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

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

doi:10.1186/s12864-020-07340-0

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

BMC Genomics. 2021 Jan 9;22(1):43. doi: 10.1186/s12864-020-07340-0.

Authors

Xiaoting Xia¹, Shunjin Zhang¹, Huaju Zhang², Zijing Zhang³, Ningbo Chen¹, Zhigang Li², Hongxia Sun², Xian Liu⁴, Shijie Lyu³, Xianwei Wang⁴, Zhiming Li⁴, Peng Yang¹, Jiawei Xu¹, Xiaoting Ding¹, Qiaoting Shi³, Eryao Wang³, Baorui Ru⁴, Zejun Xu⁴, Chuzhao Lei¹, Hong Chen¹, Yongzhen Huang⁵

Affiliations

¹ Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, 712100, Shaanxi, China.
² Pingdingshan animal husbandry technology promotion station, Pingdingshan, 467000, Henan, China.
³ Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China.
⁴ Henan Provincial Animal Husbandry General Station, Zhengzhou, 450008, Henan, China.
⁵ Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, 712100, Shaanxi, China. hyzsci@nwafu.edu.cn.

Abstract

Background: 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. 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.

Results: The 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, F_ST 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 (F_ST 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).

Conclusion: We 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.

Keywords: Bos indicus; Bos taurus; Chinese cattle; Genetic diversity; Genetic signatures; Population structure.

Publication types

Review

MeSH terms

Animals
Cattle / genetics
Genomics
Phenotype
Plant Breeding*
Polymorphism, Single Nucleotide*
Selection, Genetic
Whole Genome Sequencing

Abstract

Publication types

MeSH terms

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