Genome-wide mapping of Quantitative Trait Loci for fatness, fat cell characteristics and fat metabolism in three porcine F2 crosses

<p>Abstract</p> <p>Background</p> <p>QTL affecting fat deposition related performance traits have been considered in several studies and mapped on numerous porcine chromosomes. However, activity of specific enzymes, protein content and cell structure in fat tissue probably depend on a smaller number of genes than traits related to fat content in carcass. Thus, in this work traits related to metabolic and cytological features of back fat tissue and fat related performance traits were investigated in a genome-wide QTL analysis. QTL similarities and differences were examined between three F₂crosses, and between male and female animals.</p> <p>Methods</p> <p>A total of 966 F₂animals originating from crosses between Meishan (M), Pietrain (P) and European wild boar (W) were analysed for traits related to fat performance (11), enzymatic activity (9) and number and volume of fat cells (20). Per cross, 216 (M × P), 169 (W × P) and 195 (W × M) genome-wide distributed marker loci were genotyped. QTL mapping was performed separately for each cross in steps of 1 cM and steps were reduced when the distance between loci was shorter. The additive and dominant components of QTL positions were detected stepwise by using a multiple position model.</p> <p>Results</p> <p>A total of 147 genome-wide significant QTL (76 at P < 0.05 and 71 at P < 0.01) were detected for the three crosses. Most of the QTL were identified on SSC1 (between 76-78 and 87-90 cM), SSC7 (predominantly in the MHC region) and SSCX (in the vicinity of the gene <it>CAPN6</it>). Additional genome-wide significant QTL were found on SSC8, 12, 13, 14, 16, and 18. In many cases, the QTL are mainly additive and differ between F₂crosses. Many of the QTL profiles possess multiple peaks especially in regions with a high marker density. Sex specific analyses, performed for example on SSC6, SSC7 and SSCX, show that for some traits the positions differ between male and female animals. For the selected traits, the additive and dominant components that were analysed for QTL positions on different chromosomes, explain in combination up to 23% of the total trait variance.</p> <p>Conclusions</p> <p>Our results reveal specific and partly new QTL positions across genetically diverse pig crosses. For some of the traits associated with specific enzymes, protein content and cell structure in fat tissue, it is the first time that they are included in a QTL analysis. They provide large-scale information to analyse causative genes and useful data for the pig industry.</p

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

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