2012 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, approved for funding, and is planned for August/September 2012. In cooperation with USDA/ARS collaborators, herbarium specimens of 75 accessions of wild carrot were gathered. The original and larger focus of this study was a numerical taxonomic study of Daucus, but because of an unusually warm year in the preceding winter, insect vectors spreading aster yellows disease infected the plants from this field plot and this study is postponed until next year.
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. Species boundaries were clarified in the wild potato Conicibaccata group, the Piurana Group, and all four cultivated potato species, and clarified the ecological similarities of wild potato populations 4000 km apart in central Mexico and northern Bolivia. In addition, a method, single strand conformation polymorphism, was optimized to physically separate out different forms of a gene (allelic variants).
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.
An analysis of the origin of the European cultivated potato. Potato is one of the most important food crops worldwide, but its origin has been the subject of long speculation and debate. Our modern potato is quite different from indigenous primitive cultivars (landraces) of potato that occur in two broad geographic regions; the high Andes from western Venezuela south to northern Argentina (Andigenum landraces), and lowland south central Chile (Chilotanum landraces). Chilotanum landraces are adapted to long days and have a characteristic deoxyribonucleic acid (DNA) signature and differ in minor appearances from Andigenum landraces. The modern "Irish" potato clearly originated from Chilotanum landraces. Our research investigated the origin of Chilotanum landraces, with one hypothesis proposing an origin from Andigenum landraces, and another hypothesis suggesting an origin from a native Chilean wild potato species technically called S. maglia. Our data obtained from starch grain analysis do not support S. maglia as the parent of Chilean landraces but the molecular results do support this idea. This research alerts breeders to starch grain variation in Andean and Chilean potatoes, and highlights molecular similarities between Solanum maglia and cultivated potatoes.
The significance of field work in taxonomic studies. A taxonomic monograph is a comprehensive and synthetic publication used in all phases of plant biology ranging from ecology to biodiversity conservation to breeding. It presents identification keys, illustrations, descriptions, localities, habitat data, distribution maps, synonymies, cytological and molecular data, and hypotheses of relationships. This Spooner (2011) paper listed below in “Publications” outlines the many advantages of conducting field work to improve the completeness and accuracy of a taxonomic monograph as a result of access to data available only in the field or in associated herbaria where these plants grow. While the significance of field work is clear to most taxonomists, this paper classifies and clarifies these advantages to a non-taxonomic audience and justifies the need for field work to granting agencies.
Optimization of a technique to more efficiently and cheaply conduct molecular marker analyses. Wild and cultivated potatoes, technically grouped in the genus Solanum, section Petota, are very similar. Their formal classification into species is difficult, and there are many conflicting publications (taxonomies) that recognize different numbers of species. Molecular data from deoxyribonucleic acid (DNA) sequences provides a powerful and very useful method to help identify a species and to determine how species are related. ARS scientists have developed a relatively fast and inexpensive method that increases the accuracy of comparing DNA sequences, technically termed asymmetric single-strand polymorphism. It will be used by scientists to obtain more accurate DNA sequence data and has the advantages of being faster, cheaper, and more accurately than traditionally used methods.
A geographic information system based locator of a disjunct population of wild potato. The cultivated potato of world commerce has about 100 wild species relatives that are of great value to improve, through plant breeding, disease resistances and quality traits. Hence, there is great effort to collect and study the distributions of the wild potato species that are distributed from the southeastern United States to Uruguay and adjacent central Argentina and south-central Chile. One of these species, Solanum morelliforme, was previously known only from Mexico and Central America. Recently it was discovered in Bolivia, representing the first species known from both Mexico and Central America and South America. ARS scientists utilized a procedure known as maximum entropy analyses to locate compatible environmental conditions (such as rainfall and temperature) to predict where Solanum morelliforme could be found. Maximum entropy analysis predicted with great precision that Solanum morelliforme could be found where it occurs in Bolivia, and showed other places in South America (in Bolivia and Peru) where it may also exist. This study not only demonstrates the value of this technique, but alerts collectors to look for this species in these new places in South America. It also alerts botanists to the value of geographic information system tools to better predict where species may be found in unexpected places.
Simon, R., Fuentes, A.F., Spooner, D.M. 2011. Biogeographic implications of the striking discovery of a 4000 kilometer disjunct population of the wild potato Solanum morelliforme in South America. Systematic Botany. 36(4):1062-1067.
Spooner, D.M., Jansky, S.H., Del Rosario Herrera, M., Montenegro, J.D., Nunez, J., Clausen, A., Ghislain, M. 2012. The enigma of Solanum maglia in the origin of the Chilean cultivated potato, Solanum tuberosum Chilotanum group. Economic Botany. 66(1):12-21.
Egan, A., Schleiter, J., Spooner, D.M. 2012. Applications of next-generation sequencing techniques in plant biology. American Journal of Botany. 99(2):175-185.
Spooner, D.M. 2011. The significance of field work in monographic studies. Journal of the International Association of Plant Taxonomy. 153:25-32.
Rodriquez, F., Cai, D., Teng, Y., Spooner, D.M. 2011. Asymmetric single-strand polymorphism: an accurate and cost-effective method to amplify and sequence allelic variants. American Journal of Botany. 98:1061-1067.
Zheng, X., Hu, C., Spooner, D.M., Liu, J., Cao, J., Teng, Y. 2011. Molecular evolution of Adh and LEAFY and the phylogenetic utility of their introns in Pyrus (Rosaceae). BMC Evolutionary Biology. 11:255.
Fajardo, D., Spooner, D.M. 2011. Phylogenetic relationships of Solanum series Conicibaccata and related species in Solanum section Petota inferred from five conserved ortholog sequences. Systematic Botany. 36(1):163-170.