Identification of Genomic Structural Variations in Xinjiang Brown Cattle by Deep Sequencing and Their Association with Body Conformation Traits

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 (<i>NFKBIZ</i> and <i>PTPRT</i>), growth and development (<i>HDAC4</i> and <i>MEF2A</i>), and milk production (<i>TP63</i>, <i>FABP4</i>, and <i>MEF2A</i>). 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 (<i>CLINT1</i>, <i>EBF1</i>, <i>PAM16</i>, <i>GRIP1</i>, <i>CFAP54</i>, <i>SLC22A16</i>, <i>DOK5</i>, <i>ETAA1</i>, and <i>IPMK</i>) 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.