Population structure, genetic diversity, and selective signature of Chaka sheep revealed by whole genome sequencing

NWIPB OpenIR

	Population structure, genetic diversity, and selective signature of Chaka sheep revealed by whole genome sequencing
	Cheng, Jie; Zhao, Huangqing; Chen, Ningbo; Cao, Xiukai; Hanif, Quratulain; Pi, Li; Hu, Linyong; Chaogetu, Buren; Huang, Yongzhen; Lan, Xianyong; Lei, Chuzhao; Chen, Hong
	2020
发表期刊	BMC GENOMICS
卷号	21 期号:1
摘要	BackgroundChaka sheep, named after Chaka Salt Lake, are adapted to a harsh, highly saline environment. They are known for their high-grade meat quality and are a valuable genetic resource in China. Furthermore, the Chaka sheep breed has been designated a geographical symbol of agricultural products by the Chinese Ministry of Agriculture.ResultsThe genomes of 10 Chaka sheep were sequenced using next-generation sequencing, and compared to that of additional Chinese sheep breeds (Mongolian: Bayinbuluke and Tan; Tibetan: Oula sheep) to explore its population structure, genetic diversity and positive selection signatures. Principle component analysis and a neighbor-joining tree indicated that Chaka sheep significantly diverged from Bayinbuluke, Tan, and Oula sheep. Moreover, they were found to have descended from unique ancestors (K=2 and K=3) according to the structure analysis. The Chaka sheep genome demonstrated comparable genetic diversity from the other three breeds, as indicated by observed heterozygosity (Ho), expected heterozygosity (He), runs of homozygosity (ROH), linkage disequilibrium (LD) decay. The enrichment analysis revealed that in contrast to Mongolian or Tibetan lineage groups, the genes annotated by specific missense mutations of Chaka sheep were enriched with muscle structure development (GO:0061061) factors including insulin-like growth factor 1 (IGF1), growth differentiation factor 3 (GDF3), histone deacetylase 9 (HDAC9), transforming growth factor beta receptor 2 (TGFBR2), and calpain 3 (CAPN3), among others. A genome-wide scan using Fst and XP-CLR revealed a list of muscle-related genes, including neurofibromin 1 (NF1) and myomesin 1 (MYOM1), under potential selection in Chaka sheep compared with other breeds.ConclusionsThe comprehensive genome-wide characterization provided the fundamental footprints for breeding and management of the Chaka sheep and confirmed that they harbor unique genetic resources.
关键词	Chaka sheep Population structure Specific variation Fst and XP-CLR
文献类型	期刊论文
条目标识符	http://210.75.249.4/handle/363003/60288
专题	中国科学院西北高原生物研究所
推荐引用方式 GB/T 7714	Cheng, Jie,Zhao, Huangqing,Chen, Ningbo,et al. Population structure, genetic diversity, and selective signature of Chaka sheep revealed by whole genome sequencing[J]. BMC GENOMICS,2020,21(1).
APA	Cheng, Jie.,Zhao, Huangqing.,Chen, Ningbo.,Cao, Xiukai.,Hanif, Quratulain.,...&Chen, Hong.(2020).Population structure, genetic diversity, and selective signature of Chaka sheep revealed by whole genome sequencing.BMC GENOMICS,21(1).
MLA	Cheng, Jie,et al."Population structure, genetic diversity, and selective signature of Chaka sheep revealed by whole genome sequencing".BMC GENOMICS 21.1(2020).