Rich maternal and paternal genetic diversity and divergent lineage composition in wild yak (<i>Bos mutus</i>)

Ma, Zengyi; Li, Guangzhen; Chen, Shengmei; Han, Jianlin; Hanif, Quratulain

doi:10.1080/10495398.2021.1895187

Cited by 6 publications

(4 citation statements)

References 21 publications

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“…Combining shotgun and captured sequencing data, we obtained sequencing depths for the five bovine mitogenomes ranging from 7.16× to 256.72× (table S6). Next, we assigned the species of the five bovine mitogenomes by placing them within the currently known matrilineal ancestries of 76 present-day yak and cattle (45)(46)(47)(48)(49) (table S7). The maximum likelihood (ML) tree revealed that four of the five mitogenomes fell within domestic taurine cattle haplogroup T, while the remaining mitogenome was within the yak clade III of haplogroup A (Fig.…”

Section: Molecular Identification Of the Species Of The Bangga Bovine...mentioning

confidence: 99%

Evidence for early domestic yak, taurine cattle, and their hybrids on the Tibetan Plateau

Chen,

Zhang,

Hou

et al. 2023

Sci. Adv.

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Domestic yak, cattle, and their hybrids are fundamental to herder survival at high altitudes on the Tibetan Plateau. However, little is known about their history. Bos remains are uncommon in this region, and ancient domestic yak have not been securely identified. To identify Bos taxa and investigate their initial management, we conducted zooarchaeological analyses of 193 Bos specimens and sequenced five nuclear genomes from recently excavated assemblages at Bangga. Morphological data indicated that more cattle than yak were present. Ancient mitochondrial DNA and nuclear genome sequences identified taurine cattle and provided evidence for domestic yak and yak-cattle hybridization ~2500 years ago. Reliance on diverse Bos species and their hybrid has increased cattle adaptation and herder resilience to plateau conditions. Ancient cattle and yak at Bangga were closely related to contemporary livestock, indicating early herder legacies and the continuity of cattle and yak husbandry on the Tibetan Plateau.

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Section: Molecular Identification Of the Species Of The Bangga Bovine...mentioning

confidence: 99%

Evidence for early domestic yak, taurine cattle, and their hybrids on the Tibetan Plateau

Chen,

Zhang,

Hou

et al. 2023

Sci. Adv.

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“…According to our previous reports on genetic variations in Y-chromosomal markers, both wild and domestic yak in Qinghai have relatively high paternal genetic diversity with weak phylogeographic structures and two paternal origins (Ma et al, 2018;Ma et al, 2022). In addition, maternal genetic diversity of the wild and domestic yak in Qinghai indicates that wild and domestic yak have high levels of genetic diversity and can be clustered into three lineages (Wang et al, 2021;Li et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

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

Luo²,

Wang³

et al. 2023

Front. Genet.

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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. FST 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 (CDK2AP2, PLEC, and CYB5B), heat stress (NFAT5, HSF1, and SLC25A48), pigmentation (MCAM, RNF26, and BOP1), vision (C1QTNF5, MFRP, and TAX1BP3), milk quality (OPLAH and GRINA), neurodevelopment (SUSD4, INSYN1, and PPP1CA), and meat quality (ZRANB1), using the integrated PI, composite likelihood ratio (CLR), and FST 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.

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“…The exploration of population genetic structure of yak has become a prominent field in domestic animal. Studies have been conducted on the genetic diversity of yaks using microsatellites and mitochondrial DNA (Qiu et al, 2015;Wang et al, 2021;Hameed et al, 2022;Ma et al, 2022). Moreover, the assembly and publication of the first yak reference genome in 2012, followed by subsequent improvements, have resulted in a highly complete and accurate yak reference genome at the chromosome level (Qiu et al, 2012;Ji et al, 2021;Zhang et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

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

Zhang,

Li,

Zhao

et al. 2024

Front. Genet.

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The Sichuan-Yunnan region is the main production area of yaks in southwestern China, with rich genetic resources of Yaks. Nevertheless, there have been limited study on the genetic characteristics of the entire yak populations in Tibet and southwestern China. In this study, we performed whole-genome resequencing to identify genetic variation information in a total of 198 individuals from six yak breeds (populations) in Sichuan (Muli yak, Jinchuan yak, Changtai yak, Maiwa yak), Yunnan (Zhongdian yak), and Tibet (Tibetan yak). The aim was to investigate the whole-genome genetic diversity, population genetic structure, and genome selection signatures. We observed that all six populations exhibit abundant genetic diversity. Except for Tibetan yaks, which showed low nucleotide diversity (0.00104), the remaining yak populations generally displayed high nucleotide diversity (0.00129–0.00153). Population genetic structure analysis revealed that, among the six yak populations, Muli yak exhibited greater differentiation from other yak populations and formed a distinct cluster independently. The Maiwa yak population displayed a complex genetic structure and exhibited gene exchange with Jinchuan and Changtai yaks. Positive selection signals were detected in candidate genes associated with growth (GNB4, HMGA2, TRPS1, and LTBP1), reproduction (PI4KB, DYNC1I1, and GRIP1), immunity (CD200 and IL1RAP), lactation (SNX13 and CPM), hypoxia adaptation (NDUFB6, PRKN, and MRPS9), hair (KRT24, KRT25, and KRT26), meat quality (SUCLG2), digestion and absorption (CLDN1), and pigment deposition (OCA2) using the integrated Pi and FST methods. This study provides significant insights into understanding the whole-genome genetic characteristics of yak populations in Tibet and southwestern China.

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Rich maternal and paternal genetic diversity and divergent lineage composition in wild yak (Bos mutus)

Cited by 6 publications

References 21 publications

Evidence for early domestic yak, taurine cattle, and their hybrids on the Tibetan Plateau

Evidence for early domestic yak, taurine cattle, and their hybrids on the Tibetan Plateau

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

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

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