DOI: 10.5061/dryad.8c930
title: Data from: Genome-wide analysis reveals artificial selection on coat colour and reproductive traits in Chinese domestic pigs

description: 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&gt;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.
description: SNPs called from
 Tongcheng pool and seven Chinese wild boarsThis 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 poolSNPs_bwteen_tongcheng_pool_and_Chinese_wild_boars.txtSNPs called from 54 individually sequenced pigs at 32.475-32.775 Mb on chromosome 3This 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 pigschr3.txtSNPs called from 54 individually sequenced pigs at 102.3-102.675 Mb on chromosome 13This 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 pigschr13.txtSNPs called from 54 individually sequenced pigs at 71.775-72.15 Mb on chromosome 14This 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 pigschr14.txtSNPs called from 54 individually sequenced pigs at 60-109.95 Mb on chromosome XThis 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 pigschrX.txt