Fine-mapping of quantitative trait loci in half-sib families using current recombinations

Two groups of methods are being developed to fine-map quantitative trait loci (QTLs): identity-by-descent methods or methods using historical recombinations, and genetic chromosome dissection methods or methods utilizing current recombinations. Here we propose two methods that fall into the second group: contrast mapping and substitution mapping. A QTL has previously been detected via linkage mapping in a half-sib design (granddaughter or daughter design), and sires (grandsires) likely to be heterozygous at the QTL have been identified. A sire (grandsire) and its recombinant offspring are then genotyped for a series of ordered markers spanning the initial marker interval. Offspring are grouped by paternal multi-marker haplotype with haplotypes differing in the location of the recombination event. In the contrast method, contrasts between the phenotypic averages of haplotypes or offspring groups are calculated which correspond to marker intervals within the original interval. The expected value of the contrast for the true QTL interval is always maximum, hence the interval with maximum observed contrast is assumed to contain the QTL. Alternative statistics for determining the interval most likely to contain a QTL are presented for contrast mapping, as well as a bootstrap estimation of the probability of having identified the correct interval. For an initial marker bracket of 20 cM and 10 additional equidistant markers, the probability of assigning the QTL to the correct 2 cM marker interval or to a combined 4 cM interval was calculated. For substitution effects of 0.093, 0.232, 0.464, 0.696 and 0.928 (in additive genetic SD), power values near 0.14, 0.26, 0.48, 0.67 and 0.80 (0.25, 0.53, 0.86, 0.97 and 0.99) are achieved for a family of 200 (1000) sons, respectively. In substitution mapping, QTL segregation status of recombinant sons must be determined using daughter genotyping. Combinations of two haplotypes with their segregation status are required to assign the QTL to an interval. Probabilities of correct QTL assignment were calculated assuming absence of the mutant QTL allele in dams of sons. For a 2 cM interval and a QTL at the midpoint of an interval, power near 0.95 (0.90) is reached when the number of recombinant sons is 70 (60), or total number of sons is 424 (363). For QTL positions away from the midpoint, power decreases but can be improved by combining marker intervals. For a QTL located halfway to the midpoint, and 182 sons in a family resulting in 30 recombinant sons, probability is 0.94 for assignment to either a 2 cM or a combined 4 cM interval. Effect of type I and type II errors in segregation status determination on power of QTL assignment was found to be small. Errors in segregation status due to QTL segregation in dams have an impact if the frequency of the mutant QTL allele is intermediate to high.