Genome sequencing
We sampled a total of 28 cattle, from four different regions of China
(Mongolia, Yanbian, Hainan and Yunnan). DNA was extracted from the blood
of each individual and degradation was monitored based on its
concentration by spectrometry, fluorometry, and 1% agarose gel
electrophoresis. Paired-end libraries with insert size of 150 bp were
constructed for each individual and sequenced using the a HiSeq X Ten
Sequencing System (Illumina Inc., San Diego, CA, USA). We mapped the
clean reads after filtering sequencing data to the Bos Taurusgenome assembly (version UMD_3.1.1) using BWA [49]. All the
potential single-nucleotide polymorphisms site (SNPs) were extracted and
filtered by GATK [50]. ANNOVAR [51] and existing Genome
annotation file (GFF/GTF) made corresponding annotations on the detected
SNPs. 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.