Location: Temperate Tree Fruit and Vegetable Research
2023 Annual Report
Objectives
Develop or identify new breeding lines, germplasm and named cultivars with superior quality, disease and pest resistance, and nutritional value. This will involve collaborative and independent work by our three-person team using our respective expertise in potato breeding, molecular physiology and plant pathology. The three objectives below undertake complimentary approaches to germplasm improvement. Objective 1 involves largely breeding for targeted traits. Objective 2 seeks to determine basic mechanisms that govern trait expression. Objective 3 will develop new or improved methods to evaluate breeding lines and germplasm. We will work closely with the TriState Breeding Program, as we have for over 20 years.
Objective 1: Evaluate, identify, breed, and release potato germplasm with improved traits of interest, especially improved disease and pest resistance, and increased amounts of phytonutrients.
Subobjective 1A. Develop breeding lines, cultivars or identify germplasm with enhanced amounts of phytonutrients and visual appeal.
Subobjective 1B. Develop breeding lines, cultivars or identify germplasm with superior disease resistance with a focus on soil-borne diseases.
Objective 2: Characterize genetic, environmental, molecular, physiological, and biochemical factors that control accumulation of potato phytonutrients and mechanisms that lead to plant disease resistance, and use this knowledge to produce new superior potato cultivars.
Subobjective 2A: Determine mechanisms that mediate tuber phytonutrient expression.
Subobjective 2B: Increase information and develop methods with potential to be used for control of Potato Cyst Nematode (PCN) and for improved disease resistance.
Objective 3: Develop improved pathogen diagnostic techniques and phenotyping approaches that can be used for potato germplasm evaluation, development of host-resistance, and identification of emerging potato diseases.
Subobjective 3A. Identify and characterize emerging and evolving pathogens and pests in the Pacific Northwest.
Subobjective 3B: Characterize Tobacco rattle virus (TRV)-potato interactions to develop better detection methods and determine the relationship between viral titer, cultivar, symptoms and resistance.
Objective 4. Determine the value of advanced potato germplasm with particular attention to disease, pest, and stress resistance, yield, quality characteristics, and profitability parameters. Define cultural conditions which will optimize yield and quality of each clone.
Approach
1A. Germplasm will be intercrossed and progeny evaluated in the field. Replicated plots will be grown in successive years across multiple locations. Lines will be analyzed for carotenoids, anthocyanins, antioxidants, total protein, potassium and iron. Molecular markers will be used to characterize high carotenoid lines. Liquid chromatography mass spectrometry (LC-MS) will be used to quantitate phytonutrients. If germplasm does not provide the desired traits, we will import additional germplasm.
1B. Resistance to nematodes, viruses and fungi will be developed using resistant lines to make crosses and evaluating progeny in field trials. Selected clones will be evaluated under high disease pressure and molecular markers used for Meloidogyne chitwoodi breeding. If progeny have lower selection rates than expected the size of the initial population will be increased.
2A. Expression of structural genes and transcription factors in potatoes or organs that have low or high amounts of phenolics, are cold-treated, or wounded will be analyzed using reverse transcription quantitative polymerase chain reaction (RT-qPCR) and LCMS. We will use ribonucleic acid sequencing (RNA-seq) to generate transcriptomic data. Effect of environment on glycoalkaloids will be assessed by growing 13 genotypes in six locations and methanolic extracts from freeze-dried tubers analyzed by LCMS. If key genes are identified, resources will be redirected to apply this knowledge through precision breeding efforts.
2B. Potato cyst nematode (PCN) trap crop seed will be produced by sowing true seed directly into the soil at ¼ inch depth. Hatching factor purification will be tested on diverse High-performance liquid chromatography (HPLC) columns and fractions tested for activity. If a hatching factor is identified and quantitated by LCMS, increased resources will be directed.
