2011 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 Morocco was written and submitted, and approved for funding. In cooperation with USDA/ARS collaborators in Ames, IA, morphological data for 80 accessions of cultivated and wild carrot were gathered, 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. Published papers examined clarifications of species boundaries in the wild potato Conicibaccata group, the Piurana Group, and all four cultivated potato species. Papers currently in press examine the ecological similarities of wild potato populations 4000 km apart in central Mexico and northern Bolivia, and developing a method to physically separate out different forms of a gene (allelic variants) efficiently in a technique called single strand conformational polymorphism.
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 116 accessions of 37 potato species for the potato virus Y (PVY). PVY resistance was identified in 17 of the 38 species tested. Of the 870 plants tested, 115 (13%) were resistant to PVY. These included four species for which PVY resistance has been previously reported, and 11 species for which PVY resistance has not been previously published. Five of these species are easily crossed to diploid cultivated potato, and represent promising sources of PVY resistance for cultivar development. Resistance was identified in nine of the 14 series represented in the study and in all four clades plus the outgroup. Consequently, broad taxonomic groupings do not seem to predict the distribution of PVY resistance genes.
Ecogeography of ploidy variation in cultivated potatoes. The taxonomy of cultivated potatoes has been highly controversial, with current estimates of species numbers ranging from 3 to 17. Chromosome numbers were one of the major factors defining many of these species, and ARS researchers in Madison, Wisconsin, and collaborators tested the environmental associations of different chromosome numbers to the many names of cultivated species recognized by others. They found that except for cultivated potatoes in the extreme northern and southern range extensions, chromosome numbers have no association with ecological differences. These distributional and ecological data, in combination with prior results from morphology, molecular data, and crossing data, provide yet additional information to support a major reclassification of cultivated potatoes into only four species, providing a rational and stable taxonomy of this major crop plant. This new taxonomy, published in the scientific journal Proceedings of the National Academy of Sciences (PNAS) in 2007, will greatly aid potato breeders, gene bank managers, evolutionary biologists, and literally all users and investigators of cultivated potato.
Revised phylogeny of the Solanum series Piurana group based on multiple nuclear deoxyribonucleic acid (DNA) sequences. Taxonomic complexity in wild potatoes has led to widely conflicting ideas of how many species exist and how these species are interrelated. One group of these species, termed the Solanum ser. Piurana group, comprises 40 species, confined to northern South America, that were distinctive as a group, but with uncertain definitions of species within the group. In the present study, ARS researchers in Madison, Wisconsin, and collaborators used a set of five conserved single copy nuclear DNA markers to clarify the species that belonged to the Piurana group and show that many recognized species within the group were not worthy of taxonomic recognition and should be placed in synonymy. These molecular data are being used, in combination with recently published morphological data of the Solanum Piurana group, to form a taxonomic revision of the potatoes of South America.
Hybrid origins of cultivated potatoes. The taxonomy of wild and cultivated potatoes is difficult, partly because the species can hybridize among each other and blur their species boundaries. Using deoxyribonucleic acid (DNA) sequence data of the waxy gene, ARS researchers in Madison, Wisconsin, and collaborators confirmed the hybrid origins of the four species of cultivated potatoes accepted in the latest taxonomic treatment (S. ajanhuiri, S. curtilobum, S. juzepczukii and S. tuberosum, the latter divided into the Andigenum and Chilotanum Cultivar Groups). These results greatly clarify not only the reasons for the taxonomic difficulty in cultivated potatoes, but will inform potato breeders of the complex genetic makeup of these species that will aid them when planning their use in breeding programs.
