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- Navarre, Duroy - Roy
- Feldman, Max
- Swisher Grimm, Kylie
- 2023
- Publications
- Plant Genetic Resources, Genomics and Genetic Improvement (301)

Research Project: Potato Germplasm Development for Improved Sustainability, Disease Resistance, Nutrition, and Quality **Location:
                            Temperate Tree Fruit and Vegetable Research** 2023 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 progress for project 2092-21220-003-000D, "Potato Germplasm Development for Improved Sustainability, Disease Resistance, Nutrition, and Quality", which started May 2023 and continues research from project 2092-21220-002-000D, "Developing New Potatoes with Improved Quality, Disease Resistance, and Nutritional Content".

In support of Sub-objective 1A, ARS scientists in Prosser, Washington, and Aberdeen, Idaho, developed a machine vision workflow to count the numbers of tubers in a sample and measure tuber size, shape, skin, and flesh color from photograph images. As part of this effort a deep learning model was constructed to classify tubers affected by ‘hollow heart’ defect. In addition, two ARS employees have obtained their FAA Part 107 drone pilot license and flights to capture multispectral drone data from breeding experiment trials in Pasco and Othello, Washington, and being performed each week.

In support of Sub-objective 1B, ARS scientists in Prosser, Washington, successfully completed a potato crossing block in the spring of 2023 that generated thousands of recombinant seeds that will be evaluated in future field trials and through marker assisted selection. Progress was made by introgressing extreme resistance to viral diseases (Potato Virus Y, Tobacco rattle virus) and nematode infection (Columbia root knot nematode, Potato cyst nematodes) into susceptible genetic backgrounds in the processing and fresh market classes. ARS researchers have generated a large multi-parent population segregating for Columbia root-knot nematode (CRKN) resistance. This population is comprised of three CRKN resistant females crossed with 12 other russet potato breeding clones for a total of 32 breeding families. This population (38–50 clones per family) is currently being trialed under center pivot irrigation in Othello, Washington, as un-replicated 5-hill plots.

In support of Sub-objective 1C, ARS scientists in Prosser, Washington, performed a screen of 20 diploid accessions (10 individual plants/accession) derived from nine different potato wild relative species. Varying levels of Potato mop-top virus (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.

In support of Sub-objective 1D, ARS scientists in Prosser, Washington, grew out and evaluated multi-parent breeding populations focused on transferring Potato virus Y (PVY) and Golden cyst nematode resistance into specialty potato germplasm. Five cultivars of yellow, red, and purple potatoes were hybridized with disease resistant parent ‘Barbara’ and individual clones from each family (100 each) were grown as five-hill plots in Pasco, Washington. Plots were harvested and evaluated for yield, specific gravity, and an index score of tuber shape and color was collected. This population is being evaluated again in FY2023. In the spring of 2023, a crossing block was completed that focused on trying to move the high-tuber set trait from 35-4 into diverse germplasm to develop high-tuber set lines that have additional characteristics desired by the baby potato market and consumers, including shape, various skin and flesh colors, and uniformity. Berries from these crosses have been harvested and are being processed to collect true seed that will be planted in greenhouses in Hermiston, Oregon, by collaborators at Oregon State University in order to provide seed for single-hill field trials next year in Klamath Falls, Oregon.

In support of Sub-objective 2A, experiments exposing tubers to light for varying times have been initiated to characterize the effect of light on tuber flavonol amounts and types. Towards this same goal, potatoes silenced for the enzyme dihydroflavonol reductase are in the process of being generated and constructs have been made. In support of Sub-objective 2B, attempts are underway to develop a lab assay that can determine if tubers from multiple cultivars are resistant to physiological disorders. ARS researchers in Prosser, Washington, already determined this works for blackheart and are now testing whether the approach can work for heat necrosis and hollow heart. A specialty breeding line that seems exceptionally susceptible to heat necrosis in the field and that will be a useful control for our heat necrosis work was discovered. To explore the effect of high temperatures on potato glycoalkaloid amounts, collaborators at Texas A&M University have planted potatoes at two different sites in Texas and will ship these to us for analysis this summer.

To address Objective 3, ARS researchers in Prosser, Washington, partnered with ARS scientists in Wapato, Washington, and extension scientists at Washington State University and Oregon State University. Yellow sticky traps and preservative traps have been deployed at potato and/or other vegetable and seed crops across the Columbia and Klamath Basins. Non-potato psyllid species have been removed from these traps and tested for the Liberibacter pathogen, with a low percentage (5.4%) showing infection with the bacterium. ARS collaborators in Wapato, Washington, have collected numerous psyllid species belonging to the Craspedolepta, Aphalara, Trioza, and Pershivora genera. These specimens are currently being tested for the presence of Liberibacter. As non-potato psyllids are collected throughout the growing season on sticky traps or in preservative traps, testing for the Liberibacter pathogen will continue. Live collections of specific psyllid species will begin during the summer of 2023 for maintenance in greenhouse cultures. **Accomplishments**


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