2013 Annual Report
1a.Objectives (from AD-416):
Objective 1: Through standard morphometric and novel genetic marker (e.g., COS sequences) approaches, determine the genetic profiles and systematic and genetic relationships for species and populations of carrot, potato, and related wild species.
Sub-objective 1.A. Generate classical and practical morphological descriptions of 39 key taxonomic traits for carrot, assess their value as phylogenetic and/or taxonomic characters, and incorporate these taxonomic data into GRIN.
Sub-objective 1.B. Develop and apply new DNA markers for phylogenetic and genetic analyses of carrot genetic resources, and incorporate resultant characterization data into GRIN and/or other databases such as GenBank, or on-line repositories of aligned DNA sequences of peer-reviewed scientific journals.
Sub-objective 1.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 and for potato.
Objective 2: Apply state-of-the-art systematic, genetic and geospatial analyses to identify taxonomic and/or ecogeographical gaps in the coverage of NPGS collections of carrot and potato genetic resources, and then strategically acquire new accessions to fill the preceding gaps.
Sub-objective 2.A. Identify and establish contacts in Latin America, Europe and Asia who may enable acquisition of wild relatives of potato (Solanum) and carrot (Daucus) species.
Sub-objective 2.B. 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 potential material that would fill gaps in NPGS collections, and begin acquiring and characterizing the missing species.
Sub-objective 2.C. When feasible, strategically acquire, via at least three field expeditions, genetic diversity of cultivars and wild relatives of either potato (Solanum) or carrot (Daucus) that are currently underrepresented in the U. S. National Plant Germplasm System (NPGS).
Objective 3: Critically assess the utility of core subsets for enhancing the efficiency of crop genetic resource management, especially for planning and conducting effective and comprehensive evaluations of the intrinsic horticultural merit of carrot, potato, and other crop genetic resources.
1b.Approach (from AD-416):
For objective 1, information about boundaries of carrot species will be obtained from taxonomic treatments. Characters used for carrot descriptions will be obtained from the literature and used to reassess taxonomic boundaries. For molecular analyses, next-generation “targeted” sequencing technology will begin with a collection of 100 accessions of Daucus and outgroups with 90 orthologous DNA markers to.
1)determine the generic limits of Daucus,.
2)determine the interspecific relationships within the genus, and.
3)determine the genetic diversity within and among the species. The data will be analyzed with concatenated analyses and analyses of individual loci with Bayesian analyses. As this project progresses we will be able to select a subset of the DNA and morphological markers that provide maximum discrimination of the species of carrot (and generic ingroups) that can then be used for more rapid assessment of phylogeny and diversity of a high-confidence, statistically well-supported phylogeny of many more carrot genetic resources present in the US National Plant Germplasm System. This will incorporate additional material collected in field explorations that are of problematic identity. Two monographic treatments are planned, one for wild potatoes of northern South America (Venezuela, Colombia, Ecuador, Peru). For Daucus, a shorter taxonomic treatment is planned to include keys and distribution maps.
For objective 2, if germplasm collecting regulations are relaxed for Peru, Solanum collections will be attempted in central and northern Peru. For Daucus, we will inquire of some of the larger world genebanks (VIR, IPK, PGRC, Vegetable centre in Taiwan) which may have Daucus germplasm not yet incorporated into the US collection. Herbarium specimens will be examined for species differences and locality data. 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 GIS software to analyze distributional data to indicate gaps in the collections. The carrot collection has very poor herbarium specimen representation and this plan is to collect 100 herbarium specimens/year with a focus on the wild species. Collecting expeditions will involve cooperators at the National Germplasm Resources Laboratory (NGRL) to identify legal requirements and permit possibilities in different countries and obtain in-country contacts. The PI will present a collecting plan and seek their concordance and support from the root and bulb CGC, and submit collecting proposals to the NGRL and conduct collecting expeditions based on available permits and funding.
For objective 3, the PI will accumulate a literature database of references on core collections and diversity assessments of germplasm evaluations, with a primary focus on those relying primarily on neutral molecular markers but also including non-neutral markers, breeders’ opinions or genetic traits, as criteria to establish core collections. He also will assemble literature on the history and development of the core collection concept to reassess the core collection concept.
This research relates to sub-objectives 1A, 1B, 2B, and 2C. The morphological data and herbarium specimens collected from these fulfill the need for practical taxonomic descriptors and voucher specimens needed to document the United States germplasm collection of Daucus. The germplasm collections made in Morocco fulfill the need to expand the collection regarding species or geographic representatives not presently there. The gathering and organization of the species description literature are needed to properly identify these collections and write taxonomic monographs. This project is new, began in March 2013. One hundred accessions of wild carrots from the United States Germplasm System have been planted in greenhouses and are successfully growing, ready to be harvested in September or October 2013 when they are mature. Morphological data and herbarium specimens are being collected from these accessions. Deoxyribonucleic acid (DNA) sequences are obtained for 100 conserved orthologous nuclear DNA sequences (COS) of 102 accessions of Daucus and related genera. Contacts have been made of germplasm cooperators in Europe, and a proposal to collect Daucus in Spain in 2014 has been submitted to the National Germplasm Resources Laboratory. Floristic literature has been obtained for Daucus and all Umbelliferae where Daucus grows from throughout the world, organized by geographic regions, and bound into books. Original descriptions of all 220 known Daucus taxonomic descriptions have been gathered, organized alphabetically, and bound into books. A germplasm collecting expedition was conducted in Morocco for three weeks in June 2013, resulting in 32 new collections to the United States Germplasm System.
The genus Daucus includes about 20 species. The most widespread and economically important species, Daucus carota (cultivated carrot), occurs on almost every continent. However, the diversity of Daucus carota, and the relationships of this species to the other 20 Daucus species is poorly understood. This hinders the naming and organization of the 1370 USDA collections of Daucus at the North Central Regional Plant Introduction Station (NCRPIS) in Ames, Iowa. To address this problem we planted out representative germplasm collections in an experimental field at the NCRPIS and measured plant parts used in the past to study diversity and species boundaries, with the long-term goal of developing a practical system to classify Daucus. We measured 36 morphological characters from multiple individuals within each of 155 accessions of D. carota, and the morphologically and related species within D. carota. Results were able to distinguish only two subspecies, but even these showed great overlap of individual characters. In combination with molecular data and field collections, these results help to develop an accurate classification, to understand relationships, and to predict the distribution of genetic variation in Daucus. These results help the NCRPIS curators to organize these collections and carrot breeders to better choose populations for their carrot breeding programs.