Location: Temperate Tree Fruit and Vegetable Research
2025 Annual Report
Objectives
A priority need for agricultural research in the coming years is to help ensure food security despite challenges such as an increasing population, climate uncertainty, rising input costs, and loss of arable land. Another need for potato is research that helps the industry adapt to evolving consumer preferences because consumers are increasingly prioritizing sustainability and nutritional value when making their food purchasing decisions. Our research will address these needs using both pre-breeding and breeding approaches to identify or develop potato germplasm with better disease and pest resistance, nutritional value, sustainability, and product quality. Our project has three interrelated objectives, all of which are ultimately intended to facilitate the development of superior new potato cultivars.
OBJECTIVE 1: Utilize high-throughput phenotyping, molecular breeding strategies, and genomic prediction to characterize, breed, and release potato germplasm with improved traits, especially those related to disease and pest resistance, sustainability, and increased amounts of phytonutrients.
Sub-objective 1A: Develop and deploy high-throughput phenotyping workflows to quantify foliar and tuber characteristics of individual clones within potato breeding populations.
Sub-objective 1B: Generate and characterize multi-parent breeding populations that segregate for dominantly inherited, large-effect, pathogen resistance alleles.
Sub-objective 1C: Screen cultivars, landraces, and wild species for resistance to soil-borne pathogens and develop self-compatible, diploid introgression populations.
Sub-objective 1D: Develop new baby potato lines and characterize the genetics of traits important for a baby potato cultivar, especially the tuber high-set trait.
OBJECTIVE 2: Characterize genetic, molecular, physiological, and biochemical factors that control potato key traits, including disease and other stress resistance, yield, and processing and nutritional qualities.
Sub-objective 2A: Delineate mechanisms that mediate small molecules involved in tuber nutritional value and appearance.
Sub-objective 2B: Examine the effect of heat-stress on tuber internal defects, phenylpropanoids, and glycoalkaloid metabolism.
OBJECTIVE 3: Develop improved molecular diagnostic tools for pathogen detection to facilitate epidemiological studies of important pathogens of potato.
Sub-objective 3.A: Develop new tools for rapid identification of Lso and BLTVA phytoplasma in planta and explore the role of new genetic variants of Lso in potato in the Northwest.
Sub-objective 3B: Generate and maintain a PMTV-infected Spongospora subterranea population in the greenhouse for use in germplasm screens.
Approach
OBJECTIVE 1: We will use modern breeding methods, and develop and deploy high-throughput phenotyping methods. Drones will collect weekly multispectral images of field trials. Tubers will be phenotyped using digital imaging and a self-built conveyor belt system with sensors to automate phenotyping of tuber number, size, shape, color, eyes, and physiological defects. Parental lines containing disease resistance alleles will be used to develop mapping populations. Populations will be genotyped using DArTseq. Diploids and germplasm from wild potato showing disease resistance will be used to produce self-compatible diploid clones. A factorial breeding population will be used to assess trait correlation and mapping. Joint linkage or association mapping will be used to map QTL and calculate GEBVs for key traits. A major breeding effort will be russet potatoes, but baby and specialty potatoes will be bred with traits including appearance, taste, high tuber number and nutritional value.
OBJECTIVE 2: The factors that influence tuber nutritional value and quality, including phenylpropanoids and glycoalkaloids will be analyzed. Time-course studies will use tubers exposed to continuous light. Flavonols will be extracted and measured with LCMS. Gene expression and transcriptomic studies will be conducted if samples show large flavonol increases. Tuber flavonol synthesis will be reprogramed by silencing anthocyanin biosynthesis to test whether this increases flavonols. Terpenoid metabolism will be analyzed in tubers exposed to light. Chlorophyll and carotenoids will be measured by spectroscopy. Glycoalkaloids will be quantitated by LCMS. Relevant genes will be measured by qRT-PCR and network analysis of gene-metabolite interactions visualized. We will develop a lab assay for defects like blackheart and heat necrosis by exposing tubers to varying temperatures. The effect of high temperatures on glycoalkaloids will be assessed in potatoes grown in WA and TX in a randomized complete block design.
OBJECTIVE 3: Molecular tools for BLTVA detection will be optimized and validated. Non-potato psyllids found on sticky traps in the Columbia Basin will be analyzed for Lso and transmission to potato tested. At two, four, and six weeks post-inoculation, symptoms will be recorded, and plant tissue will be collected and tested for the presence of Lso to assess whether successful inoculation occurred. To develop and maintain a potato mop top virus (PMTV) infected Spongospora subterranea f. sp. Subeterranea (Sss) population, various potential host plants will be inoculated in the greenhouse with Sss-infested soil. To ensure persistence of the PMTV infected Sss, we will try different methods to ensure inoculum is maintained. One method will cycle potato plants and tomato/N. benthamiana to ensure that the soil always has a potato plant present to maintain PMTV-infected Sss when the tomato needs to be replaced. A second method does not rely on the continual cycling of potato but will grind up the tomato. A third method utilizes PMTV-infected potato obtained each year by planting tubers alongside the tomato or plants to enable transmission to the host plant.
