2010 Annual Report
1a.Objectives (from AD-416)
The long-term objective of this project is to develop improved national plant germplasm collections of potato, carrots, and their wild relatives (including tomato), and to improve understanding of the species boundaries and taxonomic relationships of these crops and their wild relatives. Over the next 5 years we will focus on the following three objectives: Objective 1: Strategically expand and improve collections of priority potato and carrot genetic resources and associated information. Sub-objective 1.A. When feasible, strategically acquire via at least three field expeditions for either potato (Solanum) or carrot (Daucus) genetic diversity (especially wild relatives of these crops) currently underrepresented in the U. S. National Plant Germplasm System (NPGS). Sub-objective 1.B. Identify and establish contacts in Latin America, Europe and Asia who may enable acquisition of Solanum and Daucus species, especially wild relatives of potato and carrot. Sub-objective 1.C. In cooperation with USDA/ARS collaborators at the USDA/ARS North Central Regional Plant Introduction Station in Ames, IA, survey existing U.S. domestic collections of Daucus, identify material that would fill gaps in NPGS collections, and begin acquiring and characterizing them. Objective 2: Elucidate the systematic relationships and assess the amount and apportionment of genetic diversity in priority specialty crops of potato, tomato, carrots, and their wild relatives. Sub-objective 2.A. Generate classical and practical morphological descriptions of up to 50 key taxonomic traits for each crop and their wild relatives, analyze them for their value as phylogenetic and/or systematic characters, and incorporate this taxonomic evidence into GRIN. Sub-objective 2.B. Develop and apply new and appropriate DNA markers for phylogenetic and genetic analyses of potato, tomato, and/or carrot genetic resources, and incorporate resultant characterization data into GRIN and/or other databases, such as SolGenes (for potato and tomato), GenBank, or on-line repositories of aligned DNA sequences of peer-reviewed scientific journals. Sub-objective 2.C. In cooperation with USDA/ARS, university, and international collaborators, synthesize and integrate the preceding data and other lines of systematic evidence into monographic treatments and systematic revisions of the preceding taxa. Objective 3: Building on earlier tests of taxonomic prediction, critically assess the utility of taxonomic classifications and/or ecogeographical information as tools for planning and conducting effective, efficient, and comprehensive assessments of the intrinsic horticultural merit of potato genetic resources. Sub-objective 3.A. In collaboration with ARS Madison and Wisconsin collaborators, evaluate 150 accessions of 50 different species for host-plant resistance for Alternaria early blight, Colorado Beetle, potato virus Y, and potato late blight. Sub-objective 3.B. Drawing on the preceding new data and other lines of evidence, assess the ability of systematic/ecogeographic factors to help crop breeders effectively choose the optimal new genetic resources to incorporate into a breeding program.
1b.Approach (from AD-416)
For objective 1, the PI has obtained a list of current germplasm holdings of Daucus and is actively planning germplasm collecting expeditions. Through GRIN, he obtained accepted taxonomic names for carrot and associated taxonomic information. For Solanum, he will collect in Peru as a priority country if permits can be obtained. He will discuss collection needs with personnel from the National Germplasm Resources Laboratory, and seek collecting permits. He will attend the annual meetings of the Root and Bulb Crop Germplasm Committee to present a collecting plan and seek their concordance and support, and submit collecting proposals to the U.S. Germplasm Laboratory and conduct collecting expeditions based on available permits and funding. Based on current collecting needs and potential collaborations carrot expeditions are planned for Pakistan, Tunisia, and the United States. He will obtain locality data from herbarium and genebank curators. He will survey taxonomic treatments of carrot and floras worldwide and visit key herbaria to assess collection needs.