3A. Samples from symptomatic plants will be collected. Grafting experiments will evaluate transmissibility. Established molecular tools will be used to detect any pathogens present. If targeting known pathogens does not identify a biological agent, primers that target unknown pathogens will be used. Psyllid involvement in beet-leafhopper transmitted virescence agent (BLTVA) will be tested using field and cage experiments. Development of improved diagnostic tools for BLTVA and Candidatus Liberibacter solanacearum (Lso) will be assessed using a single-tube nested PCR technique, RT-qPCR or Kompetitive allele-specific PCR. If unable to identify any known pathogen in a sample, next generation sequencing platforms will be used.
3B. Tobacco Rattle Virus (TRV) sampling methods will be evaluated for efficacy. Lines will be evaluated for resistance in field trials. PCR will be used to compare viral titer with symptom severity. Varieties will be exposed to TRV and differences in resistance/insensitivity and susceptibility compared. Daughter tuber symptoms and viral titer will be compared to mother tuber symptoms, viral titer, plant emergence, and daughter tuber yield. If TRV infection becomes sporadic, we will focus on the genotypes that were subject to sufficient disease pressure.
Progress Report
This is the final report for project 2092-21220-002-000D, "Developing New Potatoes with Improved Quality, Disease Resistance, and Nutritional Content", replaced by project 2092-21220-003-000D, "Potato Germplasm Development for Improved Sustainability, Disease Resistance, Nutrition, and Quality". For additional information, see the new project report.
In support of Objective 1, researchers in Prosser, Washington, completed five crossing blocks, performed hundreds of hybridizations, and generated tens-of- thousands of recombinant seeds that were/are being evaluated though field trials and marker assisted selection. Progress was made for Sub-objective 1A, by crossing pigmented and elongated diploid breeding selections acquired from the U.S. Potato Genebank with high performing, self-compatible diploid breeding clones. ARS scientists generated and field tested a multi-parent parent tetraploid breeding population focused on transferring Potato virus Y (PVY) and Golden cyst nematode resistance into specialty potato germplasm. To address Sub-objective 1B, ARS scientists identified Tobacco rattle virus (TRV) immunity as the mechanism of Corky ringspot disease resistance observed in Castle Russet and mapped a quantitative trait locus (QTL) conferring TRV immunity to Chromosome 9. Crosses were performed to introgress sources of PVY, Verticillium wilt, TRV and nematode resistance from wild potato relatives into high performing, self-compatible diploid genetic backgrounds for the purpose of genetic mapping and clone development. A large multi-parent tetraploid population segregating for Columbia root-knot nematode (CRKN) resistance were generated. This population is comprised of three CRKN resistant females crossed with 12 other russet potato breeding clones for a total of 32 breeding families. To address Sub-objective 1B, researchers in Prosser, Washington, developed a method to screen potato germplasm for resistance to TRV under field conditions and Potato mop-top virus (PMTV) under greenhouse conditions to identify clones with resistance/insensitivity to one or both of these economically concerning tuber necrotic viruses. In collaboration with the Tri-State Breeding Program, USDA scientists screened advanced breeding lines for resistance to TRV by planting a replicated trial each year in a stubby root nematode/TRV-infested field maintained in Prosser, Washington. Due to the lack of consistent PMTV infected soil, a greenhouse screen was established by USDA scientists to identify germplasm that fails to test positive for PMTV in root tissue. Screening of additional material identified potential wild potato accessions with resistance to PMTV. Results from these studies were provided to potato breeders for introgression into breeding programs and eventual development of resistance markers for faster identification of resistant material.
In support of Objectives 1 and 2 scientists in Prosser, Washington, analyzed potato glycoalkaloids that influence potato disease resistance, nutritional value and marketability. Transgenic potatoes with altered amounts of sterols were made to assess the effect on tuber greening and glycoalkaloid amounts. Expression of genes involved in glycoalkaloid metabolism were measured in the transgenic lines. In a separate study, light treatments administered to whole tubers were used to determine the effect on greening, glycoalkaloids, and gene expression. Transcriptomic and metabolomic approaches were used to monitor levels of glycoalkaloids, chlorophyll, carotenoids, and 35 genes in potatoes exposed to light. Network analysis was used to look at relationships between metabolites and gene expression. Not all potato genotypes were found to respond the same way to light, some more resistant to greening or light-induced SGA increases than others. In some cases, little or no increase in glycoalkaloids was observed in potatoes that had greened.
