3.3 Phylogenetic analysis of five yak breeds/populations
Phylogenetic analysis revealed that 29 haplotypes was separated into eight haplogroups (A-H), among which four haplogroups (A, B, C, and G) were found in wild yak population, four haplogroups (A, B, C, and F) in Qinghai-Gaoyuan yak breed, three haplogroups (A, B, and C) in Huanhu yak breed, six haplogroups (A, B, C, D, E, and G) in Xueduo yak breed, and six haplogroups (A, B, C, D, F, and H) in Yushu yak breed. Furthermore, only three haplogroups (A, B, and C) were shared by wild yak population and four domestic yak breeds (Figure 1, Table S2).
In our present study, a neighbor-joining tree and a network diagram of 166 yak individuals was constructed to explore the yak phylogeny (Figure 4 and Figure 5). Our results showed that the diagram comprised three branches, eight haplogroups were separated into three distinct maternal lineages (Mt-I, Mt-II, and Mt-III), indicating three maternal origins in yak. Here, Mt-I showed the highest frequency (77.71%) of the total yak individuals, followed by Mt-II (21.08%), and Mt-III (1.21%). Of these, Mt-I, Mt-II, and Mt-III including 4 haplogroups (A, B, E, and F), 3 haplogroups (C, D, and H), and 1 haplogroup (G), respectively. It was worth noting that Mt-III included only one Xueduo yak and one wild yak (Figure 2 and Figure 4). Compared with the previous findings of wild yak and Qinghai domestic yak breeds/populations based on the whole-mito genome variants (Ma et al., 2021; Wang et al., 2010; Wang et al., 2021; Li et al., 2022), this experiment reconfirmed that yak consisted of three maternal lineages, dominated by Mt-I, and presumably has three maternal origins.
As one of the five major pastoral areas in China, Qinghai has extremely abundant yak resources. In this study, five yak breeds/populations have high genetic diversity and each yak breed/population owns unique haplotypes. Both domestic and wild yak were clustered into three lineages, probably with three maternal origins. Based on the above results, we provide baseline information for the wild yak and Qinghai local yak breed and the genetic relationship among each other, which is conducive to the preservation of these valuable yak genetic resources. Overall, further exploration of Qinghai domestic yak and wild yak based on the whole-genome level in the future is of critical importance.