Whole-genome resequencing reveals genetic diversity, differentiation, and selection signatures of yak breeds/populations in Qinghai, China.

The Qinghai Province of China is located in the northeast region of the Qinghai-Tibetan Plateau (QTP) and carries abundant yak genetic resources. Previous investigations of archaeological records, mitochondrial DNA, and Y chromosomal markers have suggested that Qinghai was the major center of yak domestication. In the present study, we examined the genomic diversity, differentiation, and selection signatures of 113 Qinghai yak, including 42 newly sequenced Qinghai yak and 71 publicly available individuals, from nine yak breeds/populations (wild, Datong, Huanhu, Xueduo, Yushu, Qilian, Geermu, Tongde, and Huzhu white) using high-depth whole-genome resequencing data. We observed that most of Qinghai yak breeds/populations have abundant genomic diversity based on four genomic parameters (nucleotide diversity, inbreeding coefficients, linkage disequilibrium decay, and runs of homozygosity). Population genetic structure analysis showed that Qinghai yak have two lineages with two ancestral origins and that nine yak breeds/populations are clustered into three distinct groups of wild yak, Geermu yak, and seven other domestic yak breeds/populations. values showed moderate genetic differentiation between wild yak, Geermu yak, and the other Qinghai yak breeds/populations. Positive selection signals were detected in candidate genes associated with disease resistance (, , and ), heat stress (, , and ), pigmentation (, , and ), vision (, , and ), milk quality ( and ), neurodevelopment (, , and ), and meat quality (), using the integrated PI, composite likelihood ratio (CLR), and methods. These findings offer new insights into the genetic mechanisms underlying target traits in yak and provide important information for understanding the genomic characteristics of yak breeds/populations in Qinghai.

Li G ，Luo J ，Wang F ，Xu D ，Ahmed Z ，Chen S ，Li R ，Ma Z ... -  《Frontiers in Genetics》

Whole-genome resequencing reveals genetic diversity, differentiation, and selection signatures of yak breeds/populations in southwestern China.

Zhang S ，Li J ，Zhao Y ，Tang Y ，Li H ，Song T ，An T ，Guan J ，Li X ，Zhang M ... -  《Frontiers in Genetics》

Identification and diversity of Y-chromosome haplotypes in Qinghai yak populations.

The aim of the present study was to perform a preliminary analysis of the characterization and diversity of Y-chromosome haplotypes/haplogroups in yak of Qinghai Province, China. A total of 322 male yaks from nine populations belonging to three officially recognized breeds (Gaoyuan, Huanhu and Datong) were sampled. Animals were genotyped using six previously reported Y-SNPs present in the SRY, USP9Y, UTY, AMELY and OFD1Y genes and four new Y-SNPs in the OFD1Y gene (g.569A>C, g.578A>C, g.608G>T and g.653G>C) identified in this study. Seven Y-chromosome haplotypes (H1-H7) were identified according to the combination of the 10 Y-SNPs. H1, H2 and H6 were the most common and shared haplotypes across all yak populations/breeds. Private haplotypes H3 and H7 were detected in the Datong breed; H4 in Guoleimude, Qumalai, Qilian, Tianjun and Ganglong populations; and H5 in Qumalai of Gaoyuan breed. Haplotype clustering and network analyses inferred two haplogroups, Y1 and Y2, indicating two divergent lineages of paternal origins of Qinghai yak. The analysis of molecular variance showed a significant difference among individuals (P < 0.0001) with more than 93% of the total genetic variation present within populations, suggesting a weak genetic structure among Qinghai yak populations. The overall Y-haplotype diversity was 0.538 ± 0.028, showing a relatively high diversity in Qinghai yak. The Gaoyuan and Datong breeds had similar haplotype diversities (0.547 ± 0.030 and 0.553 ± 0.083, respectively), which were higher than that of the Huanhu breed (0.441 ± 0.098). Our results support the conservation and sustainable use of unique yak genetic resources in Qinghai.

Ma ZJ ，Xia XT ，Chen SM ，Zhao XC ，Zeng LL ，Xie YL ，Chao SY ，Xu JT ，Sun YG ，Li RZ ，Guanque ZX ，Han JL ，Lei CZ ... -  《-》

Paternal genetic diversity, differentiation and phylogeny of three white yak breeds/populations in China.

