Assessing Genomic Diversity and Selective Pressures in Bohai Black Cattle Using Whole-Genome Sequencing Data.

Xiaohui Ma,Enliang Song,Wei You,Luyang Sun,Yangkai Liu,Chuzhao Lei,Fugui Jiang,Baoheng Zhang,Ningbo Chen,Zhangang Yang,Haijian Cheng

doi:10.3390/ani12050665

Abstract

Simple SummaryBohai Black cattle are one of the indigenous black coat cattle breeds in China, which are famous for their excellent meat quality. Whole-genome sequencing technology has been extensively developed to study species genome genetic diversity, population structure, selection pressure, demographic events, etc. However, a limited number of studies have reported genomic diversity and selection pressures in Bohai Black cattle. The purpose of this study is to analyze population structure and genomic differences between Bohai Black cattle and five “core” cattle populations from all over the world, mainly oriented on the identification of selection signatures using whole-genome sequencing data. In addition, we identify a series of candidate genes that can potentially be related to black coat color, meat quality, immunity, and reproduction in this breed. This study provides valuable genomic resources and theoretical basis for the future breeding of Bohai Black cattle.Bohai Black cattle are one of the well-known cattle breeds with black coat color in China, which are cultivated for beef. However, no study has conducted a comprehensive analysis of genomic diversity and selective pressures in Bohai Black cattle. Here, we performed a comprehensive analysis of genomic variation in 10 Bohai Black cattle (five newly sequenced and five published) and the published whole-genome sequencing (WGS) data of 50 cattle representing five “core” cattle populations. The population structure analysis revealed that Bohai Black cattle harbored the ancestry with European taurine, Northeast Asian taurine, and Chinese indicine. The Bohai Black cattle demonstrated relatively high genomic diversity from the other cattle breeds, as indicated by the nucleotide diversity (pi), the expected heterozygosity (HE) and the observed heterozygosity (HO), the linkage disequilibrium (LD) decay, and runs of homozygosity (ROH). We identified 65 genes containing more than five non-synonymous SNPs (nsSNPs), and an enrichment analysis revealed the “ECM-receptor interaction” pathways associated with meat quality in Bohai Black cattle. Five methods (CLR, θπ, FST, θπ ratio, and XP-EHH) were used to find several pathways and genes carried selection signatures in Bohai Black cattle, including black coat color (MC1R), muscle development (ITGA9, ENAH, CAPG, ABI2, and ISLR), fat deposition (TBC1D1, CYB5R4, TUSC3, and EPS8), reproduction traits (SPIRE2, KHDRBS2, and FANCA), and immune system response (CD84, SLAMF1, SLAMF6, and CDK10). Taken together, our results provide a valuable resource for characterizing the uniqueness of Bohai Black cattle.

Highlights

Abundant cattle resources are essential for the diversified development of husbandry in China are anfor important constituent form of agriculturalAbundant cattle resources are and essential the diversified development of animaleconomy.have established a close relationship with human beings in economic and cultural a husbandry in China and are an important constituent form of agricultural economy
A total of 25,982,011 SNPs were detected in Bohai Black cattle (Table S3), of which 1,863,158 SNPs were specific to Bohai black cattle (Figure S1a)
This study provides a comprehensive overview of genomic diversity and selective pressures of Bohai Black cattle using whole-genome sequencing data

Summary

Introduction

Have established a close relationship with human beings in economic and cultural a husbandry in China and are an important constituent form of agricultural economy. Since cattle domestication [2], have established a close relationship with human beings in economic and cultural aspects range of natural artificial selection events in cattle have greatly by providing most of the leather,and meat, and milk [1]. [5–7 behavior and appearance cattle breeds still show considerable diversity of national programs, there a needWith to conduct g in terms of milk the andlatest meatdevelopment production, fertility, coat breeding color, body size, horns, etc.is[5–7]. Research on important phenotypic traits and economic traits (such as coat the latest development of national breeding programs, there is a need to conduct genetic color an quality)phenotypic of cattle breed.

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