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Gigascience. 2017 Jun 1;6(6):1-5. doi: 10.1093/gigascience/gix026.

Genomic data for 78 chickens from 14 populations.

Author information

1
Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
2
Novogene Bioinformatics Institute, Beijing 100083, China.
3
Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
4
Department of Animal Science, Oklahoma State University, Stillwater, OK 74078, USA.
5
Hubei Key Laboratory of Cell Homeostasis, Laboratory of Molecular and Developmental Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, China.

Abstract

Since the domestication of the red jungle fowls ( Gallus gallus ; dating back 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. 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 ∼21.30 gigabases (Gb) of high-quality data from each individual to the reference chicken genome, we identified ∼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. 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.

KEYWORDS:

chicken; genetic diversity; population genomics; whole genome resequencing

PMID:
28431039
PMCID:
PMC5449643
DOI:
10.1093/gigascience/gix026
[Indexed for MEDLINE]
Free PMC Article

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