A new method of QTL identification for undersaturated maps

Abstract

In many species, low levels of polymorphism prevent the assembly of linkage maps that are used to identify genetic markers related to the expression of quantitative trait loci (QTLs). This study compared two methods of locating QTLs in association studies that do not require a previous estimation of linkage maps. Method I (MI) was a Bayesian multiple marker regression and Method II (MII) combined multiple QTL mapping and “moving away from markers”. In this method, markers are not directly regressed to the phenotype, but are used as pivots to search for QTLs along the genome. To compare methods, we simulated 300 individuals from an F2 progeny with two levels of marker loss (20 and 80%). A total of 165 markers and seven QTLs were spread along 11 chromosomes (roughly emulating the genetic structure of the common bean, Phaseolus vulgaris). A real data example with 186 progenies of a F2:4 generation of the species was analyzed using 59 markers (17 simple sequence repeats, 31 amplified fragment length polymorphisms, and 11 sequence-related amplified polymorphisms). MII was more precise than MI for both levels of marker loss. For real data, MII detected 17 candidate positions for QTLs, whereas MI did not detect any. MII is a powerful method that requires further studies with actual data and other designs such as crossover, and genome-wide studies.