Analysis of genetic diversity and phylogenetic evolution of cattle population in the Ili River Valley region, Xinjiang, based on mtDNA D-loop sequence.

This study used mitochondrial DNA (mtDNA) D-loop region sequence polymorphisms as molecular markers to investigate the genetic structure and maternal origin of six cattle breeds in the Ili River Valley region of Xinjiang, China. Blood samples were collected from six cattle breeds in the region, including Xinjiang Brown cattle (n = 30), Kazakh cattle (n = 33), Altay White-headed cattle (n = 33), Chinese Simmental cattle (n = 34), Chinese Holstein cattle (n = 31), and Angus cattle (n = 22), for DNA extraction. Complete mtDNA D-loop region sequences were obtained from 183 individuals. Sequence alignment, correction and SNP screening were implemented to characterize sequence variation and base composition. Genetic diversity parameters and pairwise genetic distances were estimated, and a neighbor-joining (NJ) phylogenetic tree was constructed. The complete sequences of the mtDNA D-loop region in the six cattle breed populations were 910-911 bp. The average contents of A, G, T, and C were 32.76%, 13.83%, 28.79%, and 24.62%, respectively, and the overall AT content was higher than GC content. A total of 147 SNPs were detected, accounting for 16.10% of the total sequence length. In total, 107 haplotypes were identified, of which 92 were classified as Bos taurus and 15 as Bos indicus. The k, Hd, and Pi values were 14.24, 0.99, and 0.02, respectively. The constructed NJ phylogenetic tree revealed two major maternal origins-Bos taurus and Bos indicus-among the six cattle breeds. The six cattle breeds in the Ili River Valley region exhibit rich genetic diversity and two maternal origins, predominantly influenced by Bos taurus. These findings provide a theoretical basis for the conservation and rational use of cattle genetic resources in the region.