Abstract
BackgroundImproving meat quality is a high priority for the pork industry to satisfy consumers’ preferences. GWAS have become a state-of-the-art approach to genetically improve economically important traits. However, GWAS focused on pork quality are still relatively rare.ResultsSix genomic regions were shown to affect loin pH and Minolta colour a* and b* on both loin and ham through GWAS in 1943 crossbred commercial pigs. Five of them, located on Sus scrofa chromosome (SSC) 1, SSC5, SSC9, SSC16 and SSCX, were associated with meat colour. However, the most promising region was detected on SSC15 spanning 133–134 Mb which explained 3.51% - 17.06% of genetic variance for five measurements of pH and colour. Three SNPs (ASGA0070625, MARC0083357 and MARC0039273) in very strong LD were considered most likely to account for the effects in this region. ASGA0070625 is located in intron 2 of ZNF142, and the other two markers are close to PRKAG3, STK36, TTLL7 and CDK5R2. After fitting MARC0083357 (the closest SNP to PRKAG3) as a fixed factor, six SNPs still remained significant for at least one trait. Four of them are intragenic with ARPC2, TMBIM1, NRAMP1 and VIL1, while the remaining two are close to RUFY4 and CDK5R2. The gene network constructed demonstrated strong connections of these genes with two major hubs of PRKAG3 and UBC in the super-pathways of cell-to-cell signaling and interaction, cellular function and maintenance. All these pathways play important roles in maintaining the integral architecture and functionality of muscle cells facing the dramatic changes that occur after exsanguination, which is in agreement with the GWAS results found in this study.ConclusionsThere may be other markers and/or genes in this region besides PRKAG3 that have an important effect on pH and colour. The potential markers and their interactions with PRKAG3 require further investigationElectronic supplementary materialThe online version of this article (doi:10.1186/s12863-015-0192-1) contains supplementary material, which is available to authorized users.
Highlights
Improving meat quality is a high priority for the pork industry to satisfy consumers’ preferences
Genomic regions Population stratification with Identity-by-State (IBS) showed that all animals from the two commercial populations could be classified into two clusters, which correspond to the populations from which the individuals were derived
A total of 26 Single nucleotide polymorphism (SNP) in this region explained the major proportion of the total genetic variance for the five traits, with 17.06%, 8.68%, 12.91%, 9.26% and 3.51% for colour b* (QFCOL b*) and a* (QFCOL a*) measured on the quadriceps femoris on the ham, colour b* measured on the thawed loin (TMCOL b*), pH 24 h post-mortem measured on fresh loin (FpH24) and pH measured on thawed loin (TMpH), respectively
Summary
Improving meat quality is a high priority for the pork industry to satisfy consumers’ preferences. Improving meat quality has become a high priority for the pork industry to satisfy consumers’ preferences for a better eating experience. Colour and pH are highly correlated with other pork quality measurements (e.g. drip loss, texture score) and carcass yield (e.g. carcass weight, loin depth, loin length) as reported in our recent work [2]. Improving these traits by traditional breeding methods is a challenge due to the wide range of reported heritability (0.04 - 0.57) in different breeds [3], the high cost of measurement and the limited amount of data available post-mortem. Nearly 900 QTLs (PigQTLdb, release 25, December 2014. http://www. animalgenome.org/cgi-bin/QTLdb/SS/index) and a few gene variants, such as PRKAG3 (Protein Kinase, AMPActivated, Gamma 3 Non-Catalytic Subunit) [1,4,5], have
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