For Objective 2, ARS researchers assessed how flavonol biosynthesis is regulated in potatoes. Flavonols are phenylpropanoids with numerous health-promoting benefits that are dietarily desirable but are present in low amounts in tubers. ARS scientists identified transcription factors that regulate flavonols and showed a regulatory loop between sucrose and myeloblastosis (MYB) transcription factors, demonstrated that transcription factors that regulate potato phenylpropanoid metabolism bind the promoters of genes that degrade sucrose, identified one of the first microRNAs ever found in potatoes, which we showed regulates flavonol amounts, and showed light induces dramatic increases in tuber flavonol content. Potatoes can be a significant source of other health-promoting phenylpropanoids such as chlorogenic acid, but a concern about breeding cultivars with higher amounts of phenylpropanoids is that they might be more prone to bruising or discoloration. Studies found no correlation between phenylpropanoid amounts and discoloration. In support of Sub-objective 2B, a line of reduced thorn Litchi Tomato was examined for its efficacy against potato cyst nematode in Idaho, working with APHIS-PPQ. Solanacous plants produce “hatching factors” that promote potato cyst nematode eggs to hatch, and that potentially can be used to promote a “suicide hatch” by causing hatch in the absence of a host. By using high performance liquid chromatography (HPLC), discovery that numerous distinct hatching factors are present in potato root exudates were found. Separated HPLC fractions were used to show that these various hatching factors have markedly different efficacy in inducing hatch.
Baby potatoes are a growing market and among the best options for the potato industry to target emerging consumer preferences like nutrition, taste, novelty, ease of preparation, and visual appeal. One limitation to the development of this market is reduced yields, which are far less than when potatoes are grown to maturity. For Sub-objectives 1A, 1B, and 2A a promising breeding line, 35-4, that produces an exceptionally high-set of small tubers was developed. Because of this unusual, highly-desirable trait, this line was used to make numerous additional crosses in an attempt to fast-track development of a high-tuber set potato with additional desirable traits and accelerate the breeding process that normally takes over 12 years.
Supporting Objective 3, scientists in Prosser, Washington, deployed novel machine vision-based phenotyping techniques to assess the genetics of tuber characteristics (proximal imaging) and field resistance to Colorado potato beetle defoliation (drone). A screen of 20 diploid accessions derived from nine different potato wild relative species to assess resistance to PMTV was done. Varying levels of PMTV infection was found in 17 of these accessions, whereas three accessions derived from S. boliviense, S. chachoense, and S. vernei exhibited no viral infection after 12 weeks of exposure to infected soil.
To address Sub-objective 3A, researchers in Prosser, Washington, with collaborators at Washington State University developed improved molecular assays for the rapid detection of beet leafhopper-transmitted pathogens that affect vegetable and seed crops in the Pacific Northwest. A qualitative real-time polymerase chain reaction (PCR) protocol was developed to detect the beet leafhopper transmitted virescence agent phytoplasma from both insect and plant samples that decreased the amount of time, reagents, and supplies required to detect this pathogen. In addition, a multiplex real-time qualitative PCR protocol was developed to simultaneously detect all three beet leafhopper-associated pathogens. These novel tools were used to provide weekly pathogen prevalence data on the Washington State University Decision Aid System online tool for growers and fieldman in 2022-2023. Field trials were conducted to determine the role of symptom severity and viral titer in TRV transmission to daughter tubers in the field. Effort is currently focused on finishing all daughter tuber laboratory testing, but preliminary analyses suggests that the presence of TRV does not induce delayed emergence or impact yield, regardless of internal tuber symptom severity of the seed piece. Contrary to this, virus presence in the seed piece does lead to a statistically significant increase in internal necrosis in the daughter tubers, though only minor compared to internal symptoms caused by current-season infection. In a separate trial conducted over two years, the effects of planting TRV-infected seed in the presence or absence of the vector, Paratrichodorus allius was assessed. Emergence in the P. allius-infested field was delayed by about one week compared to the fumigated field, but the effects of planting infected seed were less significant.
