Location: Small Grains and Potato Germplasm Research
2025 Annual Report
Objectives
Potato breeding in the United States is mainly a collaborative undertaking between public institutions with the time necessary to develop new varieties taking up to fifteen years. Molecular techniques, including high throughput marker assisted selection (MAS), can reduce the timeframe. The discovery of new or emerging diseases makes it imperative that resistance be incorporated into potato to reduce losses. Climate changes, historic droughts and the need for lower nitrogen and pesticide inputs also drive the development of new varieties. This breeding program has been in place for more than seven decades with a large germplasm base to draw upon for resistance and quality traits. The program contributes to the Northwest Potato Variety (Tri-State) Program (NPVP) representing collaborations among ARS and land grant universities of Idaho, Oregon, Washington, and the potato commissions of these states. The program has a pipeline of potential new varieties allowing release of one to three varieties each year. Industry is very involved in this program providing input that helps direct research to solve problems and develop ready to use varieties. The end result is varieties with lower environmental impact that economically support, and address industry needs.
Objective 1: Develop and release new potato varieties having traits for improved processing, pest and pathogen resistance, nutrient and water utilization, greater resiliency to environmental stress, and enhanced tuber qualities that benefit the productivity and profitability of the potato industry.
Sub-objective 1.A: Develop potato varieties with improved processing and fresh market traits.
Sub-objective 1.B: Develop potato varieties with improved pest and pathogen resistance.
Sub-objective 1.C: Develop varieties with more efficient nutrient and water utilization and greater resiliency to environmental stress.
Objective 2: Discover and incorporate resistance genes from wild and domestic potato to improve varietal resilience.
Objective 3: Develop and deploy molecular markers to accelerate the improvement of new potato varieties to meet the needs of the potato industry.
Objective 4: Research the biology of new and emerging diseases and pests in potato such as Potato mop-top virus and potato cyst nematodes and incorporate virus and nematode resistance genes.
These objectives will be reached using the dedicated efforts of a Plant Breeder Geneticist, a Molecular Geneticist, and a Plant Pathologist. Together this team with the help of five technicians will use field, greenhouse, and lab resources to execute beneficial trait hybridizations, research disease interactions, seek new molecular markers and obtain and incorporate resistance genes from multiple sources. Within the scope of the project plan’s timeline, up to fifteen new varieties will be released, higher throughput evaluations will be developed to identify and select resistant progeny, and a better understanding of interactions between pests and host resistance genes will be developed.
Approach
Sub-objective 1.A: Improve process and fresh market traits by selected hybridizations on russet-skin, round white, red-skin, and specialty types. Modified backcross with different parent clones will be used each cycle to reduce inbreeding depression. First year field selections and subsequent trials for yield, processing, storage, and nutritional qualities will be done as entries progress.
Sub-objective 1.B: Developing pest and pathogen resistance in selections to be done in randomized complete block (RCB) trials for bacterial, fungal, virus and nematode resistance.
Sub-objective 1.C: Development of varieties resilient to environmental stress (nutrient and water) will be done in RCB and split plot trials. Applications of varying amounts of water and nitrogen will mimic commercial center pivot system application. Where research doesn’t result in a new variety, germplasm releases with desirable traits will be useful in multiple breeding programs. Also, increased number of progenies can be developed to allow success. If better host resistance to pests/pathogens is unsuccessful due to low disease pressure, subsequent assays will be done on the most resistant clones. If trials for environmental resilience fail, resistant germplasm in the literature will be incorporated into trials. To increase gains over time more rigorous reduced water/nitrogen regimes will be used.
Objective 2: Discover and incorporate resistance genes to be done by germplasm exchange and backcrossing, including the use of wild diploid species to introgress traits into tetraploid potato. Marker assisted selection will increase breeding efficiencies and be used for mining germplasm for resistant sources. Unsuccessful efforts may arise due to difficulties in obtaining international germplasm or be due to different environmental flowering conditions or male sterility. Project scientists’ knowledge of phytosanitary requirements will help facilitate movement of germplasm. For male sterility, reciprocal crosses can be made with germplasm used as a female parent.
