Paternal Genetic Diversity, Differentiation, and Phylogeny of Three Breeds/Populations of White Yaks in China – Scientific Reports

Identification of haplotype/haplogroup Y in white yak

The amplified fragment lengths of the five Y-SNPs (SRY4, USP9Y, UTY19, AMELY3and OFD1Y10) were 969 bp, 470 bp, 290 bp, 971 bp, and 763 bp, respectively. The corresponding sequences had been submitted to GenBank (Accession No. SRY4: MF683848, USP9Y: MF683849, UTY19: MF683850, AMELY3: MF683851, and OFD1Y10:MF683852). The sequencing results of each of the Y-SNPs were analyzed by multiple sequence alignment and 10 previously reported Y-SNPs were also detected (Table S1)^9.10. In Y-STR typing analysis INRA189 marker, three alleles of 155 bp, 157 bp and 161 bp were detected. Notably, the 161 bp allele was only detected in Tianzhu white yak, while others were found in all three breeds/populations (Table S1).

Haplotypes/haplogroups were jointly identified based on Y-SNP and Y-STR alleles. According to the previous judgment criterion for haplotype Y of yak^ten, a total of six Y haplotypes were determined in three breeds/populations of white yaks, namely H1Y1, H9Y1, H10Y1, H11Y2, H12Y2 and H13Y2 (Table 1, Table S1). The six Y haplotypes could be divided into two Y haplogroups (Y1 and Y2): haplogroup Y1 included three haplotypes (H1Y1, H9Y1 and H10Y1), while haplogroup Y2 contained haplotypes H11Y2, H12Y2 and H13Y2 (Table S1) . .

White yak Y-chromosome haplotype diversity

The frequencies of six Y haplotypes were different among three breeds/populations of white yaks (Fig. 1, Table 1). Overall, haplotype H11Y2 was predominant (37.1%) and H13Y2 (1.0%) was rare in white yak. Three haplotypes (H1Y1, H10Y1 and H11Y2) were common and shared by the three breeds/populations of white yak; however, H12Y2 was only shared by the Tianzhu and Huzhu white yak populations. Haplotypes H9Y1 and H13Y2 were found exclusively in white yak Menyuan and Tianzhu, respectively. These results showed that the Menyuan and Tianzhu white yak breeds/populations possessed unique paternal genetic information. In our previous study, 5, 3, and 43 specific maternal haplotypes were detected in Menyuan, Huzhu, and Tianzhu white yak breeds/populations, respectively.¹¹. Based on the studies of maternal and paternal genetic markers, it can be concluded that the Menyuan and Tianzhu white yak populations possessed specific genetic information; therefore, conservation and enforcement should be done independently for these genetic units in the future.

In this study, the total haplotype diversity of three breeds/populations of white yaks was 0.7567 ± 0.0233. Compared to previous report^ten, it showed that the white yak had a higher total haplotype diversity (0.7567 ± 0.0233) than 15 other Chinese domestic yak breeds/populations (0.6946 ± 0.0143), but lower than the population of wild yaks (0.8214 ± 0.1007). This total haplotype diversity revealed that the white yak also possessed rich paternal genetic diversity. The haplotype diversities of the Huzhu, Tianzhu, and Menyuan white yak breeds/populations in this study were 0.7500 ± 0.0349, 0.6881 ± 0.0614, and 0.5720 ± 0.0657, respectively (Table 1) . He reported that the diversity of Y haplotypes was highest in white yak Huzhu but lowest in white yak Menyuan. Surprisingly, the haplotype diversity of the Huzhu white yak was higher than that of other previously reported Chinese domestic yak breeds/populations (0.1174–0.7273), but only lower than that of the wild yak population (0. 8214 ± 0.1007)^ten. At the same time, the haplotype diversities of the Menyuan and Tianzhu white yak breeds/populations were also higher than those of most Chinese domestic yak breeds/populations (0.1174–0.7273)^ten. The present results indicate rich paternal genetic diversity in the three Chinese white yak breeds/populations. While Huzhu’s white yak showed the highest level of paternal genetic diversity.

Relationship of differentiation and clustering among white yak populations

The genetic differentiation index (F_ST) was used to assess the degree of differentiation between races/populations of white yaks. The F_ST values ​​ranged from −0.0050 to 0.0763, whereas, R_ST values ​​(linearized F_ST values) ranged from 0 to 0.0826 (Table S2), indicating the varying degree of differentiation between the three breeds/populations of white yaks. Refer to Wright’s standard²⁰the F_ST values ​​indicated moderate differentiation between Tianzhu and Menyuan white yak breeds/populations (0.0763, P< 0.05), however, the Huzhu white yak population displayed a weaker genetic differentiation from Tianzhu white yak (0.0186, P >0.05) and Menyuan white yak (-0.0050, P > 0.05) (Table S2). The differentiation between the three races/populations of white yaks may have been the result of differences in diverse living environment, geographic isolation, and human selection.

The UPGMA tree was constructed using R_ST values ​​among populations for cluster analysis (Fig. S1). The result showed that the Huzhu and Menyuan white yak populations clustered first, and then with the Tianzhu white yak. The clustering relationship results revealed that there was a close genetic relationship between the white yak Huzhu and Menyuan, but a distant genetic relationship with the white yak Tianzhu.

White yak phylogenetic network analysis

Network analysis showed that six Y haplotypes were divided into two haplogroups/lineages (Y1 and Y2), suggesting two paternal origins of the white yak. The current observation is consistent with the results of previous research on wild and domestic yak breeds.^ten. In the present study, the Y1 and Y2 lines had three haplotypes in each line (Fig. 2). Haplogroup/lineage Y1 was observed in 48.45% (47/97) of individuals and haplogroup/lineage Y2 in 51.55% (50/97) of individuals (Table 1), indicating that Y2 was a dominant haplogroup/lineage in the white yak. Meanwhile, the proportions of Y1 in Menyuan, Huzhu and Tianzhu white yak were 41.94%, 43.75% and 58.82%, respectively; however, the proportions of Y2 in white yaks from Menyuan, Huzhu, and Tianzhu were 58.06%, 56.25%, and 41.18%, respectively (Table 1). The observed data indicated the dominance of Y1 haplogroup/lineage in Tianzhu white yak and Y2 haplogroup/lineage in Menyuan and Huzhu white yak populations. Previous studies showed that the Y1 haplogroup/lineage was the dominant haplogroup/lineage in most domestic and wild yak populations, with the exception of the Pali yak breed.^ten. Therefore, our current results showed that the population structure composition of Menyuan and Huzhu white yak is different from most other Chinese domestic yak breeds, but similar to Pali yak breed. Further exploration at the genome level would be needed to unravel the genomic differences between yak breeds/populations.

Median junctional network of six Y haplotypes identified in three breeds/populations of Chinese white yaks based on Y-SNP and Y-STR makers. The colors correspond to the different races/populations. The size of each haplotype circle indicates the number of individuals observed.