Research Project: Potato Genetic Improvement for Enhanced Tuber Quality and Greater Productivity and Sustainability in Western U.S. Production

Location: Small Grains and Potato Germplasm Research

2022 Annual Report

Objectives
This project intends to produce improved potato germplasm and varieties with emphasis on the predominant market class for the western U.S. which is characterized by long tubers and russet skin. Improved varieties will be suitable for potato processing, as well as fresh consumption. The objectives below will be the specific focus for the next five years for the project scientists Novy and Whitworth: Objective 1: Use conventional and genomic technologies to develop improved potato germplasm and varieties representative of the primary market classes grown in the western U.S. with the following enhancements being emphasized: • Subobjective 1A: Improve Disease and Pest Resistance • Subobjective 1B: Improve Tuber Qualities for Processing and Fresh Use • Subobjective 1C: Reduce Production Inputs • Subobjective 1D: Enhance Nutritional Value Objective 2: Accelerate breeding for resistance to potato pathogens and pests using genomic technologies. Objective 3: Identify and utilize pathogen and pest resistance specific to potato cyst nematode (PCN) and tuber necrotic viruses (Potato virus Y, Potato mop-top virus, and Tobacco rattle virus), and characterize foliar and tuber responses of potato varieties and germplasm to the tuber necrotic viruses.

Approach
Objective 1 is non-hypothesis driven research with the goal of developing potato germplasm and varieties with tuber qualities, disease and pest resistance, and sustainable production that is superior to current industry varieties, with emphasis on primary market classes grown in the western U.S. Varieties and germplasm obtained from other breeding programs, as well as breeding clones of species and their enhanced progeny from ARS collaborators, will be hybridized with adapted parent material in our program using a modified backcross where different cultivated parent clones are used in each backcross to minimize inbreeding depression. Progenies will be screened over multiple years for enhanced traits and agronomic performance in replicated multi-site field trials in the western U.S. Use of molecular technologies (i.e. SNP microarrays, genotyping by sequencing, MAS, and genomic selection) will accelerate development of improved germplasm and varieties. Breeding clones with enhanced traits compared to industry standard varieties will be released as new varieties or as breeding germplasm. As needed, additional germplasm from outside of our program will be requested and utilized as parental material in hybridizations to generation unique populations that expedite trait enhancement. Objective 2 is non-hypothesis driven research utilizing molecular markers with close linkage to genes conferring pest and disease resistance. Molecular markers to resistance genes for Potato virus Y, Potato leafroll virus (PLRV), and potato cyst nematode will be utilized in marker-assisted selection (MAS). Genomic technologies, including SNP microarrays, will be used to identify new genes and quantitative trait loci (QTLs) for resistance. Mapped genes and QTLs will be sequenced and primers developed for MAS. Development of new MAS protocols is important for breeding resistance to emerging diseases (i.e. Potato mop-top virus (PMTV) and zebra chip disease. MAS application will fast-track identification of resistant individuals and facilitate the development and release of potato germplasm and varieties with enhanced disease resistance. If markers in the literature prove unsatisfactory for MAS, then we would work to identify suitable markers, as was previously done by our project for a PLRV resistance gene. Objective 3 is non-hypothesis research focusing on the screening of diverse potato germplasm and characterization of infection-response to potato cyst nematode and three tuber necrotic viruses: PVY, (PMTV), and Tobacco rattle virus (TRV). Field evaluations for response to infection will be conducted by our project (PVY), as well as with collaborators in Washington and North Dakota (PMTV and TRV). Resistant individuals will be utilized in the breeding program as parents with incorporation of resistance conducted utilizing the modified backcross method describe in Objective 1. If levels of resistance for PCN and the tuber necrotic viruses cannot be identified within project germplasm, then new parental material with desired characteristics will be obtained from the U.S. Potato Genebank and other national and international public and private breeding programs

