A NONPARAMETRIC BOOTSTRAP METHOD FOR TESTING CLOSE LINKAGE VS. PLEIOTROPHY OF COINCIDENT QUANTITATIVE TRAIT LOCI

A novel method using the nonparametric bootstrap is proposed for testi ng whether a quantitative trait locus (QTL) at one chromosomal positio n could explain effects on two separate traits. If the single-QTL hypo thesis is accepted, pleiotropy could explain the effect on two traits. If it is rejected, then the effects on two traits are due to linked Q TLs. The method can be used in conjunction with several QTL mapping me thods as long as they provide a straightforward estimate of the number of QTLs detectable from the data set. A selection step was introduced in the bootstrap procedure to reduce the conservativeness of the test of close linkage vs, pleiotropy, so that the erroneous rejection of t he null hypothesis of pleiotropy only happens at a frequency equal to the nominal type I error risk specified by the user. The approach was assessed using computer simulations and proved to be relatively unbias ed and robust over the range of genetic situations tested. An example of its application on a real data set from a saline stress experiment performed an a recombinant population of wheat (Triticum aestivum L.) doubled haploid lines is also provided.