Assessing genomic diversity and signatures of selection in Jiaxian Red cattle using whole-genome sequencing data

Xiaoting Xia,Yongzhen Huang,Huaju Zhang,Zhiming Li,Xianwei Wang,Xiaoting Ding,Chuzhao Lei,Hongxia Sun,Shunjin Zhang,Qiaoting Shi,Ningbo Chen,Zhigang Li,Zijing Zhang,Xian Liu,Peng Yang,Shijie Lyu,Baorui Ru,Hong Chen,Eryao Wang,Zejun Xu,Jie Xu

doi:10.1186/s12864-020-07340-0

Abstract

BackgroundNative cattle breeds are an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and tough feeding conditions. Jiaxian Red, a Chinese native cattle breed, is reported to have originated from crossbreeding between taurine and indicine cattle; their history as a draft and meat animal dates back at least 30 years. Using whole-genome sequencing (WGS) data of 30 animals from the core breeding farm, we investigated the genetic diversity, population structure and genomic regions under selection of Jiaxian Red cattle. Furthermore, we used 131 published genomes of world-wide cattle to characterize the genomic variation of Jiaxian Red cattle.ResultsThe population structure analysis revealed that Jiaxian Red cattle harboured the ancestry with East Asian taurine (0.493), Chinese indicine (0.379), European taurine (0.095) and Indian indicine (0.033). Three methods (nucleotide diversity, linkage disequilibrium decay and runs of homozygosity) implied the relatively high genomic diversity in Jiaxian Red cattle. We used θπ, CLR, FST and XP-EHH methods to look for the candidate signatures of positive selection in Jiaxian Red cattle. A total number of 171 (θπ and CLR) and 17 (FST and XP-EHH) shared genes were identified using different detection strategies. Functional annotation analysis revealed that these genes are potentially responsible for growth and feed efficiency (CCSER1), meat quality traits (ROCK2, PPP1R12A, CYB5R4, EYA3, PHACTR1), fertility (RFX4, SRD5A2) and immune system response (SLAMF1, CD84 and SLAMF6).ConclusionWe provide a comprehensive overview of sequence variations in Jiaxian Red cattle genomes. Selection signatures were detected in genomic regions that are possibly related to economically important traits in Jiaxian Red cattle. We observed a high level of genomic diversity and low inbreeding in Jiaxian Red cattle. These results provide a basis for further resource protection and breeding improvement of this breed.

Highlights

Native cattle breeds are an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and tough feeding conditions
There are a limited number of studies on the genomic variation of native cattle breeds in China, and even fewer reports have been reported from Jiaxian Red cattle [2, 7, 8]
We annotated 24,800,431 biallelic Single nucleotide polymorphism (SNP) that were discovered in 30 Jiaxian Red cattle

Summary

Introduction

Native cattle breeds are an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and tough feeding conditions. Based on WGS many studies initially focused on the genetic architecture and economic traits under positive selection of European commercial breeds [3, 4], and gradually focused on the adaptable indigenous breeds, such as African cattle [5, 6]. They identified genomic variations characteristics (new genes or genetic pathways) of native cattle adapting to local environments, such as climate challenges and disease resistance [5, 6]. There are a limited number of studies on the genomic variation of native cattle breeds in China, and even fewer reports have been reported from Jiaxian Red cattle [2, 7, 8]

Methods

Results

Discussion

Conclusion