Source: MICHIGAN STATE UNIV submitted to NRP
DEVELOPMENT OF MULTIPURPOSE POTATO CULTIVARS WITH ENHANCED QUALITY, DISEASE AND PEST RESISTANCE – NORTH CENTRAL REGION 2021-23
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
SPECIAL GRANT
Reporting Frequency
Annual
Accession No.
1026969
Grant No.
2021-34141-35447
Cumulative Award Amt.
$1,644,777.37
Proposal No.
2021-06091
Multistate No.
(N/A)
Project Start Date
Sep 1, 2021
Project End Date
Aug 31, 2024
Grant Year
2022
Program Code
[AN]- Potato Research
Recipient Organization
MICHIGAN STATE UNIV
(N/A)
EAST LANSING,MI 48824
Performing Department
PLANT SOIL MICROBIAL
Non Technical Summary
Potato production is in the North Central US is vital to the regional economy and plays an important role in the national potato supply. The four states of Michigan, Minnesota, North Dakota, and Wisconsin accounted for almost a quarter of the US acreage, with a farm-gate value of about $1 billion. All sectors of the potato market are present in this region, dominated by fry and chip processing markets, with a successful fresh market and expanding specialty market niches. Changes in climate, consumer preference, production economics, and environmental regulations require continual innovation in the potato industry, and plant breeding leading to variety commercialization is critical to meeting these evolving demands. This proposal, which is a joint effort of the potato breeding and genetics programs at four North Central land-grant universities (UW, MSU, NDSU, UM). There are four specific objectives detailed: 1) Identify new varieties with superior agronomics and end-used quality via sexual hybridization and selection at the tetraploid and diploid level, 2) Screen elite germplasm for resistance to key pests, 3) Leverage genomic tools to enhance breeding efficiency, and 4) Commercialization of new variety releases for stakeholder adoption. The four project directors and their collaborators have the requisite experience, facilities, and stakeholder relationships to successfully complete these objectives. The expected outcomes from the two-year grant include the release of new varieties, the selection of new breeding lines, new markers for marker-assisted selection, and preliminary data on the feasibility of using a rapid cycling genome-wide marker analyses for improving variety development.
Animal Health Component
40%
Research Effort Categories
Basic
20%
Applied
40%
Developmental
40%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2011310108050%
2011310108150%
Knowledge Area
201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
1310 - Potato;

Field Of Science
1081 - Breeding; 1080 - Genetics;
Goals / Objectives
1. Identify new varieties with superior agronomic traits and end-used quality via sexual hybridization and selection at the tetraploid and diploid levels.2. Screen elite germplasm for resistance to key pests.3. Leverage genomics tools to enhance breeding efficiency.4. Commercialization of new variety releases for stakeholder adoption.
Project Methods
Objective 1.The current timeline from crossing to varietal release is over 12 years. The four cooperating breeding programs will establish crossing blocks at university greenhouses using favorable clones as parental lines from within and among breeding programs. Elite clones are intercrossed to synthesize new segregating seedling populations. We also make crosses to less adapted clones (e.g., wild-elite hybrids) developed by USDA collaborators (e.g., from the Vegetable Crops Research Unit, Madison, WI) and others to incorporate novel genes for disease resistance and other key traits. True potato seed will be sown in greenhouses and harvested to generate seedling tubers for the first field generation. Phenotypic evaluation of clones over time and locations is the current state of art for potato breeding. As many as 200,000 unique clones will be evaluated as single-hill plots, over 95% of which will be culled based on visual selection. Around 5,000 second-year clones will be planted in larger plots (4, 8, or 12-hill), and the number of third-year clones is typically 1,000-2,000. Across the four breeding programs, approximately 400 Year 4 clones will be evaluated in replicated trials within their originating state and in unreplicated trials at the other three locations.Objective 2.Late Blight:MSU will screen clones that have pedigrees with a known source of late blight resistance at the MSU campus in East Lansing. A US-23 P. infestans isolate will be applied through the irrigation system to conduct inoculated field trials. The advanced breeding lines are evaluated as three replicates of 5-hill plots, whereas the early generation material is a 5-hill single plot observation. The border of the field and spreader rows are planted to susceptible lines to promote disease development. MSU has the capacity to screen up to 500 early generation and 200 advanced breeding lines per year. Individual lines and mapping populations are also assayed using detached leaf bioassays. NDSU and UW employ a detached leaf assay to evaluate segregating populations. Replicated field trials in subsequent generations at NDSU are used to quantify foliar resistance and to test for tuber resistance.Colorado potato beetle:The Montcalm Research Center (MSU) has maintained a field nursery to evaluate foliar damage by the Colorado potato beetle for over 40 years. Border field and spreader rows are planted to a susceptible variety and used to attract over-wintering Colorado potato beetle adults. The percent plot