期刊
GIGASCIENCE
卷 6, 期 6, 页码 -出版社
OXFORD UNIV PRESS
DOI: 10.1093/gigascience/gix026
关键词
chicken; genetic diversity; population genomics; whole genome resequencing
资金
- China Agricultural Research System [CARS-41]
- 12th Five Year Plan for Breeding Program in Sichuan-Selective breeding of new breeds and the synthetic strains in laying hens [2011NZ0099-7]
- National Natural Science Foundation of China [31402063, 31522055]
- Sichuan Provincial Department of Science and Technology Program [2015JQO023]
- National Program for Support of Top-notch Young Professionals
- Young Scholars of the Yangtze River
Background: Since the domestication of the red jungle fowls (Gallus gallus; dating back to similar to 10 000 B.P.) in Asia, domestic chickens (Gallus gallus domesticus) have been subjected to the combined effects of natural selection and human-driven artificial selection; this has resulted in marked phenotypic diversity in a number of traits, including behavior, body composition, egg production, and skin color. Population genomic variations through diversifying selection have not been fully investigated. Findings: The whole genomes of 78 domestic chickens were sequenced to an average of 18-fold coverage for each bird. By combining this data with publicly available genomes of five wild red jungle fowls and eight Xishuangbanna game fowls, we conducted a comprehensive comparative genomics analysis of 91 chickens from 17 populations. After aligning similar to 21.30 gigabases (Gb) of high-quality data from each individual to the reference chicken genome, we identified similar to 6.44 million (M) single nucleotide polymorphisms (SNPs) for each population. These SNPs included 1.10 M novel SNPs in 17 populations that were absent in the current chicken dbSNP (Build 145) entries. Conclusions: The current data is important for population genetics and further studies in chickens and will serve as a valuable resource for investigating diversifying selection and candidate genes for selective breeding in chickens.
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