Location: Vegetable Crops Research
2020 Annual Report
Objectives
Objective 1: Efficiently and effectively expand the U.S. National Plant Germplasm System’s collection of priority carrot genetic resources and associated information.
Sub-objective 1.A. Identify and establish contacts in Latin America, Europe, North Africa, and Asia who may enable acquisition of wild relatives of carrot (Daucus) species.
Sub-objective 1.B. When feasible, strategically acquire, via at least three field expeditions, genetic diversity of cultivars and wild relatives of carrot (Daucus) that are currently underrepresented in the U. S. National Plant Germplasm System (NPGS).
Objective 2: Develop more effective characterization and phylogenetic analysis methods and apply them to carrot genetic resources to elucidate systematic relationships and to assess the amount, apportionment, and nature of the genetic diversity they contain. Record and disseminate characterization data via GRIN-Global and other data sources.
Sub-objective 2.A. Develop and apply new and appropriate DNA markers for phylogenetic and genetic analyses of carrot genetic resources, and incorporate resultant characterization data into GRIN-Global and/or other databases such as GenBank, or into on-line repositories of aligned DNA sequences operated by peer-reviewed scientific journals.
Sub-objective 2.B. Examine the criteria for defining core subsets of plant genetic resource collections and the predicative value of these subsets in plant taxonomy from the perspective of the relative importance of different food plants, such as carrots and potatoes.
Sub-objective 2.C. In cooperation with USDA/ARS, university, and international collaborators, synthesize and integrate the preceding data and other lines of taxonomic evidence into monographic treatments and taxonomic revisions for carrot.
Objective 3: Complete the curation and re-organization of the USDA/ARS collection of potato herbarium specimens, and transfer it to the University of Wisconsin-Madison Herbarium.
Approach
For obj. 1, contacts will be made with floristic workers or germplasm curators in foreign countries to initiate collecting for Daucus. Collecting goals and analyses of distributional patterns will be made with geographic information systems software. As in past collections, we will identify target species for Daucus with these taxonomic and locality data, construct a locality database and planning route map, consult with in-country collaborators, and initiate collecting. Solicitation of collecting funds and coordination of collections will be made with local cooperators and with personnel at The National Germplasm Resources Laboratory, who will identify legal requirements and permit possibilities in different countries and obtain in-country permits. PI 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 will submit collecting proposals to the U.S. Germplasm Laboratory and conduct collecting expeditions based on available permits and funding.
For obj. 2, morphological characters used for carrot descriptions will be obtained from the literature and used to reassess taxonomic boundaries. For molecular analyses of interspecific relationships, next-generation “targeted” sequencing technology will assess taxonomically representative and taxonomically ambiguous accessions of Daucus and outgroups with 10 orthologous DNA markers and separately with whole DNA sequencing of plastid genomes to determine 1) the generic limits of Daucus, 2) the interspecific relationships within the genus, and 3) the genetic diversity within and among the species. The data will be analyzed with standard phylogenetic procedures. These analyses will incorporate additional material collected in field explorations that are of problematic identity. For species-level taxonomic questions of subspecies of Daucus carota we will use GBS data. For studies to establish core collections, we will associate data from important traits often targeted by plant breeders: productivity, plant vigor, disease resistance and quality with GBS data, and compare molecular-based and standard core collection strategies.
For obj. 3, the PI will work with collaborators to curate the approximately 15,000 herbarium specimens in the former PTIS potato herbarium in Sturgeon Bay, Wisconsin and approximately 1000 specimens of carrots grown from germplasm samples of the U.S. carrot collection in Ames, Iowa. The majority of these specimens have been obtained from grow-outs needed to serve as taxonomic vouchers for routine genebank identifications, but many of these lack complete label data (collector, date of collection, locality, habitat), and many of them have outdated identifications. Every specimen will be checked for proper identification, and full label data will be added from information in GRIN-Global or collector’s field notes. In addition, hundreds of photos of type specimens will be printed on archival paper and mounted on herbarium sheets and labeled as to the source of the type. Specimens of duplicate herbarium vouchers will be mailed to herbaria after execution of the appropriate agreements.
Progress Report
The priorities this year were devoted to publishing results of prior years and working with the Wisconsin State Herbarium (WIS) for a final herbarium upgrade. The most significant and practical project was the transfer and incorporation of the Potato Introduction Station herbarium in Sturgeon Bay to the WIS as this makes these specimens up-to-date in taxonomy with new herbarium labels and making sure all are properly mounted on archival quality herbarium sheets and properly organized. In addition, two molecular phylogenetic studies were published, one using DNA sequences from the mitochondrial genome, and one using DNA sequences for a well-characterized set of ten nuclear genes previously shown to give maximum results. The mitochondrial research showed results similar to many other mitochondrial phylogenies to not be the best marker for phylogenetic reconstruction. The ten nuclear genes, however, examined wild carrot species not examined before, and provided new information about the validity of species and relationships of these species. These results are significant in providing a modern and updated set of relationships to wild carrot species that serve as predictors and guideposts for carrot breeders and other researchers using the wild carrot species in their research.
