Pigs from Asia and Europe were independently domesticated from c. 9000 years ago. During this period, strong artificial selection has led to dramatic phenotypic changes in domestic pigs. However, the genetic basis underlying these morphological and behavioural adaptations is relatively unknown, particularly for indigenous Chinese pigs. Here, we performed a genome-wide analysis to screen 196 regions with selective sweep signals in Tongcheng pigs, which are a typical indigenous Chinese breed. Genes located in these regions have been found to be involved in lipid metabolism, melanocyte differentiation, neural development and other biological processes, which coincide with the evolutionary phenotypic changes in this breed. A synonymous substitution, c.669T>C, in ESR1, which colocalizes with a major quantitative trait locus for litter size, shows extreme differences in allele frequency between Tongcheng pigs and wild boars. Notably, the variant C allele in this locus exhibits high allele frequency in most Chinese populations, suggesting a consequence of positive selection. Five genes (PRM1, PRM2, TNP2, GPR149 and JMJD1C) related to reproductive traits were found to have high haplotype similarity in Chinese breeds. Two selected genes, MITF and EDNRB, are implied to shape the two-end black colour trait in Tongcheng pig. Subsequent SNP microarray studies of five Chinese white-spotted breeds displayed a concordant signature at both loci, suggesting that these two genes are responsible for colour variations in Chinese breeds. Utilizing massively parallel sequencing, we characterized the candidate sites that adapt to artificial and environmental selections during the Chinese pig domestication. This study provides fundamental proof for further research on the evolutionary adaptation of Chinese pigs.
SNPs called from Tongcheng pool and seven Chinese wild boars
This table includes the genome-wide SNP data called from Tongcheng pool and seven Chinese wild boars. column 1 & 2: chromosome and position according to Sscrofa 10.2 assembly. column 3: the reference allele according to Sscrofa 10.2 assembly. column 4: the variant allele identified from sequencing data. column 5-11: genotypes of Chinese wild boars, and “00”means the missing genotype. column 12: count of reference allele reads identified from the Tongcheng sequencing pool. column 13: count of variant allele reads identified fromthe Tongcheng sequencing pool
SNPs_bwteen_tongcheng_pool_and_Chinese_wild_boars.txt
SNPs called from 54 individually sequenced pigs at 32.475-32.775 Mb on chromosome 3
This table includes the SNP data at 32.475-32.775 Mb on chromosome 3, and the variants are called from 54 individually sequenced pigs from 11 populations. “00” indicates the missing genotype. column 1 & 2: chromosome and position according to Sscrofa 10.2 assembly. column 3: the reference allele according to Sscrofa 10.2 assembly. column 4: the variant allele identified from sequencing data. column 5- 8: genotypes of four Duroc pigs. column 9-12: genotypes of four Meishan pigs. column 13-19 genotypes of seven Chinese wild boars. column 20-22 genotypes of three Jinhua pigs. column 23-28 genotypes of six Landrace pigs. column 29-42 genotypes of 14 Large White pigs. column 43-45 genotypes of three Neijiang pigs. column 46-48 genotypes of three Penzhou pigs. column 49-52 genotypes of four Tongcheng pigs. column 53-55 genotypes of three Wujin pigs. column 56-58 genotypes of three Yanan pigs
chr3.txt
SNPs called from 54 individually sequenced pigs at 102.3-102.675 Mb on chromosome 13
This table includes the SNP data at 102.3-102.675 Mb on chromosome 13, and the variants are called from 54 individually sequenced pigs from 11 populations. “00” indicates the missing genotype. column 1 & 2: chromosome and position according to Sscrofa 10.2 assembly. column 3: the reference allele according to Sscrofa 10.2 assembly. column 4: the variant allele identified from sequencing data. column 5- 8: genotypes of four Duroc pigs. column 9-12: genotypes of four Meishan pigs. column 13-19 genotypes of seven Chinese wild boars. column 20-22 genotypes of three Jinhua pigs. column 23-28 genotypes of six Landrace pigs. column 29-42 genotypes of 14 Large White pigs. column 43-45 genotypes of three Neijiang pigs. column 46-48 genotypes of three Penzhou pigs. column 49-52 genotypes of four Tongcheng pigs. column 53-55 genotypes of three Wujin pigs. column 56-58 genotypes of three Yanan pigs
chr13.txt
SNPs called from 54 individually sequenced pigs at 71.775-72.15 Mb on chromosome 14
This table includes the SNP data at 71.775-72.15 Mb on chromosome 14, and the variants are called from 54 individually sequenced pigs from 11 populations. “00” indicates the missing genotype. column 1 & 2: chromosome and position according to Sscrofa 10.2 assembly. column 3: the reference allele according to Sscrofa 10.2 assembly. column 4: the variant allele identified from sequencing data. column 5- 8: genotypes of four Duroc pigs. column 9-12: genotypes of four Meishan pigs. column 13-19 genotypes of seven Chinese wild boars. column 20-22 genotypes of three Jinhua pigs. column 23-28 genotypes of six Landrace pigs. column 29-42 genotypes of 14 Large White pigs. column 43-45 genotypes of three Neijiang pigs. column 46-48 genotypes of three Penzhou pigs. column 49-52 genotypes of four Tongcheng pigs. column 53-55 genotypes of three Wujin pigs. column 56-58 genotypes of three Yanan pigs
chr14.txt
SNPs called from 54 individually sequenced pigs at 60-109.95 Mb on chromosome X
This table includes the SNP data at 60-109.95 Mb on chromosome X, and the variants are called from 54 individually sequenced pigs from 11 populations. “00” indicates the missing genotype. column 1 & 2: chromosome and position according to Sscrofa 10.2 assembly. column 3: the reference allele according to Sscrofa 10.2 assembly. column 4: the variant allele identified from sequencing data. column 5- 8: genotypes of four Duroc pigs. column 9-12: genotypes of four Meishan pigs. column 13-19 genotypes of seven Chinese wild boars. column 20-22 genotypes of three Jinhua pigs. column 23-28 genotypes of six Landrace pigs. column 29-42 genotypes of 14 Large White pigs. column 43-45 genotypes of three Neijiang pigs. column 46-48 genotypes of three Penzhou pigs. column 49-52 genotypes of four Tongcheng pigs. column 53-55 genotypes of three Wujin pigs. column 56-58 genotypes of three Yanan pigs
chrX.txt