College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China.
Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
Int J Mol Sci. 2024 Sep 30;25(19):10557. doi: 10.3390/ijms251910557.
Body conformation traits are linked to the health, longevity, reproductivity, and production performance of cattle. These traits are also crucial for herd selection and developing new breeds. This study utilized pedigree information and phenotypic (1185 records) and genomic (The resequencing of 496 Xinjiang Brown cattle generated approximately 74.9 billion reads.) data of Xinjiang Brown cattle to estimate the genetic parameters, perform factor analysis, and conduct a genome-wide association study (GWAS) for these traits. Our results indicated that most traits exhibit moderate to high heritability. The principal factors, which explained 59.12% of the total variance, effectively represented body frame, muscularity, rump, feet and legs, and mammary system traits. Their heritability estimates range from 0.17 to 0.73, with genetic correlations ranging from -0.53 to 0.33. The GWAS identified 102 significant SNPs associated with 12 body conformation traits. A few of the SNPs were located near previously reported genes and quantitative trait loci (QTLs), while others were novel. The key candidate genes such as , , and were annotated within 500 Kb upstream and downstream of the significant SNPs. Therefore, factor analysis can be used to simplify multidimensional conformation traits into new variables, thus reducing the computational burden. The identified candidate genes from GWAS can be incorporated into the genomic selection of Xinjiang Brown cattle, enhancing the reliability of breeding programs.
体躯结构性状与牛的健康、长寿、繁殖力和生产性能有关。这些性状对于牛群选择和培育新品种也至关重要。本研究利用新疆褐牛的系谱信息和表型（1185 条记录）和基因组（对 496 头新疆褐牛进行重测序产生了约 749 亿个reads）数据，估计了这些性状的遗传参数，进行了因子分析，并进行了全基因组关联研究（GWAS）。结果表明，大多数性状表现出中等至高度的遗传力。主因子解释了总方差的 59.12%，有效地代表了体躯结构、肌肉发达度、臀部、脚和腿以及乳房系统性状。它们的遗传力估计值在 0.17 到 0.73 之间，遗传相关系数在-0.53 到 0.33 之间。GWAS 确定了 102 个与 12 个体躯结构性状相关的显著 SNP。少数 SNP 位于先前报道的基因和数量性状位点（QTL）附近，而其他 SNP 则是新的。关键候选基因如 、 、 等在显著 SNP 上下游 500 Kb 范围内被注释。因此，因子分析可用于将多维结构性状简化为新的变量，从而降低计算负担。从 GWAS 中鉴定的候选基因可被整合到新疆褐牛的基因组选择中，提高了育种计划的可靠性。
