Data_Sheet_6_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.pdf

Linear type traits describing the skeletal characteristics of an animal are moderately to strongly genetically correlated with a range of other performance traits in cattle including feed intake, reproduction traits and carcass merit; thus, type traits could also provide useful insights into the morphological differences among animals underpinning phenotypic differences in these complex traits. The objective of the present study was to identify genomic regions associated with five subjectively scored skeletal linear traits, to determine if these associated regions are common in multiple beef and dairy breeds, and also to determine if these regions overlap with those proposed elsewhere to be associated with correlated performance traits. Analyses were carried out using linear mixed models on imputed whole genome sequence data separately in 1,444 Angus, 1,129 Hereford, 6,433 Charolais, 8,745 Limousin, 1,698 Simmental, and 4,494 Holstein-Friesian cattle, all scored for the linear type traits. There was, on average, 18 months difference in age at assessment of the beef versus the dairy animals. While the majority of the identified quantitative trait loci (QTL), and thus genes, were both trait-specific and breed-specific, a large-effect pleiotropic QTL on BTA6 containing the NCAPG and LCORL genes was associated with all skeletal traits in the Limousin population and with wither height in the Angus. Other than that, little overlap existed in detected QTLs for the skeletal type traits in the other breeds. Only two QTLs overlapped the beef and dairy breeds; both QTLs were located on BTA5 and were associated with height in both the Angus and the Holstein-Friesian, despite the difference in age at assessment. Several detected QTLs in the present study overlapped with QTLs documented elsewhere that are associated with carcass traits, feed intake, and calving difficulty. While most breeding programs select for the macro-traits like carcass weight, carcass conformation, and feed intake, the higher degree of granularity with selection on the individual linear type traits in a multi-trait index underpinning the macro-level goal traits, presents an opportunity to help resolve genetic antagonisms among morphological traits in the pursuit of the animal with optimum performance metrics.

线性型性状描述动物骨骼特征，与牛的多种性能性状，包括饲料摄入量、繁殖特性和肉品质，存在中等至强烈的遗传相关性；因此，型性状亦能提供关于动物形态差异的有价值见解，这些形态差异是支撑复杂性状表型差异的基础。本研究的目的是识别与五个主观评分的骨骼线性性状相关的基因组区域，确定这些相关区域是否在多个肉牛和乳牛品种中普遍存在，并进一步确定这些区域是否与先前提出的相关性能性状的关联区域重叠。分析分别在对1,444头安格斯牛、1,129头赫雷福德牛、6,433头夏洛来牛、8,745头利木赞牛、1,698头西门塔尔牛和4,494头荷斯坦-弗里斯牛的线性型性状进行评分的基础上，使用线性混合模型对全基因组序列数据进行推断。牛肉牛和乳牛在评估年龄上平均相差18个月。虽然大多数已识别的性状特异性QTL和相应基因均为性状特异性和品种特异性，但位于BTA6上的具有NCAPG和LCORL基因的大效应多效性QTL与利木赞牛群中的所有骨骼性状以及安格斯牛的背高相关。除此之外，其他品种中检测到的骨骼型性状的QTL之间几乎没有重叠。只有两个QTL在肉牛和乳牛品种之间重叠；这两个QTL均位于BTA5上，并与安格斯牛和荷斯坦-弗里斯牛的高度相关，尽管在评估年龄上存在差异。在本研究中检测到的几个QTL与之前记录的、与肉品质、饲料摄入量和分娩难度相关的QTL重叠。尽管大多数育种计划会选择像胴体重、胴体形状和饲料摄入量这样的宏观性状，但通过对多性状指数中支撑宏观目标性状的个体线性型性状进行选择的更高粒度，提供了帮助解决形态性状间遗传对抗性的机会，以追求具有最佳性能指标的家畜。