For Objective 4, large field trials of breeding lines were conducted in multiple locations in Idaho, Oregon, and Washington, with the help of researchers at the University of Idaho, Oregon State University, and Washington State University over five years. Tens of thousands of breeding line tubers were obtained from true seed planted in greenhouses. These greenhouse-generated tubers were provided to collaborators and evaluated in field trials around the Pacific Northwest. Performance was evaluated and tubers were collected from the most promising lines to be further evaluated for consistency and numerous quality traits in the next growing season. With collaborators at Washington State University, a dedicated study to determine optimum potassium fertilizer rates for newly established cultivars was conducted to facilitate the acceptance of newer Russet cultivars in the and to mitigate the economic and environmental costs of over-fertilization. A field study was conducted to examine the effect of plant architecture on greening. The below ground plant architecture of some varieties positioned tubers closer to the soil surface, which led to premature and excessive tuber greening.
Accomplishments
1. Novel machine vision techniques to quantify tuber shape and classify hollow heart defect in potato breeding populations. Potato tuber size, shape, and defect susceptibility are a few of the most important characteristics that influence cultivar acceptance within the potato processing industry. Tuber size and shape determine compatibility with potato processing machines (peelers, cutters, fryers, etc.), whereas all three factors, size, shape, and defect susceptibility influence the portion of usable raw product after cutting and trimming. USDA-ARS scientists in Prosser, Washington, and Aberdeen, Idaho, developed a latent trait approach (tuber biomass profile) to quantify potato shape features that are independent of tuber size and aspect ratio (length-to-width ratio). As part of this effort, scientists also developed a deep learning model to classify tubers affected by an internal tuber defect called ‘hollow heart’. The ability to inexpensively and reproducibly quantify these features on the large volume of clones/samples (hundreds-to-thousands) generated in each breeding and evaluation cycle is needed to apply statistical genetics models and marker assisted selection on these traits within our potato breeding program. This result will significantly improve our ability to identify and select for cultivars that are compatible with the needs of the potato processing industry.
2. Improved method to screen for potato physiological defects. Among the many traits needed for any successful new potato cultivar is resistance to physiological disorders that result in discoloration. A limitation in developing such resistant cultivars is that the only way to screen for such disorders are slow, costly field trials that are highly variable depending on poorly understood, uncontrollable environmental conditions. Scientists in Prosser, Washington, developed a rapid 4-day assay for blackheart resistance that can be conducted in the lab using elevated temperatures to induce this physiological disorder that causes reduced yields and potato quality. This method provides new capability to determine the physiological basis of blackheart and will improve the ability of potato breeding programs to evaluate breeding lines for resistance and decrease the occurrence of blackheart, one of the leading causes of consumer complaints.
3. Potato mop-top virus is entering commercial potato fields in Washington State through infected seed. The tuber necrotic viruses, Potato mop-top virus (PMTV) and Tobacco rattle virus (TRV), are found in the Northwest United States, where they cause internal tuber damage that renders tubers unmarketable. A seven-year study was conducted by ARS researchers in Prosser, Washington, in collaboration with Washington State University scientists, to access the presence of PMTV and TRV in commercial seed lots entering Washington State each year. Findings indicate that PMTV is present in seed of 23 cultivars, with an infection rate from 1.73 to 5.5% each year in lots from at least six different states and one province in Canada, which indicates this pathogen is a widespread problem for seed production. The presence of the PMTV vector in grower fields across the northwest suggests that planting PMTV-infected seed could lead to serious economic losses for growers and continual monitoring of PMTV in seed lots is essential in order to provide growers with a real-time look at how this pathogen prevalence changes each year. Overall, this study indicated that PMTV testing in seed is needed to prevent economic losses from PMTV infections from worsening and to protect growers, the industry, and food security.
