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

Jie Cheng,Linyong Hu,Buren Chaogetu,Chuzhao Lei,Li Pi,Ningbo Chen,Yongzhen Huang,Xianyong Lan,Hong Chen,Huangqing Zhao,Quratulain Hanif,Xiukai Cao

doi:10.1186/s12864-020-06925-z

Abstract

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.

Highlights

Chaka sheep, named after Chaka Salt Lake, are adapted to a harsh, highly saline environment
Chinese indigenous sheep breeds include Mongolian, Kazakh, and Tibetan lineage groups according to their geographical distribution and genetic relationships (China National Commission of Animal Genetic Resources 2011) [2]
TAN and BYK sheep are within the Mongolian lineage, OLA is within the Tibetan lineage, and the lineage of CKA sheep has not yet been identified

Summary

Introduction

Chaka 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. Called Qinghai plateau half-fine wool sheep for fur and meat, the breed has been designated a geographical symbol of agricultural products by the Chinese Ministry of Agriculture. The Mongolian lineage (ML) has the largest population and is widely distributed in northern, central, and eastern areas of China Among these populations, Chaka (CKA), Tan (TAN), Bayinbuluke (BYK), and Oula (OLA) sheep are widespread in Qinghai, Ningxia, Xinjiang, and Qinghai, respectively, in China (Supplementary Figure 1). TAN and BYK sheep are within the Mongolian lineage, OLA is within the Tibetan lineage, and the lineage of CKA sheep has not yet been identified

Methods

Results

Conclusion