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

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. © The Author(s) 2020. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article' s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article'

Genomic Regions Associated With Skeletal Type Traits in Beef and Dairy Cattle Are Common to Regions Associated With Carcass Traits, Feed Intake and Calving Difficulty

“…Furthermore, some of the top 140 QTLs were also previously associated with carcass weight (McClure et al, 2010;Saatchi et al, 2014a) and residual feed intake (Nkrumah et al, 2007;Lu et al, 2013;Saatchi et al, 2014a) in cattle. Nineteen QTLs identified in the present study have also been identified previously as being associated with linear type traits describing the muscular characteristics of cattle (Doyle et al, 2020).…”

“…This indicates the existence of breed-specific and trait-specific QTL for skeletal traits, which has implications for the usefulness of such QTL in across-breed genomic evaluations where only purebreds are used. Previous studies have documented both across-breed and breed-specific QTL associated with carcass traits, birth weight, weaning weight, and mature weight (Saatchi et al, 2014b), as well as dry matter intake, growth and feed efficiency (Saatchi et al, 2014a), carcass traits (Purfield et al, 2019), and muscular type traits (Doyle et al, 2020) in beef cattle. Excluding stature (Bouwman et al, 2018), the present study is the first published genome study on the skeletal linear type traits in beef cattle using imputed sequence data and is one of few genome-based studies comparing QTLs across multiple breeds of cattle.…”

Assessing the genetic background and genomic relatedness of red cattle populations originating from Northern Europe

“…A genome-wide association study in Holstein cattle discovered a significant SNP for milk yield located in the P4HA3 gene at 54.4 Mb on BTA15 [ 107 ]. Moreover, Doyle et al [ 108 ] reported suggestive SNPs for beef traits that are located in the CHRDL2 and NEU3 genes on BTA15. Beyond that, NEU3 was demonstrated to have functional effects on fertility and production traits in Holstein Friesian [ 109 ].…”

Genome-wide association study of trypanosome prevalence and morphometric traits in purebred and crossbred Baoulé cattle of Burkina Faso

“…This genomic region was also identified to harbor a selection signature for body weight in Korean breeds [ 35 ]. The gene TMEM178A was found to be suggestively associated with loin muscularity in multiple beef cattle breeds [ 36 ]. In the same region was the MAP4K3 gene, involved in the Trypanosome resistance of the N’Dama cattle [ 37 ].…”