Maternal genetic diversity,population structure and phylogenetic analysis of Qaidam cattle based on mitochondrial whole genome variations
[Objective]This study explored maternal genetic diversity,population structure and genetic relationship between Qaidam cattle and other cattle breeds at the genome level.[Method]The whole ge-nome resequencing technology was used for resequencing 60 Qaidam cattle to obtain the complete mito-chondrial genome sequence of each individual.A total of 129 corresponding mitochondrial genome se-quences from 5 northern cattle breeds(Mongolian cattle,Tibetan cattle,Kazakh cattle,Yanbian cattle and Anxi cattle)in China and 2 foreign breeds(Holstein cattle and Japanese Wagyu)were downloaded from GenBank for comprehensive analysis.[Result](1)A total of 346 polymorphic loci were found in the align-ment analysis of mitochondrial whole genome sequence of Qaidam cattle,including 51 single nucleotide mu-tation sites and 295 parsimony informative sites.A total of 37 haplotypes(H1-H37)were determined according to the nucleotide variation between sequences.Genetic diversity analysis showed that the haplo-type diversity of the mitochondrial genome was(0.981 0±0.006 0),and the nucleotide diversity was(0.003 3±0.000 2),suggesting that the genetic diversity of Qaidam cattle was relatively rich.(2)Phylo-genetic analysis showed that Qaidam cattle had two maternal genetic branches of Bos taurus and Bos indi-cus,and the T branch was the main lineage.There were six sub-haplogroups of T1,T2,T3,T4,I1 and I2,suggesting that Qaidam cattle had two maternal origins of Bos taurus and Bos indicus.(3)The analysis of population genetic differentiation showed that the differentiation degree of Qaidam cattle was very weak with Mongolian cattle,Tibetan cattle,Kazakh cattle,Yanbian cattle and Japanese Wagyu,while it reached moderate genetic differentiation with Anxi cattle and Holstein cattle.Cluster analysis showed that Qaidam cattle had the closest clustering relationship with Mongolian cattle,relatively close to Tibetan cattle,Ka-zakh cattle,Anxi cattle and Yanbian cattle,and farthest from Japanese Wagyu and Holstein cattle.The clustering results were basically consistent with the degree of differentiation.[Conclusion]Qaidam cattle had rich maternal genetic diversity,which was composed of two maternal branches of Bos taurus and Bos indicus.It contained six sub-haplogroups of T1,T2,T3,T4,I1 and I2,and it was speculated to have two maternal origins.It was closely related to Mongolian cattle and genetically related to Tibetan cattle,Kazakh cattle,Yanbian cattle and Anxi cattle,while it was far with Japanese Wagyu and Holstein cattle.
万方数据
维普
