title: A meta analysis of genome-wide association studies for limb bone lengths in four pig populations.
abstract: BACKGROUND
  Limb bone length is an economically important trait in pigs, because it is negatively correlated with backfat thickness, and is also a determinant to the yield of hip and loin. Moreover, abnormal growth of the limb bone leads to leg structural weakness. Until now, the genetic architecture of the pig lime bone length remains poorly understood. The object of this study was to map genomic loci for limb bone length by genome-wide association study (GWAS) on 4 pig populations.
  
  
  RESULTS
  We measured the lengths of five limb bones including scapula, humerus, ulna, femur and tibia that were dissected from the right-side carcass of 925, 331, 314 and 434 animals from White Duroc × Erhualian F2 intercross, Erhualian, Laiwu and Sutai populations, respectively. We genotyped the 2004 pigs for 62,163 single nucleotide polymorphisms (SNPs) on the Porcine SNP60 BeadChip, and performed GWAS and a GWAS meta analysis in the 4 populations. In total, we identified 12 and 4 loci associated with the limb bone lengths at suggestive and genome-wide significant levels respectively, of which 4 loci were reported for the first time. The most prominent locus was identified in a 924-kb (kilo base pairs) linkage disequilibrium block on Sus Scrofa chromosome (SSC) 7, and High Mobility Group AT-hook 1 (HMGA1) appears to be a strong candidate gene in this region. Another promising locus is located in the middle of SSC4, and Pleiomorphic Adenoma Gene 1 (PLAG1) is a functionally plausible candidate gene underlying the locus. Because the lengths of the 5 limb bones are highly correlated to each other, most of significant loci were associated with all of the 5 traits; however, several loci showed specific effect on the length of one limb bone, such as the locus at the proximal end of SSC2 associated with only the scapula length.
  
  
  CONCLUSIONS
  To our knowledge, this study was the first GWAS meta analysis for limb bone lengths in pigs. As expected, the meta analysis is more powerful to identify genomic loci. A total of 16 loci were identified in this study, including four novel loci. HMGA1 and PLAG1 are two appearing candidate genes for pig limb bone lengths, which warrant further investigations.
authors.affiliation: State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China. gyuanmei@hotmail.com.
authors.forename: Yuanmei
authors.initials: Y
authors.lastname: Guo
authors.affiliation: State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China. 397999166@qq.com.
authors.forename: Lijuan
authors.initials: L
authors.lastname: Hou
authors.affiliation: State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China. 604120811@qq.com.|Current address: Wenzhou Medical University, WenZhou, 325000, China. 604120811@qq.com.
authors.forename: Xufei
authors.initials: X
authors.lastname: Zhang
authors.affiliation: State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China. 1549765280@qq.com.
authors.forename: Min
authors.initials: M
authors.lastname: Huang
authors.affiliation: State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China. maohuirong82@hotmail.com.
authors.forename: Huirong
authors.initials: H
authors.lastname: Mao
authors.affiliation: State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China. 378639708@qq.com.
authors.forename: Hao
authors.initials: H
authors.lastname: Chen
authors.affiliation: State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China. ma_junwu@hotmail.com.
authors.forename: Junwu
authors.initials: J
authors.lastname: Ma
authors.affiliation: State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China. chcy75@hotmail.com.
authors.forename: Congying
authors.initials: C
authors.lastname: Chen
authors.affiliation: State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China. aihsh@hotmail.com.
authors.forename: Huashui
authors.initials: H
authors.lastname: Ai
authors.affiliation: State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China. renjunjxau@hotmail.com.
authors.forename: Jun
authors.initials: J
authors.lastname: Ren
authors.affiliation: State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China. lushenghuang@hotmail.com.
authors.forename: Lusheng
authors.initials: L
authors.lastname: Huang
mesh_terms: D000818:Animals; D001842:Bone and Bones / Q000033:anatomy & histology*; D002874:Chromosome Mapping; D005121:Extremities / Q000033:anatomy & histology*; D005828:Genetics, Population; D055106:Genome-Wide Association Study; D015810:Linkage Disequilibrium; D015233:Models, Statistical; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D019655:Quantitative Trait, Heritable; D013552:Swine / Q000033:anatomy & histology* / Q000235:genetics*