Teagasc, Animal and Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland.
Department of Science, Waterford Institute of Technology, Cork Road, Waterford, Co. Waterford, Ireland.
Genet Sel Evol. 2020 Jan 30;52(1):2. doi: 10.1186/s12711-020-0523-1.
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.
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.
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.
线性体型特征反映了动物的肌肉特征，可深入了解在某些情况下，形态非常不同的动物如何产生相同的胴体重量。这种可变性可能导致胴体整体价值的差异，因为主要切块的价格差异很大；这种可变性也可能阻碍基于基因组的成功关联研究。因此，我们的研究目的是鉴定与五个肌肉线性体型特征相关的基因组区域，并确定这些显著区域是否在五个不同品种中普遍存在。在每个品种中，分别使用线性混合模型对推断的全基因组序列数据进行分析。然后，利用每个品种内的分析结果，对每个性状进行跨品种元分析。
我们鉴定了许多位于整个基因组上的数量性状基因座（QTL），这些 QTL 与每个品种中的每个特征相关。品种和特征之间唯一的共同点是 BTA2 上的一个大效应的多效性 QTL，该 QTL 包含 MSTN 基因，该基因与夏洛莱牛和利木赞牛品种的所有特征相关。还确定了其他一些有希望的候选基因，包括 PDE1A、PPP1R1C 和多个胶原蛋白和 HOXD 基因。此外，与肌肉特征相关的（基因本体论）GO 术语和 KEGG 途径在品种之间和特征之间往往不同，尤其是在安格斯牛、海弗牛和西门塔尔牛这些数量较小的品种中。与任何特征相关的大多数 SNP 都是位于基因组调控区域内的基因间或内含子 SNP。
夏洛莱牛和利木赞牛品种之间的共同点表明，由于它们的起源相似，肌肉特征的遗传结构可能在这些品种中相似。相反，安格斯牛、海弗牛和西门塔尔牛的肌肉特征相关的 QTL 存在巨大差异。了解品种之间遗传结构的这些差异对于开发可以在品种间有效运行的准确基因组预测方程是有用的。总体而言，根据特征的不同，相关的 QTL 也不同，这表明未来可能有可能培育出形态不同（例如更长更宽与更短更小）但效率更高的动物。
