Genomic regions associated with muscularity in beef cattle differ in five contrasting cattle breeds

Doyle, Jennifer L. and Berry, Donagh P. and Veerkamp, Roel F. and Carthy, Tara R. and Evans, Ross D. and Walsh, Siobhán W. and Purfield, Deirdre C. (2020) Genomic regions associated with muscularity in beef cattle differ in five contrasting cattle breeds. Genetics Selection Evolution, 52 (1). ISSN 0999-193X

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Abstract

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.

Item Type:	Article
Additional Information:	Funding Information: Funding from the Science Foundation Ireland principal investigator award grant (SF 14/IA/2576) and Research Centres Award (16/RC/3835) is greatly appreciated. Funding Information: This work was in part funded by a research grant from Science Foundation Ireland award number 14/IA/2576 and as well as a research grant from Science Foundation Ireland and the Department of Agriculture, Food and Marine on behalf of the Government of Ireland under the Grant 16/RC/3835 (VistaMilk; Dublin, Ireland).The authors would also like to thank the 1000 Bull Genomes consortium for the reference population used to impute genotypes to sequence. Publisher Copyright: © 2020 The Author(s).
Uncontrolled Keywords:	/dk/atira/pure/subjectarea/asjc/1100/1105
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Depositing User:	Admin SSL
Date Deposited:	19 Oct 2022 23:11
Last Modified:	14 Aug 2023 19:30
URI:	http://repository-testing.wit.ie/id/eprint/4595

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