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. 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, 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). 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.
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 indicinecattle; 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 Redcattle. Furthermore, we used 131 published genomes of world-wide cattle to characterize the genomic variation of Jiaxian Redcattle. RESULTS: The population structure analysis revealed that Jiaxian Redcattle 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 Redcattle. We used θπ, CLR, FST and XP-EHH methods to look for the candidate signatures of positive selection in Jiaxian Redcattle. 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). CONCLUSION: We provide a comprehensive overview of sequence variations in Jiaxian Redcattle genomes. Selection signatures were detected in genomic regions that are possibly related to economically important traits in Jiaxian Redcattle. We observed a high level of genomic diversity and low inbreeding in Jiaxian Redcattle. These results provide a basis for further resource protection and breeding improvement of this breed.
Entities:
Keywords:
Bos indicus; Bos taurus; Chinese cattle; Genetic diversity; Genetic signatures; Population structure
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