Towards Strategic Genotype Selection for Allelic Mining: Genome Diversity Assessment in the Wild Potato, Solanum bulbocastanum Bradeen, J.M., R.L. Syverson, and M.J. Sanchez

Plant & Animal Genome XII (San Diego, CA Jan 2004)

We are actively optimizing methods for rapid and efficient extraction of intact gene copies for the late blight resistance locus, RB, from a wide collection of potato species. Our goals include the generation of a deep sequence library reflecting allelic diversity at this locus for evolutionary analyses, and testing and eventual deployment of allelic variants for cultivated potato protection. To aid in selecting genotypes that maximize the likelihood of mining diverse alleles, we have initiated a study examining potential predictive factors for RB allele diversity. RB was isolated using a map-based cloning approach from the wild diploid potato, Solanum bulbocastanum. The USDA Potato Genebank maintains approximately 50 S. bulbocastanum accessions. We have established a 38 genotype reference collection for S. bulbocastanum encompassing three morphologically-defined subspecies and reflecting the entire geographic distribution of the species (predominantly Mexico and Guatemala). These genotypes, and up to 5 randomly selected seed-derived genotypes from each of 43 S. bulbocastanum accessions, were subjected to AFLP analysis. AFLP markers, of unknown genome location, failed to cluster genotypes into groups representing described subspecies. Furthermore, geographic origin for a given genotype did not correlate well with total genome diversity. Finally, within population marker diversity was measured to exceed between population diversity. Solanum bulbocastanum is a facultative outcrossing species, which likely contributes to the observed diversity patterns. Our results will be interpreted with regard to using total genome diversity, geographic origin, or subspecies affiliation as possible predictors of RB allelic diversity in our 38 genotype reference collection.