Genome-wide association analyses for meat quality traits in Chinese Erhualian pigs and a Western Duroc × (Landrace × Yorkshire) commercial population

Abstract

BackgroundUnderstanding the genetic mechanisms that underlie meat quality traits is essential to improve pork quality. To date, most quantitative trait loci (QTL) analyses have been performed on F2 crosses between outbred pig strains and have led to the identification of numerous QTL. However, because linkage disequilibrium is high in such crosses, QTL mapping precision is unsatisfactory and only a few QTL have been found to segregate within outbred strains, which limits their use to improve animal performance. To detect QTL in outbred pig populations of Chinese and Western origins, we performed genome-wide association studies (GWAS) for meat quality traits in Chinese purebred Erhualian pigs and a Western Duroc × (Landrace × Yorkshire) (DLY) commercial population.MethodsThree hundred and thirty six Chinese Erhualian and 610 DLY pigs were genotyped using the Illumina PorcineSNP60K Beadchip and evaluated for 20 meat quality traits. After quality control, 35 985 and 56 216 single nucleotide polymorphisms (SNPs) were available for the Chinese Erhualian and DLY datasets, respectively, and were used to perform two separate GWAS. We also performed a meta-analysis that combined P-values and effects of 29 516 SNPs that were common to Erhualian, DLY, F2 and Sutai pig populations.ResultsWe detected 28 and nine suggestive SNPs that surpassed the significance level for meat quality in Erhualian and DLY pigs, respectively. Among these SNPs, ss131261254 on pig chromosome 4 (SSC4) was the most significant (P = 7.97E-09) and was associated with drip loss in Erhualian pigs. Our results suggested that at least two QTL on SSC12 and on SSC15 may have pleiotropic effects on several related traits. All the QTL that were detected by GWAS were population-specific, including 12 novel regions. However, the meta-analysis revealed seven novel QTL for meat characteristics, which suggests the existence of common underlying variants that may differ in frequency across populations. These QTL regions contain several relevant candidate genes.ConclusionsThese findings provide valuable insights into the molecular basis of convergent evolution of meat quality traits in Chinese and Western breeds that show divergent phenotypes. They may contribute to genetic improvement of purebreds for crossbred performance.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-015-0120-x) contains supplementary material, which is available to authorized users.

Genome-wide association study identifies candidate genes for piglet splay leg syndrome in different populations

“…Only the nearest genes to the significant SNPs were considered in view of linkage disequilibrium (LD) decay as the distance between marker and QTL increased [28–32]. …”

Joint QTL mapping and gene expression analysis identify positional candidate genes influencing pork quality traits

“…For instance, when we compared our a*, b* and pH 24 data with those described in six additional GWAS studies4629303132 we only found one positional coincidence between the SSC10 (70.6 Mb) genomic region associated with LD a* in the Lipgen population (Table 3) and the SSC10 (72.8 Mb) region identified by Ma et al 4. as associated with the same trait in the semimembranosus muscle of White Duroc × Erhualian F 2 pigs.…”

“…These shared regions were: (a*) SSC4 (80–85 Mb)630, SSC6 (17–22 Mb)430, SSC7 (31–32 Mb)431, SSC12 (58–63 Mb)3031, SSC15 (133–136 Mb)303132; (b*) SSC15 (129–133 Mb)3032; and (pH 24 ), SSC3 (15–19 Mb)3031, SSC15 (133–136 Mb)2932. This latter region on SSC15 (133–136 Mb) appeared to be associated with a*, b*, pH 24 , shear force and cook loss in many independent studies29303132 but not in ours. Interestingly, this SSC15 region contains the protein kinase AMP-activated non-catalytic subunit gamma 3 ( PRKAG3 ) gene, whose polymorphism has causal effects on muscle glycogen depletion, a parameter that can have a strong influence on meat quality traits33.…”

Identification of Novel Genes and Variations Associated to Glycolytic Potential Based on Pig Model

“…Recent years, the genome sequences and high-density SNP chips are widely used for detection of variations significantly associated to economic traits in livestock (Liu et al 2015; Ma et al 2014; Rubin et al 2012; Rubin et al 2010; Verardo et al 2016). In this study, we found 1,076 potential specific SNPs between the higher and the lower GP group ( File S1–9 ) using the trancriptome sequencing data, which are the potential variations associated to GP-related traits.…”