Genomic data for 78 chickens from 14 populations

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.

Figure 1:

Sample information and comparison of identified SNPs in each breed/population with the chicken variants database (dbSNP, Build 145). Known SNPs are SNPs already in chicken dbSNP. The map displayed here is the geographic distribution of domestic chicken populations; numbers above the dashed lines are altitudes. Red and green localities represent eight lowland and six highland chicken populations respectively, sampled in this study. ^aIndividual distribution to each group can be found in Additional File 1: Table S1. ^bThe whole genome sequencing data of eight game fowls and five RJFs were downloaded from the NCBI.

Figure 2:

Population genetics of studied chickens. A) Rooted neighbor-joining phylogenetic tree with the Japanese quail as an outgroup. The reliability of each branch was evaluated by bootstrapping with 1000 replicates. Different groups of chicken populations: Sichuan local chickens (red), Tibetan chickens (green), Xishuangbanna game fowls (purple), RJFs (gray), and Japanese quail (black). B) Principal component plots. The first dimension and second dimension are shown. The fraction of the variance explained was 8.91% for eigenvector 1 (P < 0.05, Tracy-Widom test) and 7.43% for eigenvector 2 (P < 0.05, Tracy-Widom test).