all_breed_data_3_1.map

A total of 397 individual pigs from seven indigenous breeds (Laiwu, Dapulian, Licha Black, Yantai Black, Yimeng Black, Wulian Black, and Zaozhuang Heigai) and five Western commercial breeds (Yorkshire, Landrace, Duroc, Berkshire, and Pietrain) were used in the study. All animals were genotyped using Porcine SNP55K BeadChips according to the manufacturer’s protocol. The BeadChip was designed and promoted by Compass Biotechnology Corporation, Beijing, China (http://www.kangpusen.com/), and manufactured by Illumina (San Diego, CA, USA). Using PLINK v1.90 [12], SNPs were filtered with call rate ≧95% and MAF ≧0.05. A total of 39,300 informative SNPs , out of 43,832 SNPs contained in the BeadChip, were obtained. The SNP positions within a chromosome were based on the current pig genome assembly (Sscrofa11.1).