Progress Report
In support of Sub-objective 1A, research continued using several thousand potato breeding clones that were planted, maintained, and evaluated at multiple sites. Evaluations included yield and disease screening within the project and with collaborators throughout the United States. Seed of all breeding clones was maintained at three increase sites in Idaho. Stocks of breeder seed representing these clones were tested for viruses to mitigate infection in seed used for planting. An advanced clone was released and named ‘Becca Rose’. It is a bright red-skin, white-flesh potato variety. It has a high percentage of 2-6 ounce tuber compared to ‘Chieftain’ and ‘Dark Red Norland’ varieties, the industry standards. There is industry interest in this variety from Mid-West producers. One hundred and fifty-two parental clones representing a total of 608 plants were grown in greenhouses in 2022 at Aberdeen, Idaho. Hybridizations were made among them for the generation of true potato seed, which is the starting point for the generation of new populations in the breeding program. From the successful hybridizations, true potato seed was extracted, counted, and organized in the fall of 2021. This spring, seedlings from that true potato seed were generated and grown in greenhouses to produce ‘seedling’ tubers for planting in the field in 2023. A second greenhouse crop of seedlings will be grown this fall and those seedling tubers will be planted with the spring-produced seedling tubers. Last year, this same process yielded 311 families produced in the greenhouse. The harvested seedling tubers are planted each year on approximately 25 acres in Aberdeen and selections are made in the fall from this first field year material principally based on tuber type and shape. Each plant from a tuber represents unique genetics with the potential to be developed as a new variety. Directed hybridizations are made specifically for disease and pest resistance, as well as for better tuber quality, enhanced nutritional qualities, traits that require less fertilizer, water, and other inputs to make potato more sustainable. These research efforts contribute to all four sub-objectives of Objective 1. As a part of Sub-objective 1B, the National Fry Processing Trials (NFPT), financially supported by the potato processing industry, included 66 entries (breeding clones) from seven states in 2022. Thirty-two of those entries originated from this project. The NFPT program seeks to identify advanced breeding clones that perform well under multiple environments and have low tuber sugars (reducing sugars) for processing. Our project serves as one of six trial sites for the NFPT where entries were planted, maintained, and data collected and provided to the national project. In support of Sub-objective 1C, research continued by evaluating advanced breeding clones for nitrogen use efficiencies, with further development of protocols for water use efficiency trials. This work was done in collaboration with the University of Idaho as part of the Northwest Potato Variety Development Program. These trials were conducted at Aberdeen, Idaho. In support of Sub-objective 1D, research continued with collaborators in assessment of advanced breeding clones from the Aberdeen potato breeding program. This included evaluating vitamin C and glycoalkaloid content in tubers as well as assessments for protein and other components present in potato tubers. Collaborating institutions included the University of Idaho and Washington State University. In support of Objective 2, the use of the project’s recently developed multi-plex PCR assay that streamlines the identification of Potato virus Y resistance genes has led to more efficient identification of resistant plants for selection as new breeding lines. This selection is done at harvest and the breeder is provided with resistance data. Other molecular markers that identify nematode resistance are also being evaluated by a collaborator for use on this project’s germplasm. In support of Objective 3, research continues through greenhouse experiments for potato variety expression of Potato virus Y symptoms. This is done prior to release of a new variety with the information being included in the variety publication. Potato mop-top virus trials are ongoing in infested fields. Two trials are in place; one has industry accepted varieties and the other has new germplasm. They are both evaluated in a similar manner for tuber symptoms and for the presence of virus in asymptomatic tubers to determine virus resistance. Hybridizations are also being done for resistance to the white potato cyst nematode (PCN) (G. pallida). These hybridizations were crossed using pollen and flowers from parent clones where at least one had PCN resistance. In the spring of 2022, nine families comprising 1,013 clones were planted. From the 2021 harvest, 195 PCN breeding lines were selected and planted in the field in 2022 as second year selected material. For context, this equals 14.8% of this second year material.

Accomplishments
1. Release of new potato variety ‘Becca Rose’. ARS researchers in Aberdeen, Idaho, released a new potato variety to the industry named ‘Becca Rose’. It is a bright red-skin, white-flesh potato variety. It retains its red skin color following extended storage. Reduction of red color occurs in many red-skin varieties. It was compared to ‘Dark Red Norland,’ an industry standard, and both have short natural dormancy, with longer dormancy maintained in storage with sprout suppressants or inhibitors. ‘Becca Rose’ has a smaller size profile than ‘Dark Red Norland’ at 4.4 oz. compared to 6.4 oz., respectively. The smaller size is a premium size for this market class. Total yield and premium yield (2-6 oz. size) are higher for ‘Becca Rose’ both in weight and percentage of yield than for ‘Dark Red Norland’ and ‘Chieftain’, another industry standard red. There is industry interest in this variety from mid-west producers.

