Chiese_indigenous_chickens.ped and Chiese_indigenous_chickens.map are included in the compressed Chinese_indigenous_chickens.rar file, including 46,239 informative SNPs for 1,187 samples. The first two columns in PED file represent Family ID and Individual ID, respectively. We add population information in the Individual ID column. e.g. for 2 samples 385 5297000013_R06C02_WL 758 A00001_WC The first individual has family id: 385 and individual id: 5297000013_R06C02_WL which belong to White Leghorn (WL) population. The second individual has family id: 758 and individual id: A00001_WC which belong to Wenchang (WC) population. You can find details of those chickens in our manuscript.