Location: Temperate Tree Fruit and Vegetable Research
2021 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
In support of Sub-objectives 1A, 1B, and 2A, scientists in Prosser, Washington, conducted a potato crossing block in generating thousands of recombinant seeds for future field trials in Idaho, Oregon, and Washington. New breeding lines were made by introgressing extreme resistance to viral diseases [Potato Virus Y (PVY), Tobacco rattle virus (TRV), nematode infection (Columbia root knot nematode (CRKN),and potato cyst nematodes (PCN)]. True potato seed from a test panel designed to assess general and specific combining ability of CRKN resistant material (30 families derived from three resistant clones) is being grown out for evaluation. Long day adapted diploid clones were crossed with three donor lines (M6, PI 654351, US-W4) that confer self-compatibility via S-locus inhibitor (Sli) alleles. We identified more than 140 diploid gene bank accessions reported to be resistant to viral, bacterial, fungal, nematode, and insect pathogens, and we are acquiring these lines from the United States Potato Genebank as true potato seed. Breeding lines were analyzed for nutritional value, focusing on anti-nutritional glycoalkaloids, along with compounds called phenylpropanoids that have numerous health-promoting effects, including anti-inflammatory and anti-cancer properties and promotion of gut-health.
A third year of data was collected on virus symptomology and molecular detection of TRV in a tetraploid linkage mapping population segregating for TRV and PVY resistance. Faster ways to phenotype breeding lines are being developed, which is perhaps the biggest bottleneck in cultivar development. Foliar characteristics of individual clones are being assessed using aerial drone based multispectral remote sensing techniques. Tuber traits including yield and specific gravity were acquired gravimetrically; whereas tuber number, tuber size, shape, and colorimetric features were measured using computer vision methods. The inheritance of these traits is currently being assessed using linkage mapping based upon genetic marker data collected in 2020.
In support of Sub-objectives 1A, 1B, and 2A scientists in Prosser, Washington, studied potato glycoalkaloids (GLKs) that influence both potato disease/pest resistance and nutritional value. True seed was planted out from crosses between high and low GLK lines. Hundreds of tubers from this segregating population were collected and processed. These will be used in the future to search for genes that control GLK amounts. Light-induced accumulation of GLKs and the concurrent greening of tubers is a major problem, which some have estimated can cause up to 15% - 17% of the crop to be culled. 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 genotypes were found to respond the same way to light, with some more resistant to greening or light-induced GLK increases than others. In some cases, little or no increase in GLKs was observed in potatoes that had greened.
In support of Sub-objectives 1A and 2A, flavonol biosynthesis regulation was assessed in potatoes. Flavonols have numerous health-promoting benefits and are dietarily desirable, but tubers only contain low amounts. Studies were initiated to assess the role of light in flavonol accumulation in potato, following up on findings that light may be a possible key factor. A concern about breeding new cultivars with higher amounts of phenylpropanoids is that they might be more prone to bruising or discoloration. Studies were conducted to evaluate whether phenylpropanoids are primary determinants of discoloration. Phenylpropanoid amounts and their precursors were analyzed in potatoes from numerous cultivars that were subjected to various treatments that cause discoloration. Results suggest higher amounts of phenylpropanoids do not necessarily predispose potatoes to discoloration.
In support of Sub-objectives 1A and 2A, potatoes that produce large amounts of small tubers are being developed for baby potato production. Baby potatoes are a growing market and among the best options for the potato industry to target emerging consumer preferences, such as nutrition, taste, ease of preparation, and visual appeal. Field trials revealed that one exceptionally high-set line we developed has an inconsistent phenotype across years and locations, including a variable red-splash around eyes that is undesirable for marketing. New crosses were made using this line with an objective of keeping the high-set trait but eliminating the red-splash.