Progress Report
This report documents the FY 2025 progress of project 2092-21220-003-000D, “Potato Germplasm Development for Improved Sustainability, Disease Resistance, Nutrition, and Quality”, which began in March 2023.
In support of Sub-objective 1A, ARS scientists in Wapato, Washington, utilized a novel, low-cost machine vision workflow to quantify tuber number, size, shape, color characteristics, starch content, and defect frequency of more than 2,000 field-grown breeding lines. In addition, more than 30 flights were performed at weekly intervals to capture multispectral drone data from breeding experiment trials in Hermiston, Oregon, and Othello, Washington. Plant height, canopy volume, and multispectral reflectance values were extracted from georectified orthomosaics from all flights. Machine vision based post-harvest assays to evaluate susceptibility to blackheart, tuber greening, and oxidative browning were also developed.
For Sub-objective 1B, ARS scientists in Wapato, Washington, successfully completed a potato crossing block in the spring of 2025 that generated thousands of recombinant seeds that will be evaluated in future field trials and via marker assisted selection. Progress was made in introgressing extreme resistance to viral diseases (Potato Virus Y (PVY), Tobacco rattle virus (TRV)) and nematode infection (Columbia root knot nematode (CRKN), Potato cyst nematodes (PCN)) into susceptible genetic backgrounds in the processing and fresh market classes. Researchers are continuing to generate multi-parent populations segregating for Potato virus Y, Tobacco rattle virus, and Columbia root-knot nematode resistance in both russet and specialty germplasm.
In support of Sub-objective 1C, ARS scientists in Wapato, Washington, completed a screen of more than 175 accessions (ten individual plants/accession) derived from more than 35 different potato wild relative species. Roots from each plant were assessed by molecular pathogen detection, with an S. subterranea infection rate of approximately 89 percent and Potato mop-top virus (PMTV) infection rate of approximately 57 percent, showing successful assay design. Varying levels of PMTV infection was found in these accessions, whereas 15 accessions derived from S. acuale, S. berthaultii, S. boliviense, S. brevicaule, S. chachoense, and S. vernei exhibited no viral infection after 12 weeks of exposure to infected soil. Three of these accessions exhibited no infection in a follow-up validation assay. Several diploid accessions which are reported to carry resistance to verticillium wilt, PVY, Colorado potato beetle, and cyst nematodes were hybridized with self-compatibility donors. This research identified numerous diploid potato species with no resistance to the S. subterranea vector or PMTV, enabling breeders to look elsewhere for resistance.
For Sub-objective 1D, ARS scientists in Wapato, Washington, planted and evaluated more than 80 specialty potato clones representative of the most popular varieties within red, yellow, and purple-skinned market classes based upon seed acreage between 2018 – 2023. Clones were evaluated for their productivity, type, and potential as breeding parents. Both early and late harvest evaluations were performed, with each plot evaluated for yield, specific gravity, tuber size, shape, color and external defects. In addition, diploid breeding clones from the red, yellow, purple-skinned market class were acquired from the U.S. potato genebank and hybridized with self-compatibility donors to generate F1 progeny for field selection. Four diploid clones selected in 2023 containing self-compatibility were self-pollinated to generate F2 mapping populations. In the winter and spring of 2025, a crossing block was completed that focused on trying to develop specialty lines with a high-tuber number and visually appealing skin, along with additional characteristics desired by the baby potato market and consumers, including shape, flesh colors, uniformity and phytonutrients. Berries from these crosses were harvested and processed to collect true seed that will be planted in greenhouses in Hermiston, Oregon, by collaborators at Oregon State University. This will provide seed for single-hill field trials in Klamath Falls, Oregon, 2026. Six thousand seedlings from our previous crossing block were planted in Klamath Falls, Oregon and evaluated in the field in fall, 2024 and several lines were selected for advancement.
In support of Sub-objective 2A, ARS researchers in Wapato, Washington, treated tubers from over 40 cultivars with light to evaluate the effect on skin, greening, and glycoalkaloids. Tubers are in the process of being freeze-dried for biochemical analysis of flavonols, carotenoids, glycoalkaloids and chlorophyll. Analysis of glycoalkaloid changes in response to light in hundreds of primitive tubers was completed and provided to ARS collaborators in Aberdeen, Idaho, to be used in a mapping study attempt to identify greening resistance.
In support of Sub-objective 2B, ARS researchers completed analysis of glycoalkaloids in potatoes heat-treated by researchers at Texas A&M University to study the effect of heat on glycoalkaloids in different cultivars and to evaluate heat tolerance among cultivars. ARS scientists in Wapato, Washington, determined that post-harvest heat treatments were not useful for evaluating resistance to heat necrosis or hollow heart, but were effective for evaluating blackheart resistance. The method to induce blackheart was further optimized and a final protocol used to evaluate over 40 TriState breeding lines in the spring of 2025, which identified some lines that were highly resistant to blackheart. A machine vision method was developed to phenotype the material, thereby automating the evaluation of blackheart, while allowing collection of data on additional traits.
