Genome-wide association studies (GWAS) identify a QTL close to PRKAG3 affecting meat pH and colour in crossbred commercial pigs
| Autor: | Patrick Charagu, Younes Miar, Tianfu Yang, Graham Plastow, Zhiquan Wang, Heather L. Bruce, Robert Kemp, Chunyan Zhang |
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| Jazyk: | angličtina |
| Rok vydání: | 2015 |
| Předmět: |
Linkage disequilibrium
Meat Swine Quantitative Trait Loci SNP Single-nucleotide polymorphism Genomics Genome-wide association study Biology Quantitative trait locus AMP-Activated Protein Kinases Crossbreed Genome-wide association studies Polymorphism Single Nucleotide Chromosomes Linkage Disequilibrium 03 medical and health sciences Quantitative Trait Heritable Genetic variation Genetics Animals Genetics(clinical) Gene Regulatory Networks Genetics (clinical) Genetic Association Studies 030304 developmental biology 2. Zero hunger 0303 health sciences Pig Haplotype 0402 animal and dairy science 04 agricultural and veterinary sciences 040201 dairy & animal science Meat pH and colour Phenotype Haplotypes Hybridization Genetic Research Article Genome-Wide Association Study |
| Zdroj: | BMC Genetics |
| ISSN: | 1471-2156 |
| Popis: | Background Improving 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. Results Six 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. Conclusions There 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 investigation Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0192-1) contains supplementary material, which is available to authorized users. |
| Databáze: | OpenAIRE |
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