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ARS Home » Midwest Area » Madison, Wisconsin » Vegetable Crops Research » Research » Publications at this Location » Publication #343681

Research Project: Genetic Characterization, Taxonomy, and Acquisition of Genetic Resources for Carrot, Potato, and Their Related Wild Species

Location: Vegetable Crops Research

Title: Greatly reduced phylogenetic structure in the cultivated potato clade of potatoes, Solanum section Petota

Author
item Spooner, David
item Ruess, Holly
item Arbizu, Carlos - University Of Wisconsin
item Rodriguez, Flor - International Potato Center
item Solis-lemus, Claudia - University Of Wisconsin

Submitted to: American Journal of Botany
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/8/2017
Publication Date: 2/15/2018
Citation: Spooner, D.M., Ruess, H.M., Arbizu, C., Rodriguez, F., Solis-Lemus, C. 2018. Greatly reduced phylogenetic structure in the cultivated potato clade of potatoes, Solanum section Petota. American Journal of Botany. 105(1):60–70. https://doi.org/10.1002/ajb2.1008.
DOI: https://doi.org/10.1002/ajb2.1008

Interpretive Summary: Wild and cultivated potatoes are technically classified in the genus Solanum, section Petota, that includes about 110 species worldwide. These species are of tremendous use to plant breeders because they contain useful traits, such as disease resistance, that can be incorporated, through breeding efforts, into the cultivated potato crop. Taxonomy represents a way to understand the diversity and relationships of plants of use to breeders and other scientists, but for a variety of biological reasons the taxonomy of the species in section Petota are difficult and controversial among different taxonomists. We here provide the first in-depth taxonomic study of the most difficult portion of section Petota, “the cultivated potato clade” to explore possible causes of these problems. We examined 131 diploid populations, using a large data set of DNA sequences that were appropriate for phylogenetic study. We found that these DNA sequences were difficult to use to differentiate the species in the cultivated potato clade, unlike other portions of section Petota. Our results document the close relationships of many of the species in the cultivated potato clade, provide insight into the cause of their taxonomic problems, and support a recent taxonomic treatment that reduced the number of species in the cultivated potato clade. These data serve to inform potato breeders and other users of potato wild species that these species are very similar and that species designations should be taken with caution in this group when choosing germplasm (living collections) for their breeding studies.

Technical Abstract: The species boundaries of wild and cultivated potatoes, Solanum section Petota, are controversial with most of the taxonomic problems in a clade containing cultivated potatoes. We here provide the first in-depth phylogenetic study of the cultivated potato clade to explore possible causes of these problems. We examined 131 diploid accessions, using 12 nuclear orthologs, producing an aligned dataset of 14,072 DNA characters, 2,171 of which are parsimony informative. We analyzed the data for phylogeny, concordance analysis, and goodness-of-fit tests. There is good phylogenetic structure in clades traditionally referred to as clade 1+2 (North and Central American diploid potatoes exclusive of S. verrucosum), clade 3, and a newly discovered “basal” clade, but drastically reduced phylogenetic structure in clade 4, the cultivated potato clade. A newly discovered nuclear clade ‘neocardenasii’, in South America, sister to clade 1+2, possesses key morphological traits typical of diploids in Mexico and Central America. Goodness-of-fit tests test suggest potential hybridization between some species of the cultivated potato clade. However, we do not have enough signal with the data at hand to explicitly estimate such hybridization events with species networks methods. Our results document the close relationships of many of the species in the cultivated potato clade, provide insight into the cause of their taxonomic problems, and support the recent reduction of recognized species in this clade. The discovery of the ‘neocardenasii’ clade provides data to revise the biogeographic hypotheses of section Petota.