To address Sub-objectives 2 A and 2B, trials aimed at identifying physical and biological factors associated with soil health status relative to corky ringspot (CRS) and CRKN infections were performed. Potato cultivars susceptible or resistant to TRV infection were planted in a CRS disease infested field in Prosser, Washington. Samples representative of bulk soil, rhizosphere associated soil, and plant root tissue were collected from each plot at three time points during the growing season to assess microbial content. Total yield, size categorization, and virus damage was determined for each plot to assess the economic impacts of TRV infection relative to the costs of fumigation. Seed of the potato cyst nematode trap crop, Litchi Tomato, with reduced thorn numbers and size, and that produces hatching factors, was provided to collaborators in Idaho. However, while field trial results indicate Litchi Tomato is an effective trap crop, the finding that the plants can carry viroids may complicate its use.
For Objective 3, multispectral remote sensing techniques were tested to evaluate breeding line response to pathogens, nitrogen fertilizer (N) application, and predict phenotypic characteristics of breeding populations. Experiments designed to assess the capacity of multispectral sensors to detect TRV and predict tuber characteristics were performed in Prosser, Washington. Data acquisition was performed on a weekly basis generating more than 50 successful data collection missions throughout the 2020 field season. This large data set is being analyzed.
In support of Objective 3, ARS researchers in Prosser, Washington, increased understanding of TRV and the disease that it causes in potato. A field trial was completed to assess the effects of planting TRV-infected seed in the presence or absence of the vector. Emergence in the P. allius-infested field was delayed by approximately one week compared to the fumigated field, but the effects of planting infected seed were less significant. Additionally, there was no effect of planting clean or infected seed in the P. allius-infested field, as no below ground stem distortion was observed. Results from controlled greenhouse trials suggest that TRV does not move systemically throughout the root system, and as a result, if the infected P. allius 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 CRS disease.
The second year of a field trial was conducted by ARS scientists in Prosser, Washington, to compare transmission of TRV from infected seed of susceptible cultivars with varying internal CRS disease symptoms and resistant (insensitive) cultivars. compared to plant emergence of the insensitive cultivars, despite whether TRV and/or PVY was present. When compared to insensitive cultivars, daughter tuber yield and quantity per plant was decreased and the disease severity and percent of disease incidence in daughter tubers was greater from TRV and/or PVY symptomatic seed with more severe tuber necrosis. These results would suggest that planting seed that has moderate to severe internal tuber necrosis caused by either TRV or PVY, even in the absence of the nematode and aphid vectors, will decrease overall yield at harvest and will lead to greater internal defects at processing.
Researchers at the USDA-ARS 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 (Objective 3). Analysis of the ‘Ca. L. solanacearum’ identified three new haplotypes of the bacterium, including two variants of one haplotype. Haplotype F was not identified in this study, 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.
To meet 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. Tens of thousands of breeding line tubers were obtained from true seed planted in greenhouses. Subsequently 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. 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, leading to premature and excessive tuber greening. Tuber underground arrangement varies by cultivar and cultivars that produce more green tubers have more tubers closer to the soil surface. Tubers of some varieties in this study were eight times as likely to green as others due to phenotype, regardless of grower management.
Accomplishments
1. Factors influencing potato greening and glycoalkaloids identified. Light-induced tuber greening and accumulation of glycoalkaloids can cause up to 15% - 17% of the crop to be culled. Factors that control how a genotype responds to environmental signals that cause greening or increases in glycoalkaloids are not well understood. ARS scientists at Prosser, Washington, and Washington State University researchers, used transcriptomic, metabolomic, and network analysis to monitor amounts of glycoalkaloids, chlorophyll, carotenoids, and 35 target genes in potatoes exposed to light. Some genotypes were more resistant to greening or light-induced glycoalkaloid increases, while others had greening but no glycoalkaloid increase. Transcription factors were identified that correlated with glycoalkaloid amounts, and an inverse relationship was observed between increases in carotenoids and glycoalkaloids in response to light. These findings provide insights into mechanisms that control spiking of glycoalkaloid amounts and suggest potato breeding programs may benefit from evaluating the spiking potential of lines, not just base amounts.
