Haplotypic QTL mapping in an outbred pedigree

An offspring genome can be viewed as a mosaic of chromosomal segments or haplotypes contributed by multiple founders in any quantitative trait locus (QTL) detection study but tracing these is especially complex to achieve for outbred pedigrees. QTL haplotypes can be traced from offspring back to individual founders in outbred pedigrees by combining founder-origin probabilities with fully informative flanking markers. This haplotypic method was illustrated for QTL detection using a three-generation pedigree for a woody perennial plant, Pinus taeda L. Growth rate was estimated using height measurements from ages 2 to 10 years. Using simulated and actual datasets, power of the experimental design was shown to be efficient for detecting QTLs of large effect. Using interval mapping and fully informative markers, a large QTL accounting for 11.3% of the phenotypic variance in the growth rate was detected. This same QTL was expressed at all ages for height, accounting for 7.9-12.2% of the phenotypic variance. A mixed-model inheritance was more appropriate for describing genetic architecture of growth curves in P. taeda than a strictly polygenic model. The positive QTL haplotype was traced from the offspring to its contributing founder, GP3, then the haplotypic phase for GP3 was determined by assaying haploid megagametophytes. The positive QTL haplotype was a recombinant haplotype contributed by GP3. This study illustrates the combined power of fully informative flanking markers and founder origin probabilities for (1) estimating QTL haplotype magnitude, (2) tracing founder origin and (3) determining haplotypic transmission frequency.