2013 Annual Report
1a.Objectives (from AD-416):
The long-term objective of this project is to develop improved national plant germplasm collections of potato, carrots, and their wild relatives (including tomato), and to improve understanding of the species boundaries and taxonomic relationships of these crops and their wild relatives. Over the next 5 years we will focus on the following three objectives: Objective 1: Strategically expand and improve collections of priority potato and carrot genetic resources and associated information. Sub-objective 1.A. When feasible, strategically acquire via at least three field expeditions for either potato (Solanum) or carrot (Daucus) genetic diversity (especially wild relatives of these crops) currently underrepresented in the U. S. National Plant Germplasm System (NPGS). Sub-objective 1.B. Identify and establish contacts in Latin America, Europe and Asia who may enable acquisition of Solanum and Daucus species, especially wild relatives of potato and carrot. Sub-objective 1.C. 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 material that would fill gaps in NPGS collections, and begin acquiring and characterizing them. Objective 2: Elucidate the systematic relationships and assess the amount and apportionment of genetic diversity in priority specialty crops of potato, tomato, carrots, and their wild relatives. Sub-objective 2.A. Generate classical and practical morphological descriptions of up to 50 key taxonomic traits for each crop and their wild relatives, analyze them for their value as phylogenetic and/or systematic characters, and incorporate this taxonomic evidence into GRIN. Sub-objective 2.B. Develop and apply new and appropriate DNA markers for phylogenetic and genetic analyses of potato, tomato, and/or carrot genetic resources, and incorporate resultant characterization data into GRIN and/or other databases, such as SolGenes (for potato and tomato), GenBank, or on-line repositories of aligned DNA sequences of peer-reviewed scientific journals. Sub-objective 2.C. In cooperation with USDA/ARS, university, and international collaborators, synthesize and integrate the preceding data and other lines of systematic evidence into monographic treatments and systematic revisions of the preceding taxa. Objective 3: Building on earlier tests of taxonomic prediction, critically assess the utility of taxonomic classifications and/or ecogeographical information as tools for planning and conducting effective, efficient, and comprehensive assessments of the intrinsic horticultural merit of potato genetic resources. Sub-objective 3.A. In collaboration with ARS Madison and Wisconsin collaborators, evaluate 150 accessions of 50 different species for host-plant resistance for Alternaria early blight, Colorado Beetle, potato virus Y, and potato late blight. Sub-objective 3.B. Drawing on the preceding new data and other lines of evidence, assess the ability of systematic/ecogeographic factors to help crop breeders effectively choose the optimal new genetic resources to incorporate into a breeding program.
1b.Approach (from AD-416):
For objective 1, the PI has obtained a list of current germplasm holdings of Daucus and is actively planning germplasm collecting expeditions. Through GRIN, he obtained accepted taxonomic names for carrot and associated taxonomic information. For Solanum, he will collect in Peru as a priority country if permits can be obtained. He will discuss collection needs with personnel from the National Germplasm Resources Laboratory, and seek collecting permits. He 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 submit collecting proposals to the U.S. Germplasm Laboratory and conduct collecting expeditions based on available permits and funding. Based on current collecting needs and potential collaborations carrot expeditions are planned for Pakistan, Tunisia, and the United States. He will obtain locality data from herbarium and genebank curators. He will survey taxonomic treatments of carrot and floras worldwide and visit key herbaria to assess collection needs.
For objective 2, the PI will gather information about species boundaries of carrot from taxonomic treatments. Morphological studies will be conducted at the Ames germplasm station using species-specific morphological characters, and the data will be analyzed with standard multivariate techniques. For interspecific relationships, DNA phylogenies will be generated for a subset (50) of wild and cultivated potato and all available (12) carrot species. In addition, outgroups identified as possibly congeneric with Daucus will be examined using COSII (nuclear DNA) markers, and be examined with standard cladistic techniques. While COSII genes will be explored as new markers, plastid rpoC1 intron and rpl16 intron sequences, and plastid matK coding sequences also will be examined. The PI will write a taxonomic monograph of the wild potato species from the Southern Cone of South America and will write taxonomic treatments of Solanum series Conicibaccata and the Solanum series Piurana group.
