Große-Brinkhaus, Christine: Epistatic effects on carcass composition and meat quality in pigs. - Bonn, 2012. - Dissertation, Rheinische Friedrich-Wilhelms-Universität Bonn.
Online-Ausgabe in bonndoc:
author = {{Christine Große-Brinkhaus}},
title = {Epistatic effects on carcass composition and meat quality in pigs},
school = {Rheinische Friedrich-Wilhelms-Universität Bonn},
year = 2012,
month = aug,

note = {The analysis of epistasis is not yet a routine, but it has been shown by few studies in livestock animals that interaction effects contribute with considerable proportions to the phenotypic variance. Therefore the objective of this study was to evaluate the importance of epistatic effects in the Bonn Duroc × Pietrain resource population (DuPi) for carcass composition and meat quality traits. This population was investigated so far for single quantitative trait loci (QTL) considering additive, dominance and imprinting effects.
In the first approach, 585 F2 pigs of DuPi were used to perform a two dimensional QTL scan. All animals were genotyped using 125 genetic markers (microsatellites and SNP) spread across the 18 pig autosomes. Phenotypic information for 26 carcass composition and meat quality traits was available for all F2 animals. Linkage analysis was performed in a two-step procedure using a maximum likelihood approach implemented in the QxPak program. A number of 56 interacting QTL was observed for 19 different traits. These interacting QTL pairs explained up to 8% of the phenotypic variance. Based on these results a variety of networks among chromosomal regions throughout the porcine genome were identified. Moreover, considering interactions between loci allowed to detect several novel QTL and trait-specific relationships of loci within and across chromosomes.
In a second step the causes of an epistatic QTL pair between Sus scrofa chomsosome (SSC) 8 and 15 influencing pH value 1 h post mortem in M. long. dorsi were investigated. Gene expression data was obtained from loin tissue of 74 F2 which were selected from 585 animals. Gene expression profiles, genotypes and phenotypes of these pigs were investigated jointly applying three alternative models. Method A considered the phenotypic differences in pH values between groups of pigs with extreme values. Method B was based on differences between the genotype combinations of relevant epistatic QTL pairs between SSC8 and SSC15. Finally, method C was a linear model comprising the epistatic QTL genotypes as fixed effects. Overall method A, B and C revealed 1182, 480 and 1823 differentially expressed or associated genes, respectively. By means of a functional analysis it was possible to set up networks which contained mainly interactions between genes located within the specific regions on SSC8 and SSC15 and allowed a meaningful biological discussion. Expression QTL (eQTL) analyses were performed for functional and positional transcripts in order to assume regulations patterns. This approach showed that combining phenotype, genotype and transcriptome data helped to uncover the involved molecules of observed epistasis.
In conclusion, this study revealed the importance of epistasis for the expression of complex traits. Furthermore, it was possible to uncover potential biological causes of observed epistatic QTL pairs applying different statistical models as well as bioinformatic tools.},

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