SNP Discoveries and Population Genetic Analyses for Chinese Indigenous Chickens using RAD Sequencing

Single nucleotide polymorphism (SNP) discovery and genotyping are essential to population genetic variation and diversity. Here we performed restriction-site-associated DNA sequencing (RAD-seq) to discover SNPs and made population genetic analyses among Chinese indigenous chickens. 620 million reads were obtained by using the next-generation sequencing platform (Illumina Hiseq2000). A total of 72 individuals from 13 indigenous populations and 3 introduced populations were sampled. We genotyped average 75,587 SNPs for each individual and constructed a map including 474,933 SNPs, and 238 InDels. Further filtering validated 28,527 SNPs candidates for the total population. There were higher heterozygosity in most of the populations, with all loci contributing significantly to polymorphisms (Expected Heterozygosity arranged from 0.097 to 0.157). A pairwise Fst was calculated between populations to explore genetic diversity and genetic distance through all SNPs loci. In order to evaluate genetic distances among populations, a phylogenetic tree was constructed using the Neighbour-Joining method. In this study, we applied RAD-seq on Chinese indigenous chickens, confirmed its availability, predictability, low cost, and high-through characteristics and showed its effectiveness and potential applications on population genetic analysis and whole-genome selection in chicken.

Keywords: RAD-seq, SNP discovery, genotyping, Chinese indigenous chicken, population genetic analysis