Genome-wide mapping of quantitative trait loci for fatness, fat cell characteristics and fat metabolism in three porcine F2 crosses

Abstract

Background: 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 F2 crosses, and between male and female animals.

Methods: A total of 966 F2 animals 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 (MxP), 169 (WxP) and 195 (WxM) 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.

Results: 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 CAPN6). 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 F2 crosses. 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.

Conclusions: 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.

Figure 1

Genomic distribution of QTL. The distribution of the QTL detected in the Hohenheim crosses (M: Meishan; P: Pietrain; W: European wild boar) and with F ratio values above the genome-wide thresholds P = 0.05 is shown on the pig chromosomes (SSC); for each cross, the sex-averaged map in Kosambi morgan (M) is adjusted to the length calculated for the Hohenheim M × P cross; results for SSCX were obtained from female animals; the different symbols for the three trait groups represent major QTL peaks (black) and minor QTL peaks (red) that show distances > 20 cM to the major peak and to other minor peak observed for the same trait.

Figure 2

Examples of F ratio profiles in the different Hohenheim crosses shown for chromosomes 1, 7 and X. The solid line indicates the P = 0.01, the dashed line the P = 0.05 genome-wide thresholds, and the dotted line the P = 0.05 chromosome-wide threshold for F ratio values; traits are defined in Table 2; positions of markers are given in Kosambi centimorgan (cM) on the linkage maps of Hohenheim crosses; results for SSCX were obtained from female animals; markers are described in Additional file 1; data sets for the two sexes are shown with the averaged linkage map distances whereas for SSCX the female map distances are used; M: Meishan; P: Pietrain; W: European wild boar.

Figure 3

Examples of F ratio profiles calculated for all (females and males), female or male F₂ animals. For further explanations see Figure 2.