Location: Small Grains and Potato Germplasm Research
2024 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
Objective 1 -develop and release improved trait potato varieties. Sub-obj.1a -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-obj.1b -developing pest and pathogen resistance in selections to be done in randomized complete block (RCB) trials for bacterial, fungal, virus and nematode resistance. Sub-obj.1c -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 progress for project 2050-21000-036-000D, titled, “Genetic Improvement of Potato for Sustainable Production and Enhanced Tuber Qualities for the Western United States”, which started in March 2023.
In support of Objective 1, research continued with Plant Variety Protection (PVP) and licensing was completed on new varieties ‘Becca Rose’ and ‘Rainier Russet’. Both varieties originated from the breeding program with release by USDA and the associated university Cooperative Research and Development Agreement partners (CRADA). ‘Rainier Russet’ has similar total yield when compared with ‘Russet Burbank’, the industry standard but has higher marketable (U.S. No. 1 tuber) yields. In addition, to good nutritional characteristics such as high protein, it also has good processing characteristics for French fries and other frozen products. ‘Rainier Russet’ also has resistance to common scab, a significant skin defect and dry rot, a tuber defect caused by the fungus Fusarium solani var. sambucinum. This variety also has a long tuber dormancy comparable to ‘Russet Burbank’ allowing longer off-season storage times compared to other varieties. Seed acreage of this variety is just starting to get into grower fields with 8.5 acres of seed produced in 2024 which represents enough to plant 85 commercial acres.
The variety ‘Becca Rose’ had 11 seed acres in 2023, enough to produce 100 acres of red skin-colored potatoes. This variety has a better fresh market profile than the industry standards with a high percentage in the two-to-six-ounce range, very desirable for the market. Interest has also been expressed in the commercialization of ‘Becca Rose’ in Uruguay, where trials there have shown high merit for this variety.
Development of these two varieties also supports Sub-objective 1.A for improved processing and fresh market traits and Sub-objective 1.B for improving pest and pathogen resistance.
Upcoming possible releases include A12305-2adg and AFA5661-8. The A12305-2adg breeding line has the Ryadg marker that identifies an important key gene that provides complete resistance to Potato virus Y (PVY). These possible releases support Sub-objective 1.B. PVY causes yield loss and in some cases causes tuber defects, that at a rate of 5% or higher, makes the crop unmarketable. Both lines have higher total and U.S. No. 1 tuber yields at both an early and a late harvest time than the industry standard ‘Russet Burbank’ (in 2022 and 2023). These types of yields indicate that these lines can be grown profitably across many different environments and harvest dates. These advanced breeding lines have been trialed in the National Fry Processing Trials which are conducted across multiple states and represent industry engagement on the decision to release them as new varieties.
In support of Objective 1 and Objective 3, using second year field material, 47 out of 163 entries were selected for agronomic type and Potato virus Y (PVY) resistance (28.8%) utilizing marker assisted selection (MAS). Of those, 41 were confirmed for the presence of the Ry genes with marker assisted selection which ultimately provides complete resistance to all strains of PVY. PVY is a significant seed certification and production problem for potato in the United States and found in most places where potatoes are grown. This represents a large increase in the incorporation of these Ry genes in this potato breeding program. In 2020, only 14 entries with Ry genes were selected out of 187 entries (7.5%) and has resulted in the program developing a multiplex PCR assay to more rapidly test for desired traits via marker assisted selection (Objective 3).
For potato cyst nematode resistance, in support of Objectives 1 and 4, three entries were selected for agronomic type and potential nematode resistance. Parental background on two of these have the GpaIV gene from the variety 'Eden' obtained from the United Kingdom and one has the Gpa5 gene from the South American variety 'Maria Huanca'. Both of these genes have some resistance to Globodera pallida, a cyst nematode present in Idaho. Work is ongoing in the program to pyramid these resistance genes to give higher levels and more durable resistance to potato cultivars. These selections and nine others have been sent for testing for resistance against G. pallida to a collaborating scientist at the University of Idaho. Previous results from the lab showed high resistance scores (7 and 8 from a 1-9 scale where 9 is highly resistant) have been reached.
In support of Objective 2, research on sequencing and assembling wild potato genomes that were identified as important to breeding programs due to the diverse traits they harbor compared to cultivated potato, has made significant progress. Thirty-five wild genomes were identified and sequenced using next generation sequencing technologies (PE150 short Illumina reads). The data was filtered and assembled de novo and reference guided to produce an initial assembly of each genome. Assembly statistics were calculated to demonstrate the quality of each sequenced and assembled genomes. Twenty-three of those genomes were compared to one another and submitted for publication. The remaining genomes are undergoing further data analysis by collecting long sequencing reads to improve the quality of the assemblies and identifying key traits of importance in their genomes. Because many of these genomes are highly heterozygous and have more than two copies of DNA (polyploid), they are more complex to produce a good quality genome, thus, long reads may help to improve the current assemblies.
Also in support of Objective 2, a biparental mapping population that includes a Solanum tuberosum (cultivated) x Solanum microdontum hybrid (wild x cultivated) parent has also been evaluated. This population is of interest due to the parents segregating for tuber greening resistance which is an important trait to the potato industry. This population has been genotyped and evaluated for resistance to tuber greening, total glycoalkaloids and morphological traits. Additional, phenotyping and data analysis is forthcoming.
