Abstract
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 hbox {F}_3 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.
Highlights
Diploid hybrid potato and quantitative trait loci (QTL) mappingDiploid hybrid potato breeding promises a paradigm shift in potato breeding consisting of replacing the tetraploid clones with diploid hybrids propagated by true seed (Lindhout et al 2011; Jansky et al 2016)
In this article we focus on another aspect of QTL mapping in the ‘‘diploid hybrid’’ era, which is the development of diploid potato breeding populations
This population is a set of F3 families with a defined pedigree structure derived from a cross between an inbred (Solanum chacoense) and an outbred parent (Solanum tuberosum). It is a diploid potato QTL mapping population with exceptionally high level of inbreeding. We here use it as a proxy of a complex plant breeding pedigree on the grounds that it has more than two alleles segregating, it is under selection and it represents an important part of the breeding germplasm
Summary
Diploid hybrid potato breeding promises a paradigm shift in potato breeding consisting of replacing the tetraploid clones with diploid hybrids propagated by true seed (Lindhout et al 2011; Jansky et al 2016). This transition is based on the development of selfcompatible diploid potato germplasm and, subsequently, the gradual selection against the genetic load through selfing. Besides the consequences regarding breeding and crop management (Lindhout et al 2018), this shift influences quantitative trait loci (QTL) mapping methodology. Selfing was hindered by the self-incompatibility and inbreeding depression of diploid potato and the use of selfed material has been limited to the study of segregation distortion and self-fertility (Peterson et al 2016; Zhang et al 2019)
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