Objective 3: Develop and deploy molecular markers to be done by testing and incorporating applicable markers. Mapping populations will be geno- and phenotyped to discover QTLs associated with targeted traits. If marker development is longer than five years, incorporation of validated markers and development of QTLs for markers will occur.
Objective 4: Researching the biology of new and emerging diseases to be done by using RCB trials in infested fields. Trials will examine variety reaction to Potato mop-top virus (PMTV) and include germplasm screening for resistance. Resistant sources can be hybridized and used to develop segregating populations for genetic studies. For potato cyst nematode (PCN), putative resistant potato lines will be phenotyped in labs with Globodera nematode populations. Difficulties in finding PMTV resistant germplasm/varieties may exist in which other more diverse material will be sought, screened, and hybridized. For PCN, high G. pallida resistance may be lacking. Pyramiding genes should increase overall resistance and provide horizontal resistance.
Progress Report
This report documents FY 2025 progress for project 2050-21000-036-000D, “Genetic Improvement of Potato for Sustainable Production and Enhanced Tuber Qualities for the Western United States”, which began in March 2023.
In support of Objective 1, research continued with the selection of seedling tubers for field production. True potato seed (botanical seed) was selected from hybridizations done over the last five years. This seed was used to plant greenhouse seedlings from which ‘seedling’ tubers will be harvested for field planting in 2026. This seed was selected from 144 families, with 80 percent of them having at least one parent with a Ry gene providing potato virus Y (PVY) immunity. The Ry gene segregates in a dominant fashion, meaning that in crosses with one Ry parent, 50 percent of the progeny should also carry the resistance gene. The remainder of the families used were selected for potato cyst nematode resistance or potato chipping characteristics. New varieties developed with PVY immunity will result in fewer pesticide inputs for production and increased sustainability for the industry, especially for the seed potato grower who faces rejection or downgrading of seed lots high in PVY.
Plant variety protection (PVP) data has been collected on two advanced breeding lines (A12305-2adg and AFA5661-8), which will be used to develop a plant variety release to be submitted to the Plant Protection Committee for approval. A12305-2adg is a breeding line which carries the Ry gene for PVY immunity. This line and AFA5661-8 both have high total U.S. and marketable yields (defined as U.S. No. 1 potatoes) which are better than the industry standard variety, Russet Burbank.
Under Objective 2, to discover and incorporate resistance genes from wild and domestic potato, a set of 220 individuals derived from Solanum microdontum species has been sequenced to identify beneficial genes that have not been part of previous genomic studies. To identify potential DNA segments that code for traits linked to tuber greening tolerance, tubers from this population were exposed to continuous light for five days and then measured for total chlorophyll, chlorophyll A, and chlorophyll B contents. From this assay, a segment on chromosome 2 was identified as significantly associated with total chlorophyll content and therefore tuber greening. The same segment remained consistently significant across two seasons of data collection. Additionally, a segment on chromosome 5 related to carotenoid content (pigment) was identified and was significant in both seasons. These segments associated with tuber greening can be used to further identify markers to screen for this characteristic which negatively impacts marketable tubers by causing green skin. Additionally, tuber biochemistry traits associated with nutritional content in potatoes were evaluated for associated DNA segments, including total glycoalkaloids (TGA), sugars content, antioxidants, vitamin C, and protein. A single segment was found to be significant for TGA content, confirming preliminary results from a smaller sample of this population. High TGA causes a bitter taste and is not desirable in tubers. Two segments were also identified as significant for antioxidants, three for protein, and three for vitamin C content. All these newly discovered DNA segments will need to be tested again over a second season.
For marker development and to improve genetic maps based on the DNA data, DArT sequencing was done on all 220 S. microdontum individuals. Sequencing was also done as long read sequencing on the S. microdontum parent and grandparent of the population. DArT sequencing was conducted on 13 wild and domestic potato accessions utilized in the breeding program to help better characterize the genetics in the germplasm used for crossing.