For objective 2, the PI will gather information about species boundaries of carrot from taxonomic treatments. Morphological studies will be conducted at the Ames germplasm station using species-specific morphological characters, and the data will be analyzed with standard multivariate techniques. For interspecific relationships, DNA phylogenies will be generated for a subset (50) of wild and cultivated potato and all available (12) carrot species. In addition, outgroups identified as possibly congeneric with Daucus will be examined using COSII (nuclear DNA) markers, and be examined with standard cladistic techniques. While COSII genes will be explored as new markers, plastid rpoC1 intron and rpl16 intron sequences, and plastid matK coding sequences also will be examined. The PI will write a taxonomic monograph of the wild potato species from the Southern Cone of South America and will write taxonomic treatments of Solanum series Conicibaccata and the Solanum series Piurana group.
For objective 3, associations will be made of potato taxonomy to the potato diseases late blight, Colorado potato beetle, and potato virus Y Disease resistance data will then be associated to taxonomic variables by nonparametric methods based on rank scores using the Mann–Whitney test when comparisons between two groups are made and the Kruskal–Wallis test when comparisons among more than two groups are made. Post hoc pairwise comparisons following a significant Kruskal–Wallis test will be performed using the Mann–Whitney test with an appropriate Bonferroni correction. To determine the relative contributions of species, accessions, and individual plants of days to infection or insect pressure, a linear model will be fit with random effects of species and accession. These statistical tests for associations of disease and biogeography are standard. To test the question of whether geographic provenance of samples is a predictor of disease resistance, we will analyze biogeographic variables using spatial autocorrelation, followed by a regression analysis against possible predictors using Moran’s I.
Objective 1 addressed the goal: Strategically expand and improve collections of priority potato and carrot genetic resources and associated information. A proposal to collect wild carrots in the western and southern USA in September was submitted. In cooperation with USDA/ARS collaborators at the USDA/ARS North Central Regional Plant Introduction Station in Ames, IA, surveyed existing U. S. domestic collections of carrot, identified material that would fill gaps in National Plant Germplasm System (NPGS) collections, and began acquiring and characterizing them. In cooperation with personnel at the North Central Regional Plant Introduction Station worked on a morphological analysis of 100 wild carrot accessions, with a particular focus on the species most closely related to cultivated carrot.
Objective 2 addressed the goal: Elucidate the taxonomic relationships and assessment of the amount and apportionment of genetic diversity in priority specialty crops of potato and carrots, and their wild relatives. This accomplishment was fulfilled by molecular morphological assessments of diversity and taxonomy in potato. Five published peer-reviewed scientific papers used molecular data to answer the following questions related to potato taxonomy and germplasm organization: 1. One paper examined, and showed to be false, an idea that simple standardized molecular deoxyribonucleic acid (DNA) markers could be used to easily identify wild potato species; 2. Another paper used molecular markers to disprove a long-standing idea that a group of breeding materials was selected from upland Andean, vs. lowland Chilean potatoes; 3. Two other papers used molecular markers of high discriminatory value to show the evolutionary relationships of wild potato species; 4. A final paper used morphological data to describe a new species closely related to wild potatoes. These combined results have improved our knowledge of practical and high-resolution molecular tools to discriminate species in wild potatoes, have helped us to show how these species are interrelated, and have aided potato breeders and genebank managers in the organization and use of wild potatoes for breeding.
Objective 3 addressed the goal: Critically assess the utility of taxonomic classifications and/or ecogeographical information as tools for planning and conducting effective, efficient, and comprehensive assessments of the intrinsic horticultural merit of potato genetic resources. Research this year screened, in an experimental greenhouse setting, a germplasm panel of 128 accessions of 38 potato species for the potato spoiling disease bacterial soft rot. The data show that taxonomy and location of collection of the potato germplasm have poor power to predict where this disease will be located in a germplasm collection. Based on these results, a more effective strategy than taxonomic and biogeographic prediction is probably a careful screening of core collections.
Do potatoes and tomatoes have a single evolutionary history, and what proportion of the genome supports this history? Our understanding of relationships among plants has been greatly improved in recent years by the use of molecular (DNA) data, yet oftentimes, different molecular tools give different answers about these relationships. In an effort to remedy this situation, ARS researchers at Madison, Wisconsin examined the utility of eleven sets of a new class of deoxyribonucleic acid (DNA) markers technically called “conserved orthologous set (COSII)” markers to examine the relationships of 29 wild potato and tomato species. The results showed that when all eleven molecular markers were used together, a single well-resolved “family tree of relationships” was shown, but that some individual markers gave other well-supported trees. This study confirms and quantifies the utility of COSII markers in understanding plant relationships and alerts researchers that relationships constructed from limited numbers of markers may give misleading results.
