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The general goal of this study was to test a combined model that uses breed and family information in a double backcross (BC) design to detect QTL. Each BC consisted of a set of eight half-sib (HS) families with 32 progeny per sire. A finite locus model was considered with eleven independently segregating QTLs, ten small and one large. The large QTL had three alleles and explained 24 percent of the total genetic variance. The first study aimed at the theoretical development of two models relevant to detection of QTL in inbred line cross (BC) and outbred population (HS) with the goal of establishing the basis for joint analysis. Expected marker contrasts and theoretical power were computed analytically. For a marker positioned at 0.1 cM from the QTL, theoretical power was 0,26 and 0.46 for single and double BC analyses, and 0.27 and 0.40 for single and double HS analyses, respectively. The second study simulated thirteen markers at 10 cM intervals to bracket the large QTL. Single marker regression analysis was applied. Progeny phenotype was regressed on the probability that the maternal allele came from breed A, in the BC analyses, or the probability that the progeny inherited the first sire allele, in the HS analyses. Double BC and double HS were combined into one design by multiple regression. Empirical power for 13 markers was estimated. Power estimates for double BC and double HS analyses were 0.20 and 0.33, respectively, and increased to 0,42 for the combined model analysis. This proved that combined model was more powerful than either BC or HS models alone. In the third study, validation of the combined model was done using field marker data from 422 animals from a three-breed swine cross. Association of polymorphic loci in four candidate genes--fatty acid binding protein ('FABP') '3, 4, 5' and histone deacetylase ('HDAC') '1'--with body weight and back fat thickness traits was tested. Four models were compared in terms of the number of significant associations, residual error variance and log likelihood ratio values. Combined model of breed and family information could be used jointly to improve the power of QTL detection in crosses of outbred populations. |
