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Chinese indigenous pig breeds have been undergoing selection for thousands of years, and have become invaluable genetic sources over the world. To investigate the population structure and genetic diversity of Jinhua (JH), Longyou Black (LYW), Shengxian Spotted (SXH), and Lanxi Spotted (LXH) breeds, a total of 200 pigs belonging to 10 diverse population were genotyped using SNP chips. The results showed that LYW pigs exhibited higher level of heterozygosity than the other indigenous pigs. In addition, gene introgression from intensively reared commercial pig breeds to LYW pigs was detected. Moreover, selection signature analysis revealed the possibility of differences between Chinese indigenous and intensively reared commercial pig breeds were mainly present for meat and carcass traits. Furthermore, we found that ANXA13, DISP1, and SRSF6 were the nearest genes located around the common selection signatures detected between each indigenous pig breed and Chinese wild boars. Our findings provide new insights into the selection signatures of Chinese indigenous pigs, and may contribute to future pig breeding. [ABSTRACT FROM AUTHOR]