Resequencing diverse Chinese indigenous breeds to enrich the map of genomic variations in swine

•2,530,248 SNVs and 3,456,626 INDELs were firstly discovered compared with dbSNP 143.•208,687 SNVs and 24,161 INDELs were uniquely observed in Chinese pigs.•Significantly high correlation between SNV and INDEL was detected.•LoF genes were found to be under weaker evolutionary constraints.

To enrich the map of genomic variations in swine, we randomly sequenced 13 domestic and wild individuals from China and Europe. We detected approximately 28.1 million single nucleotide variants (SNVs) and 3.6 million short insertions and deletions (INDELs), of which 2,530,248 SNVs and 3,456,626 INDELs were firstly identified compared with dbSNP 143. Moreover, 208,687 SNVs and 24,161 INDELs were uniquely observed in Chinese pigs, potentially accounting for phenotypic differences between Chinese and European pigs. Furthermore, significantly high correlation between SNV and INDEL was witnessed, which indicated that these two distinct variants may share similar etiologies. We also predicted loss of function genes and found that they were under weaker evolutionary constraints. This study gives interesting insights into the genomic features of the Chinese pig breeds. These data would be useful in the establishment of high-density SNP map and would lay a foundation for facilitating pig functional genomics study.