While working with this population, it was observed that the S. microdontum parent showed signs of potential soft rot resistance. Based on this observation, tubers from each individual were collected and assessed in a Pectobacterium soft rot assay to identify any potential DNA segments associated with soft rot resistance. Five cm-thick slices were taken from each tuber and placed on separate Petri dishes for inoculation. Tuber slices were inoculated with soft rot bacteria in the center of each slice and incubated for 48 hours. After incubation, soft rot lesions were measured. Segregation for soft rot resistance and susceptibility was observed in the population. This information is being shared with collaborators to advance the development of genetic markers for use by potato breeders. Developing markers for introgression of beneficial markers will allow breeders to more effectively select and track the incorporated markers.
For Objective 3, to develop and deploy molecular markers in the breeding program, increased testing of third year field material has been done. In previous years, only potato virus Y resistance markers were utilized in the breeding program, and these were used only on material from virus-specific crosses at the second-year field stage. This year, that testing was moved to the third-year selections. At this stage in the program, the advancing breeding lines have been vetted for yield, processing quality, specific gravity (which influences processing), and internal defects. Although there are fewer entries at this stage, more markers can be used. The markers now include potato virus Y, tobacco rattle virus, potato leafroll virus, and potato cyst nematode (PCN). With the smaller number of entries in the advanced material, all lines were tested for the available markers, not just those with maker pedigrees, allowing for the identification of markers in germplasm not previously characterized for virus resistance.
In support of Objective 4, for research on new and emerging diseases such as potato mop-top virus (PMTV) and PCN, work was done to finish analyses of samples from field plots for PMTV. These samples represented three standard industry varieties which are susceptible to PMTV and four new varieties that have been reported to have resistance or at least tolerance to PMTV. This work represents four years of field trials in two locations in Idaho. Results show the incidence of symptoms and include reverse transcription-polymerase chain reaction (RT-PCR) testing to determine if the varieties with no tuber symptoms are virus-positive and therefore asymptomatic. Results show that all varieties tested are susceptible, and except for Castle Russet, have some level of asymptomatic virus infection. These results show that it is difficult to control this disease by relying on visual tuber symptoms alone.
To improve PMTV testing efficiency and accuracy, work was done to determine the effect of cross contamination when sampling and the distribution of viral particles across tuber samples. To determine viral distribution of PMTV across tuber samples, viral loads across several different sections of infected tubers were tested. Subsections of different tubers were taken across many tuber sections and included necrotic and non-necrotic tissue. Each subsection was tested for virus quantity using quantitative polymerase chain reaction (qPCR) to look for differences across the tubers. This study showed that at high PMTV infection rates, the virus is evenly distributed in all parts of the tuber and effective sampling can be taken from any part of the tuber. Samples taken from tubers using different tools and decontamination strategies were evaluated to determine the effect of cross contamination in PMTV sampling. Potato cores and knives were used to test decontamination times using ethanol, flaming, Virkon® disinfectant, bleach, and boiling vinegar. In testing these tools and decontamination methods, several produced false positives. This work has demonstrated not only the efficacy of qPCR in detecting PMTV, but also the risk of false positives from cross contamination when testing for PMTV.
Accomplishments
1. Advanced potato breeding line with potato cyst nematode resistance. Potato cyst nematodes are a quarantine pest limiting export throughout the world. Resistant varieties are a sustainable tool that can be used to reduce nematode populations and allow potato production in previously infested areas. Without the use of fumigants or resistant varieties, this pest can reduce yields by up to 80%. ARS researchers in Aberdeen, Idaho, have created a potato breeding line, A16261-2PCN, which has now reached the advanced stage in the potato breeding program. This line has resistance to the potato cyst nematode, Globodera pallida, at a level of 5 and to G. ellingtonae at an 8 (scale is 1-9, with 9 most resistant). This breeding line is now 4-5 years away from release as a new variety. Development of a new variety typically takes 12-15 years. This is the first line to reach this stage of development. At the advanced trial stage, all further trials of this line are conducted by university partners in anticipation of a variety release.