Genomic Heterogeneity of Potato

Cultivated potato is unique among major crops due to its autotetraploid nature, vegetative propagation, high genetic load and highly heterogeneous genome. Potato breeding over the past century has been a numbers game where tens of thousands of progeny obtained from crosses between tetraploid cultivars are screened annually, with most subsequently discarded due to the loss of the beneficial epistatic interactions and allele combinations required to maintain complex agronomic traits. Inbreeding commercial cultivars generally results in infertile, weak progenies that cannot be advanced through many generations without loss of fertility. Sequencing the autotetraploid genome is not yet possible due to the difficulties in assembly of four similar yet divergent haplotypes of each homologous chromosome. The current potato genome sequence (DM 1-3 516 R44) is therefore based on a doubled monoploid clone obtained by anther culture from a diploid cultigen of Solanum tuberosum Group Phureja. Although commercially useless, DM provides a draft genome annotated with 39,428 genes, allowing genomic comparisons between potato germplasm. Comparisons among other available monoploid and doubled monoploid germplasm revealed rampant copy number variation in potato where dispensable genes reflect recent evolutionary lineage, and a possible role in adaptation. Monoploids obtained from F₁ hybrids between DM and the heterozygous diploid clone, RH89_039_16, are being used to resolve the RH haplotypes. In addition, phenotypic characterizations and sequencing of dihaploid populations extracted by prickle pollination of cvs. Atlantic and Superior have been used to associate alleles, heterozygosity, and copy number variation with phenotypic traits in cultivated potato.