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Research Project: Maximizing the Impact of Potato Genebank Resources: Development and Evaluation of a Wild Species Genotype Diversity Panel

Location: Vegetable Crops Research

2020 Annual Report


1a. Objectives (from AD-416):
Objective 1: Identify and maintain a set of wild potato plants, determine the DNA sequence of each, evaluate the distribution of genetic diversity among these wild potatoes, and use this information to guide breeders in developing improved potato germplasm. Objective 2: Characterize the set of wild potato plants from Objective 1 for resistance to major potato diseases and pests, including late blight, early blight, Verticillium wilt, and Colorado potato beetle, and map these resistance traits to identify the genetic regions responsible for these traits. Objective 3: Create hybrids between diploid cultivated potato and the set of wild potato plants from Objective 1, characterize these hybrids for plant and tuber traits, and provide the data to the breeding community to use in developing improved potato germplasm.


1b. Approach (from AD-416):
Objective 1: We have identified 10 wild diploid Solanum species with demonstrated utility in potato breeding. Within each species, we will choose 10 accessions for this project based on published resistance data, personal experience, and genebank passport data. Multiple individuals from each wild species will have their S-locus RNase alleles sequenced. Fertility of individuals will be assessed by assaying for pollen viability and production of berries with viable seeds. Disease and pest resistance screens will be carried out on multiple plants in each accession for which a specific resistance trait has been reported previously. Based on these data, twenty individuals from each species will be selected for SNP genotyping, detailed phenotyping and clonal maintenance. Objective 2: Individual clones identified in Objective 1 will be characterized for resistance to major potato diseases and pests, including late blight, early blight, Verticillium wilt, and Colorado potato beetle. For each disease or pest, we will perform disease inoculations or beetle challenges that generate quantitative resistance scores using previously published methods. R-genes within each individual will be sequenced using RenSeq and the position of R-genes will be mapped to the potato genome. Objective 3: We will create hybrids by crossing flowers of diploid cultivated potato with pollen from the 200 wild potato plants identified in Objective 1. Resulting hybrids will be characterized for plant growth and tuber traits including size, shape, color and yield. These phenotypic data will be shared with the potato breeding community to use in developing improved potato germplasm. Phenotypic data and genotypic data will be deposited into GRIN and the clones used for this research will be donated to the NRSP-6 potato genebank for use by others.


3. Progress Report:
384 accessions of wild potato species were screened for resistance to potato late blight (Phytophthora infestans) using the late blight clonal lineage US23, which is the most prevalent genotype in the United States. We found that 107 accessions had some resistance to late blight. All individuals from 39 accessions were resistant. Individuals in the remaining accessions were segregated for resistance, susceptibility, and partial resistance. Selected resistant clones were added to the wild species diversity collection. Five accessions in total from Solanum berthaultii (3), S. chacoense (1), and S. microdontum (1), were crossed with diploid potato clones US-W4 and MSEE736-01. 260 accessions were screened for resistance to potato early blight (Alternaria solani) using detached leaf assays. Of these, 73 accessions showed some level of resistance and were chosen for rescreening. Data from the second round of screening were used to select two individuals from each of seven accessions for inclusion in the wild species diversity collection. This work directly relates to Objective 2 of the project. Hybrids between wild species clones and the cultivated diploids W4 and MSEE736-01 were created. Subsequent analysis of progeny for potato spindle tuber viroid indicated that all MSEE736-01 hybrids were susceptible and infected with this disease. The plants were discarded and disease-free hybrids will be generated in FY21. In consultation with staff at the NRSP-6 potato genebank, we devised a naming system for clones in the wild species diversity collection. Clones will be linked to their accession and given a clone identifier that includes standardized three-letter initials for the species name and a clone number. Entries into the Germplasm Resources Information Network (GRIN) will include a descriptor indicating that the clone is a member of the wild species diversity collection.