Accomplishments
1. PTIS Potato Herbarium Transferred to WIS, the Wisconsin State Herbarium. Herbarium specimens document the morphology of a plant in order to serve as a permanent reference point for species identifications and locality and other collection data. Herbarium specimens can last hundreds of years and serve as critical elements to gene banks and taxonomic research. The Potato Introduction Station (PTIS) in Sturgeon Bay, Wisconsin, has made and maintained herbarium specimens as part of its operations, documenting the morphology of the approximately 5000 germplasm collections in the gene bank, with most of the specimens grown from seeds in the field plots or greenhouses, but also were original specimens made during germplasm collecting expeditions. The PTIS herbarium was transferred from the potato gene bank in Sturgeon Bay, Wisconsin, to the Wisconsin State Herbarium (WIS) at the University of Wisconsin-Madison, where it is now fully integrated, curated, and funded by WIS; PTIS is discontinued and is no longer maintained as a separate herbarium. After transfer, the herbarium specimens were upgraded with new specimen labels representing the modern taxonomy of wild and cultivated potatoes made over the last 35 years. This herbarium transfer is significant in that it makes the specimens more widely available in a modern and world-class herbarium, yet are still available locally to the USDA and state potato research community in Wisconsin.
2. Mitochondrial DNA sequence phylogeny of Daucus. The mitochondrion is one of three DNA-containing genomes in plants, in addition to plastids and nuclei. The mitochondrion codes for some of the genes necessary for proteins that produces the energy carrier molecule in plants. ARS researchers in Madison, Wisconsin, explored the utility of mitochondrial DNA sequences in wild carrots (members of the genus Daucus) for their ability to determine at relationships among wild carrots and compared the results with prior relationship results using the same 36 accessions of Daucus with plastid DNA sequences and with other results from nuclear DNA. They obtained data from 47 of 71 total mitochondrial genes. Mitochondrial DNA turned out to be a poor method to look at relationships, judging from its comparison to other result from the plastid and nucleus. The results are significant in that they provide additional data from other studies in other plant groups showing that mitochondrial DNA has too many complicating biological factors precluding its general use as a good molecule to investigate relationships.
3. Extended studies of relationships of wild and cultivated carrots (genus Daucus) using DNA sequences from ten single-copy nuclear DNA regions. Wild and cultivated carrots technically belong to the genus Daucus. There are about 25-40 species of wild carrots, depending on the classification, and they all have potential value as breeding stock to improve the cultivated carrot crop. ARS researchers in Madison, Wisconsin, obtained DNA sequences of ten regions of the nuclear genome to provide information about the relationships of wild and cultivated carrots, using a large collection of different species gathered from gene banks in England, France, and recent expeditions to Spain, where many wild carrots are native. The data results provide new information about wild carrot relationships, including new knowledge of the hybrid nature of one of the species, and knowledge of how one of the species is really two species. This new knowledge of the relationships of members of the genus Daucus provide carrot breeders with guideposts about Daucus species to use in their carrot breeding programs.
Review Publications
Mezghani, N., Khoury, C.K., Carver Jr, D.P., Achicanoy, H.A., Simon, P.W., Spooner, D.M. 2019. Distributions and conservation status of carrot (Daucus L.) wild relatives in Tunisia: A case study in the Western Mediterranean basin. Crop Science. 59:1-12. https://doi.org/10.2135/cropsci2019.05.0333.
Spooner, D.M., Simon, P.W., Bamberg, J.B., Cameron, K.M. 2019. PTIS potato herbarium transferred to WIS, the Wisconsin State Herbarium. American Journal of Potato Research. https://doi.org/10.1007/s12230-019-09751-6.
Spooner, D.M., Jansky, S.H., Rodriguez, F., Reinhard, S., Ames, M., Fajardo, D., Castillo, R. 2019. Taxonomy of wild potatoes in northern South America (Solanum section Petota). Systematic Botany Monographs. 1-209. https://www.jstor.org/stable/25027915.
Spooner, D.M., Ruess, H., Simon, P.W., Senalik, D.A. 2020. Mitochondrial DNA sequence phylogeny of daucus. Systematic Botany. Volume 46 / Pages 403-408(6). https://doi.org/10.1600/036364420X15862837791311.
Fernando Martínez, F., Crespo, M.B., Geoffriau, E., Allender, C., Ruess, H.M., Simon, P.W., Spooner, D.M. 2019. Extended studies of interspecific relationships of Daucus using DNA sequences from ten nuclear orthologs. Botanical Journal of the Linnean Society. 164-187. https://doi.org/10.1093/botlinnean/boz042.
