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Genome-Wide Selection Sweep Analysis to Identify Candidate Genes with Black and Brown Color in Tibetan Sibu Yaks

文献类型： 外文期刊

作者： Wu, Xinming 1 ; Xu, Lu 1 ; Zhang, Haoyuan 1 ; Zhu, Yong 2 ; Zhang, Qiang 2 ; Zhang, Chengfu 2 ; Guangxin, E. 1 ;

作者机构： 1.Southwest Univ, Coll Anim Sci & Technol, Chongqing 400715, Peoples R China

2.Tibet Acad Agr & Anim Husb Sci, Inst Anim Husb & Vet Med, Lhasa 850009, Peoples R China

关键词： yak; pigment; coat color; wide-genome selection; ROH

期刊名称：ANIMALS （ 影响因子：2.7； 五年影响因子：3.2 ）

ISSN： 2076-2615

年卷期： 2024 年 14 卷 17 期

页码：

收录情况： SCI

摘要： Simple Summary We performed a genome-wide selection sweep analysis on 50 domesticated yaks to investigate the genetic basis of coat color phenotypes. We identified numerous candidate genes (e.g., PLCB1, LEF1, and DTNBP1) that play key roles in melanin synthesis. Unique candidate genes for different coat color groups may explain the variations in coat color. Additionally, a range of selected genes associated with melanin and pigment deposition were identified within the ROH islands. This study provides a solid theoretical basis for understanding yak coat color.Abstract Although coat color is an important economic phenotype in domesticated yaks (Bos grunniens), its genetic basis is not yet fully understood. In this study, a genome-wide selective sweep and high-frequency runs of homozygosity (ROH) identification were performed on 50 yaks with different coat colors to investigate candidate genes (CDGs) related to coat color. The results suggested that 2263 CDGs were identified from the 5% interaction windows of the FST and theta pi ratio, along with 2801 and 2834 CDGs from black and brown yaks with iHS, respectively. Furthermore, 648 and 691 CDGs from black and brown yaks, which were widely enriched in pathways related to melanogenesis, melanocyte differentiation, and melanosome organization via GO and KEGG functional enrichment, respectively, were confirmed on the basis of the intersection of three parameters. Additionally, the genome of brown yaks presented more ROH, longer ROH fragments, and higher inbreeding levels than those of black yaks. Specifically, a large number of genes related to melanin synthesis and regulation (e.g., UST, TCF25, and AHRR) from the ROH islands were confirmed to be under strong selection. In summary, the results of this study enhance the understanding of the genetic basis for determining yak coat color.

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