defoliation data will be collected throughout the growing season and resistant clones identified. NDSU also screens for CPB defoliation in the field using a similar field design as at the MSU site. In the off-season MSU also uses detached leaf bioassays to assess CPB resistance. Beetle populations are maintained in cages using greenhouse-grown foliage as beetle fodder.Common scab:Advanced and early generation lines are evaluated for scab at the Montcalm Research Center, Entrican, MI, at university fields dedicated to maintaining high disease pressure. Furthermore, a commercial site in Michigan with extremely high disease pressure is being used to evaluate elite chip-processing crosses for scab resistance. The evaluation criteria include number, severity, and percent area of lesions observed on harvested tubers. Advanced breeding lines (in replicated 5-hill plots), as well as first, second- and third-year selections are screened. UW has a scab nursery at the Hancock Research Farm that follows a similar design and assessment. UMN began development of a scab nursery at the Sand Plains Research Farm in the summer of 2020 which will be ready for evaluation of samples in 2023. NDSU is utilizing a commercial site to evaluate selections across market types for scab resistance.Objective 3. We are actively converting the original PCR-based markers, which were evaluated with gels, to more high-throughput platforms, such as KASP and iPLEX. In early 2019 we partnered with International Potato Center (CIP) to validate KASP markers for PVY resistance (Ryadg and Rysto); we have successfully used them during the 2020 field season and will continue to do so for this project. A similar collaboration is underway with PepsiCo for the late blight resistance genes RB and R8.The progeny of the crosses segregating for these marker-linked traits are produced as greenhouse seedling tubers in the first year. The second year these tubers are planted in the field as single hill selections. This evaluation process selects only lines with marketable tuber types and reduces the number of selections to a manageable number for DNA sampling. In the fall, a tuber is sampled for DNA isolation, followed by PCR-based marker analysis. After three to four years the marker data, in combination with the field and storage data, are used to select those lines from the early generation phase, should be advanced to the replicated trial phase of the breeding cycle. Furthermore, some lines may be designated as parents for the 2022 crossing blocks.Objective 4. Commercialization of new variety releases for stakeholder adoption.Our commercialization pipeline has two main components. The first involves producing high quality breeder's seed that can be given to commercial growers for trialing. This participatory research provides valuable feedback about advanced lines and incipient varieties, and it stimulates interest from the growers and industry professionals who are early adopters.

Progress 09/01/23 to 08/31/24

Outputs
Target Audience:Potato breeding and genetics community and the state/national potato industries (growers, processors and marketers. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Each breeding program has graduate students, undergraduates, research technicians and post docs that are conducting research. During their graduate and post graduate training and research they are participating in the breeding program activities of hybridization, planting, field variety trials, disease assessment, grading of trials, post-harvest assessment, dataanalysis, etc. which provides practical training in potato breeding. At the University of Wisconsin 2 undergraduates have gained experience with potato breeding and variety development. At Michigan State University 6undergraduates and 4graduate students gained experience within the potato breeding and genetics field program. At NDSU 5undergraduate student and 2graduate students have gained experiences in agronomic and convention breeding efforts. At the University of Minnesota 1graduate studentcompleted their theses (Hussain Agha). Three graduate students and three undergraduate students received training and experience in the areas of potato breeding and cultivar development. Additionally presentations were made by technicians, graduate students and post docs at the December 2023NCCC215 Breeding and Genetics Technical Committee meeting in Chicago IL and at the July 2023Potato Association of America Meeting to an audience of plant breeders and geneticists. How have the results been disseminated to communities of interest?Research results from this project are reported to the state potato industries in Michigan, Wisconsin, Minnesota and North Dakota through written reports, winter research meetings and summer field days. Information about new varieties and breeding technologies has been presented to stakeholders at several forums, including the January 2024National Potato Expo, the December 2023National Chip and Fry Processing programs of Potatoes USA, the December 2023USDA multistate project NCCC215 (Potato Breeding & Genetics Technical Committee), the annual meeting of the Potato Association of America. Results have been presented at the North Plains Potato Growers' Association (NPPGA) and the Minnesota Area II Potato Research and Promotion Council (Area II) summer field days in Hoople, ND, Inkster, ND, Larimore, ND, and Becker, MN; the NPPGA and Area II joint research planning meeting in Alexandria MN, the winter NPPGA research reporting meeting in East Grand