Genomic Diversity of Chinese Cattle

We sampled a total of 114 cattle, including 111 Chinese domestic cattle (1–9 individuals for each of the 22 geographically diverse populations) and 3 indicine cattle in India (Fig. 1a and Supplementary Tables 1 and 2). DNA was extracted from the ear tissues or blood of each individual. Paired-end libraries with insert size of 500 bp were constructed for each individual and sequenced using the HiSeq 2000 platform (Illumina) (Supplementary Note 1). In addition, we downloaded the genome data of 146 individuals across the world from the NCBI database, including 83 European taurine cattle, 26 Northeast Asian taurine cattle, 8 Iranian cattle, 17 American indicine cattle and 12 African cattle (Supplementary Tables 1 and 2). All experimental procedures were performed in accordance with the Regulations for the Administration of Affairs Concerning Experimental Animals approved by the State Council of People’s Republic of China. The study was approved by Institutional Animal Care and Use Committee of Northwest A&F University (Permit number: NWAFAC1019).