Review Publications
Park, J., Massa, A.N., Douches, D., Coombs, J., Akdemir, D., Yencho, G.C., Whitworth, J.L., Novy, R.G. 2021. Linkage and QTL mapping for tuber shape and specific gravity in a tetraploid mapping population of potato representing the russet market class. Biomed Central (BMC) Plant Biology. 21. Article 507. https://doi.org/10.1186/s12870-021-03265-2.
Elison, G.L., Novy, R.G., Whitworth, J.L. 2021. Russet potato breeding clones with extreme resistance to potato virus Y conferred by Rychc as well as resistance to late blight and cold-induced sweetening. American Journal of Potato Research. 98:411-419. https://doi.org/10.1007/s12230-021-09852-1.
Luttringhaus, S., Pradel, W., Suarez, V., Manrique-Carpintero, N., Anglin, N.L., Ellis, D., Hareau, G., Jamora, N., Smale, M., Gomez, R. 2021. Dynamic guardianship of potato landraces by Andean communities and the genebank of the International Potato Center. CABI Agriculture and Bioscience (CABI A&B). 2. Article 45. https://doi.org/10.1186/s43170-021-00065-4.
Novy, R.G., Whitworth, J.L., Stark, J.C., Spear, R.R., Schneider, B.L., Pavek, M.J., Knowles, N.R., Knowles, L.O., Charlton, B.A., Sathuvalli, V., Yilma, S., Brown, C.R., Brandt, T.L., Wang, Y., Thornton, M., Olsen, N. 2021. La Belle Russet: An early maturing, dual-purpose variety having a high percentage of marketable yield, long tuber dormancy, and a reduced incidence of sugar ends. American Journal of Potato Research. 98:395-410. https://doi.org/10.1007/s12230-021-09853-0.
Hoopes, G., Meng, X., Hamilton, J.P., Achakkagari, S.R., De Alves Freitas Guesdes, F., Bolger, M.E., Coombs, J.J., Esselink, D., Kaiser, N.R., Kodde, L., Kyriakidou, M., Lavrijssen, B., van Lieshout, N., Shereda, R., Tuttle, H.K., Vaillancourt, B., Wood, J.C., de Boer, J.M., Bornowski, N., Bourke, P., Douches, D., van Eck, H.J., Ellis, D., Feldman, M.J., Gardner, K.M., Hopman, J.C., Jiang, J., De Jong, W.S., Kuhl, J.C., Novy, R.G., Oome, S., Sathuvalli, V., Tan, E.H., Ursum, R.A., Vales, M.I., Vining, K., Visser, R.G., Vossen, J., Yencho, C., Anglin, N.L., Bachem, C.W., Endelman, J.B., Shannon, L.M., Stromvik, M.V., Tai, H.H., Usadel, B., Buell, C.R., Finkers, R. 2022. Phased, chromosome-scale genome assemblies of tetraploid potato reveal a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity. Molecular Plant. 15(3):520-536. https://doi.org/10.1016/j.molp.2022.01.003.
Prager, S., Cohen, A., Cooper, W.R., Novy, R.G., Rashed, A., Wenninger, E., Wallis, C.M. 2022. A comprehensive review of zebra chip disease in potato and its management through breeding for resistance/tolerance to 'Candidatus Liberibacter solanacearum' and its insect vector. Pest Management Science. 78:3731-3745. https://doi.org/10.1002/ps.6913.
Ramirez-Villegas, J., Khoury, C.K., Achicanoy, H., Diaz, M.V., Mendez, A.C., Sosa, C.C., Kehel, Z., Guarino, L., Abberton, M., Aunario, J., Awar, B., Alarcon, J.C., Amri, A., Anglin, N.L., Azevedo, V., Azia, K., Capilit, G.L., Chavez, O., Chebotarov, D., Costich, D.E., Debouck, D.G., Ellis, D., Falalou, H., Fiu, A., Ghanem, M.E., Giovannini, P., Goungoulou, A., Gueye, B., Hobyb, A.I., Jamnadass, R., Jones, C.S., Kpeki, B., Lee, J., McNally, K.L., Muchugi, A., Ndjiondjop, M., Oyatomi, O., Payne, T.S., Ramachandran, S., Rossel, G., Roux, N., Ruas, M., Sansaloni, C., Sardos, J., Setiyono, T., Tchamba, M., van den Houwe, I., Velazquez, J.A., Venuprasad, R., Wenzl, P., Yazbek, M., Zavala, C. 2022. State of ex situ conservation of landrace groups of 25 major crops. Nature Plants. 8:491-499. https://doi.org/10.1038/s41477-022-01144-8.
Perez, W., Alarcon, L., Rojas, T., Correa, Y., Juarez, H., Andrade-Piedra, J., Anglin, N.L., Ellis, D. 2022. Screening South American potato landraces and potato wild relatives for novel sources of late blight resistance. Plant Disease. 106(7):1845-1856. https://doi.org/10.1094/PDIS-07-21-1582-RE.
Eastwood, R.J., Tambam, B.B., Aboagye, L.M., Akparoz, Z.I., Aladele, S.E., Allen, R., Amri, A., Anglin, N.L., Araya, R., Arrieta-Espinoza, G. 2022. Adapting agriculture to climate change: a synopsis of coordinated national crop wild relative seed collecting programs across five continents. Plants. 11(14). Article 1840. https://doi.org/10.3390/plants11141840.