High-density linkage map constructed from a skim sequenced diploid potato population reveals transmission distortion and QTLs for tuber and pollen production

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 relies 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 a R implementation of the OutcrossSeq pipeline for diploids and applied it 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 (TRD) including epistatic ones, indicative of large effect deleterious mutations. Finally, we identified QTLs for seedling tuber yield in pots and pollen production. This study showcases the range of genetic analyses, from marker inference, TRD identification and linkage map construction to QTL mapping, resulting in new insights that contribute to breeding diploid potato.