Abstract
BackgroundLimb 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.ResultsWe 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.ConclusionTo 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-015-0257-1) contains supplementary material, which is available to authorized users.
Highlights
Limb bone length is an economically important trait in pigs, because it is negatively correlated with backfat thickness, and is a determinant to the yield of hip and loin
An additional table shows the phenotypic correlation coefficients among the 5 measured traits related to limb bone length [see Additional file 1]
Distribution of the Z value in the meta analysis In this study, we used a Z test to detect the association between Single Nucleotide Polymorphism (SNP) and limb bone lengths in the genome-wide association study (GWAS) meta analysis
Summary
Limb bone length is an economically important trait in pigs, because it is negatively correlated with backfat thickness, and is a determinant to the yield of hip and loin. Abnormal growth of the limb bone leads to leg structural weakness. It has been reported that body height is negatively correlated with backfat thickness, and is a determinant to the yield of hip, loin, picnic shoulder and shoulder butt [1, 2]. Abnormal growth of the limb bone could lead to leg structural weakness, and unsound legs would cause huge economic loss, especially in breeding pigs [3]. Deciphering the genetic basis of limb bone growth in pigs will provide insight to understanding of the complex genetic architecture of human height
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