To address Sub-objective 3A, ARS researchers in Wapato, Washington, conducted inoculation assays to assess the ability of ‘Candidatus Liberibacter solanacearum’ (Lso)-infected non-potato psyllid species to transmit the pathogen to potato and other related crops/weeds. Recently, three new haplotypes of Lso were discovered by ARS scientists in Wapato, Washington, in four different non-potato psyllid species. Three cage trials were conducted whereby naturally infected populations of the non-potato psyllid, Aphalara loca, were released on potato, carrot, or a weedy host plant of another Aphalara psyllid species. The plants were then assessed for the presence of Lso. Other Lso-free Aphalara species were caged on the plants to determine if the pathogen can move between different insect species. Transmission and acquisition did not occur, but Lso infection rates in the psyllids were likely too low to draw accurate conclusions. Follow-up trials are ongoing. To determine the prevalence of the new Lso haplotypes occurring naturally in the potato- and carrot-growing regions of Washington State, non-potato psyllid species captured on sticky traps near vegetable and seed fields continue to be tested for the presence of Lso. Efforts are underway to identify Lso haplotype at the molecular level, as well as psyllid species to accurately depict pathogen trends in the region.
For Sub-objective 3B, ARS researchers in Wapato, Washington, continued to generate cultures of Potato mop-top virus-infected Spongospora subterranea maintained on tomato plants in the greenhouse as a source of inoculum and for ongoing efforts to generate a disease field that can be used for consistent pathogen screening of breeding lines. Infected tomato plants maintained in the greenhouse for inoculum were transplanted into this field. Currently, there are no commercial potato cultivars resistant to PMTV, so greenhouse screens were designed, validated and subsequently conducted in high numbers to identify PMTV- and/or S. subterranea-resistant material. During the current growing season, healthy potato seeds were planted in this field. Inoculation success will be assessed at harvest, with hopes of identifying some level of S. subterranea and PMTV in this field. To generate additional inoculum, potato plants of four different cultivars were grown in the greenhouse and inoculated with Potato mop-top virus-infected S. subterranea.
Accomplishments
1. Development of a greenhouse assay to screen potato germplasm for resistance to Potato mop-top virus and its vector, Spongospora subterranea. Potato mop-top virus, vectored by the protist, Spongospora subterranea, causes tissue death that can lead to unmarketable tubers. Because there are no cultivars in the United States with resistance to the virus, ARS researchers in Wapato, Washington, designed, optimized, and validated a greenhouse assay to screen a high number of plants and identify virus-resistant potato germplasm. The pathogen rate, inoculation time, and molecular detection methods were optimized on 13 commercial cultivars or breeding lines with known susceptibility to the virus and vector. Successful assay design was confirmed and enables maximization of greenhouse space for screening a greater number of plants. This new assay could be used to quickly and efficiently screen wild relatives of potato for sources of resistance to this economically devastating virus.
2. Identifying opportunities for innovation in the fresh market potato sector. Roughly a quarter of U.S. potato production is sold as a fresh market product. Historically, market classes within this sector are dominated by a small number of varieties which are familiar to industry practitioners but often susceptible to disease and quality defects. ARS researchers at Wapato, Washington, performed an analysis of historical seed acreage data and evaluated the productivity and adherence to ideal traits of more than 80 potato varieties in a common garden experiment. Results from this study highlight the differences in cultivar dominance among market classes and suggest that market demand is largely driven by historical consumer preference not necessarily cultivar productivity. This work suggests that grower profitability and sustainability could be improved by growing various newer lines developed by ARS and the Tri-State Potato Breeding Program, which have superior traits, performance and virus-resistance compared to the standard varieties.
3. New methods to phenotype potato disorders. A bottleneck for potato breeding programs is that evaluating breeding lines for desired traits is time consuming, and some traits are not even evaluated because no screen is available. USDA-ARS researchers at Wapato, Washington, developed new methods to treat tubers that allow the measurement of tuber periderm color stability, blackheart resistance, and greening resistance with results measured using machine vision. These new methods were used to identify lines resistant to blackheart, specialty potato lines with periderm color that does not darken when exposed to light, and lines with slower greening in the light. Collectively, these methods will help in the development of superior new potato cultivars that have lower amounts of the type of defects that are a major cause of consumer complaints.
Review Publications
Swisher Grimm, K.D., Quick, R.A., Feldman, M.J., Charlton, B.A. 2025. Development of a greenhouse screen for the identification of potato mop-top virus and Spongospora subterranea resistance in Solanum tuberosum. PhytoFrontiers. https://doi.org/10.1094/PHYTOFR-11-24-0127-R.
Anglin, N.L., Yellarreddygari, S.K., Gudmestad, N.C., Sathuvalli, V., Brown, C., Feldman, M.J., De Jong, W.S., Douches, D.S., Novy, R.G., Coombs, J.J. 2023. A genome wide association study (GWAS) identifies SNPs associated with resistance to Tobacco rattle virus (TRV) and Potato mop-top virus (PMTV) in a tetraploid mapping population of potato. American Journal of Potato Research. 101:1–16. https://doi.org/10.1007/s12230-023-09933-3.