3.1 Maternal genetic diversity of five yak breeds/populations
The sequences of two wild yak and three Qinghai-Gaoyuan yak were deposited in GenBank under the accession numbers ON077034-ON077035 and OP389990-OP389992, respectively. A set of the 166 mtDNA Cytbsequences from one wild yak population and four Qinghai domestic yak breeds was analyzed, which revealed 34 polymorphic sites, including 16 singleton variable sites and 18 parsimonious informative sites. A total of 11 variable sites were detected, and 11, 11, 11,12, and 25 haplotypes were identified in Qinghai-Gaoyuan, Huanhu, Xueduo, Yushu, and wild yak, respectively (Table S2). Totally, 29 haplotypes were defined in 166 yak samples (Figure 2,Table S2). Of these, H1, H4, and H10 were the most frequent, being represented in 86 (51.81%), 26 (15.66%), and 20 (12.05%) individuals of all samples respectively, followed by H14 identified in three yak (1.81%). H2, H5, H19, H21, H22, and H28 were each found in two yak individuals and the remaining 19 haplotypes were found in single individual (Figure 2.). At the same time, a total of 7 haplotypes were found in Qinghai-Gaoyuan yak (4 specific haplotypes), 5 in Huanhu yak (2 specific haplotypes), 8 in Xueduo yak (3 specific haplotypes), 9 in Yushu yak (4 specific haplotypes), and 13 in wild yak (8 specific haplotypes), respectively, indicating that both wild yak and four Qinghai domestic yak breeds/populations own unique maternal genetic information. The analysis of genetic diversity of five yak breeds/populations showed that the haplotype and nucleotide diversities of wild yak (0.883±0.044 and 0.004±0.002) were higher than that of the total haplotype diversity (0.646±0.040) and nucleotide diversity (0.003±0.001) of four Qinghai domestic yak breeds, respectively (Table S2), indicating a rich genetic diversity in five yak breeeds/populations, but the wild yak population have highest maternal genetic diversity. Of the four domestic yak breeds, the haplotype diversity reached a maximum in the Yushu yak breed (0.770±0.053) and a minimum in the Huanhu yak breed (0.501±0.088). Notably, the result was broadly consistent with the previous studies on domestic and wild yak breeds/populations in Qinghai (Li et al., 2022).
3.2 Genetic differentiation and clustering relationships among five yak breeds/populations
F ST (Fixation Index) is the index of genetic differentiation among populations, which can be used to evaluate the degree of differentiation among populations. The genetic differentiation index of 0 to 0.05 shows a very weak population differentiation, that of 0.05-0.15 shows moderately differentiated populations, whereas, 0.15-0.25 indicates significant population difference. The degree of differentiation is considered extremely significant when the index reaches above 0.25 (Curnow & Wright, 1978). Here, our analysis revealed that the FST values between wild yak and three Qinghai local yak breeds (Qinghai-Gaoyuan, Xueduo, and Yushu) exhibited a very weak genetic differentiation (-0.021<FST <0.037), but a moderate differentiation was observed between wild yak population and Huanhu yak breed (F ST = 0.058) (Table S3). Additionally, of four domestic yak breeds, the results suggested a moderate differentiation was found between Yushu yak breed and Huanhu yak breed (F ST = 0.052). In contrast, a very weak genetic differentiation was observed between the other domestic yak breeds (Table S3). Overall, the genetic differentiation among the wild yak population and four Qinghai domestic yak breeds showed a weak level, which was largely consisted with the previous results based on paternal genetic differentiation (Li et al., 2022)
According to the analysis of multi-dimensional scale (MDS) among five yak breeds/populations in this study, the five yak breeds/populations were divided into four groups/categories. In dimension one, wild yak and Yushu yak were separated into one group, Qinghai-Gaoyuan, Xueduo, and Huanhu yak were separated into another one group. In dimension two, Qinghai-Gaoyuan yak was separated from Xueduo and Huanhu yak, wild yak and Yushu yak were separated again (Figure 3). Based on the results of genetic differentiation and cluster analysis, the cluster relationship between Yushu yak and wild yak was closer, while the cluster of Xueduo, Huanhu, and Qinghai-Gaoyuan yak was closer.