2. Remote sensing platform developed to assess resistance to Colorado potato beetle. High-throughput, quantitative evaluation of cultivar performance in response to insect pests is a major bottleneck in potato breeding programs that require quantitative measurements of 100s-to-1000s of clones for genetic mapping. To alleviate this bottleneck, ARS scientists in Prosser, Washington, developed and deployed a multispectral remote sensing platform to assess cultivar performance using unmanned aerial systems. Through collaboration with scientists at Oregon State University in Hermiston, Oregon, ARS scientists identified a substantial correlation (r2 > 0.7) between several multispectral indices and manual measurement of insect damage over the most dynamic period of insect pressure, indicating that these remote sensing techniques are both reliable and scalable enough for evaluation of breeding populations. Information about the performance of individual cultivars will help guide decision making for stakeholders faced with Colorado potato beetle pressure in their fields.
3. Beet curly top virus identified in symptomatic Coriandrum sativum. In 2020, two fields of coriander seed crops were identified in the Columbia Basin of Washington State with leaf and stem discoloration ranging from mild to severe. In collaboration with Washington State University and Oregon State University scientists, ARS researchers in Prosser and Wapato, Washington, were able to identify the causal agent of these symptoms as Beet curly top virus, which is also a potato pathogen. A single beet leafhopper specimen, known to vector this pathogen to many different crops, was collected near one symptomatic coriander field and was also identified with the Beet curly top virus pathogen. Beet curly top virus has caused millions of dollars in losses to major crops within the United States, and the detection in coriander seed indicates that insect pest management strategies must be implemented to mitigate the devastating economic effects of this pathogen and its insect vector.
Review Publications
Lin, S., Singh, R., Hninsi, M., Navarre, D.A. 2021. R2R3-MYB transcription factors, StmiR858 and sucrose mediate potato flavonol biosynthesis. New Phytologist. 8. Article 25. https://doi.org/10.1038/s41438-021-00463-9.
Krey, K.L., Cooper, W.R., Renkema, J.M. 2020. Revealing the diet of generalist insect predators in strawberry fields: not only pests, but other predators beware. Environmental Entomology. 49(6):1300-1306. https://doi.org/10.1093/ee/nvaa125.
Qin, R., Moparthi, S., Feldman, M.J., Charlton, B.A., Sathuvalli, V. 2020. Effect of foliar application of 2,4-D and calcium on four red-skinned potato cultivars. Agronomy Journal. 113(1):88-89. https://doi.org/10.1002/agj2.20444.
Swisher Grimm, K.D., Crosslin, J.C., Cooper, W.R., Frost, K.E., du Toit, L.J., Wohleb, C.H. 2021. First report of curly top of Coriandrum sativum L. caused by beet curly top virus in the Columbia Basin of Washington State. Plant Disease. 105(10):3313. https://doi.org/10.1094/PDIS-01-21-0041-PDN.
Rondon, S., Feldman, M.J., Thompson, A., Thompson, I., Oppedisano, T., Shrestha, G. 2021. Identifying resistance to the Colorado potato beetle (Leptinotarsa decemlineata Say) in potato germplasm: review update. Frontiers in Agronomy. 3. Article 642189. https://doi.org/10.3389/fagro.2021.642189.
Swisher Grimm, K.D., Porter, L.D. 2021. KASP markers reveal established and novel sources of resistance to Pea seed-borne mosaic virus in pea genetic resources. Plant Disease. https://doi.org/10.1094/PDIS-09-20-1917-RE.
Cohen, A.L., Wohleb, C.H., Rondon, S., Swisher Grimm, K.D., Esquivel, I., Munyaneza, J.E., Jones, V., Crowder, D.W. 2020. Seasonal population dynamics of potato psyllid (Hemiptera: Triozidae) in the Columbia River Basin. Environmental Entomology. 49(4):974-982. https://doi.org/10.1093/ee/nvaa068.
