Abstract
BackgroundLinear 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.ResultsWe 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.ConclusionsThe 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.
Highlights
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
Hereford No significant SNPs were detected for any of the muscularity linear type traits in the HE population, suggestive SNPs were identified for all five traits
No genomic window was common to all five type traits; six 1-kb windows i.e. on BTA5 (n = 1), BTA7 (n = 4), and BTA25 (n = 1) were shared between development of the hind quarter (DHQ) and DIT with three 1-kb regions on BTA20 shared between DIT and TW
Summary
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. The genetic merit of a young animal for these traits may be a good representation of its merit for carcass traits While both carcass value and conformation have been reported to be correlated with linear type traits [9], the correlation with any one type trait is not equal to 1 which implies that the same carcass value can be achieved with morphologically different animals; by extension this implies that, for example, an animal with a better developed loin and a shallow chest may have the same yield as an animal with a lesser developed loin and a deep chest. The objective of the present study was to identify genomic regions associated with five muscularity linear type traits and to determine if these associated regions are common across multiple beef cattle breeds
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