2008 Annual Report
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.
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.
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
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.