2009 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. Permission is obtained and travel plans in place to collect carrot (Daucus) on a field exploration to Tunisia, from August 7-21, 2009. For collections in 2010, this involved communicating with the Officer in charge of germplasm collections in Portugal, Estação Agronómica Nacional, Instituto Nacional dos Recursos Biológicos (EAN/INRB), Portugal, to initiate germplasm collections in Portuguese Macronesia.
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 and morphological assessments of diversity and taxonomy in potato. A taxonomic monograph was published of tomato and all of its wild relatives. Three separate papers used morphological data to assess species boundaries in the wild potato; these serve as reference data for taxonomic monographs. A Deoxyribonucleic acid (DNA) sequencing study was used to elucidate the diploid parents of polyploid species, and a companion study, using a technique called genomic in-situ DNA hybridization, was used to corroborate these results. Another study used a molecular marker called DNA microsatellites to refute a long-held idea of the origin of a germplasm collection of breeding materials called Neo-Tuberosum. Finally, a widely used technique called DNA barcoding was tested in wild potatoes. The technique failed in potatoes, and the results were extrapolated to other groups that are similar to potatoes to alert biologists to problems of DNA barcoding.
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 a germplasm panel of 150 accessions of 34 potato species that represent the diversity of wild potatoes as assessed by traditional and more recent molecular methods. These were evaluated for 10,738 disease and pest evaluations, derived from the literature and genebank records, of 32 pest and diseases in five classes of organisms (bacteria, fungi, insects, nematodes, and virus). The data show that ratings for only Colorado potato beetle and one pathogen (Potato M Carlavirus) are reliably predicted both by host taxonomy and climatic variables. Based on these results, a more effective strategy than taxonomic and biogeographic prediction is probably a careful screening of core collections.
Tests of taxonomic and biogeographic predictivity: resistance to multiple disease and insect pests in wild relatives of cultivated potato. A major justification for taxonomic and biogeographic research is its assumed ability to predict the presence of traits in a group for which the trait has been observed in only a representative subset of the group, but this assumption has rarely been tested. This study tested taxonomic and biogeographic associations with 10,738 disease and pest evaluations, derived from the literature and genebank records, of 32 pest and diseases in five classes of organisms (bacteria, fungi, insects, nematodes, and virus). The data show that ratings for only Colorado potato beetle and one pathogen (Potato M Carlavirus) are reliably predicted both by host taxonomy and climatic variables. While it is logical to initially take both taxonomy and geographic origin into account while screening genebank materials for pest and disease resistances, such associations will hold for only a small subset of resistance traits. Based on these results, a more effective strategy than taxonomic and biogeographic prediction is probably a careful screening of core collections.
The single Andigenum origin of Neo-Tuberosum materials is not supported by microsatellite and plastid marker analyses. Neo-Tuberosum refers to an artificially selected group of cultivated potatoes adapted to long-day tuberization and a syndrome of related morphological and physiological traits, developed by intercrossing and selection of short-day adapted tetraploid native (landrace) potatoes native from the Andes of western Venezuela to northern Argentina ("Andigenum" potatoes). This re-creation of the modern (short-day adapted) potato helped support the theory of an Andigenum Group origin of potato in temperate regions and the possibility to access the largely untapped diversity of the Andigenum germplasm in breeding programs. This study showed, with molecular data, that the Neo-Tuberosum germplasm did not arise from Andigenum potatoes, but rather from landraces occurring much farther south in lowland Chile ("Chilotanum" potatoes). These results question the long-standing Neo-Tuberosum derived theory and have implications in breeding programs and phylogenetic reconstructions of potato.
A morphometric study of species boundaries of the wild potato Solanum series Piurana (Solanaceae) and putatively related species from seven other series in Solanum sect. Petota. Recent estimates of the number of wild potatoes are about 190 species, distributed from the southwestern United States to central Argentina and adjacent Chile and Uruguay, but this estimate of 190 species is thought to be too large. Solanum series Piurana and related species are distributed from southern Colombia, south through Ecuador to central Peru, and like section Petota as a whole, contains many species that may not be valid. This was the first comprehensive morphological analysis of this group, through an examination of 188 living germplasm accessions of 33 species, planted in replicated plots in a field station in Andean Peru. Only four morphologically well-defined groups were supported, giving useful data, that in concert with ongoing molecular studies will be needed to give a more definitive understanding of the number of valid species of wild potatoes.
DNA barcoding will frequently fail in complicated groups: an example in wild potatoes. The goal of DNA barcoding is to find a simple, cheap, and rapid DNA assay that can be converted to a readily accessible technical skill that bypasses the need to rely on highly trained taxonomic specialists for identifications of the world's biota. This study tested DNA barcoding in wild potatoes with 72 species using the barcoding regions ITS, trnH-psbA, and matK. None of these regions were very accurate at distinguishing or serving as markers for species boundaries in wild potatoes. The results were extrapolated to other groups with similar biological traits as wild potatoes to shed caution on the widespread use of DNA barcoding to identify species.
Spooner, D.M., Clausen, A., Peralta, I. 2009. Taxonomic Treatment of Solanum Section Petota (Wild Potatoes) in Catálogo de Plantas Vasculares del Cono Sur (Argentina, Chile, Paraguay, Uruguay, y sur del Brasil). Systematic Botany Monographs. 107:3011-3053.
Pendinen, G., Gavrilenko, T., Jiang, J., Spooner, D.M. 2008. Allopolyploid speciation of the Mexican tetraploid potato species Solanum stoloniferum and S. hjertingii revealed by genomic in situ hybridization. Genome. 51(9):714-720(7).
Spooner, D.M., Salas, A., Ames, M. 2008. Revision of the Solanum medians complex (Solanum section Petota). Systematic Botany. 33(3):579-588.
Ghislain, M., Nunez, J., Del Rosario Herrera, M., Pignataro, J., Guzman, F., Spooner, D.M. 2009. Robust and Highly Informative Microsatellite-Based Genetic Identity Kit for Potato. Molecular Breeding. 23:377-388.
Jansky, S.H., Liping, J., Kaiyun, X., Xie, C., Spooner, D.M. 2009. Potato Production and Breeding in China. American Journal of Potato Research. 52(1):57-65.