Simple Summary
The Xinjiang Brown cattle is a dual-purpose dairy and beef breed independently developed in China, exhibiting excellent performance in both milk and meat production, and is highly favored by farmers and herders. Genetic analysis was conducted on 750 Xinjiang Brown cattle from three breeding farms using a high-density SNP chip. This study revealed abundant genetic diversity within the population, with breeding farm 3 exhibiting particularly high diversity. However, we also identified closely related individuals and assessed the population’s inbreeding level. By identifying regions of shared genomic segments (ROHs) across numerous individuals, we identified 61 candidate genes (including LCORL, FAM110B, and NR4A1) likely associated with important economic traits in Xinjiang Brown cattle. These findings provide a crucial genetic foundation for conserving Xinjiang Brown cattle genetic resources and will directly support future genotyping-based selection breeding programs.
Abstract
The Xinjiang Brown cattle (XJBC) is one of China’s five major dual-purpose dairy and beef breeds. Analyzing the genetic diversity of the Xinjiang Brown cattle population lays the theoretical groundwork for identifying and conserving its genetic resources. This study employed the Illumina Bovine SNP 150K chip to analyze genetic diversity, inbreeding coefficient, kinship, and genetic distance in a population of 750 Xinjiang Brown cattle from three breeding farms in Xinjiang. Genetic diversity was assessed by calculating minimum allele frequency (MAF), observed heterozygosity (Ho), expected heterozygosity (He), polymorphic information content (PIC), and linkage disequilibrium (LD). Population structure was analyzed using PCA. ROH was calculated to derive ROH-based inbreeding coefficients, pedigree-based inbreeding coefficients (FPED) were estimated using CFC software for comparison, and candidate genes within high-frequency ROH regions in Xinjiang Brown cattle were identified. A G matrix was constructed to analyze population kinship. Results revealed 94,173 high-quality SNP loci in Xinjiang Brown cattle, with an average MAF of 0.276, PIC of 0.376, Ho of 0.345, and He of 0.376. Breeding farm 3 exhibited the fastest LD decay, indicating relatively high genetic diversity across Xinjiang Brown cattle populations, with farm 3 demonstrating greater diversity. The IBS genetic distance was 0.313. The G matrix results aligned with the IBS distance matrix, both indicating close kinship among some individuals within the Xinjiang Brown cattle population. The ranges for average FPED and average FROH across farms were 0.0017–0.0189 and 0.0609–0.0878, respectively. Short ROH segments (0.5–2 Mb) constituted the largest proportion (51.31%) of all ROHs. Within high-frequency ROH enrichment regions, 61 genes, including LCORL, FAM110B, NR4A1, and PER2, were identified as potentially associated with economic traits in Xinjiang Brown cattle. These findings provide relevant marker sites for genomic selection in Xinjiang Brown cattle and lay a theoretical foundation for subsequent research.