Genome diversity of tuber-bearing <i>Solanum</i> uncovers complex evolutionary history and targets of domestication in the cultivated potato.

Abstract

Cultivated potatoes (<i>Solanum tuberosum</i> L.), domesticated from wild <i>Solanum</i> species native to the Andes of southern Peru, possess a diverse gene pool representing more than 100 tuber-bearing relatives (<i>Solanum</i> section <i>Petota</i>). A diversity panel of wild species, landraces, and cultivars was sequenced to assess genetic variation within tuber-bearing <i>Solanum</i> and the impact of domestication on genome diversity and identify key loci selected for cultivation in North and South America. Sequence diversity of diploid and tetraploid <i>S</i><i>tuberosum</i> exceeded any crop resequencing study to date, in part due to expanded wild introgressions following polyploidy that captured alleles outside of their geographic origin. We identified 2,622 genes as under selection, with only 14-16% shared by North American and Andean cultivars, showing that a limited gene set drove early improvement of cultivated potato, while adaptation of upland (<i>S</i><i>tuberosum</i> group Andigena) and lowland (<i>S. tuberosum</i> groups Chilotanum and Tuberosum) populations targeted distinct loci. Signatures of selection were uncovered in genes controlling carbohydrate metabolism, glycoalkaloid biosynthesis, the shikimate pathway, the cell cycle, and circadian rhythm. Reduced sexual fertility that accompanied the shift to asexual reproduction in cultivars was reflected by signatures of selection in genes regulating pollen development/gametogenesis. Exploration of haplotype diversity at potato's maturity locus (<i>StCDF1</i>) revealed introgression of truncated alleles from wild species, particularly <i>S</i><i>microdontum</i> in long-day-adapted cultivars. This study uncovers a historic role of wild <i>Solanum</i> species in the diversification of long-day-adapted tetraploid potatoes, showing that extant natural populations represent an essential source of untapped adaptive potential.