Abstract
BackgroundIn pig, limb bone length influences ham yield and body height to a great extent and has important economic implications for pig industry. In this study, an intercross population was constructed between the indigenous Chinese Minzhu pig breed and the western commercial Large White pig breed to examine the genetic basis for variation in limb bone length. The aim of this study was to detect potential genetic variants associated with porcine limb bone length.MethodsA total of 571 F2 individuals from a Large White and Minzhu intercross population were genotyped using the Illumina PorcineSNP60K Beadchip, and phenotyped for femur length (FL), humerus length (HL), hipbone length (HIPL), scapula length (SL), tibia length (TL), and ulna length (UL). A genome-wide association study was performed by applying the previously reported approach of genome-wide rapid association using mixed model and regression. Statistical significance of the associations was based on Bonferroni-corrected P-values.ResultsA total of 39 significant SNPs were mapped to a 11.93 Mb long region on pig chromosome 7 (SSC7). Linkage analysis of these significant SNPs revealed three haplotype blocks of 495 kb, 376 kb and 492 kb, respectively, in the 11.93 Mb region. Annotation based on the pig reference genome identified 15 genes that were located near or contained the significant SNPs in these linkage disequilibrium intervals. Conditioned analysis revealed that four SNPs, one on SSC2 and three on SSC4, showed significant associations with SL and HL, respectively.ConclusionsAnalysis of the 15 annotated genes that were identified in these three haplotype blocks indicated that HMGA1 and PPARD, which are expressed in limbs and influence chondrocyte cell growth and differentiation, could be considered as relevant biological candidates for limb bone length in pig, with potential applications in breeding programs. Our results may also be useful for the study of the mechanisms that underlie human limb length and body height.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-014-0056-6) contains supplementary material, which is available to authorized users.
Highlights
In pig, limb bone length influences ham yield and body height to a great extent and has important economic implications for pig industry
The aim of this study was to detect potential genetic variants associated with limb bone length in a Large White × Minzhu intercross population using a genome-wide association studies (GWAS) and to identify candidate genes that are near these polymorphisms or that include them with major effects on this trait
Genome-wide association study After quality control, 48 238 single nucleotide polymorphisms (SNP) and 564 F2 individuals were used for the GWAS
Summary
Limb bone length influences ham yield and body height to a great extent and has important economic implications for pig industry. An intercross population was constructed between the indigenous Chinese Minzhu pig breed and the western commercial Large White pig breed to examine the genetic basis for variation in limb bone length. The aim of this study was to detect potential genetic variants associated with porcine limb bone length. The aim of this study was to detect potential genetic variants associated with limb bone length in a Large White × Minzhu intercross population using a GWAS and to identify candidate genes that are near these polymorphisms or that include them with major effects on this trait
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