Location: Temperate Tree Fruit and Vegetable Research
2022 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
For Objective 1, ARS scientists in Prosser, Washington, successfully completed a potato crossing block in the spring of 2022 that generated thousands of recombinant seeds for evaluation in future field trials and through marker assisted selection. Progress was made by introgressing extreme resistance to viral diseases; Potato Virus Y (PVY), Tobacco rattle virus (TRV), several sources of late blight resistance, and nematode resistances (Columbia root knot nematode, Potato cyst nematodes) into susceptible genetic backgrounds in the processing and table stock market classes. Long day adapted diploid clones maintained by our program were crossed with three donor lines (M6, PI 654351, US-W4) that confer self-compatibility via S-locus inhibitor (Sli) alleles. We acquired and began growing out 30 diploid Solanum tuberosum breeding stocks clones and ~200 accessions from 40 potato wild relative species reported to be resistant to viral, bacterial, fungal, nematode, and insect pathogens. Another crossing block focused on developing cultivars suitable for baby potato production. The baby potato market is growing, and these types of potatoes have traits that appeal to evolving consumer preferences. Plants used as parents were selected based on the number of tubers produced and appearance, especially shape, color and eye depth. Thousands of true seed were generated and will be planted in the greenhouse to generate tubers for 2023 field trials in Klamath Falls, Oregon. Tubers from breeding line seed produced in 2021 were planted in Klamath Falls, Oregon, in the spring of 2022. Breeding lines generated in 2020 and planted in the spring of 2021 were evaluated in field trials in the fall of 2021, and selections were made of lines to be advanced for further analysis were planted this spring for 2022 field trials.
Approximately 330 clones were cultivated and maintained by our program and the U.S. Potato Genebank for phenotypic analysis as twice replicated 5-hill plots and are constructing a digital catalog of this material using gravimetric measurement of yield, specific gravity, tuber number, size, shape, skin color, and flesh color.
A progeny test panel (North Carolina II design) is being planted to assess the general and specific combining ability of Columbia root-knot nematode resistant germplasm developed by our program when combined with different russet germplasm. This population is being grown in two locations: One for harvest and estimation of yield in 20-hill bulked plots (replicated 5X) and the other is for single hill selection activities as part of the Tri-State potato breeding program.
To address Objective 2, we are planting a trial to assess segregation of yield, tuber size, shape, and color traits in five breeding families that we believe have either potato clone Barbara (PVY resistance, golden cyst nematode resistance, late blight resistance) and/or POR16PG35-4 (high tuber set) as parental lines. These breeding families will be grown out as 5-hill plots this season and tuber phenotypes will be evaluated in FY2023. The structure of this population (five clones crossed to a common female parent, Barbara) will enable us to select for PVY and potato cyst nematode resistance using kompetitive allele specific PCR (KASP) genotyping, potentially map quantitative trait loci (QTL) linked to additional quantitative traits, and construct genomic prediction models that improve trait introgression from Barbara by identifying progeny with high estimated breeding value.
In further support of Objective 2, we are analyzing factors that influence phytonutrient amounts in tubers, with a focus on phenylpropanoids and glycoalkaloids. Previously, we identified transcription factors that regulate anthocyanin amounts in tubers and are working on approaches to make red skin even brighter for increased visual appeal. Working with researchers at the University of Idaho, we tried treatments, including 2,4-D, on various red-skin cultivars being grown in the field. This treatment is anecdotally thought to increase skin color, which is desirable for marketing but it also can be a research tool to study changes in gene expression that promote brighter skin color. However, over multiple years the treatments did not produce a measurable increase in skin color intensity (anthocyanins), leading us to hypothesize that increased temperatures of recent years suppress anthocyanin formation, which raises the possibility that higher temperatures in the Pacific Northwest might have a detrimental effect on potato market classes (specialty potatoes for example) that benefit from an attractive skin. We have identified transcriptional regulators of tuber flavonol metabolism but these don’t explain why tubers have low amounts of health-promoting flavonols. Using light treatments on post-harvest tubers, we showed light induces dramatic increases in tuber flavonol content. Because light also results in undesirable greening and an undesirable increase in glycoalkaloids, it would not be a suitable treatment to increase flavonols, but this enables a new approach to study tuber flavonol regulation.
