A Haplotype‐Based Method for QTL Mapping of F1 Populations in Outbred Plant Species

The integration of quantitative trait loci (QTL) analysis into breeding strategies rather than being seen as separated processes has been proposed to increase the power and accuracy of QTL detection and to allow the two activities to be joined. The main objective of this research is to develop a specific scheme for mapping QTL in actual breeding F1 populations of outbred plant species with a high degree of accuracy. The proposed method groups populations by common founders and statistically associates founder‐origin probabilities that trace the common founder haplotypes in a given region of the progeny genome with the phenotypic expression, using a linear model with a structured covariance matrix. The method was applied to computer simulated data sets, corresponding to five F1 populations of 100 individuals each obtained from the crosses of a common founder with several other founders. We are currently using this scheme with cocoa (Theobroma cacao L.) crosses, using selected clones resistant to specific diseases to widen the genetic base of disease resistance. The results indicate that the position and effect of QTLs in the common founder, that explain each at least 14% of the phenotypic variance, can be estimated with good precision and accuracy. The theoretical assumptions on which this approach was developed render the method appropriate for outbred plant species that are highly heterozygous, which is often the case in tropical tree crops like cocoa, and have phenotypic traits that show few interlocus interaction effects.