A strategy for QTL detection in half-sib populations

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Abstract
A statistical analysis strategy for the detection of quantitative trait loci (QTLs) in half-sib populations is outlined. The initial exploratory analysis is a multiple regression of the trait score on a subset of markers to allow a rapid identification of possible chromosomal regions of interest. This is followed by multiple marker interval mapping with regression methods within and across families fitting one or two QTLs. Empirical thresholds are determined by experiment-wise permutation tests for different significance levels and empirical confidence intervals for the QTLs' positions are obtained by bootstrapping methods. For traits with evidence for a significant single-QTL effect, an approximate maximum likelihood analysis is performed to obtain estimates of QTL effect and the probability of the QTL genotype for each parent of a group of half-sibs. The strategy is demonstrated in an analysis of previously published data on chromosome 6 and five production traits from a granddaughter design in dairy cattle. The results confirm and extend evidence for QTLs affecting protein percentage. Informativeness of markers limited the possibility of mapping more than one QTL on the same linkage group.