In support of Objective 3, ARS researchers in Prosser, Washington, continued research to identify novel haplotypes of ‘Candidatus Liberibacter solanacearum’ and 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. In these analyses of the ‘Ca. L. solanacearum’ 16S RNA, and nucleic and amino acid sequence analysis of the 50S ribosomal proteins L10/L12 and the outer membrane protein genes, three new haplotypes of the bacterium, including two variants of one haplotype were identified. The insect specimens harboring these new ‘Ca. L. solanacearum’ haplotypes were not of high quality, so a collaborative project with ARS researchers in Wapato, Washington, was initiated to taxonomically identify insect specimens of the Aphalara species collected in the Pacific Northwest to pair this data with molecular analysis of a barcoding gene. This study enabled the ‘Ca. L. solanacearum’-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. ‘Ca. L. solanacearum’ haplotype F has still not been identified, suggesting that the vector of this economically important haplotype remains unknown, and that further studies are necessary to help determine the best pest management strategies to implement.
ARS researchers in Prosser, Washington, continued testing tubers from Washington State University’s Seed Lot Trial for the tuber necrotic viruses, Potato mop top virus (PMTV) and Tobacco rattle virus. Findings indicate that PMTV is entering commercial potato fields through seed, with an infection rate ranging from 1.73 to 5.97% each year. These lots are originating from at least six different states in the United States, as well as from one province in Canada. Infection was found in 22 different cultivars to date. Transmission from the infected seed to healthy host plants of the virus was confirmed in the greenhouse when planted in soil containing the vector, Spongospora subterranea. These results are striking, as the presence of the tuber necrotic virus in seed could cause economic losses for growers if the vector is present in the soil.
In support of Objectives 1 and 4, efforts continued to improve the quality and sustainability of potato cultivation. Sustainability can be enhanced by developing new cultivars with superior traits and by crop management. Excessive irrigation during the last half of the production season is wasteful and can reduce potato tuber quality. Efficient irrigation becomes even more critical if climate change reduces water availability for agriculture. ARS researchers at Prosser, Washington, with colleagues at Washington State University planted six potato cultivars, Alturas, Clearwater Russet, Ranger Russet, Russet Burbank, and Umatilla Russet, and managed using grower-typical irrigation between emergence and midseason. Grower-typical irrigation was delivered at 100% ET modeled evapotranspiration (ET) estimated using the Washington State University’s (WSU) irrigation scheduler web-based program. When cumulative growing day-degrees reached 1500 heat units beyond planting (base temperature of 45 degrees F and an upper limit of 95 degrees F), approximately 95-105 days after planting (DAP), five levels of irrigation, 120% ET, 100% ET (considered the grower standard), 80% ET, 60% ET, and 40% ET were implemented. This treatment start-date was selected because the canopy had reached its peak and the root system has fully developed. The irrigation treatments ended at vine kill (approximately 150 DAP) and the soil was kept moist until harvest. Tuber yield and quality were assessed, and grower return calculated using a standard french-fry processing contract. Irrigation exceeding 100% ET failed to improve total yield across cultivars. Across the five cultivars, process adjusted gross was optimized by irrigating between 80% ET and 100% ET.
In further support of Objectives 1 and 4, field trials and post-harvest evaluation of breeding lines were conducted in Idaho, Oregon, and Washington, with the help of researchers at the University of Idaho, Oregon State University, and Washington State University. Numerous performance and quality traits were assessed, including post-harvest traits like storability and culinary properties.
Accomplishments
1. Tobacco rattle virus does not move systemically through the potato root system. Tobacco rattle virus (TRV), vectored by the stubby root nematode, causes internal tuber necrotic symptoms that cause tubers to be rejected for processing because of corky ringspot disease symptoms that range from internal flecks to larger necrotic arcs and blemishes. A replicated trial was conducted by ARS researchers located in Prosser, Washington, using a unique split-pot design to assess the ability of TRV to move systemically through the potato root system. Half of the roots from each plant were inoculated with TRV-infected stubby root nematodes and half were grown in un-infested soil. Roots grown in the un-infested soil were not infected with TRV at harvest, and tubers collected from these un-infested pots did not contain TRV or disease symptoms. Results suggest that TRV does not move systemically throughout the root system, and as a result, if the infected stubby root nematode population is adequately eliminated from soil, it will prevent symptoms from developing to high incidence levels. These studies will ultimately benefit growers seeking improved management strategies and control measures for TRV and corky ringspot disease.
