QTL detection in a pedigreed breeding population of diploid potato
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QTL detection in a pedigreed breeding population of diploid potato George Korontzis . Marcos Malosetti . Chaozhi Zheng . Chris Maliepaard . Han A. Mulder . Pim Lindhout . Roel F. Veerkamp . Fred A. van Eeuwijk
Received: 15 March 2020 / Accepted: 2 August 2020 Ó The Author(s) 2020
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 F3 families under selection derived by a cross between an inbred Solanum chacoense and an outbred diploid Solanum
G. Korontzis (&) M. Malosetti C. Zheng F. A. van Eeuwijk Biometis, Wageningen University and Research, Droevendaalsesteeg 1, P.O. Box 16, 6700 AA Wageningen, The Netherlands e-mail: [email protected] F. A. van Eeuwijk e-mail: [email protected] C. Maliepaard Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, P.O. Box 386, 6700 AJ Wageningen, The Netherlands H. A. Mulder R. F. Veerkamp Animal Breeding and Genomics, Wageningen University and Research, Droevendaalsesteeg 1, P.O. Box 338, 6700 AH Wageningen, The Netherlands P. Lindhout Solynta, Dreijenlaan 2, 6703 HA Wageningen, The Netherlands
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. Keywords QTL mapping Diploid potato Hybrid potato GWAS Identity-by-descent Pedigree
Introduction Diploid hybrid potato and QTL mapping 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. The resulting inbred lines enable the exploitation of heterosis through hybrid breeding, the introgression of genes through backcrossing and the
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utilization of all breeding methods and genomic tools developed for diploid crops. Besides the consequences regarding breeding and crop management (Lindhout et al. 2018), this shift also influences quantitative trait loci (QTL) mapping methodology. In potato, QTLs h
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