High-Density Linkage Map Constructed from a Skim Sequenced Diploid Potato Population Reveals Transmission Distortion and QTLs for Tuber Yield and Pollen Shed

Corentin R. Clot, Xulan Wang, Joey Koopman, Alejandro Thérèse Navarro, Johan Bucher, Richard G.F. Visser, Richard Finkers, Herman J. van Eck*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

3 Citations (Scopus)

Abstract

The reinvention of potato, from a tetraploid clonal crop into a diploid seed-based hybrid crop, requires insight in the mutational load, recombination landscape, and the genetic basis of fertility. Genomics-based breeding and QTL discovery rely on efficient genotyping strategies such as skim sequencing, to gather genotypic information. The application of skim sequencing to full-sib population of non-inbred parents remains challenging. Here, we report on an R implementation of the OutcrossSeq pipeline for diploids. We applied this pipeline to a large diploid skim sequenced potato population. We used the resulting bin-markers for the construction of high-density parent specific linkage maps, highlighting variation in parental recombination rate and structural variations. We subsequently explored transmission ratio distortion and non-independent assortment of alleles, indicative of large-effect deleterious mutations. Finally, we identified QTLs for seedling tuber yield in pots and pollen shed. This study showcases the range of genetic analyses, from marker inference, identification of transmission ratio distortion, and linkage map construction to QTL mapping, resulting in new insights that contribute to breeding diploid potato.

Original languageEnglish
Pages (from-to)139-163
JournalPotato Research
Volume67
Issue number1
Early online date19 May 2023
DOIs
Publication statusPublished - 2024

Keywords

  • Diploid potato
  • Linkage map
  • Pollen shed
  • Transmission ratio distortion

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