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United States Department of Agriculture

Agricultural Research Service

Research Project: SYSTEMATICS, GENETIC DIVERSITY ASSESSMENT, AND ACQUISITION OF POTATOES, CARROTS, AND THEIR RELATED WILD RELATIVES

Location: Vegetable Crops Research Unit

2008 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.


3.Progress Report
The Peer Review process for the Project has been certified by OSQR as complete. Start date of project is 3/12/2008.

For objective 1, Strategically expand and improve collections of priority potato and carrot genetic resources and associated information, visited cooperators in carrot (Daucus) collections at the North Central Regional Plant Introduction Station in Ames, Iowa to plan the needs of new collections. Hired a summer student to assemble all 220 original descriptions (basionyms) of wild and cultivated carrot names, organized these alphabetically, and bound these into three books. Gathered the entire carrot family (Umbelliferae) floristic treatments worldwide wherever Daucus grows, organized these by geographic regions, and bound them into six books.

For objective 2, this project is a continuation of that in the prior OSQR plan but with different traits to be evaluated; hence, the title, objectives, and potential impact is the same. The title is: Research to critically assessing 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. Scientists worldwide need better tools for setting priorities for genomic research efforts, horticultural evaluations, and biotechnological research. This research 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 the insect pest Colorado potato beetle and the bacterial pathogen soft rot. A scientific paper was written on Colorado potato beetle. This research has tremendous impact for genebank managers who wish to advise potato breeders on resistances in the US National Potato Collection. It showed that taxonomic relationships and ecogeographic data cannot be reliably used to predict where additional sources of white mold resistance genes will be found but alternatively suggests that a "core collection" strategy" may be a more efficient way to screen for early blight resistance in potato. The research addresses National Program 301, Component 1: Plant and Microbial Genetic Resource Management; Problem statement 1B: Assess the Systematic Relationships and Genetic Diversity of Crop Genetic Resources.

Awarded the USDA Midwest Area Scientist of the Year Award for 2008.


4.Accomplishments
1. Extensive simple sequence repeat genotyping of potato landraces supports a major reevaluation of their gene pool structure and classification.

Contrasting taxonomic treatments of potato landraces have continued over the last century, with the recognition of anywhere from 1 to 21 distinct Linnean species, or of Cultivar Groups within the single species Solanum tuberosum. This study provides one of the largest molecular marker studies of any crop landraces to date, to include an extensive study of 742 landraces of all cultivated species (or Cultivar Groups) and 8 closely related wild species progenitors, with 50 nuclear simple sequence repeat (SSR) (also known as microsatellite) primer pairs and a plastid DNA deletion marker that distinguishes most lowland Chilean from upland Andean landraces. Neighbor-joining results highlight a tendency to separate three groups: (i) putative diploids, (ii) putative tetraploids, and (iii) the hybrid cultivated species S. ajanhuiri (diploid), S. juzepczukii (triploid), and S. curtilobum (pentaploid) and supports the classification of only four cultivated potato species: S. ajanhuiri, S. curtilobum, S. juzepczukii, and S. tuberosum. This research greatly clarifies the taxonomy of cultivated potatoes. For other classifications, consistent and stable identifications are impossible, and their classification as species is artificial and only maintains the confusion of users of the gene banks and literature.

This research addresses National Program 301, Component 1: Plant and Microbial Genetic Resource Management; Problem statement 1B: Assess the Systematic Relationships and Genetic Diversity of Crop Genetic Resources.

2. Genomic Origins of Potato Polyploids: GBSSI Gene Sequencing Data.

Chromosome pairing relationships within cultivated potato (Solanum tuberosum) and its wild tuber-bearing relatives (Solanum sect. Petota) have been interpreted by genome formulas, developed in the early 1900s, through techniques of classic meiotic analysis of interspecific hybrids, but there was no agreement on these genomic designations. This study reexamined potato genome hypotheses with the first phylogenetic analysis of all major genomes of sect. Petota using cloned DNA sequences of the single-copy nuclear gene GBSSI (waxy). The results provide the first molecular confirmation of allopolyploidy in wild potato and both support prior hypotheses and identify novel genome origins never before proposed. The data will be useful to help design crossing strategies to incorporate wild species germplasm into cultivated potato. This research addresses National Program 301, Component 1: Plant and Microbial Genetic Resource Management; Problem statement 1B: Assess the Systematic Relationships and Genetic Diversity of Crop Genetic Resources.

3. DNA from herbarium specimens settles a controversy about origins of the European potato.

Landrace potato cultivars are native to two areas in South America: the high Andes from eastern Venezuela to northern Argentina and the lowlands of south-central Chile, and two competing hypotheses suggested the origin of the "European" potato from the Andes or from lowland Chile, but the Andean origin has been widely accepted over the last 60 years. Through a plastid DNA deletion marker from historical herbarium specimens, this study reports that the Andean potato predominated in the 1700s, but the Chilean potato was introduced into Europe as early as 1811 and became predominant long before the late blight epidemics in the UK beginning in 1845, a time proposed by the proponents of the Andean introduction hypothesis to be a key event in the introduction of the Chilean potato into Europe. These results provide the first direct evidence of these events and change the history of introduction of the European potato. They shed new light on the value of past breeding efforts to recreate the European potato from Andean forms and highlight the value of herbarium specimens in investigating origins of crop plants. This research addresses National Program 301, Component 1: Plant and Microbial Genetic Resource Management; Problem statement 1B: Assess the Systematic Relationships and Genetic Diversity of Crop Genetic Resources.

4. Monograph of tomatoes and their wild relatives.

Tomato is a vegetable crop of world-wide importance and the wild species have proven use in tomato breeding efforts, but the last taxonomic monograph of tomatoes was 60 years old and the delimitation and relationships of wild tomatoes have differed widely depending upon whether morphological or biological species concepts are considered more important. This monograph summarizes recent morphological and molecular studies of tomato and its wild relatives technically classified in Solanum section Lycopersicon, section Juglandifolia, and section Lycopersicoides, using data from herbarium specimens and observations of germplasm accessions of all species grown in gardens. It recognizes 13 tomato species and four species in closely related groups, and provides descriptions and synonymies (including designations of lectotypes), illustrations, distribution maps, and an extensive list of localities are provided for all of tomato and outgroup species. Tomato breeders, geneticists, and biogeographers now have a much better set of facts about these key data that will aid planning their programs. This research addresses National Program 301, Component 1: Plant and Microbial Genetic Resource Management; Problem statement 1B: Assess the Systematic Relationships and Genetic Diversity of Crop Genetic Resources.


5.Significant Activities that Support Special Target Populations
None.


6.Technology Transfer

None

Review Publications
Jimenez, J., Brenes, A., Fajardo, D., Salas, A., Spooner, D.M. 2008. The Use and Limits of AFLP Data in the Taxonomy of Polyploid Wild Potato Species in Solanum Series Conicibaccata. Conservation Genetics. 9(2):381-387.

Ames, M., Salas, A., Spooner, D.M. 2008. 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. Systematic Botany. 33:183-192.

Last Modified: 10/1/2014
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