The white yak, a type of unique and valuable farm animals on the Qinghai-Tibet Plateau, are mainly distributed in Tianzhu (County of Gansu Province), Menyuan, Huzhu and Ledu (three Counties of Qinghai Province) in China. In the present study, the Y-chromosomal genetic diversity, differentiation and phylogeny of three Chinese white yak breeds/populations (Tianzhu, Huzhu and Menyuan) were comprehensively explored using five Y-SNPs (SRY4, USP9Y, UTY19, AMELY3 and OFD1Y10) and one Y-STR (INRA189) markers. The results showed that six Y-haplotypes (H1Y1, H9Y1, H10Y1, H11Y2, H12Y2 and H13Y2) were identified in 97 male yak from three white yak breeds/populations. Among these haplotypes, H1Y1, H10Y1 and H11Y2 were shared by all of breeds/populations and H12Y2 was shared by Tianzhu and Huzhu populations. However, H9Y1 and H13Y2 haplotypes were only detected in Menyuan and Tianzhu white yak populations, respectively. The Y-haplotype diversity was maximum in Huzhu white yak (0.7500 ± 0.0349), the medium in Tianzhu white yak (0.6881 ± 0.0614) and the lowest in Menyuan white yak (0.5720 ± 0.0657). The total Y-haplotype diversity of three white yak breeds/populations was 0.7567 ± 0.0233, indicating rich paternal genetic diversity in white yak. The F values showed a moderate differentiation between Tianzhu and Menyuan (F = 0.0763, P < 0.05) populations, but a weak differentiation between Huzhu and Tianzhu white yak breeds/populations (F = 0.0186, P > 0.05) and Huzhu and Menyuan (F = - 0.005, P > 0.05) populations. The clustering analysis revealed a close genetic relationship between Huzhu and Menyuan white yak, both were far from Tianzhu white yak breed. The phylogenetic analyses showed that white yak had two Y-haplogroups/lineages (Y1 and Y2) with two potential paternal origins. The findings of present study provide new insight into the basic information for the formulation of molecular breeding programs of white yak. Moreover, it also contributes to the conservation and utilization of this special animal genetic resource.

Luo J ，Wei X ，Liu W ，Chen S ，Ahmed Z ，Sun W ，Lei C ，Ma Z ... -  《Scientific Reports》

Maternal genetic diversity, differentiation and phylogeny of three white yak breeds/populations in China.

White yak is a unique economic livestock animal on the Qilian Mountains of Qinghai-Tibet Plateau (QTP). Here, 369 mitochondrial D-loop sequences from three Chinese white yak breeds/populations (Tianzhu, Menyuan and Huzhu) were comprehensively analyzed to indicate their maternal genetic diversity, differentiation and phylogenetic relationship. Our results showed that the haplotype diversity (Hd) was found to be highest in Tianzhu white yak (Hd ± SD = 0.9501 ± 0.0058), while the lowest was recorded in Huzhu white yak (Hd ± SD = 0.7178 ± 0.0474). Totally, the haplotype and nucleotide diversities of white yak were 0.9407 ± 0.0069 and 0.0187 ± 0.0094, respectively, indicating an abundant maternal genetic diversity in white yak. Estimates of (Fixation Index) values showed a high genetic differentiation between Tianzhu and Menyuan populations ( = 0.2928,  < 0.05) as well as that between Tianzhu and Huzhu populations ( = 0.2721,  < 0.05), but a moderate genetic differentiation between Menyuan and Huzhu populations ( = 0.1352,  > 0.05) was observed. Cluster analysis based on values among populations indicated that the genetic relationship between Menyuan and Huzhu white yak was closer, but they had a far genetic relationship with Tianzhu white yak. Maternal phylogenetic analysis revealed that white yak represented two maternal lineages (I and II), suggesting two maternal origins. In addition, it is notable that taurine mtDNA haplotypes were detected in Tianzhu and Huzhu white yak populations, indicating taurine genetic introgression to some extent. Our study would provide useful information for the conservation and utilization of white yak.

Li G ，Luo J ，Chen S ，Hanif Q ，He D ，Ma Z ... -  《-》