Population Structure, and Selection Signatures Underlying High-Altitude Adaptation Inferred From Genome-Wide Copy Number Variations in Chinese Indigenous Cattle.

Yang Zhou,Liguo Yang,Jinming Huang,Han Zhao,Xiaochao Wei,Yan Hu,Yaping Gao,Yaran Zhang,Jiachen Bai,Xiuge Wang,Zhihua Ju,Qiang Jiang,Jinpeng Wang

doi:10.3389/fgene.2019.01404

Abstract

Copy number variations (CNVs) have been demonstrated as crucial substrates for evolution, adaptation and breed formation. Chinese indigenous cattle breeds exhibit a broad geographical distribution and diverse environmental adaptability. Here, we analyzed the population structure and adaptation to high altitude of Chinese indigenous cattle based on genome-wide CNVs derived from the high-density BovineHD SNP array. We successfully detected the genome-wide CNVs of 318 individuals from 24 Chinese indigenous cattle breeds and 37 yaks as outgroups. A total of 5,818 autosomal CNV regions (683 bp–4,477,860 bp in size), covering ~14.34% of the bovine genome (UMD3.1), were identified, showing abundant CNV resources. Neighbor-joining clustering, principal component analysis (PCA), and population admixture analysis based on these CNVs support that most Chinese cattle breeds are hybrids of Bos taurus taurus (hereinafter to be referred as Bos taurus) and Bos taurus indicus (Bos indicus). The distribution patterns of the CNVs could to some extent be related to the geographical backgrounds of the habitat of the breeds, and admixture among cattle breeds from different districts. We analyzed the selective signatures of CNVs positively involved in high-altitude adaptation using pairwise Fst analysis within breeds with a strong Bos taurus background (taurine-type breeds) and within Bos taurus×Bos indicus hybrids, respectively. CNV-overlapping genes with strong selection signatures (at top 0.5% of Fst value), including LETM1 (Fst = 0.490), TXNRD2 (Fst = 0.440), and STUB1 (Fst = 0.420) within taurine-type breeds, and NOXA1 (Fst = 0.233), RUVBL1 (Fst = 0.222), and SLC4A3 (Fst=0.154) within hybrids, were potentially involved in the adaptation to hypoxia. Thus, we provide a new profile of population structure from the CNV aspects of Chinese indigenous cattle and new insights into high-altitude adaptation in cattle.

Highlights

Copy number variations (CNVs), which include insertions, duplications, and deletions of genomic segments among individuals within species, are currently known to be 50 bps to several Mbps in length (Mills et al, 2011; Iskow et al, 2012; Zarrei et al, 2015)
These CNV regions (CNVRs) corresponded to ~14.34% of bovine genome (UMD3.1 assembly), and included 2,872 deletions, 742 insertions or duplications and 2,204 both events (Supplementary Table S3)
In ALT, the largest number of CNVRs was found on chromosome 6, and the coverage ratio ranged from 0.62% of chromosome 8 to 7.52% of chromosome 25, while in ZT, the largest number presented on chromosome 1 and the coverage ratio varied from 1.41% of chromosome 18 to 8.84% of chromosome 12

Summary

Introduction

Copy number variations (CNVs), which include insertions, duplications, and deletions of genomic segments among individuals within species, are currently known to be 50 bps to several Mbps in length (Mills et al, 2011; Iskow et al, 2012; Zarrei et al, 2015). A growing body of evidence shows that CNVs are crucial drivers of phenotypic diversity, evolution, and adaptation in humans and animals (Perry et al, 2008; Iskow et al, 2012; Sudmant et al, 2015; Romero et al, 2017; Rinker et al, 2019). Emerging evidence demonstrates that CNVs have been implicated in the adaptation of Nellore cattle to the tropical environment (Lemos et al, 2018). These findings indicate that artificial and natural selection may have shaped the landscape of CNVs in cattle genomes, thereby contributing to adaptive evolution, diversity, and breed differentiation

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Conclusion