Forks, and the Area II short course. Results from yearly trials were reported during the February 2024NPPGA Research Reporting Conference, February 2024Michigan Winter Potato Conference and the February 2023Wisconsin Winter Potato conference in February. National Outreach Activities: Endelman, Shannon, and Thompson participated in the National Fry Processing Trial and associated meetings. All four co-PDs participated in the National Chip Processing Trial and associated meetings. Douches, representing the NC team, spoke at the January 2024 Potato Expo in Austin Texas to highlight the breeding efforts in the North Central Region. Endelman JB. Feb. 6, 2024. Potato Breeding & Variety Selection: Fundamentals. UW-Madison Extension and WPVGA Grower Education Conference, Stevens Point, WI. Endelman JB. Feb. 8, 2024. Potato Breeding & Genetics. UW-Madison Extension and WPVGA Grower Education Conference, Stevens Point, WI. Douches, DS. February 1, 2024. Potato Breeding and Genetics research report. Michigan Winter Potato Conference. East Lansing, MI. Shannon LM. Feb. 6, 2024. Using Image Analysis to Breed for Potato Quality Traits. UW-Madison Extension and WPVGA Grower Education Conference, Stevens Point, WI. Shannon LM. Feb. 6, 2024. Improving Nitrogen Use Efficiency in Potato. UW-Madison Extension and WPVGA Grower Education Conference, Stevens Point, WI. Shannon LM. Feb 27, 2024. Moving Towards Minnesota Varieties. Area II Short Course, St. Cloud, MN. Thompson, S. Breeding and Development of Resilient Potato Cultivars for the Northern Plains. 2024 International Crops Expo. February 21, 2024. Invited. Thompson, S. Reducing Bruising. 2024 International Crops Expo. February 22, 2024. Invited. Thompson, S. Grand Farm Field Day Crop Breeder Panel. Casselton, ND. March 13, 2024. Invited. Thompson, S. Spuddles, Vader Tots and Small Fries: Let's Talk Potatoes! Field to Fork Series. NDSU Extension. Virtual. March 13, 2024. Invited. Thompson, S. Next Gen Ag Panel 'Everything Potatoes'. Fargo, ND. April 10, 2024. Invited. Thompson, S. NDSU Potato Breeding. NDSU Horticulture Club. NDSU Ag Week. April 16, 2024. Invited Academic Presentations: Shannon LM. May 30, 2024. Exploring potato diversity from multiple angles. National Potato Day. Universidad Nacional Toribio Rodriguez de Mendoza de Amazonas, Peru. Shannon LM. May 24, 2024. Potato 2.0. Center for Precision Plant Genomics Symposium. St. Paul, MN. Shannon LM. March, 2024. The Loaded Potato Genome. The Allied Genetics Conference, Washington DC. Shannon LM. January, 2024. Foundational Germplasm for a New Era of Potato Breeding. Plant and Animal Genome Meeting, San Diego, CA. Yusuf M, Miller M, Stefaniak TR, Shannon LM. January, 2024. Improving genomic prediction of quality related traits using image-based analysis in potato. Polyploid Tools Meeting. San Diego, CA. Yusuf M, Miller M, Stefaniak TR, Shannon LM. December, 2023. Genomic selection of quality traits measured using image-based tools in potato. NCCC215 Potato Breeding and Genetics Technical Committee Meeting, Chicago, IL. Agha HI, Shannon LM. December, 2023. Potato adaptation to environment. NCCC215 Potato Breeding and Genetics Technical Committee Meeting, Chicago, IL. Stefaniak TR, Shannon LM. December, 2023. Introducing Elk River Russet. NCCC215 Potato Breeding and Genetics Technical Committee Meeting, Chicago, IL. Coronejo S, Shannon LM. December, 2023. Diversity in the potato dihaploid panel. NCCC215 Potato Breeding and Genetics Technical Committee Meeting, Chicago, IL. Tuttle H, del Rio A, Bamberg J, Shannon LM. December, 2023. Potato Soup: analysis of cultivated potato genebank populations reveals high diversity and little structure. NCCC215 Potato Breeding and Genetics Technical Committee Meeting, Chicago, IL. Yusuf M, Miller M, Stefaniak TR, Shannon LM. 2023. Genomic selection of quality traits measured using image-based tools in potato. Crop and Soil Science Society, St. Louis, MO. Agha HI, Shannon LM. August, 2023. Evidence of local adaptation in the National Chip Processing Trial. Midwest PopGen Meeting, Ann Arbor, MI. Shannon LM. November, 2023. Baked Boiled and Fried: Potato Diversity Served Three Ways. International Solanaceae Genomics Meeting, Montreal, Canada. Yusuf M, Miller M, Stefaniak TR, Shannon LM. July, 2023. Genomic selection of quality traits measured using image-based tools in potato. Potato Association of America Meeting, Charlottetown, Canada. Stefaniak TR, Harder M, Yusuf M, Shannon LM. July, 2023. Yield and Quality of Red Potato Clones in Response to Variable Nitrogen Application Timings. Potato Association of America Meeting, Charlottetown, Canada. What do you plan to do during the next reporting period to accomplish the goals?In the fall we spend a majority of the time conducting evaluation and selection of the potato germplasm within the breeding program. That involves disease assessment for scab and late blight. We also conduct post-harvest analyses and store potato samples for processing analysis. The data is summarized and used to determine what material to advance as well as what material to consider for commercialization. In the winter crossing blocks are established to initiate the next cycle of the breeding program. DNA marker analysis and genotyping is also conducted in the post-harvest season. Winter is also the reporting season to the stakeholders as well new variety releases. There are also plans to continue expand our genomic selection models to encompass the russets and wider variety of traits. Diploid breeding will also be expanded.