For objective 3, associations will be made of potato taxonomy to the potato diseases late blight, Colorado potato beetle, and potato virus Y Disease resistance data will then be associated to taxonomic variables by nonparametric methods based on rank scores using the Mann–Whitney test when comparisons between two groups are made and the Kruskal–Wallis test when comparisons among more than two groups are made. Post hoc pairwise comparisons following a significant Kruskal–Wallis test will be performed using the Mann–Whitney test with an appropriate Bonferroni correction. To determine the relative contributions of species, accessions, and individual plants of days to infection or insect pressure, a linear model will be fit with random effects of species and accession. These statistical tests for associations of disease and biogeography are standard. To test the question of whether geographic provenance of samples is a predictor of disease resistance, we will analyze biogeographic variables using spatial autocorrelation, followed by a regression analysis against possible predictors using Moran’s I.
The progress of this project relates to the objectives through four main goals:.
1)collect new germplasm or living plant parts of carrot and potato to be used by plant breeders,.
2)study the taxonomy of carrots and potatoes,.
3)study the taxonomy and genetic diversity of carrots and potatoes, and.
4)see how useful taxonomy is as a tool for choosing germplasm with desirable characteristics, based on what we know from other accessions where these characteristics are well studied. During the five-year course of this project, four wild carrot collecting expeditions were made, Tunisia in 2009, the Western United States in 2010, and Morocco in 2012 and 2013. These new collections greatly expanded the taxonomic diversity and geographic distributions of carrot genetic resources. Taxonomic treatments were published in natural groups of potato and carrot, aided by a combination of molecular and morphological studies. Studies were conducted of the association of disease and pest resistances of wild potato species, showing that taxonomy serves as a poor predictor of disease and pest resistances in potatoes. These results were published in 40 peer-reviewed scientific papers, making these results well organized and publically available to scientists and others interested in the taxonomy, germplasm resources, and breeding value of potatoes and carrots.
Wild and cultivated potatoes often have disease resistances useful for breeding. Potato wart disease is an extremely virulent potato disease, caused by a fungal pathogen that can ruin a potato crop and make it unsuitable for use. ARS researchers at Madison, WI studied the disease resistances in 52 collections of wild and cultivated potatoes and found some collections with good resistances to potato wart and alerted potato breeders of these useful collections. We also showed that these collections were not associated with the name given to these collections, alerting breeders that such names (taxonomy) have little value in predicting the incidence of this important disease. These results help improve the disease resistances of the potato crop.
Domestication refers to the process of adapting a wild plant into one of use to humans. ARS researchers in Madison, WI used deoxyribonucleic acid (DNA) to study the domestication of carrot, asking where and what populations gave rise to domesticated carrots. Our results suggested that carrots were domesticated in Central Asia. Furthermore, we found that wild carrots from North America were most closely related to European wild accessions. These results provide answers to long-debated questions of carrot evolution and domestication and inform germplasm curators and breeders on genetic substructure of carrot genetic resources. These results improve the efficiency of breeding research and curation of USDA genetic resources of carrot.
DNA investigations in carrot. Deoxyribonucleic acid (DNA) is the molecule that determines what an organism will look like and how it will act. This research studied DNA structure to better understand how this comes about. ARS researchers at Madison, WI used DNA sequencing to determine the sequence of DNA subunits, or “bases,” that give different DNA sections this power to govern these properties of an organism. Various studies this year determined.
“Chromosome painting” studies chromosome differences. Most wild potatoes have 24 chromosomes, but some potatoes have 2 sets of chromosomes called tetraploids, and some have three sets called hexaploids. ARS researchers at Madison, WI used chromosome painting to color or “paint” deoxyribonucleic acid (DNA) from different parents and to use this DNA to understand the species that were the parents of tetraploid and hexaploid wild potatoes. We used this method to study the parents of both tetraploid and hexaploid potatoes. In some cases the parents matched those suspected by other methods, and in some cases they were different. These new data alert potato breeders to the potential genes in the wild polyploid species that can be used in potato breeding.
