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.