Location: Vegetable Crops Research
2019 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
All potato publications from the prior project ending last year have been completed. The most significant potato research was using total chloroplast deoxyribonucleic acid (DNA) (about 155,000 base pairs of data per accession) on 202 accessions to produce a well-resolved phylogeny of the potato group. For carrot research, we worked with our collaborators at the University of Wisconsin to publish a paper testing the assessment of various traits of breeding interest, analyzed with different statistical methods, to assess the effectiveness of core collections in germplasm collections. Also for Objective 2 in carrot research, two review chapters in a book on the carrot genome were published. One paper summarized the current state of knowledge of carrot taxonomy, bringing up-to-date the many recent studies using molecular taxonomy that have made many changes in our knowledge of carrot relationships. The other chapter summarized the current state of knowledge on the genetics of carrot organelles (including both chloroplasts and mitochondria), and how this knowledge has been used to better understand the taxonomy and transfer of genes among the chloroplasts, mitochondria, and nucleus.
Accomplishments
1. Analyses of 202 plastid genomes elucidate the phylogeny of Solanum section Petota. Wild and cultivated potatoes are a large (over 100 species) and taxonomically complex group and it has been difficult to get sufficient molecular data to address their relationships. Recent high-throughput deoxyribonucleic acid (DNA) sequencing methods (next-generation sequencing) has the ability to generate huge amounts of high-quality data to produce well-resolved trees of relationships (phylogenetic trees). Our paper used next-generation sequencing methods to analyze full chloroplast DNA sequence data (about 155,000 base pairs of DNA per accession) of 202 wild and cultivated potatoes, technically grouped in Solanum section Petota. We compared the chloroplast phylogenetic tree to prior trees based on chloroplast and nuclear DNA that were produced with far fewer accessions and base pairs of DNA. The present chloroplast results discovered the same four major groups of species as prior chloroplast and nuclear results, but have considerable differences in species relationships within these four groups. The considerably larger plastid data highlight plastid/nuclear incongruence. This incongruence supports hypotheses of hybridization/introgression that help explain the taxonomic difficulty in section Petota. This is important because hybridization and introgression have been hypothesized to be critical evolutionary factors to explain the taxonomic difficulty at the species level in wild and cultivated potatoes.
2. Comparison of representative and custom methods of generating core subsets of a carrot (Daucus carota L.) germplasm collection. Many crop breeding programs are interested in using genetic resources but have difficulty identifying useful accessions from germplasm collections. To efficiently use the diversity present in large germplasm collections, breeders often identify a subset of accessions that represent the larger collection, called a core collection. Methods to identify these subsets do not consistently capture functional diversity and breeders would benefit from methods which help create “custom” core collections using existing data from variety trials or breeding programs. Making use of the availability of next-generation sequencing data, and existing phenotypic data for a collection of 433 domesticated carrot (Daucus carota) accessions, we tested whether it is possible to develop custom core collections for specific breeding purposes. Significantly, we find that for this collection, the next-generation sequencing data are no better than random sampling, likely because the collection itself is not strongly subdivided. Increasing the size of the core did improve prediction accuracy, suggesting that it is possible to improve the usefulness of core collections by identifying custom subsets that are large enough to represent the functional genetic diversity present in the collection. Because core collections are almost universally accepted to be useful for genebank curators our results raise significant caution in relying on this concept. This is important because it forces a reevaluation of best practices in determining the best ways to reduce the size of large germplasm collections to manageable sizes.
Review Publications
Spooner, D.M., Ruess, H.M., Arbizu, C., Rodriguez, F., Solis-Lemus, C. 2018. Greatly reduced phylogenetic structure in the cultivated potato clade of potatoes, Solanum section Petota. American Journal of Botany. 105(1):60–70. https://doi.org/10.1002/ajb2.1008.
Jansky, S.H., Spooner, D.M. 2018. The evolution of potato breeding. Plant Breeding Reviews. 41:169-214.
Huang, B., Ruess, H.M., Liang, Q., Colleoni, C., Spooner, D.M. 2019. Full genome analyses of 203 plastid genomes elucidates the phylogeny of Solanum section Petota. Scientific Reports. 9:4454. https://doi.org/10.1038/s41598-019-40790-5.
Corak, K.E., Ellison, S.L., Simon, P.W., Spooner, D.M., Dawson, J.C. 2019. Comparison of representative and custom methods of generating core subsets of a carrot germplasm collection. Crop Science. 59(3):1107-1121. https://doi.org/10.2135/cropsci2018.09.0602.
Spooner, D.M. 2019. Daucus: Taxonomy, phylogeny, distribution. In: P. Simon, M. Iorizzo, D. Grzebelus, and R. Baransky, editors. The Carrot Genome. Springer Nature: Cham, Switzerland. p. 9-26.
Spooner, D.M., Simon, P.W., Senalik, D.A., Iorizzo, M. 2019. Carrot organelle genomes: organization, diversity and inheritance. In: P. Simon, M. Iorizzo, D. Grzebelus, and R. Baransky, editors. The Carrot Genome. Springer Nature: Cham, Switzerland. p. 9-26.
