Location: Vegetable Crops Research
2021 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
Contacts were made with genebanks in France and England to obtain germplasm for ongoing projects. To provide “molecular fingerprints” for plant held in these genebanks, deoxyribonucleic acid (DNA) sequences were obtained and are being analyzed for ten nuclear conserved orthologous DNA sequences (COS) for 20 new accessions of carrot relatives not examined before. DNA sequences from genotyping by sequencing (GBS) were obtained and analyzed for 90 new accessions of carrot (Daucus carota). Using total chloroplast deoxyribonucleic acid (DNA) (about 155,000 base pairs of data per accession) on 202 accessions a well-resolved phylogeny of the potato group was produced. The transfer and incorporation of the potato herbarium in Sturgeon Bay to the Wisconsin State Herbarium as completed and 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. Using data from evaluation of carrot DNA found in the mitochondrial compartment of the cell, research showed results similar to many other evaluations of mitochondrial DNA in other plants to not be very useful to help understand familial relationships. For ten genes in the nucleus of the cell, however, for wild carrot species not examined before, new information about the validity of family relationships of these species was discovered. 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.
Significant accomplishments over the course of this project include analyses of 202 plastid genomes to elucidate the phylogeny of potatoes and its relatives; comparison of representative and custom methods of generating core subsets of a carrot germplasm collection; development of a mitochondrial DNA sequence phylogeny for wild carrots; studies of relationships of wild and cultivated carrots using DNA sequences from ten single-copy nuclear DNA regions; successful germplasm collecting expeditions in North Africa, Europe, and North America; establishment of critical international collaborative projects with scientists in North and South America, Europe, Asia, and Africa; and high-impact publications in the areas of botany, crop domestication, and evolution.
Accomplishments
1. Usefulness of DNA information to understand plant familial relationships. Usefulness of DNA information to understand plant familial relationships. DNA (deoxyribonucleic acid) sequencing has provided interesting and useful information to broaden our understanding of how closely different groups of plants are to each other, in the same way as DNA testing kits helps humans to better understand our heritage. DNA sequencing data are useful to assist in understanding familial relationships among plants. DNA is carried in three cellular compartments or locations of plant cells and in this research, ARS researchers in Madison, Wisconsin, studied DNA sequence from the three different cellular locations was compared to determine if the DNA sequence information provided similar conclusions about relationships of carrots to other plants: DNA in the nucleus, DNA in the mitochondria, and DNA in the plastid. These three cellular locations have distinct genomes in plants. Interestingly, the results were not consistent when using sequence diversity to delineate family relationships from the three cellular origins. These results raise questions concerning the best data and analytical methods to reconstruct and understand the “true” familial relationships between plants based upon DNA data, and for this reason they are of interest to plant and animal taxonomists, botanists, evolutionary biologists, and genomic researchers.
