Abstract: The study aimed to explore the maternal genetic diversity, population structure, cluster relationship and genetic background of wild yak and local yak breeds in Qinghai at molecular level. The 22 mitogenome sequences of 4 local yak breeds in Qinghai (Qinghai Plateau, Huanhu, Xueduo and Yushu) were obtained, and 142 corresponding sequences from wild yak and the above 4 local yak breeds in Qinghai were downloaded from GenBank. A total of 164 mitogenome sequences were comprehensively analyzed by using BioEdit 7.2.5, Arlequin 3.11 and Network 10.1 softwares. The results showed that:1) A total of 115 haplotypes were identified based on nucleotide variation, among which 22 haplotypes were found in wild yak and 93 haplotypes were detected in Qinghai yak breeds. The 22, 26, 18, 23 and 19 haplotypes were detected in wild yak, Qinghai Plateau, Huanhu, Xueduo and Yushu yak breeds, respectively. Genetic diversity analysis showed that the haplotype diversity of wild yak was the highest (0.992 8±0.014 4), which was higher than that of 4 local yak breeds in Qinghai (0.973 1±0.007 7). The haplotype diversities of 4 local yak breeds were 0.988 5±0.012 6 (Xueduo yak), 0.975 8±0.018 7 (Yushu yak), 0.973 0±0.016 6 (Qinghai Plateau yak) and 0.939 3±0.027 8 (Huanhu yak), respectively. 2) The fixed index (F_ST) value between wild yak and Huanhu yak was the highest (0.041 2), while the lowest (-0.008 8) between wild yak and Yushu yak. Among the 4 local yak breeds, the F_ST value between Xuduo yak and Qinghai Plateau yak was the highest (0.035 8) and the differentiation degree was the highest, while the F_ST value between Xuduo yak and Huanhu yak was the lowest (0.011 2), inferring the lowest differentiation degree. 3) The clustering analysis showed that each of the 4 yak breeds was divided into one category, suggesting that there were significant maternal genetic differences among them. In contrast, the clustering of Huanhu and Xueduo yak was closer, while the clustering of Qinghai Plateau yak and Yushu yak was also closer. The clustering relationship between wild yak and Yushu yak was closer. The clustering results among breeds (populations) was consistent with their differentiation degree and geographical distribution. 4) Phylogenetic analysis showed that 115 haplotypes were distributed in 3 maternal lineages (Mt-Ⅰ, Mt-Ⅱ and Mt-Ⅲ). The proportion of Mt-Ⅰ clade was 72.17%, consisting of 4 haplogroups (A, B, E and F), and Mt-Ⅱ clade consisted of 3 haplogroups (C, D and H), accounting for 26.09%. Mt-Ⅲ clade contained only G haplogroup, which was owned by Xueduo yak and wild yak, accounting for 1.74%, suggesting that yak had 3 maternal origins. In summary, the wild yak and the 4 local yak breeds in Qinghai Province all have rich maternal genetic diversity, and the diversity levels from high to low are the wild yak, Xueduo yak, Yushu yak, Qinghai plateau yak and Huanhu yak. The genetic differentiations among the 5 yak breeds (population) are weak, and each breed(population) had unique maternal genetic information, there are significant maternal genetic difference among them. The wild yak and Qinghai domestic yak breeds are composed of 3 maternal lineages, and it is speculated that there are 3 maternal origins in yak.

Key words: yak, mitogenome, genetic diversity, differentiation, clustering relationship, phylogeny