Genomic Interrogation of Cultivated Potato: New Insights to Improve Breeding Efficiencies.

Cultivated potato is a vegetatively propagated autotetraploid, a unique trait among major crop and model plant species. The assembly of characteristics that define cultivated potato relies on a complex balance of multiallelic loci with frequent epistatic interactions that are lost through sexual reproduction, with the result that most progeny are inferior to either parent as a consequence of inbreeding depression. Using structured populations and tetraploid cultivars, we have uncovered a high degree of heterozygosity and rampant copy number variation that result in a highly heterogenous genome and a complex transcriptome with additive and non-additive gene expression. Genes with a high degree of copy number variation tend to be evolutionarily recent with potential function in adaptation. Using a panel of wild species, landraces, and cultivars, we have identified introgressions from wild species, loci under selection, and confirmed the single origin of domestication for this important food crop. Collectively, these results provide new foundations to begin to breed potato for improved agronomic traits to meet 21^st century food security needs.