A meta analysis of genome-wide association studies for limb bone lengths in four pig populationsReport as inadecuate

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BMC Genetics

, 16:95

Complex traits and quantitative genetics


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.

KeywordsLimb bone length Meta analysis Pig Genome-wide association study AbbreviationsDNADeoxyribonucleic Acid

GWASGenome-wide Association Study

HMGA1High Mobility Group AT-hook 1

kbKilo Base Pairs

LDLinkage Disequilibrium

MbMega Base Pairs

PLAG1Pleiomorphic Adenoma Gene 1

QTLQuantitative Trait Locus

SNPSingle Nucleotide Polymorphism

SSCSus Scrofa Chromosome

Yuanmei Guo and Lijuan Hou Equal contributors

Electronic supplementary materialThe online version of this article doi:10.1186-s12863-015-0257-1 contains supplementary material, which is available to authorized users.

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Author: Yuanmei Guo - Lijuan Hou - Xufei Zhang - Min Huang - Huirong Mao - Hao Chen - Junwu Ma - Congying Chen - Huashui Ai - Jun

Source: https://link.springer.com/

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