The aim of the research was to gain a better understanding of the genomic regulation of meat quality by investigating individual and epistatic QTL in a three-generation full-sib population (Pietrain x crossbred dam line). In total, 386 animals were genotyped for 96 markers. Analysed traits included pH, reflectance value, conductivity, and meat colour. Thirteen significant individual QTL were id...

We consider some practical statistical issues in QTL analysis where several crosses originate in multiple inbred parents. Our results show that ignoring background polygenic variation in different crosses may lead to biased interval mapping estimates of QTL effects or loss of efficiency. Threshold and power approximations are derived by extending earlier results based on the Ornstein-Uhlenbeck ...

Genetic mapping of quantitative trait loci (QTLs) is performed typically by using a parametric approach, based on the assumption that the phenotype follows a normal distribution. Many traits of interest, however, are not normally distributed. In this paper, we present a nonparametric approach to QTL mapping applicable to any phenotypic distribution. The method is based on a statistic ZW, which ...

Multiple-trait analysis typically employs models that associate a quantitative trait locus (QTL) with all of the traits. As a result, statistical power for QTL detection may not be optimal if the QTL contributes to the phenotypic variation in only a small proportion of the traits. Excluding QTL effects that contribute little to the test statistic can improve statistical power. In this article, ...

INRA, UMR1313 Génétique Animale et Biologie Intégrative, F-78350 Jouy-en-Josas, France; INRA, UR444 Laboratoire de génétique cellulaire, F-31320 CastanetTolosan, France; INRA, UMR1286; CNRS, UMR5226, Laboratoire PsyNuGen, F-33076 Bordeaux, France; INRA, UE967 Génétique expérimentale en productions animales, F-17700 Surgères, France; INRA, UAR2 Services déconcentrés d’appui à la recherche – Poit...

INTRODUCTION Reducing plant height has played an important role in improving crop yields. The success of a breeding program relies on the source of dwarfing genes. For a dwarfing or semi-dwarfing gene to be successfully used in a breeding program, the gene should have minimal negative effects on yield and perform consistently in different environments. METHODS In this study, 182 doubled haplo...

Bayesian shrinkage analysis is arguably the state-of-the-art technique for large-scale multiple quantitative trait locus (QTL) mapping. However, when the shrinkage model does not involve indicator variables for marker inclusion, QTL detection remains heavily dependent on significance thresholds derived from phenotype permutation under the null hypothesis of no phenotype-to-genotype association....

MAPfastR is a software package developed to analyze quantitative trait loci data from inbred and outbred line-crosses. The package includes a number of modules for fast and accurate quantitative trait loci analyses. It has been developed in the R language for fast and comprehensive analyses of large datasets. MAPfastR is freely available at: http://www.computationalgenetics.se/?page_id=7.

We describe a method for constructing the confidence interval of the QTL location parameter. This method is developed in the local asymptotic framework, leading to a linear model at each position of the putative QTL. The idea is to construct a likelihood ratio test, using statistics whose asymptotic distribution does not depend on the nuisance parameters and in particular on the effect of the Q...