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

Abstract

Meat quality traits have an increasing importance in the pig industry because of their strong impact on consumer acceptance. Herewith, we have combined phenotypic and microarray expression data to map loci with potential effects on five meat quality traits recorded in the longissimus dorsi (LD) and gluteus medius (GM) muscles of 350 Duroc pigs, i.e. pH at 24 hours post-mortem (pH24), electric conductivity (CE) and muscle redness (a*), lightness (L*) and yellowness (b*). We have found significant genome-wide associations for CE of LD on SSC4 (~104 Mb), SSC5 (~15 Mb) and SSC13 (~137 Mb), while several additional regions were significantly associated with meat quality traits at the chromosome-wide level. There was a low positional concordance between the associations found for LD and GM traits, a feature that reflects the existence of differences in the genetic determinism of meat quality phenotypes in these two muscles. The performance of an eQTL search for SNPs mapping to the regions associated with meat quality traits demonstrated that the GM a* SSC3 and pH24 SSC17 QTL display positional concordance with cis-eQTL regulating the expression of several genes with a potential role on muscle metabolism.

Deciphering the genetic regulation of peripheral blood transcriptome in pigs through expression genome-wide association study and allele-specific expression analysis

“…The integration of eGWAS- and ASE-based approaches, together with GWAS data when relevant, facilitates the identification of candidate genes and polymorphisms that are related to complex traits. Similar integrated approaches in pigs have been recently published for complex traits related to meat properties [ 14 , 16 ], as well as for blood lipid traits linked with cardiovascular diseases [ 41 ] and traits associated with coping behavior [ 20 ]. In addition, this approach could help to pinpoint the biological and molecular bases of phenotype-genotype links that are highlighted by a GWAS-based approach.…”

“…Liaubet et al [ 13 ] analyzed gene expression in pig skeletal muscle sampled shortly after slaughtering, and showed an over-representation of genes that encoded proteins involved in processes induced during muscle development and metabolism, cell morphology, stress response, and apoptosis. More recently, eGWASs have been integrated with phenotyping studies in order to identify candidate genes and causative mutations associated with phenotypic variations in several tissues: for example, liver gene expression linked to blood and lipid traits [ 41 ], gene expression in longissimus dorsi or gluteus medius muscles associated with growth, fatness, yield, and meat quality [ 14 – 19 ], and hypothalamus gene expression connected to coping behavior [ 20 ].…”

Harnessing genomic information for livestock improvement

“…In cattle, such data sets have been generated for mammary gland, liver, blood and adrenal gland and have been used to identify causative genes underlying GWAS-identified QTL [41][42][43][44][45] . In pigs, eQTL studies have been conducted in skeletal muscle, lung, adipose tissue and liver [46][47][48][49][50][51][52][53][54][55][56][57] . In poultry, genome-wide eQTL analyses have been reported for liver, bone, adrenal gland and hypothalamus [58][59][60][61] .…”

Role of AMPK signalling pathway during compensatory growth in pigs

“…Moreover, samples of ~100 g of gluteus medius (GM) muscle were collected for laboratory analyses. Electric conductivity (EC), ultimate pH (pH 24 ), and meat colour parameters (lightness L*, redness a* and yellowness b*) were determined 24-h after slaughtering following the methods described in Gonzalez-Prendes et al [ 14 ]. Analyses of GM lipid components included the determination of percentage of intramuscular fat (IMF), cholesterol content and fatty acid composition in the C12 - C22 interval, as described in Canovas et al [ 15 ].…”