QTL detection in a pedigreed breeding population of diploid potato

Diploid hybrid potato breeding is emerging as an alternative to breeding tetraploid potato clones. The development of diploid breeding varieties involves recent, shallow pedigrees with a limited number of founders. Within this context, alternative QTL detection methodologies should be considered to enable identification of relevant QTLs and characterize the founders of the pedigree. To that end, we are using a dataset of multiple diploid potato F3\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\hbox {F}_3$$\end{document} families under selection derived by a cross between an inbred Solanum chacoense and an outbred diploid Solanum tuberosum, and identify QTLs for tuber fresh weight. We used three methods for QTL detection: (1) a Genome Wide Association Study model, (2) a linkage approach tailored to the population under study and (3) a more general approach for modelling multiallelic QTLs in complex pedigrees using identity-by-descent (IBD) probabilities. We show that all three approaches enable detection of QTLs in the population under study, but the method that makes better use of IBD information has a more direct and detailed interpretation by linking QTL alleles to the founders.