Impacts
What was accomplished under these goals? In the NC region over 5,071 certified seed acres were planted in 2023, to 34 recently released varieties and advanced breeding lines with commercial interest. Although commercial acreage is not trackedby variety, the number of commercial acres can be estimated by multiplying the seed acreage by 10-15. A number of factors are driving theadoption of new varieties developed in our region, including improved agronomic performance and storability, disease resistance, fresh market appearance, and processingquality.MSZ242-13 was released as Dundee in 2023. It is a scab resistant, high solids chip processor. MN04844 was released as Polaris Gold. It is a late season fresh market yellow potato with low internal defects. The commercial acreage for Mackinaw, a PVY, scab and late blight resistant chipper, is expanding in the US. Petoskey, Huron Chipper and Blackberry seed acreage is increasing. Certified seed potato production for Dakota Russet, a dual-purpose russet with frozen processing potential (approved for McDonald's French fry production in 2022) with resistance to the sugar end disorder, cold sweetening, pink rot and southern rot, and moderate resistance to Verticillium wilt and Pythium leak, moved into the top 10 cultivars grown in North America. Certified seed production and grower/industry evaluation of several advancing selections including ND7799c-1 (130 acres), ND113207-1R (15 acres), ND1241-1Y (50 acres), and ND13220C-3 continued to expand. A PVP certificate was filed for Lakeview Russet. Portage Russet was released as a processing variety. PVP application (PV2000389) was submitted for Dakota Dawn. Scab resistance, late blight resistance, Verticillium wilt resistance, and PVY resistance is being introgressed into advanced breeding lines for the chip processing, frozen processing, and table (red, yellow and white skins) markets. The majority of the MSU advanced breeding lines have scab resistance. Over 50% have PVY resistance. Late blight resistance is found in about 10% of the lines. Genomic selection was used for parent selection in 2023 in the UW chip program based on a multi-trait index for total yield, specific gravity, fry color, and maturity. At UMN, genomic selection was used for yield, specific gravity, tuber shape, and tuber color in fresh market and chipping potatoes. Variety releases from NDSU and MSU lead seed production acreage in the region. Variety development is the core function of the project. Across our four states, more than 900segregating populations with over 80,000 seedlings were generated in 2023/24. This leads to early generation evaluation of second, third- and fourth-year clones with increasing selection pressure taking into account disease testing, marker screening, agronomic performance and post-harvest storage testing. Over 300 lines were evaluated in in-state trials and over 200 lines were evaluated in multistate trials. These include lines for the chip processing selections from the four breeding programs that participate in the National Chip Processing Trial (NCPT), which is managed by Potatoes USA. MSU, NSDU and UW manage test sites. Fry processing selections entered the National Fry Processing Trial (NFPT), which is also managed by Potatoes USA, and for which NDSU and UW manage test sites. Disease and pest testing is integrated with the selection stages of the breeding programs. A key impact has been theRyadg gene for potato virus Y resistance. Recent variety releases from MSU, including Saginaw Chipper (2016) and Mackinaw (2018), contain this late blight and PVY resistance. A KASP marker for this gene was developed in 2021 and is now being used for marker-assisted selection. The Ryadg gene from S. tuberosum ssp. andigena and Rysto gene from S. stoloniferum are present in a number of elite parents used for crossing in the North Central region. In 2023over 750 clones have been screened for PVY resistance in the North Central region. Progress in breeding for scab tolerance has been made by conducting phenotypic selection in dedicated scab fields in MI and WI. information is used in determining continuation in the breeding pipeline, parental selection, and in development of cultivar specific management guidelines. At MSU over 1,200 scab nursery plots were evaluated for scab resistance. Scab resistance is found across a wide range of germplasm at both 4x and 2x ploidy levels. For the University of Wisconsin (UW), thegenomic selection model for the chip processing market was updated based on yield, specific gravity, vine maturity, and fry color data collected in 2023. The multi-trait selection index targets equal genetic gain (in standardized units) for yield, specific gravity and fry color, without increasing maturity. In addition to these quantitative traits, UWprioritized parents with (1) extreme PVY resistance from one of two sources, Ryadg or Rychc; (2) P- or T cytoplasm, and (3) low levels of total glycoalkaloid in tubers (<20mg/100g FW). 