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.
Highlights
Understanding the genetic mechanisms that underlie meat quality traits is essential to improve pork quality
Results of the separate genome-wide association studies (GWAS) for the Erhualian and DLY populations Overall, we identified 37 single nucleotide polymorphisms (SNPs) on 14 chromosomes that were significantly associated with pH, drip loss, meat colour, moisture content and firmness in these populations (Table 3), which demonstrates the diverse genetic architecture of meat quality traits in pigs
PH values and drip loss We identified three significant SNPs associated with pH values in the Erhualian dataset, including one for LM_pH24h, one for SM_pH24h and one for LM_pHdrop_45min-24 h, which were localized on SSC9 (SSC for Sus scrofa chromosome), SSC3 and SSC16, respectively
Summary
Understanding the genetic mechanisms that underlie meat quality traits is essential to improve pork quality. It has been shown that the genes insulin-like growth factor 2 (IGF2) [8,9], melano-cortin 4 receptor (MC4R) [9], protein kinase, AMP-activated, gamma 3 non-catalytic subunit (PRKAG3) [10] and ryanodine receptor 1 (RYR1) [11] have major effects on meat production and quality in pigs. Identification of these genes has greatly benefited the pig industry [12]
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