Characterization of quantitative trait loci for growth and meat quality in a cross between commercial breeds of swine.

A three-generation resource family was created by crossing two Berkshire grandsires with nine Yorkshire granddams to identify QTL affecting growth, body composition, and meat quality. A total of 512 F2 offspring were evaluated for 11 traits related to growth and body composition and 28 traits related to meat quality. All animals were initially genotyped for 125 markers across the genome. The objectives of this advanced phase of the project were to further identify and characterize QTL after genotyping for another 33 markers in special regions of interest, and to develop and apply methods for detecting QTL with parent-of-origin effects. New marker linkage maps were derived and used in QTL analysis based on line-cross least squares regression-interval mapping. A decision tree for identifying QTL with parent-of-origin effects was developed based on tests against the Mendelian mode of expression. Empirical significance thresholds were derived at chromosomewise and genomewise levels using specialized permutation strategies to create data under the null hypothesis appropriate for each test. Significance thresholds derived by the permutation tests were validated based on simulation of a pedigree and data structure similar to the Berkshire-Yorkshire population. The addition of 33 markers resulted in the discovery of 29 new QTL at the 5% chromosomewise level using the Mendelian model of analysis. Thirteen of the original QTL were no longer significant at the 5% chromosomewise level. A total of 33 QTL with parent-of-origin effects were identified, including QTL with paternal expression for backfat and loin muscle area on chromosome 2, near IGF2, and QTL with maternal expression for drip loss and reflectance on chromosome 9. Tests for imprinting against Mendelian expression identified much fewer QTL with parent-of-origin effects than tests based on significance of paternal and maternal alleles, which have been used in other studies. The detected QTL and their identified mode of expression will allow further research in these QTL regions and their utilization in marker-assisted improvement of meat quality.