Phylogeny of the wild potato group Solanum series Piurana based on five conserved single-copy nuclear deoxyribonucleic acid (DNA) regions. Taxonomic complexity in wild potatoes has led to widely conflicting treatments. The wild potato group technically known as Solanum series Piurana is emblematic of such taxonomic problems. These species are distributed from southern Colombia south to central Peru. Some of them are useful for potato breeding. ARS researchers at Madison, Wisconsin examined 199 collections of 66 species in this group and related species with a new class of molecular markers, technically called conserved orthologous set (COSII) markers, to infer the evolutionary relationships of members of series Piurana. The results helped us redefine the natural boundaries of series Piurana and gave us insights into readily visible traits we could observe (morphological traits) to help others better understand ways to recognize wild species in this group.
Wild and cultivated potato (Solanum section Petota) escaped and persistent outside of its natural range. Wild potato (Solanum section Petota) contains about 100 species that are native to the Americas from the southwestern United States to southern Chile and most wild potatoes are restricted to this area. One wild potato, technically known as Solanum chacoense, has been found outside of its natural range in seven sites in southern Australia, eastern China, England, New Zealand, the eastern United States, central Peru, and east-central Argentina, but it is unknown why this potato, and not others has “escaped” outside of its natural range. ARS researchers at Madison, Wisconsin, with collaborators from Peru and England, used computer-assisted geographic tools (“geographic information systems” or GIS) to model similar climatic niches where Solanum chacoense may be found in the future. A literature review summarized traits possessed by S. chacoense that may have allowed it to become an invasive species. These results inform the public of a potential new escaped wild potato that may be of importance to potato growers and landscape managers.
Taxonomy of cultivated potatoes (Solanum section Petota: Solanaceae). Solanum tuberosum, the cultivated potato of world commerce, is a primary food crop worldwide and indigenous landrace potatoes in South America are used by potato breeders to improve the potato in the face of variety of disease, environmental, and agronomic constraints. However, past taxonomic treatments of wild and cultivated potato have differed tremendously among authors regarding both the number of species recognized and hypotheses of their interrelationships, hindering their efficient organization in genebanks and use by potato breeders. ARS researchers at Madison, Wisconsin, in conjunction with collaborators from Russia and England compiled, for the first time, 602 names of cultivated potatoes, and associated these names with the modern taxonomy of cultivated potatoes. This paper also summarized the history of cultivated potato taxonomy, provided identification tools (“keys”) to identify cultivated potatoes, and descriptions to the four cultivated species. This comprehensive work will provide a reference to genebank managers and breeders alike of the natural groups of cultivated potatoes for their more efficient use.
Mione, T., Spooner, D.M. 2010. A New Species and Key to the Jaltomata (Solanaceae) of Mexico. Novon. 20(2):186-189.
Ghislain, M., Nunez, J., Del Rosario Herrera, M., Bonierbale, M., Spooner, D.M. 2009. The Single Andigenum Origin of Neo-Tuberosum Potato Materials is not Supported by Microsatellite and Plastid Marker Analyses. Theoretical and Applied Genetics. 118(5):963-969.
Spooner, D.M. 2009. DNA Barcoding Will Frequently Fail in Complicated Groups: An Example in Wild Potatoes. American Journal of Botany. 96:1177-1189.
Rodriguez, F., Tanksley, S., Wu, F., Spooner, D.M. 2009. Do potatoes and tomatoes have a single evolutionary history, and what proportion of the genome supports this history. BMC Evolutionary Biology. 9:191.
Rodriguez, F., Spooner, D.M. 2009. Nitrate Reductase Phylogeny of Potato (Solanum sect. Petota) Genomes with Emphasis on the Origins of the Polyploid Species. Systematic Botany. 34:207-219.