| SNPs (Single nucleotide polymorphisms) genetic marker has beenone of key tools for population genetics and quantitative genetics.Restriction-site-associated DNA sequencing (RAD-seq) is one of the mosteffective methods based on next-generation sequencing (NGS) technologywith restriction digestion for SNP discovery. However，so far there isn’treport about poultry sequencing by RAD-seq. Therefore, it’s necessary tointroduce RAD-seq into poultry industry, providing new method and toolfor poultry population genetics research.In the study, a total of72individuals from13Chinese chickenindigenous populations and3introduced populations were sampled. wediscovered SNPs and made population genetic analyses among Chineseindigenous chickens with restriction-site-associated DNA sequencing(RAD-seq).620million reads were obtained by using the next-generationsequencing platform, We genotyped average75,587SNPs for eachindividual and constructed a map including474,933SNPs. Furtherfiltering validated28,896SNPs candidates for the total population. In theseSNPs, there were15,404new discovery SNPs. With the individual SNPsresults, we calculated the population SNPs for perbreed，the SNPs arrangedfrom30,763to181,507, and the avarage population SNPs was101,108.Population genetic analyses showed that there were higher heterozygosity in most of the populations, with all loci contributing significantly topolymorphisms. In addition, population pairwise Fst, phylogenetic tree andpopulation structure also supported that Chinese indigenous chickensexisted abundance genetic diversity.In conclusion, firstly, genotyping and discovering high density geneticmarkers through RAD-seq is a powerful tool for studies with chickens.Secondly, it’s availability in constructing a population polymorphism mapand making population genetics analyses for Chinese indigenous chickens.Lastly, RAD-seq could be used for deeper genetic research andapplications, such as GWAS and GWS. |
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