2. Higher amounts of health promoting phenylpropanoids in potato do not necessarily cause increased tuber discoloration. With consumers increasingly prioritizing the healthfulness of food in purchasing decisions, the nutritional value of potato is of growing importance. Phenylpropanoids are highly desirable in the diet because of their numerous health-promoting effects; however, there is concern that cultivars and breeding lines with higher amounts might be more prone to discoloration, which, if true, would greatly decrease marketability. ARS and Washington State University scientists in Prosser, Washington, showed that tuber phenylpropanoid amounts do not correlate with the propensity for bruising or browning, indicating that other components are the limiting factor(s) for such discoloration. Potatoes are already one of the major sources of phenylpropanoids in the human diet and this work shows that cultivars with even higher amounts can be developed without increasing the potential for discoloration. Moreover, phenylpropanoids increase a plant’s abiotic and biotic stress resistance, which can result in enhanced crop sustainability.
3. Genetic mapping identified a genomic region that confers immunity to Tobacco rattle virus (TRV) in a mapping population. Corky ringspot disease is a soil-borne, tuber necrotic syndrome caused by Tobacco rattle virus (TRV) and vectored by stubby root nematodes. Currently, the only management strategies are fumigation of affected fields to reduce the population size of the nematode vector, or cultivation of TRV resistant cultivars. Genetic mapping and development of molecular markers linked to TRV immunity would greatly accelerate the rate at which new TRV resistance cultivars can be developed. ARS researchers in Prosser, Washington, mapped a quantitative trait locus (QTL) linked to TRV resistance in a genetic mapping population generated by crossing a TRV resistant (Castle Russet) and TRV susceptible clone (A06084-1TE). A single, large effect QTL linked to TRV resistance was mapped to the distal end of chromosome 9. This will significantly improve the ability to identify, select, and develop TRV resistant potato cultivars, reduce the need to fumigate fields affected by corky ringspot disease, and reduce the amount of virus present in infested fields.
Review Publications
Swisher Grimm, K.D., Porter, L.D. 2021. KASP markers reveal established and novel sources of resistance to Pea seedborne mosaic virus in pea genetic resources. Plant Disease. 105(9):2503-2508. https://doi.org/10.1094/PDIS-09-20-1917-RE.
Vales, I., Scheuring, D., Koym, J., Holm, D., Essah, S., Wilson, R., Sidhu, J., Jayanti, S., Novy, R.G., Whitworth, J.L., Stark, J., Spear, R., Sathuvalli, V., Shock, C., Charlton, B., Yilma, S., Knowles, N., Pavek, M., Brown, C., Navarre, D.A., Feldman, M.J., Long, C., Miller, C. 2022. Vanguard Russet: A fresh market potato cultivar with medium-early maturity and long dormancy. American Journal of Potato Research. https://doi.org/10.1007/s12230-022-09877-0.
Cooper, W.R., Horton, D.R., Swisher Grimm, K.D., Krey, K., Wildung, M.R. 2021. Bacterial endosymbionts of Bactericera maculipennis and three mitochondrial haplotypes of B. cockerelli (Hemiptera: Psylloidea: Triozidae). Environmental Entomology. 51(1):94-107. https://doi.org/10.1093/ee/nvab133.
Tan, Y., Wang, C., Schneider, T., Li, H., de Souza, R., Tang, X., Swisher Grimm, K.D., Hsieh, T., Wang, X., Li, X., Zhang, D. 2021. Comparative phylogenomic analysis reveals evolutionary genomic changes and novel toxin families in endophytic Liberibacter pathogens. Microbiology Spectrum. 9(2). Article e00509-21. https://doi.org/10.1128/Spectrum.00509-21.
