Abstract
BackgroundRecently, genome-wide association studies (GWAS) have been reported on various pig traits. We performed a GWAS to analyze 22 traits related to growth and fatness on two pig populations: a White Duroc × Erhualian F2 intercross population and a Chinese Sutai half-sib population.ResultsWe identified 14 and 39 loci that displayed significant associations with growth and fatness traits at the genome-wide level and chromosome-wide level, respectively. The strongest association was between a 750 kb region on SSC7 (SSC for Sus scrofa) and backfat thickness at the first rib. This region had pleiotropic effects on both fatness and growth traits in F2 animals and contained a promising candidate gene HMGA1 (high mobility group AT-hook 1). Unexpectedly, population genetic analysis revealed that the allele at this locus that reduces fatness and increases growth is derived from Chinese indigenous pigs and segregates in multiple Chinese breeds. The second strongest association was between the region around 82.85 Mb on SSC4 and average backfat thickness. PLAG1 (pleiomorphic adenoma gene 1), a gene under strong selection in European domestic pigs, is proximal to the top SNP and stands out as a strong candidate gene. On SSC2, a locus that significantly affects fatness traits mapped to the region around the IGF2 (insulin-like growth factor 2) gene but its non-imprinting inheritance excluded IGF2 as a candidate gene. A significant locus was also detected within a recombination cold spot that spans more than 30 Mb on SSCX, which hampered the identification of plausible candidate genes. Notably, no genome-wide significant locus was shared by the two experimental populations; different loci were observed that had both constant and time-specific effects on growth traits at different stages, which illustrates the complex genetic architecture of these traits.ConclusionsWe confirm several previously reported QTL and provide a list of novel loci for porcine growth and fatness traits in two experimental populations with Chinese Taihu and Western pigs as common founders. We showed that distinct loci exist for these traits in the two populations and identified HMGA1 and PLAG1 as strong candidate genes on SSC7 and SSC4, respectively.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-015-0089-5) contains supplementary material, which is available to authorized users.
Highlights
Genome-wide association studies (GWAS) have been reported on various pig traits
To test why the prominent loci associated with fatness and growth traits on SSC2, 4, 7 and X that were identified in the intercross pigs are absent from Sutai pigs, we further examined the most significant locus on SSC7
Fourteen quantitative trait loci (QTL) of genome-wide significance and 39 suggestive loci of chromosome-wide significance were identified on 16 chromosomes
Summary
Genome-wide association studies (GWAS) have been reported on various pig traits. Western commercial pigs show divergent phenotypes compared to Chinese indigenous pigs Large White, Landrace, Duroc and Pietrain, have experienced intensive selection for lean pork production in the past decades Their excellent performance, including fast growth and a high lean percentage, has led them to dominate the global pig industry. Chinese indigenous breeds have been historically selected for fat deposition, since fat was an important source of energy for Chinese farmers in ancient times. These breeds are characterized by obesity and a slow growth rate but good meat quality and excellent adaptability to diverse environments.
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