Patrick Stratz

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

Improvement in growth and meat quality is one of the main objectives in sire line pig breeding programmes. Mapping quantitative trait loci for these traits using experimental crosses and a linkage-based approach has been performed frequently in the past. The Piétrain breed often was involved as a founder breed to establish the experimental crosses. This breed was selected for muscularity and leanness but shows relatively poor meat quality. It is frequently used as a sire line breed. With the advent of genome-wide and dense SNP chips in pig genomic research, it is possible to also conduct genome-wide association studies within the Piétrain breed. In this study, around 500 progeny-tested sires were genotyped with 60k SNPs. Data filtering showed that around 48k SNPs were useable in this sample. These SNPs were used to conduct a genome-wide association study for growth, muscularity and meat quality traits. Because it is known that a mutation in the RYR1 gene located on chromosome 6 shows a major effect on meat quality, this mutation was included in the models. Single-marker and multimarker association analyses were performed. The results revealed between zero and eight significant associations per trait with P < 5 × 10(-5) . Of special interest are SNPs located on SSC6, SSC10 and SSC15.

Mapping quantitative trait loci for metabolic and cytological fatness traits of connected F crosses in pigs

In the present study 3 connected F(2) crosses were used to map QTL for classical fat traits as well as fat-related metabolic and cytological traits in pigs. The founder breeds were Chinese Meishan, European Wild Boar, and Pietrain with to some extent the same founder animals in the different crosses. The different selection history of the breeds for fatness traits as well as the connectedness of the crosses led to a high statistical power. The total number of F(2) animals varied between 694 and 966, depending on the trait. The animals were genotyped for around 250 genetic markers, mostly microsatellites. The statistical model was a multi-allele, multi-QTL model that accounted for imprinting. The model was previously introduced from plant breeding experiments. The traits investigated were backfat depth and fat area as well as relative number of fat cells with different sizes and 2 metabolic traits (i.e., soluble protein content as an indicator for the level of metabolic turnover and NADP-malate dehydrogenase as an indicator for enzyme activity). The results revealed in total 37 significant QTL on chromosomes 1, 2, 4, 5, 6, 7, 8, 9, 14, 17, and 18, with often an overlap of confidence intervals of several traits. These confidence intervals were in some cases remarkably small, which is due to the high statistical power of the design. In total, 18 QTL showed significant imprinting effects. The small and overlapping confidence intervals for the classical fatness traits as well as for the cytological and metabolic traits enabled positional and functional candidate gene identification for several mapped QTL.

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

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.

Genetic parameter estimates and targeted association analyses of growth, carcass, and meat quality traits in German Merinoland and Merinoland-cross lambs1

In this study, genetic parameters of nine growth, carcass, and meat quality (MQ) traits were estimated, and targeted association studies were conducted using mixed models. Phenotypic information was collected on 1,599 lambs, including both purebred Merinoland (ML) animals and five different F1 crosses. The F1 lambs were produced by mating rams of the meat-type breeds Charollais, Ile de France, German Blackheaded Mutton (Deutsches Schwarzköpfiges Fleischschaf), Suffolk, and Texel with ML ewes. Between four and six sires were used per sire breed. In total, 29 sires and 298 purebred ML sheep were genotyped with the Illumina OvineSNP50 BeadChip. All F1 individuals were genotyped for 289 SNPs located on the chromosomes 1, 2, 3, 18, and 21. These SNPs were used to impute SNPs on five chromosomes of the Illumina Ovine chip in the F1 individuals. Several Bonferroni-corrected significant associations were identified for shoulder width. A number of additional significant associations were found for other traits. Genetic parameters were estimated and single-marker association analyses were performed with breed-specific effects. Moderate heritability estimates were found for average daily gain (0.23), kidney fat weight (0.19), carcass length (0.15), shoulder width (0.33), subcutaneous fat thickness (0.22), and cutlet area (0.36). While heritability for cooking loss was found to be low (0.07), shear force (0.17) and dressing percentage (0.20) showed moderate heritability, and thus might be candidate traits to be included in the selection index in the population. In general, low phenotypic and low or moderate genetic correlations were detected between the traits.