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

BMC Genomics

Zejun Xu¹  Zhiming Li¹  Xian Liu¹  Xianwei Wang¹  Baorui Ru¹  Shijie Lyu²  Zijing Zhang²  Eryao Wang²  Qiaoting Shi²  Peng Yang³  Xiaoting Ding³  Yongzhen Huang³  Ningbo Chen³  Jiawei Xu³  Shunjin Zhang³  Hong Chen³  Xiaoting Xia³  Chuzhao Lei³  Huaju Zhang⁴  Zhigang Li⁴  Hongxia Sun⁴ 

[1] Henan Provincial Animal Husbandry General Station;Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences;Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University;Pingdingshan animal husbandry technology promotion station;

关键词: Chinese cattle;    Genetic diversity;    Population structure;    Genetic signatures;    Bos taurus;    Bos indicus;   

DOI  :  10.1186/s12864-020-07340-0

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown