Wang Dan, Zhang Tao, Zhang Menghua, Chen Qiuming, Yan Mengjie, Ma Shengchao, Wang Jiangkun, Zhang Xiaoxue, Ma Kailun, Xu Lei, Huang Xixia
College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China.
Int J Mol Sci. 2025 May 29;26(11):5234. doi: 10.3390/ijms26115234.
Xinjiang Brown cattle is an elite dual-purpose breed (raised for dairy and beef) developed in China. To elucidate its genomic architecture, we conducted whole-genome resequencing of 169 Xinjiang Brown cattle, followed by structural variation (SV) detection and a genome-wide association study (GWAS). We identified 71,668 SVs, among which deletions were the most prevalent, followed by translocations, inversions, duplications, and insertions. We further identified 1286 high-frequency SVs involving 2016 protein-coding genes. Through functional enrichment analysis of these genes, we revealed associations of genetic variation at genomic positions near genes implicated in immune response and disease resistance ( and ), growth and development ( and ), and milk production (, , and ). GWAS analysis of 31 body conformation traits revealed 58 SVs significantly associated with five traits (chest width, rear udder width, udder depth, rump width, and heel depth) at the genome-wide level. Additionally, nine candidate genes (, , , , , , , , and ) were identified as potentially involved in the genetic regulation of body conformation traits. These findings provide novel insights for genetic improvement strategies and indicate that precision breeding could further enhance the production performance of this breed in the future.
新疆褐牛是中国培育的优良兼用型品种（用于产奶和产肉）。为阐明其基因组结构，我们对169头新疆褐牛进行了全基因组重测序，随后进行结构变异（SV）检测和全基因组关联研究（GWAS）。我们鉴定出71,668个SV，其中缺失最为普遍，其次是易位、倒位、重复和插入。我们进一步鉴定出1286个高频SV，涉及2016个蛋白质编码基因。通过对这些基因的功能富集分析，我们揭示了与免疫反应和抗病性（以及）、生长发育（和）以及产奶量（、和）相关基因附近基因组位置的遗传变异关联。对31个体型性状的GWAS分析揭示了58个SV在全基因组水平上与五个性状（胸宽、后乳房宽度、乳房深度、臀宽和蹄踵深度）显著相关。此外，九个候选基因（、、、、、、、和）被鉴定为可能参与体型性状的遗传调控。这些发现为遗传改良策略提供了新见解，并表明精准育种未来可进一步提高该品种的生产性能。
