOur findings provide valuable insights into the genetic basis of MY and FY in the Thai multibreed dairy cattle population, shedding light on the underlying mechanisms of tropical adaptation. The identified genes represent promising targets for future breeding strategies aimed at improving milk and fat production while ensuring resilience to tropical challenges. This study significantly contributes to our understanding of the genetic factors influencing milk production and adaptability in dairy cattle, facilitating the development of sustainable genetic selection strategies and breeding programs in tropical environments.

Project description:BackgroundThe origin of native and locally developed Russian cattle breeds is linked to the historical, social, cultural, and climatic features of the diverse geographical regions of Russia. In the present study, we investigated the population structure of nine Russian cattle breeds and their relations to the cattle breeds from around the world to elucidate their origin. Genotyping of single nucleotide polymorphisms (SNPs) in Bestuzhev (n?=?26), Russian Black-and-White (n?=?21), Kalmyk (n?=?14), Kholmogor (n?=?25), Kostromsky (n?=?20), Red Gorbatov (n?=?23), Suksun (n?=?20), Yakut (n?=?25), and Yaroslavl cattle breeds (n?=?21) was done using the Bovine SNP50 BeadChip. SNP profiles from an additional 70 breeds were included in the analysis as references.ResultsThe observed heterozygosity levels were quite similar in eight of the nine studied breeds (HO?=?0.337-0.363) except for Yakut (Ho?=?0.279). The inbreeding coefficients FIS ranged from -0.028 for Kalmyk to 0.036 for Russian Black-and-White and were comparable to those of the European breeds. The nine studied Russian breeds exhibited taurine ancestry along the C1 axis of the multidimensional scaling (MDS)-plot, but Yakut was clearly separated from the European taurine breeds on the C2 axis. Neighbor-Net and admixture analyses, discriminated three groups among the studied Russian breeds. Yakut and Kalmyk were assigned to a separate group because of their Turano-Mongolian origin. Russian Black-and-White, Kostromsky and Suksun showed transboundary European ancestry, which originated from the Holstein, Brown Swiss, and Danish Red breeds, respectively. The lowest level of introgression of transboundary breeds was recorded for the Kholmogor, Yaroslavl, Red Gorbatov and Bestuzhev breeds, which can be considered as an authentic genetic resource.ConclusionsWhole-genome SNP analysis revealed that Russian native and locally developed breeds have conserved authentic genetic patterns in spite of the considerable influence of Eurasian taurine cattle. In this paper, we provide fundamental genomic information that will contribute to the development of more accurate breed conservation programs and genetic improvement strategies.

Dataset Information

Genome-wide association analysis for quantitative trait loci influencing Warner-Bratzler shear force in five taurine cattle breeds.

Publications

Genome-wide association analysis for quantitative trait loci influencing Warner-Bratzler shear force in five taurine cattle breeds.

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