QTL mapping in diploid potato by using selfed progenies of the cross S. tuberosum × S. chacoense

Abstract

Usually, mapping studies in potato are performed with segregating populations from crosses between highly heterozygous diploid or tetraploid parents. These studies are hampered by a high level of genetic background noise due to the numerous segregating alleles, with a maximum of eight per locus. In the present study, we aimed to increase the mapping efficiency by using progenies from diploid inbred populations in which at most two alleles segregate. Selfed progenies were generated from a cross between S. tuberosum (D2; a highly heterozygous diploid) and S. chacoense (DS; a homozygous diploid clone) containing the self-incompatibility overcoming S locus inhibitor (Sli-gene). The Sli-gene enables self-pollination and the generation of selfed progenies. One F2 population was used to map several quality traits, such as tuber shape, flesh and skin color. Quantitative trait loci were identified for almost all traits under investigation. The identified loci partially coincided with known mapped loci and partially identified new loci. Nine F3 populations were used to validate the QTLs and monitor the overall increase in the homozygosity level.

QTL detection in a pedigreed breeding population of diploid potato

“…In this study, we develop methodology for QTL detection in pedigreed breeding populations, focusing on shallow pedigrees, derived by few possibly outbred founders. To that end, we will use a population described by Meijer et al (Meijer et al 2018). This population is a set of F 3 families with a defined pedigree structure derived from a cross between an inbred (Solanum chacoense) and an outbred parent (Solanum tuberosum).…”

“…The mapping population consists of 840 individuals originating from a cross between an inbred S. chacoense genotype (we will refer to it as the ''Sc'' parent), and a highly heterozyous diploid S. tuberosum genotype (the ''St'' parent) (Meijer et al 2018). The mapping population is the third generation of this cross, as shown in Fig.…”

“…All 840 individuals were evaluated in a greenhouse experiment for a number of traits as described by Meijer et al (2018). Here, we focus on total tuber fresh weight per plant (TFW).…”

“…TFW showed continuous variation and is expected to have a polygenic inheritance. In addition, all the individuals and the two founders were genotyped, resulting in 120 SNP markers being polymorphic within all or some of the F 3 subfamilies as described by Meijer et al (2018). Those SNPs were mapped on a linkage map with 12 groups and a total length of 817.7 cM.…”

“…A change in QTL mapping methodology driven by diploid hybrid breeding is the use of inbred material in the mapping population either as parents (Endelman and Jansky 2016) and/or as offspring, such as F 2 (Endelman and Jansky 2016;Meijer et al 2018) or sib-mated F 2 (Braun et al 2017). 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.…”