Skip to main content
ARS Home » Midwest Area » Madison, Wisconsin » Vegetable Crops Research » Research » Publications at this Location » Publication #306180
Title: Taxonomy and genetic differentiation among wild and cultivated germplasm of Solanum sect. Petota

Author
item HARDIGAN, M - Michigan State University
item Bamberg, John
item BUELL, R - Michigan State University
item DOUCHES, D - Michigan State University

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/28/2014
Publication Date: 2/3/2015
Publication URL: http://handle.nal.usda.gov/10113/61567
Citation: Hardigan, M.A., Bamberg, J., Buell, C.R., Douches, D.S. 2015. Taxonomy and genetic differentiation among wild and cultivated germplasm of Solanum sect. Petota. The Plant Genome. 8(1). doi: 10.3835/plantgenome2014.06.0025.

Interpretive Summary: Potato is a major crop in the US and worldwide, with over 5,000 populations of wild relative species that can be used in breeding maintained in the US Potato Genebank. One way to facilitate the use of this resource is to assess the genetic relationships within the genebank stocks with DNA markers. A new, powerful type of DNA marker has been developed, and used for the first time to examine relationships of stocks in the genebank. Previous taxonomic relationships were mostly confirmed, but with some intriguing exceptions. This new analysis revealed which species are likely to have the most richness in genes that could be used for breeding. Since these new markers occur in genes of known function, it was possible to note that markers that differentiate very primitive wild types from those more like cultivated forms are often associated with the genetic controls that promote bigger, more nutrient-rich tubers. This research provides specific practical insights into which forms of potato germplasm in the genebank will be most useful to breeders who are searching for valuable "new blood" to improve the potato crop.

Technical Abstract: Due to their adaptation to a diverse set of habitats and stresses, wild species of cultivated crops offer new sources of genetic diversity for germplasm improvement. Using an Infinium array representing a genome-wide set of 8303 single nucleotide polymorphisms (SNPs), we evaluated phylogenetic relationships and allele diversity within a diversity panel of germplasm from Solanum sect. Petota, the group containing tuber-bearing species and landraces of potato as well as cultivated potato (Solanum tuberosum L.). This diversity panel consists of 75 plant introductions (PIs) representing 25 species and provides a diverse representation of tuber-bearing Solanum germplasm. To determine the relatedness between current species classifications and SNP-based genetic distances, we generated a phylogeny based upon random individuals from each PI that, with few exceptions, revealed general agreement with taxonomic grouping of species in Solanum sect. Petota. Genotype comparisons between our Solanum sect. Petota diversity panel and a panel of 213 tetraploid cultivars and breeding lines revealed that the average genetic distance between landraces was higher than between cultivated clones, indicating a greater extent of diversity between populations of native Andean landraces than among modern cultivars and breeding lines. Analysis of allele frequencies at individual SNP loci between the Solanum sect. Petota diversity panel and tetraploid cultivars revealed loci with extreme divergence between cultivated potato and its tuber-bearing relatives. Interestingly, a number of these loci are associated with genes related to carbohydrate metabolism and tuber development, suggesting potential roles in domestication of potato. Our SNP data offers a new taxonomic view of potato germplasm, while further identifying candidate alleles that likely differentiate wild germplasm and cultivated potato and underlie key agronomic traits.