44 unique parental combinations were realized during the January-March 2024 crossing block in the greenhouse, involving 16 different parents and totaling 43,000 true seeds.UMN has developed a series of genomic selection models for fresh market and chipping potatoes. For fresh market potatoes our models predict yield, skin color, and shape while our models for chipping potatoes predict yield, specific gravity, and shape. These models were used to choose parents for a tetraploid crossing block which forms our 2024 FY1. Over the past two years we have collected multispectral drone data at 6 time points. Including this data in our genomic selection models has significantly improved our prediction accuracy for most traits. Parents chosen using this combined data set are in our current crossing block. We are making both the predicted best crosses and crossing to PVY resistant individuals to bring resistance into our breeding program especially for fresh market material. In conclusion, the outcomes of this project is improved potato varieties such as Dakota Russet, Mackinaw, Manistee, Plover Russet and the specialty potato Blackberry, that drive economic development for the potato industry. Secondly, we develop cultivated germplasm that is enhanced for disease, virus and insect resistances and traits that will continue to improve market quality. The germplasm is shared among the breeding programs, and it leads to long-term projected impact. As a human capacity investment activity, we also train the next generation of research scientists and breeders that are hired within and beyond the potato industry and public research institutions.

Publications

  • Type: Journal Articles Status: Published Year Published: 2024 Citation: Feldman MJ, Park J, Miller N, Wakholi C, Greene K, Abbasi A, Rippner D, Navarre D, Schmitz Carley CA, Shannon LM, Novy R. (2024). A scalable, low-cost phenotyping strategy to assess tuber size, shape, and the colorimetric features of tuber skin and flesh in potato breeding populations. The Plant Phenome Journal. 7 (1)
  • Type: Other Status: Published Year Published: 2023 Citation: Potato breeding and genetics community and the state/national potato industries (growers, processors and marketers.
  • Type: Other Status: Published Year Published: 2023 Citation: Thompson, S. 2023. Crystal Fresh Market Trial  2022 Summary. Valley Potato Grower 88(302):16-21.
  • Type: Other Status: Published Year Published: 2024 Citation: Douches, DS. 2023 MSU Potato Breeding and Genetics Research Report. January 2024.
  • Type: Other Status: Published Year Published: 2024 Citation: Douches, DS. 2023 MSU Potato Variety Trial Report. January 2024.
  • Type: Journal Articles Status: Published Year Published: 2024 Citation: Endelman JB, Kante M, Lindqvist-Kreuze H, Kilian A, Shannon LM, Caraza-Harter MV, Vaillancourt B, Malloux K, Hamilton JP, Buell CR (2024) Targeted genotyping-by-sequencing of potato and data analysis with R/polyBreedR. The Plant Genome.
  • Type: Journal Articles Status: Published Year Published: 2024 Citation: Asano K, Endelman JB (2024) Development of KASP markers for the potato virus Y resistance gene Rychc using whole-genome resequencing data. American Journal of Potato Research 101:114-121. https://doi.org/10.1007/s12230-024-09944-8


Progress 09/01/21 to 08/31/24

Outputs
Target Audience:Potato breeding and genetics community and the state/national potato industries (growers, processors and marketers). Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Each of the four breeding programs has graduate students, undergraduates, research technicians and post docs that are conducting research. During their graduate and post graduate training and research they are participating in the breeding program activities of hybridization, planting, field variety trials, disease assessment, grading of trials, post-harvest assessment, data analysis, etc. which provides practical training in potato breeding. For example, at the University of Wisconsin 2 undergraduates have gained experience with potato breeding and variety development. At Michigan State University 6 undergraduates and 4 graduate students gained experience within the potato breeding and genetics field program. At NDSU 5 undergraduate student and 2 graduate students have gained experiences in agronomic and convention breeding efforts. At the University of Minnesota 1 graduate student completed their theses (Hussain Agha). Three graduate students and three undergraduate students received training and experience in the areas of potato breeding and cultivar development. Additionally presentations were made by technicians, graduate students and post docs at the annual Decembe NCCC215 Breeding and Genetics Technical Committee meeting in Chicago IL and at the annualPotato Association of America Meeting to an audience of plant breeders and geneticists. How have the results been disseminated to communities of interest?Research results from this project are reported to the state potato industries in Michigan, Wisconsin, Minnesota and North Dakota through written reports, winter research meetings and summer field days. Information about new varieties and breeding technologies has been presented to stakeholders at several forums, including the annual JanuaryNational Potato Expo, the annual DecemberNational Chip and Fry Processing programs of Potatoes USA, the annual DecemberUSDA multistate project NCCC215 (Potato Breeding & Genetics Technical Committee), the annual meeting of the Potato Association of America. The co-PDs also have results have been presented to state-wide meetings/conferences such asthe North Plains Potato Growers' Association (NPPGA) and the Minnesota Area II Potato Research and Promotion Council (Area II) summer field days in Hoople, ND, Inkster, ND, Larimore, ND, and Becker, MN; the NPPGA and Area II joint research planning meeting in Alexandria MN, the winter NPPGA research reporting meeting in East Grand Forks, and the Area II short course. Results from yearly trials are reported during the FebruaryNPPGA Research Reporting Conference, FebruaryMichigan Winter Potato Conference and the FebruaryWisconsin Winter Potato conference. