QTL mapping in diploid potato by using selfed progenies of the cross S. tuberosum\u2009\xd7\u2009S. chacoense

D Meijer,H J Van Eck,R G F Visser,W H Lindhout,Y Su,M Viquez-Zamora,R C B Hutten,R Rothengatter,A W Van Heusden

doi:10.1007/s10681-018-2191-6

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.

Highlights

Knowledge about important characters and the genes or chromosome regions underlying the genetic variation is important in molecular breeding
Not all additional genetic variation in maturity could be explained, and other factors have yet to be identified. This was expected in tetraploid populations, where small allele dosages at other loci often complicate the mapping of minor factors
Our study aimed to investigate how much variation for several potato characteristics was present in our F2 population and to compare those with known Quantitative Trait Loci (QTL)

Summary

Introduction

Knowledge about important characters and the genes or chromosome regions underlying the genetic variation is important in molecular breeding. Mapping studies in potato have been performed in both tetraploid and diploid populations (e.g., van Eck et al 1994a, b; Bradshaw et al 2008; D’hoop et al 2014; Prashar et al 2014; Endelman and Jansky 2016) In these studies, Quantitative Trait Loci (QTL) for major traits were identified. Tuber shape has a simple genetic basis, round was considered to be dominant over long, and is hardly affected by environmental factors (van Eck et al 1994b) but recently this seems to be less clear (Prashar et al 2014). In these studies, the Ro locus on chromosome 10 (van Eck et al 1994b) plays a crucial role. In addition to the Y-locus, modifying genes are known to give rise to different gradations of white and yellow

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