4. Accomplishments
1. Modification of a late blight resistance gene to avoid effector-mediated suppression. Microorganisms that cause plant diseases are a substantial burden to agriculture. Negative impacts on revenue result from reduced yield and costs associated with disease detection and control. Plant breeders are interested in the identification and incorporation of simply inherited genes that confer robust resistance to diseases. These resistance (R) genes typically encode proteins that recognize the presence of very specific pathogen molecules, termed effectors, and activate plant defense responses. Specific effectors, however, can suppress R proteins and allow the pathogen to elude recognition and cause disease. ARS researchers at Madison, Wisconsin, previously identified a late blight (Phytophthora infestans) effector that suppresses the activity of the RB resistance protein, encoded by the RB gene. By mining the sequences of natural genetic variants of RB from wild potato relatives, we identified specific amino acids in the RB resistance protein that allow it to avoid disease suppression and maintain its ability to activate defense responses. Our results demonstrate that a better understanding of the molecular interactions between plants and pathogens will foster progressive strategies to combat diseases. The specific sequence variants of the RB resistance protein identified in this research are excellent candidates for introducing strong late blight resistance into potato. Late blight is the most serious pathogen of potatoes worldwide. Late blight resistant varieties would substantially decrease costs of production by minimizing expenses associated with fungicide sprays and preventing yield losses caused by reduced tuber production and post-harvest spoilage.

2. Transitioning to diploid hybrid potato varieties. Discussions with our industry stakeholders have revealed three major constraints to their success: extreme and unpredictable weather events, the need to remain profitable with rising production costs, and expectations for environmental sustainability. These challenges can be addressed through the timely development of improved cultivars. However, the current breeding system does not take full advantage of emerging genomics and breeding tools. The common domesticated potatoes are tetraploid with four sets of chromosomes. ARS researchers in Madison, Wisconsin, have received a grant to transition potato into a diploid (two sets of chromosomes) inbred-hybrid crop, which will be more amenable to genetic manipulations. Consequently, breeders will be better able to keep pace with industry needs for new cultivars. The goals of the SCRI grant are to harness genes to allow diploids to be inbred, move commercially important genes from existing cultivars into diploid germplasm, develop inbred lines in major market classes, and explore the potential for cultivars to be grown from true seed. We are working closely with Potatoes USA to interface with growers and other industry reps. We have given presentations at the Potato Expo and at industry-sponsored meetings.


5. Record of Any Impact of Maximized Teleworking Requirement:
The use of impedance flow cytometry to measure pollen viability in partial inbreds has been postponed. Phenotyping of inbred lines and dihaploids has been reduced.


Review Publications
Frederick, C.M., Bethke, P.C. 2019. Identification of Quantitative Trait Loci for stem-end chip defect and potato chip color traits in a ‘Lenape’-derived full-sib population. American Journal of Potato Research. 96:564-577(2019). https://doi.org/10.1007/s12230-019-09746-3.
Gutierrez Sanchez, P.A., Babujee, L., Jaramillo Mesa, H., Arcibal, E., Gannon, M., Halterman, D.A., Jahn, M., Jiang, J., Rakotondrafara, A.M. 2020. Overexpression of a modified eIF4E regulates potato virus Y resistance at the transcriptional level in potato. Biomed Central (BMC) Genomics. 21(1):18. https://doi.org/10.1186/s12864-019-6423-5.
Chowdhury, R.N., Lasky, D., Karki, H.S., Zhang, Z., Goyer, A., Halterman, D.A., Rakotondrafara, A.M. 2019. HCPro suppression of callose deposition contributes to strain-specific resistance against potato virus Y. Phytopathology. 110:164-173. https://doi.org/10.1094/PHYTO-07-19-0229-FI.
Busse, J.S., Bethke, P.C. 2019. Impact of 2,4-D and potato (Solanum tuberosum L.) tuber age on anthocyanin content of skin and phellem anatomy of Red Norland. American Journal of Potato Research. 97:102-110(2020). https://doi.org/10.1007/s12230-019-09760-5.
Lee, U., Silva, R.R., Kim, C., Kim, H., Heo, S., Park, I.S., Kim, W., Jansky, S.H., Chung, Y. 2019. Image analysis for measuring disease symptom to bacterial soft rot in potato. American Journal of Potato Research. 96:303-313. https://doi.org/10.1007/s12230-019-09717-8.
Bethke, P.C., Halterman, D.A., Jansky, S.H. 2019. Potato germplasm enhancement in the genomics era. Agronomy. 9(10):575. https://doi.org/10.3390/agronomy9100575.