Genomic data for 78 chickens from 14 populations

Area of Science:

• Genomics
• Animal Science
• Evolutionary Biology

Background:

• Domestic chickens (Gallus gallus domesticus) exhibit significant phenotypic diversity due to domestication and selection.
• Population genomic variations driven by diversifying selection remain understudied.
• The red junglefowl (Gallus gallus) is the ancestor of domestic chickens, with domestication dating back approximately 10,000 years in Asia.

Purpose of the Study:

• To investigate population genomic variations in domestic chickens.
• To identify novel single nucleotide polymorphisms (SNPs) and understand diversifying selection.
• To create a valuable genomic resource for future chicken research and selective breeding.

Main Methods:

• Whole-genome sequencing of 78 domestic chickens to an average 18-fold coverage.
• Comparative genomics analysis integrating data from 5 wild red jungle fowls and 8 Xishuangbanna game fowls, totaling 91 birds from 17 populations.
• Alignment of ~21.30 gigabases (Gb) of high-quality sequencing data to the reference chicken genome.

Main Results:

• Identification of approximately 6.44 million (M) single nucleotide polymorphisms (SNPs) per population.
• Discovery of 1.10 M novel SNPs across the 17 populations, not present in existing databases (dbSNP Build 145).
• Comprehensive genomic dataset established for 91 chickens representing diverse populations.

Conclusions:

• The study provides a significant expansion of known chicken genetic variation.
• The identified novel SNPs are crucial for future population genetics studies.
• This genomic resource will facilitate research into diversifying selection and candidate genes for chicken selective breeding.