1)the DNA sequences of the carrot mitochondria (the energy factory of cells),.
2)various genes that show how different species of wild potatoes are interrelated to each other, and.
3)how various genes are arranged along a chromosome, the structure that contains DNA that make up the genes. These studies help us understand basic biological facts of carrots and potatoes that are of use to breeders and other biologists interested in how genes are arranged and interact with each other. These results improve the efficiency of breeding research and curation of USDA genetic resources of carrot.
Development of software to help organize plant specimen data. Taxonomists are scientists who determine what a species is and how these various species are related to each other. Part of the job of a taxonomist is to compile and organize huge amounts of data needed to show where these species are distributed geographically, and to organize these data to make lists of specimens and distribution maps. This is usually initiated in spreadsheets and then converted for publication into locality lists and indices to associate collectors and collector numbers. This conversion process is mostly done by hand and is time-consuming, cumbersome, and error-prone. ARS researchers at Madison, WI constructed a computer program to automate and increase the accuracy of this process. This program increases speed, efficiency, and accuracy to convert raw spreadsheet tables to publication-ready content.
Carrot germplasm collections in Morocco. Germplasm refers to living plant parts, usually in the form of seeds, useful to store in “gene banks” and to be used by breeders to improve cultivated carrot. Part of this project was devoted to the collection of germplasm of carrots in their centers of diversity. This year a germplasm collecting expedition was conducted in Morocco by ARS researchers at Madison, WI to collect wild carrot germplasm. In total, 32 accessions of wild carrots or related species in the carrot family were collected in the field and in seed stores and imported into gene banks in the United States. These collections are useful to expand the availability of useful germplasm for carrot breeders.
Cai, D., Rodriquez, F., Teng, Y., Ane, C., Bonierbale, M., Mueller, L., Spooner, D.M. 2012. Single copy nuclear gene analysis of polyploidy in wild potatoes (Solanum section Petota). BMC Evolutionary Biology. Available: http://www.biomedcentral.com/1471-2148/12/70.
Simon, R., Spooner, D.M. 2013. A new R function, exsic, to assist taxonomists in creating indices. Applications in Plant Sciences. 1(6):1-4.
Spooner, D.M. 2013. Solanum tuberosum (Potato). Encyclopedia of Genetics. In: Maloy, S.,Hughes, K. editors. Encyclopedia of Genetics, 2nd Edition. Philadelphia, PA:Elsevier Press. p. 481-483.
Spooner, D.M., Knapp, S.K. 2013. Solanum stipuloideum Rusby, the correct name for Solanum circaeifolium Bitter. American Journal of Potato Research. 90:301-305.
Pendinen, G., Spooner, D.M., Jiang, J., Gavrilenko, T. 2012. Genomic in situ hybridization reveals both auto- and allopolyploid origins of different North and Central American hexaploid potato (Solanum sect. Petota) species. Genome. 55:407-415.
Lindqvist-Kreuze, H., Cho, K., Portal, L., Rodriguez, F., Simon, R., Mueller, L., Spooner, D.M., Bonierbale, M. 2013. Linking the potato genome to the Conserved Ortholog Set (COS) markers. BioMed Central (BMC) Genetics. Available: http://www.biomedcentral.com/1471-2156/14/51/abstract.
Khiutti, A., Afanasenko, O., Antonova, O., Shuvalov, 0., Novikova, L., Krylova, E., Chalaya, N., Mironenko, N., Spooner, D.M., Gavrilenko, T. 2012. Characterization of resistance to Synchytrium endobioticum in cultivated potato accessions from the Vavilov Institute of Plant Industry (VIR) collection. Plant Breeding. 131:744-750.