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? The NC region has continued to release improved varieties. This impact is reflected through the5,071 certified seed acres were planted in 2023 (2024 data is not available yet), to 34 recently released varieties and advanced breeding lines with commercial interest. Although commercial acreage is not tracked by variety, the number of commercial acres can be estimated by multiplying the seed acreage by 10-15. A number of factors are driving the adoption of new varieties developed in our region, including improved agronomic performance and storability, disease resistance, fresh market appearance, and processing quality. MSZ242-13 was released as Dundee in 2023. It is a scab resistant, high solids chip processor. MN04844 was released as Polaris Gold. It is a late season fresh market yellow potato with low internal defects. The commercial acreage for Mackinaw, a PVY, scab and late blight resistant chipper, is expanding in the US and is one of the commercially important public varieties used by the chip processors.Petoskey, Huron Chipper and Blackberry seed acreage is increasing. Certified seed potato production for Dakota Russet, a dual purpose russet with frozen processing potential (approved for McDonald's French fry production in 2022) with resistance to the sugar end disorder, cold sweetening, pink rot and southern rot, and moderate resistance to Verticillium wilt and Pythium leak, moved into the top 10 cultivars grown in North America. Certified seed production and grower/industry evaluation of several advancing selections including ND7799c-1 (130 acres), ND113207-1R (15 acres), ND1241-1Y (50 acres), and ND13220C-3 continued to expand. A PVP certificate was filed for Lakeview Russet. Portage Russet was released as a processing variety. PVP application (PV2000389) was submitted for Dakota Dawn. Scab resistance, late blight resistance, Verticillium wilt resistance, and PVY resistance is being introgressed into advanced breeding lines for the chip processing, frozen processing, and table (red, yellow and white skins) markets. The majority of the MSU advanced breeding lines have scab resistance. Over 70% have PVY resistance. Late blight resistance is found in about 10% of the lines. Genomic selection was used for parent selection in 2023 in the UW chip program based on a multitrait index for total yield, specific gravity, fry color, and maturity. At UMN, genomic selection was used for yield, specific gravity, tuber shape, and tuber color in fresh market and chipping potatoes. Variety development is the core function of the project. Across our four states, more than 900 segregating populations with over 80,000 seedlings were generated in 2023/24. This leads to early generation evaluation of second, third- and fourth-year clones with increasing selection pressure taking into account disease testing, marker screening, agronomic performance and post-harvest storage testing. Over 300 lines were evaluated in in-state trials and over 200 lines were evaluated in multistate trials. These include lines for the chip processing selections from the four breeding programs that participate in the National Chip Processing Trial (NCPT), which is managed by Potatoes USA. MSU, NSDU and UW manage test sites. Fry processing selections entered the National Fry Processing Trial (NFPT), which is also managed by Potatoes USA, and for which NDSU and UW manage test sites. The 2023 numbers for the breeding programs reflect numbers we handle each year. Disease and pest testing is integrated with the selection stages of the breeding programs. A key impact has been the Ryadg gene for potato virus Y resistance. Recent variety releases from MSU, including Saginaw Chipper (2016) and Mackinaw (2018), contain this late blight and PVY resistance. A KASP marker for this gene was developed in 2021 and is now being used for marker-assisted selection. The Ryadg gene from S. tuberosum ssp. andigena and Rysto gene from S. stoloniferum are present in a number of elite parents used for crossing in the North Central region. In our last year of the grantover 750 clones have been screened for PVY resistance in the North Central region. Progress in breeding for scab tolerance has been made by conducting phenotypic selection in dedicated scab fields in MI and WI. information is used in determining continuation in the breeding pipeline, parental selection, and in development of cultivar specific management guidelines. At MSU over 1,200 scab nursery plots were evaluated for scab resistance. Scab resistance is found across a wide range of germplasm at both 4x and 2x ploidy levels. For the University of Wisconsin (UW), the genomic selection model for the chip processing market was updated based on yield, specific gravity, vine maturity, and fry color data collected in 2023. The multi-trait selection index targets equal genetic gain (in standardized units) for yield, specific gravity and fry color, without increasing maturity. In addition to these quantitative traits, UW prioritized parents with (1) extreme PVY resistance from one of two sources, Ryadg or Rychc; (2) P- or T cytoplasm, and (3) low levels of total glycoalkaloid in tubers (<20mg/100g FW). 