title: Genome-wide association analyses reveal significant loci and strong candidate genes for growth and fatness traits in two pig populations.
abstract: BACKGROUND
  Recently, 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.
  
  
  RESULTS
  We 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.
  
  
  CONCLUSIONS
  We 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.
authors.affiliation: Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China. qrm480@hotmail.com.
authors.forename: Ruimin
authors.initials: R
authors.lastname: Qiao
authors.affiliation: Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China. jungaochina@hotmail.com.
authors.forename: Jun
authors.initials: J
authors.lastname: Gao
authors.affiliation: Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China. bioducklily@hotmail.com.
authors.forename: Zhiyan
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China. li_lin1011@hotmail.com.
authors.forename: Lin
authors.initials: L
authors.lastname: Li
authors.affiliation: Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China. xiexianhua19880521@163.com.
authors.forename: Xianhua
authors.initials: X
authors.lastname: Xie
authors.affiliation: Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China. fanyin8662@126.com.
authors.forename: Yin
authors.initials: Y
authors.lastname: Fan
authors.affiliation: Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China. leileicui_xuan@hotmail.com.
authors.forename: Leilei
authors.initials: L
authors.lastname: Cui
authors.affiliation: Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China. ma_junwu@hotmail.com.
authors.forename: Junwu
authors.initials: J
authors.lastname: Ma
authors.affiliation: Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China. aihsh@hotmail.com.
authors.forename: Huashui
authors.initials: H
authors.lastname: Ai
authors.affiliation: Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China. renjunjxau@hotmail.com.
authors.forename: Jun
authors.initials: J
authors.lastname: Ren
authors.affiliation: Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China. lushenghuang@hotmail.com.
authors.forename: Lusheng
authors.initials: L
authors.lastname: Huang
mesh_terms: D050154:Adiposity / Q000235:genetics*; D000483:Alleles; D000818:Animals; D002874:Chromosome Mapping; D003433:Crosses, Genetic; D004268:DNA-Binding Proteins / Q000235:genetics*; D055106:Genome-Wide Association Study / Q000379:methods*; D005838:Genotype; D025741:HMGA1a Protein / Q000235:genetics*; D007335:Insulin-Like Growth Factor II / Q000235:genetics; D010641:Phenotype; D040641:Quantitative Trait Loci; D034421:Sus scrofa / Q000235:genetics / Q000254:growth & development*; D013552:Swine
chemical_list: D004268:DNA-Binding Proteins; D025741:HMGA1a Protein; D007335:Insulin-Like Growth Factor II