Under Objective 3, ARS scientists published research that helps identify genetic signals associated with virus resistance. A genome wide association study (GWAS) was carried out on a biparental mapping population that was fingerprinted and characterized for virus resistance to two significant potato diseases: Tobacco Rattle Virus (TRV) and Potato Mop Top Virus (PMTV). A clear single quantitative trait locus (QTL) was found on chromosome 9 associated with all of the collected traits for Tobacco Rattle Virus resistance. Multiple signals (QTLs) were discovered for another significant potato virus, PMTV. This data can be used as a starting point to develop molecular markers to screen and identify resistance in potato against Tobacco rattle virus (TRV) and Potato Mop-Top Virus (PMTV). For further development of molecular markers associated with agronomic traits, published research from this program showed that QTLs were discovered that influence tuber shape characteristics. These traits are prioritized by industry to help reduce waste and improve processing efficiencies and include length-width ratios along with tuber size and flatness, and specific gravity, a measurement of solids in a tuber.
For Objective 4, screening of seven widely grown russet varieties for symptom reaction and susceptibility to Potato Mop-Top Virus (PMTV) is complete and results are being reviewed. The variety 'Castle Russet' has some resistance to PMTV and many populations have been created using ‘Castle’ as a parent. This work is helping to determine the level of resistance present, and this program is working with other ARS scientists in Prosser, Washington, to identify wild species accessions that may have higher resistance.
Accomplishments
1. Helping growers and seed certification experts recognize subtle symptoms of a damaging potato virus. Potato Virus Y (PVY) is a significant potato disease that causes internal defects to the flesh and can lead to rejection of potatoes in the marketplace. Agronomic controls are available for this virus, but because it is transmitted by aphids that rapidly probe the potato plant and transfer the virus prior to the ability of applied pesticides to kill the aphid, the virus spreads easily and quickly in potato. Further, because of the changes in PVY strain composition in the U.S. with foliar infection not always showing severe morphological symptoms, the traditional seed certification process has not been as effective which traditionally has relied on unusual appearance through visual inspections to detect PVY infection. ARS researchers in Aberdeen, Idaho, have responded by coordinating a training event for seed growers and seed certifiers to showcase the issues with PVY strains by inoculating different strains of the virus onto known potato varieties and hosting field days. These demonstrations have been held four times in eight years in three states (Washington, Wisconsin, and Maine). Varieties were selected and targeted for those states in which the field day was held and included three different PVY strains planted next to healthy plants, so members of the potato industry and seed certification officials can visualize the subtle differences in symptoms by virus strain with some showing no visual symptoms at all and others being crippling to the plant’s ability to grow normally. Visitors to these field days have remarked at the uniqueness of virus symptoms which was dependent on the potato variety, virus strain, and the environment in which it was grown.
Review Publications
Park, J., Whitworth, J.L., Novy, R.G. 2024. QTL identified that influence tuber length-width ratio, and degree of flatness, tuber size, and specific gravity in a russet-skinned, tetraploid mapping population. Frontiers in Plant Science. 15. Article 1343632. https://doi.org/10.3389/fpls.2024.1343632.
Agha, H.I., Endelman, J.B., Chitwood-Brown, J., Clough, M., Coombs, J., De Jong, W.S., Douches, D.S., Higgins, C., Holm, D., Novy, R.G., Resende, M.F., Sathuvalli, V., Thompson, A.L., Yencho, G.C., Zotarelli, L., Shannon, L.M. 2024. Genotype-by-environment interactions and local adaptation shape selection in the US National Chip Processing Trial. Theoretical and Applied Genetics. 137. Article 99. https://doi.org/10.1007/s00122-024-04610-3.
Elison, G.L., Park, J., Novy, R.G., Whitworth, J.L. 2024. A potential new source of extreme resistance to Potato virus Y in the potato variety Bistra. American Journal of Potato Research. 101:248-256. https://doi.org/10.1007/s12230-024-09954-6.
Balendres, M.A., Woodhall, J., Whitworth, J.L., Cumagun, C. 2024. Powdery scab of potato: A diagnostic guide. Plant Health Progress. 25(3):334-339. https://doi.org/10.1094/PHP-11-23-0097-DG.
Bozan, I., Achakkagari, S., Anglin, N.L., Ellis, D., Tai, H., Stromvik, M. 2023. Pangenome analyses reveal impact of transposable elements and ploidy on the evolution of potato species. Proceedings of the National Academy of Sciences (PNAS). 120(31). Article e2211117120. https://doi.org/10.1073/pnas.2211117120.
Achakkagari, S., Bozan, I., Camargo-Tavares, J.C., McCoy, H.J., Portal, L., Soto, J., Bizimungu, B., Anglin, N.L., Manrique-Carpintero, N., Lindqvist-Kreuze, H., Tai, H., Stromvik, M. 2024. The phased Solanum okadae genome and Petota pangenome analysis of 23 other potato wild relatives and hybrids. Scientific Data. 11. Article 454. https://doi.org/10.1038/s41597-024-03300-5.
Anglin, N.L., Yellarreddygari, S.K., Gudmestad, N.C., Sathuvalli, V., Brown, C., Feldman, M.J., De Jong, W.S., Douches, D.S., Novy, R.G., Coombs, J.J. 2023. A genome wide association study (GWAS) identifies SNPs associated with resistance to Tobacco rattle virus (TRV) and Potato mop-top virus (PMTV) in a tetraploid mapping population of potato. American Journal of Potato Research. 101:1–16. https://doi.org/10.1007/s12230-023-09933-3.