44 unique parental combinations were realized for the crossing blockin the greenhouse, involving 16 different parents and totaling 43,000 true seeds. UMN has developed a series of genomic selection models for fresh market and chipping potatoes. For fresh market potatoes our models predict yield, skin color, and shape while our models for chipping potatoes predict yield, specific gravity, and shape. These models were used to choose parents for a tetraploid crossing block which formed the2024 FY1 germplasm. Over the past two years we have collected multispectral drone data at 6 time points. Including this data in our genomic selection models has significantly improved our prediction accuracy for most traits. Parents chosen using this combined data set are in thecurrent crossing blocks. We are making both the predicted best crosses and crossing to PVY resistant individuals to bring resistance into our breeding program especially for fresh market material. In conclusion, the outcomes of this project is improved potato varieties such as Dakota Russet, Mackinaw, Manistee, Plover Russet and the specialty potato Blackberry, that drive economic development for the potato industry. Secondly, we develop cultivated germplasm that is enhanced for disease, virus and insect resistances and traits that will continue to improve market quality. The germplasm is shared among the breeding programs, and it leads to long-term projected impact. As a human capacity investment activity, we also train the next generation of research scientists and breeders that are hired within and beyond the potato industry and public research institutions.

Publications

  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Kaiser, Natalie & Billings, Grant & Coombs, Joseph & Buell, C.Robin & Enciso, Felix & Douches, David. (2021). Self fertility and resistance to the Colorado potato beetle (Leptinotarsa decemlineata) in a diploid Solanum chacoense recombinant inbred line population. Crop Science. 10.1002/csc2.20534.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Kaiser, N. R., Coombs, J. J., Felcher, K. J., Hammerschmidt, R., Zuehlke, M. L., Buell, C. R., & Douches, D. S. (2020). Genome-Wide Association Analysis of Common Scab Resistance and Expression Profiling of Tubers in Response to Thaxtomin A Treatment Underscore the Complexity of Common Scab Resistance in Tetraploid Potato. American Journal of Potato Research, 97(5), 513-522.
  • Type: Journal Articles Status: Published Year Published: 2022 Citation: Hoopes G, Meng X, Hamilton JP, Achakkagari, SR, Guesdes FAF, Bolger ME, Coombs JJ, Esselink D, Kaiser NR, Kodde L, Kyriakidou M, Lavrijssen B, van Lieshout N, Shereda R, Tuttle HK, Vaillancourt B, Wood JC, de Boer JM, Bourke PM, Douches D, van Eck HJ, Ellis D, Feldman MJ, Gardner KM, Hopman JCP, Jiang J, de Jong WS, Kuhl JC, Novy RG, Oome S, Sathuvalli V, Tan EH, Ursem RA, Vales MI, Vining K, Visser, RGF, Vossen J, Yencho GC, Anglin NL, Bachem CWB, Endelman JB, Shannon LM, Str�mvik M, Tai HH, Usadel B, Buell CR, Finkers R. (2022). Phased, chromosome-scale genome assemblies of tetraploid potato reveals a complex genome, transcriptome, and proteome landscape that underpin phenotypic diversity. Molecular Plant. 15(3):520-536.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Alsahlany, M., Enciso-Rodriguez, F., Lopez-Cruz, M. et al. Developing self-compatible diploid potato germplasm through recurrent selection. Euphytica 217, 47 (2021). https://doi.org/10.1007/s10681-021-02785-0
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Busse JS, Jansky SH, Agha HI, Schmitz Carley CA, Shannon LM, Bethke PC. (2021). A high throughput method for generating dihaploids from tetraploid potato. American Journal of Potato Research. 98(4): 304-314.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Kaiser, N.R., Jansky, S., Coombs, J.J. et al. Assessing the Contribution of Sli to Self-Compatibility in North American Diploid Potato Germplasm Using KASP" Markers. Am. J. Potato Res. 98, 114 (2021). https://doi.org/10.1007/s12230- 021-09826-3
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Otieno, S. A., Coombs, J., & Douches, D. S. (2021). Frequency of Polyploids of Solanum tuberosum Dihaploids in 2X-2X Crosses. Journal of Agriculture and Crops, 7(2), 76-80.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Bamberg, J., Kielar, A., del Rio, A., & Douches, D. (2021). Making Hybrids with the Wild Potato Solanum jamesii. American Journal of Potato Research, 1-7.
