Paternal genetic diversity and population structure of Qaidam cattle and its genetic relationship with other yellow cattle breeds in northern China
In this study,single nucleotide polymorphism (SNP) scans were performed on the single copy gene regions of Y chromosome genome of 110 individuals from 9 cattle breeds including 25 Qaidam cattle. The paternal genetic diversity,population structure differences,differentiation,and clustering of these cattle breeds were analyzed. The results showed that a total of 14 Y chromosome genome haplotypes were identified in 9 breeds,4 of which (H7,H12,H13,and H14) were identified in Qaidam cattle. Genomic diversity analysis showed that the paternal genetic diversity of Qaidam cattle was relatively rich (Hd=0.690±0.080),but the level of paternal genetic diversity was lower than that of Mongolian cattle,Yanbian cattle,Tibetan cattle and Kazakh cattle. Phylogenetic analysis showed that the paternal inheritance of Qaidam cattle was composed of Y1,Y2a,and Y2b haplogroups/sub-haplogroups,and the Y2b sub-haplogroup was dominant,indicating that Qaidam cattle was of Bos taurus origin. The genetic differentiation analysis showed that the differentiation degrees between Qaidam cattle and Mongolian cattle or Tibetan cattle were low,and the differentiation degree between Qaidam cattle and Yanbian cattle was moderate,and the differentiation degrees between Qaidam cattle and Kazakh cattle,Simmental cattle or Angus cattle were high. Cluster analysis showed that Qaidam cattle had the closest clustering relationship with Mongolian cattle,which was closer to that of Tibetan cattle and Yanbian cattle but far from that of Kazakh cattle,Simmental cattle and Angus cattle. The results of this study provide a reference for in-depth understanding of the paternal genomic diversity,population structure and genetic relationships between Qaidam cattle and other yellow cattle breeds,enrich the genome database/dataset of Qaidam cattle,and lay a foundation for the subsequent rational protection and molecular breeding practices of Qaidam cattle.
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