A two‐step approach to map quantitative trait loci for meat quality in connected porcine F₂ crosses considering main and epistatic effects

Abstract

The aim of this study was to map QTL for meat quality traits in three connected porcine F(2) crosses comprising around 1000 individuals. The three crosses were derived from the founder breeds Chinese Meishan, European Wild Boar and Pietrain. The animals were genotyped genomewide for approximately 250 genetic markers, mostly microsatellites. They were phenotyped for seven meat quality traits (pH at 45 min and 24 h after slaughter, conductivity at 45 min and 24 h after slaughter, meat colour, drip loss and rigour). QTL mapping was conducted using a two-step procedure. In the first step, the QTL were mapped using a multi-QTL multi-allele model that was tailored to analyse multiple connected F(2) crosses. It considered additive, dominance and imprinting effects. The major gene RYR1:g.1843C>T affecting the meat quality on SSC6 was included as a cofactor in the model. The mapped QTL were tested for pairwise epistatic effects in the second step. All possible epistatic effects between additive, dominant and imprinting effects were considered, leading to nine orthogonal forms of epistasis. Numerous QTL were found. The most interesting chromosome was SSC6. Not all genetic variance of meat quality was explained by RYR1:g.1843C>T. A small confidence interval was obtained, which facilitated the identification of candidate genes underlying the QTL. Epistasis was significant for the pairwise QTL on SSC12 and SSC14 for pH24 and for the QTL on SSC2 and SSC5 for rigour. Some evidence for additional pairwise epistatic effects was found, although not significant. Imprinting was involved in epistasis.

Discovery of Candidate Genes for Muscle Traits Based on GWAS Supported by eQTL-analysis

“…RYR1 mutations, located on SSC6, frequently occur in the Pietrain breed and significantly impact meat quality, stress resistance, and carcass composition 33. Several QTL for meat quality traits were found next to RYR1 on SSC6, although RYR1 was included in the QTL mapping model as a fixed effect 32. The GL pigs in this study did not carry this mutation.…”

“…Previous studies have also identified QTL for meat quality traits on SSC6 30-32. Markljung and colleagues 31 identified QTL affecting water content, DVMLP (drip loss), and pH decline between positions 51 and 69 cM on SSC6.…”

Genome‐wide association analysis for growth, muscularity and meat quality in Piétrain pigs

“…Mohrmann et al 2006;Liu et al 2007;Boysen et al 2011). In recent studies, we conducted joint QTL analysis for growth and meat quality traits in pigs using three connected F2 crosses for which Pi etrain was used as a founder breed (R€ uckert & Bennewitz 2010;R€ uckert et al 2012;Stratz et al 2013). We were able to map numerous QTL affecting muscularity, growth and meat quality.…”

Linkage disequilibrium pattern and genome‐wide association mapping for meat traits in multiple porcine F2 crosses

“…The number of RYR1 genotypes is presented in Stratz et al . (). The locations of the markers on the Porcine 62K SNP chip were retrieved from genome assembly Sscrofa11.1 (Warr et al .…”