The great-grand-daughter design: a simple strategy to increase the power of a grand-daughter design for QTL mapping

In dairy cattle, quantitative trait loci (QTL) are usually mapped using the grand-daughter design (GDD), i.e. sets of progeny-tested paternal half-brothers. Linkage information is typically extracted from the segregation of the sire chromosomes amongst their sons. We herein propose to increase the power of a GDD by exploiting the frequently occurring relationship between sires and grandsons which has so far been ignored in most methods of analysis. The proposed approach is a multipoint interval mapping method based on the Wilcoxon sum-of-rank test. Three alternative approaches to combine information from sons and grandsons are evaluated by simulation. In these either (i) sons and grandsons are ranked separately, (ii) sons and grandsons are ranked separately but the sign of the QTL effect is constrained to be the same in both generations, or (iii) sons and grandsons are ranked jointly. The proposed methods have been applied on a real data-set in which a GDD including 907 sons is analysed with a marker map comprising nine microsatellites spanning 46 cM on bovine chromosome 6.