Genome-wide SNP discovery and evaluation of genetic diversity among six Chinese indigenous cattle breeds in Sichuan.

Wei Wang,Hui Tang,Jun Yi,Jia Gan,Huai Wang,Maozhong Fu,Donghui Fang,Gyaneshwer Chaubey

doi:10.1371/journal.pone.0201534

Abstract

Indigenous cattle in Sichuan Province, southwestern China, provide abundant genetic resources. However, their genetic diversity and population structure remain largely unknown, especially on the genome-wide scale. In the present study, we successfully employed the restriction site-associated DNA sequencing approach (RADseq) to explore genome-wide SNPs among six breeds of Sichuan cattle. A total of 238,725 high-confidence SNPs were finally obtained with a mean distance of 11,140 bp between two adjacent sites, and 43.4% were revealed to be novel in comparison with a public reference database of genetic variants. The mean nucleotide diversity and polymorphism information content (PIC) among all six breeds were 0.1878 and 0.1555, respectively. Pingwu and Ganzi cattle showed the highest and lowest genetic diversity, respectively. The inter-breed comparisons revealed that Ganzi and Ebian cattle were obviously separate from the others. Our reference set of genome-wide SNPs specific to indigenous cattle in Sichuan is the first of its kind. Moreover, our set can be used to investigate the genetic diversity and population structure and for genome-wide association studies.

Highlights

As one of the world’s earliest domesticated mammals[1], modern cattle (Bos taurus) have played an important role in livestock husbandry by providing a large amount of milk, meat, hides and other products
Sichuan Province is located in southwestern China and shows substantial diversity in geography and climate, resulting in abundant genetic resources for both wild and domesticated animals
Genome-wide single-nucleotide polymorphisms (SNPs) discovery and evaluation of genetic diversity among six Chinese indigenous cattle breeds and exploration of genetic resources are expected to be important for promoting the sustainable development of cattle husbandry

Summary

Introduction

As one of the world’s earliest domesticated mammals[1], modern cattle (Bos taurus) have played an important role in livestock husbandry by providing a large amount of milk, meat, hides and other products. Since the initial domestication in the Neolithic age, cattle have been widely disseminated along with human migrations and have adaptively developed considerable variation in appearance and performance[2]. More than 3,200 cattle breeds worldwide have been registered in the Domestic Animal Diversity Information System (DAD-IS) of FAO (http://dad.fao.org/), which systematically reviews historic and current breed classifications[3]. Chinese indigenous cattle were first imported into Northern China as taurine cattle (B. taurus) between 3000 and 2000 BC, followed by the migration of zebu cattle (B. indicus) into.

Methods

Results

Conclusion