Genome-wide scan for body composition in pigs reveals important role of imprinting

Abstract

The role of imprinting in body composition was investigated in an experimental cross between Chinese Meishan pigs and commercial Dutch pigs. A whole-genome scan revealed significant evidence for five quantitative trait loci (QTL) affecting body composition, of which four were imprinted. Imprinting was tested with a statistical model that separated the expression of paternally and maternally inherited alleles. For back fat thickness, a paternally expressed QTL was found on Sus scrofa chromosome 2 (SSC2), and a Mendelian-expressed QTL was found on SSC7. In the same region of SSC7, a maternally expressed QTL affecting muscle depth was found. Chromosome 6 harbored a maternally expressed QTL on the short arm and a paternally expressed QTL on the long arm, both affecting intramuscular fat content. The individual QTL explained from 2% up to 10% of the phenotypic variance. The known homologies to human and mouse did not reveal positional candidate genes. This study demonstrates that testing for imprinting should become a standard procedure to unravel the genetic control of multifactorial traits.

Figure 1

Test statistic profiles for three porcine chromosomes that exhibit imprinting effects for one of the body composition traits: SSC2 and back fat thickness (A), SSC6 and intramuscular fat content (B), SSC7 and muscle depth (C), and SSC7 and back fat thickness (D). The black line represents the test statistic for a Mendelian QTL vs. no QTL. The blue line represents the test statistic for a paternally expressed QTL vs. no QTL. The red line represents the test statistic for a maternally expressed QTL vs. no QTL. The black horizontal line denotes the 5% genome-wise threshold for the Mendelian model, and the blue line indicates the same threshold for the imprinting models (thresholds for maternal and paternal expression were very similar and well within the sampling variance associated with permutation testing). Homologous regions in humans are indicated as colored bars (–24, 26).^‡ Imprinted genes located within these human chromosomal areas are listed at the bottom (5, 25).