4. Three new haplotypes of ‘Candidatus Liberibacter solanacearum’ were identified in four different psyllid species in the Klamath Basin, Oregon. ‘Candidatus Liberibacter solanacearum’ (Lso) is a pathogen that causes economic losses for potato growers, including in the United States where at least three haplotypes of the bacterium are known to cause zebra chip disease symptoms. To identify novel haplotypes of Lso that could in time pose a threat to the potato industry, ARS researchers in Prosser, Washington, utilized molecular tools to compare genetic sequences of targeted genes in infected insect specimens collected in or near potato fields in the Klamath Basin of Oregon and identified three new Lso haplotypes, including two variants of one haplotype. A collaborative project with entomologists at the ARS research facility in Wapato, Washington, enabled the Lso-infected psyllids to be identified as Aphalara species, including A. loca-like, A. persicaria-like, and A. curta-like species. The impact of these novel haplotypes on Solanaceous crops, including potato, is still unknown, but the presence of these three new haplotypes in psyllid species that do not share the same host plants suggest that the different psyllid species must feed on overlapping host plants, thereby transmitting the haplotypes. The ability for the potato psyllid to transmit these new Lso haplotypes to potato must therefore be explored to protect yields. This information will be disseminated to growers through extension publications and grower-oriented meetings, allowing them to balance costly pest management with the risk of potential tuber yield or quality losses.
Review Publications
Swisher Grimm, K.D., Quick, R.A., Cimrhakl, L.L., Brown, C., Pavek, M.J. 2022. Detection of potato mop-top virus in potato seed lots entering Washington State. American Journal of Potato Research. 99:390-394. https://doi.org/10.1007/s12230-022-09889-w.
Swisher Grimm, K.D., Horton, D.R., Lewis, T.M., Garczynski, S., Jensen, A., Charlton, B. 2022. Identification of three new ‘Candidatus Liberibacter solanacearum’ haplotypes in four psyllid species (Hemiptera: Psylloidea). Scientific Reports. 12. Article 20618. https://doi.org/10.1038/s41598-022-24032-9.
Jiang, J., Feindel, W., Swisher Grimm, K.D., Harding, M., Feindel, D., Bajema, S., Feng, J. 2022. Development of a loop-mediated isothermal amplification (LAMP) method to detect the potato zebra chip pathogen ‘Candidatus Liberibacter solanacearum’ (Lso) and differentiate haplotypes A and B. Plant Disease. 107(6):1697-1702. https://doi.org/10.1094/PDIS-09-22-2258-SR.
Cooper, W.R., Walker III, W.B., Angelella, G.M., Swisher Grimm, K.D., Foutz, J.J., Harper, S.J., Nottingham, L.B., Northfield, T.D., Wohleb, C.H., Stausbaugh, C.A. 2023. Bacterial endosymbionts identified from leafhopper (Hemiptera: Cicadellidae) vectors of phytoplasmas. Environmental Entomology. 52(2):243-353. https://doi.org/10.1093/ee/nvad015.
Navarre, D.A., Zhu, M., Hellmann, H. 2022. Plant antioxidants affect human and gut health, and their biosynthesis is influenced by environment and reactive oxygen species. Oxygen. 2(3):348-370. https://doi.org/10.3390/oxygen2030025.
Baley, N., Sathuvalli, V., Charlton, B., Shock, C., Yilma, S., Qin, R., Feibert, E., Vales, M., Novy, R.G., Whitworth, J.L., Brown, C., Navarre, D.A., Stark, J.C., Pavek, M., Knowles, N.R., Knowles, L., Blauer, J., Brandt, T., Wang, Y., Spear, R., Olsen, N. 2022. Echo russet: A russet potato variety with a high yield of marketable tubers, high processing quality, and few tuber defects. American Journal of Potato Research. 100:15-26. https://doi.org/10.1007/s12230-022-09891-2.
Matias, F.I., Green, A., Lachowiec, J., LeBauer, D.S., Feldman, M.J. 2022. Bison-Fly: An open-source UAV pipeline for plant breeding data collection. The Plant Phenome Journal. 5(1). Article e20048. https://doi.org/10.1002/ppj2.20048.
