Location: Vegetable Crops Research2018 Annual Report
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.
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.
Contacts have been made for genebanks in France and England to obtain germplasm for ongoing projects. All deoxyribonucleic acid (DNA) sequences are obtained and are being analyzed for 10 nuclear conserved orthologous sequence (COS) for 20 new accessions of Daucus not examined before. DNA sequences from genotyping by sequencing (GBS) are obtained and analyzed for 90 new accessions of Daucus carota. Multiple publications are being planned. One of the two book chapters (Botanical descriptions…) is completed and the second (Carrot organelle genomes …) is being written. The transfer of the USDA/ARS collection of potato herbarium specimens to the University of Wisconsin-Madison Herbarium has already been made, and next fiscal year it is planned to curate the herbarium.