Whole-genome sequencing of eight goat populations for the detection of selection signatures underlying production and adaptive traits

Xianyong Lan,Hailong Yan,Xingui Tian,Jing Liu,Jiuzhou Song,Yulin Chen,Xiaopeng An,Yu Jiang,Yan Li,Jiazhong Guo,Chao Yuan,Xiaolong Wang,Yiyuan Niu,Rongqing Geng,Guangxian Zhou,Huangkai Zhou

doi:10.1038/srep38932

Abstract

The goat (Capra hircus) is one of the first farm animals that have undergone domestication and extensive natural and artificial selection by adapting to various environments, which in turn has resulted in its high level of phenotypic diversity. Here, we generated medium-coverage (9–13×) sequences from eight domesticated goat breeds, representing morphologically or geographically specific populations, to identify genomic regions representing selection signatures. We discovered ~10 million single nucleotide polymorphisms (SNPs) for each breed. By combining two approaches, ZHp and di values, we identified 22 genomic regions that may have contributed to the phenotypes in coat color patterns, body size, cashmere traits, as well as high altitude adaptation in goat populations. Candidate genes underlying strong selection signatures including coloration (ASIP, KITLG, HTT, GNA11, and OSTM1), body size (TBX15, DGCR8, CDC25A, and RDH16), cashmere traits (LHX2, FGF9, and WNT2), and hypoxia adaptation (CDK2, SOCS2, NOXA1, and ENPEP) were identified. We also identified candidate functional SNPs within selected genes that may be important for each trait. Our results demonstrated the potential of using sequence data in identifying genomic regions that are responsible for agriculturally significant phenotypes in goats, which in turn can be used in the selection of goat breeds for environmental adaptation and domestication.

Highlights

The goat (Capra hircus) is one of the first farm animals that have undergone domestication and extensive natural and artificial selection by adapting to various environments, which in turn has resulted in its high level of phenotypic diversity
We investigated selection signatures using pooling sequencing of eight distinct goat populations (Supplementary Table S1), including a black coated breed (Taihang Black), a highland breed (Tibetan goat), two cashmere goat breeds (Inner Mongolia Cashmere and Shaanbei Cashmere) a breed for mohair (Angora), a dairy goat population (Saanen), a meat goat breed (Boer), and a mini goat breed with small body size (Guizhou Small) (Fig. 1a and b)
whole-genome resequencing (WGS) was performed on an Illumina HiSeq 2000 platform by using the pooled DNA from each breed

Summary

Introduction

The goat (Capra hircus) is one of the first farm animals that have undergone domestication and extensive natural and artificial selection by adapting to various environments, which in turn has resulted in its high level of phenotypic diversity. We generated medium-coverage (9–13×) sequences from eight domesticated goat breeds, representing morphologically or geographically specific populations, to identify genomic regions representing selection signatures. ZHp and di values, we identified 22 genomic regions that may have contributed to the phenotypes in coat color patterns, body size, cashmere traits, as well as high altitude adaptation in goat populations. Our results demonstrated the potential of using sequence data in identifying genomic regions that are responsible for agriculturally significant phenotypes in goats, which in turn can be used in the selection of goat breeds for environmental adaptation and domestication. Our findings can be used to better understand genomic signatures under selection, as well as shed some light on genomic regions that harbor genes controlling production or adaptive traits in goats

Objectives

Methods

Results