Wild and cultivated potatoes escape and persist outside of its natural range. Wild potato contains about 100 species that are native to the Americas from the southwestern United States to southern South America. However, ARS researchers in Madison, Wisconsin, and collaborators found reports of naturalized populations of the wild potato Solanum chacoense in seven sites in southern Australia, eastern China, England, New Zealand, the eastern United States, central Peru, and east-central Argentina. It is important to understand how they got there and how they persist, because Solanum chacoense can hybridize with cultivated potatoes, potentially incorporating wild genes into cultivated potato populations. A literature review revealed that although S. chacoense possesses traits typical of an invasive species, all populations presently appear to be contained near their site of introduction. These results inform conservationists of a potential relatively recently introduced invasive species in their region and inform potato growers of the possible occurrence of Solanum chacoense in their region that could potentially hybridize with potatoes in their fields. This is important for regulators interested in possible transgene escape of transgenic potato crops.
A molecular and morphological assessment of the Russian National cultivated potato collection. Germplasm collections in Russia represent the first germplasm collection made for potatoes, now numbering 8,680 accessions. It has tremendous historical and practical importance and a rich history, having been used to document a polyploid series in the cultivated species, to formulate initial taxonomic hypotheses in potato, for studies of interspecific hybridization, and serving as the germplasm base for Russian breeding efforts. Despite its importance and size, there has never been a study of its molecular diversity, and there are many gaps in its site of collection data. ARS researchers in Madison, Wisconsin, and collaborators used morphological and molecular data and found that the taxonomic relationships were similar to a similar study done in Peru. These corroborative results bolster the need to reclassify the collection of cultivated potatoes by modern taxonomic criteria, and help potato breeders better understand the genetic diversity of these collections for their potato improvement programs.
A test of taxonomic and biogeographic predictivity using resistance to soft rot in wild relatives of cultivated potato. The concept that traits should be associated with related organisms and that nearby populations of the same species are likely to be more similar to each other than to populations spread far apart has long been accepted. Consequently, taxonomic relationships and biogeographical data are commonly believed to have the power to predict the distribution of disease resistance genes among plant species. ARS researchers in Madison, Wisconsin, and collaborators found no clear association between resistance to soft rot and taxonomic relationships, but found some associations between resistance of soft rot and environmental data such as annual precipitation and annual mean temperature. They also noted that high levels of resistance are mostly found in species that have the ability to have different morphological forms in different environments. This study informed genebank managers and potato breeders of the need to choose germplasm based on screening data of individual accessions, and to rely less on potato taxonomy to assess the best place to find soft rot resistance.
A revised taxonomy of cultivated potatoes. Solanum tuberosum is the main cultivated potato of world commerce, and has only three other cultivated species relatives, yet there are over 625 scientific names published for these four species. Because wild and cultivated potatoes form the germplasm base for international breeding efforts to improve potato in the face of a variety of disease, environmental and agronomic constraints, it was imperative to clarify the many names that greatly confused the literature. ARS researchers in Madison, Wisconsin, and collaborators compiled, for the first time, all of these cultivated potato names into a single publication, placed them in synonymy, and constructed a taxonomic identification key and descriptions of these species. The data provide a standard reference to cultivated potato taxonomy and nomenclature, species limits, distributions, and a history of the concepts that have led to these many changes. This information will be used by all users of cultivated potato germplasm resources.
Ovchinnikova, A., Krilova, E., Gavrilenko, T., Smekalova, T., Dorofeev, V., Zhuk, M., Knapp, S., Spooner, D.M. 2011. Taxonomy of cultivated potatoes (solanum section petota: solanaceae). Botanical Journal of the Linnean Society. 165:107-155.
Cai, D., Zheng, X., Teng, Y., Spooner, D.M. 2010. Genetic Relationships Among Pyrus pyrifolia Cultivars from Southeastern China and Japan. Acta Horticulturae. 859:89-92.
Spooner, D.M., Jansky, S.H., Gavrilenko, T., Ovchinnikova, A., Krilova, E., Simon, R. 2010. Ecogeography of Ploidy Variation in Cultivated Potato (Solanum Sect. Petota). American Journal of Botany. 97(12):2049-2060.