  • Type: Journal Articles Status: Published Year Published: 2022 Citation: Shelley, B., Pandey, B., Xue, W., Douches, D., Collins, P., Qu, X., ... & Clarke, C. (2022, November). Improvements to field detection and genomic characterization of Streptomyces species. In PHYTOPATHOLOGY (Vol. 112, No. 11, pp. 72- 73).
  • Type: Journal Articles Status: Published Year Published: 2022 Citation: Schlachter, E. M., Dmytryszyn, C. M., Bloomingdale, C., Kurzer, D., VanAtta, K., Douches, D., ... & Willbur, J. F. (2022, November). Evaluation of varietal responses and peroxyacetic acid application for postharvest disease management in potato storages. In PHYTOPATHOLOGY (Vol. 112, No. 11, pp. 39-39).
  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Agha HI, Schroeder L, Eikholt D, Schmitz Carely CA, Cavendar-Bares J, Shannon LM (2023). Assessing the Effectiveness of Reflectance Spectroscopy Analysis to Determine Ploidy in Potato. American Journal of Potato Research.100, pages135141.
  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Miller MD, Schmitz Carley CA, Figueroa RA, Feldman MJ, Haagenson D, Shannon LM (2023). TubAR: an R package for quantifying tuber shape and skin traits from images. American Journal of Potato Research 100,5262.
  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Endelman JB (2023) Fully efficient, two-stage analysis of multi-environment trials with directional dominance and multi-trait genomic selection. Theoretical & Applied Genetics 136:65. doi:10.1007/s00122-023-04298-x
  • Type: Journal Articles Status: Published Year Published: 2024 Citation: Endelman JB, Kante M, Lindqvist-Kreuze H, Kilian A, Shannon LM, Caraza-Harter MV, Vaillancourt B, Malloux K, Hamilton JP, Buell CR (2024) Targeted genotyping-by-sequencing of potato and data analysis with R/polyBreedR. The Plant Genome.
  • Type: Journal Articles Status: Published Year Published: 2024 Citation: Asano K, Endelman JB (2024) Development of KASP markers for the potato virus Y resistance gene Rychc using wholegenome resequencing data. American Journal of Potato Research 101:114-121. https://doi.org/10.1007/s12230-024- 09944-8
  • Type: Journal Articles Status: Published Year Published: 2024 Citation: Feldman MJ, Park J, Miller N, Wakholi C, Greene K, Abbasi A, Rippner D, Navarre D, Schmitz Carley CA, Shannon LM, Novy R. (2024). A scalable, low-cost phenotyping strategy to assess tuber size, shape, and the colorimetric features of tuber skin and flesh in potato breeding populations. The Plant Phenome Journal. 7 (1)


Progress 09/01/22 to 08/31/23

Outputs
Target Audience: Potato breeding and genetics community and the state/national potato industries (growers, processors and marketers. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Each breeding program has graduate students, undergraduates, research technicians and post docs that are conducting research. During their graduate and post graduate training and research they are participating in the breeding program activities of hybridization, planting, field variety trials, disease assessment, grading of trials, post-harvest assessment, data analysis, etc. which provides practical training in potato breeding. At the University of Wisconsin 2undergraduateshave gained experience with potato breeding and variety development. At Michigan State University 4undergraduates and 3graduate students gained experience within the potato breeding and genetics field program. At NDSU 3undergraduate student and 3graduate students have gained experiences in agronomic and convention breeding efforts.At the University of Minnesota2graduate students completed their theses (James Bjerke and Hashim Andidi).Three graduate students and three undergraduate students received training and experience in the areas of potato breeding and cultivar development. Additionally presentations were made bytechnicians, graduate students and post docs at the December 2022NCCC215 Breeding and Genetics Technical Committee meeting in Chicago IL and at the July 2022 Potato Association of America Meeting to an audience of plant breeders and geneticists. How have the results been disseminated to communities of interest? Research results from this project are reported to the state potato industries in Michigan, Wisconsin, Minnesota and North Dakota through written reports, winter research meetings and summer field days. Information about new varieties and breeding technologies has been presented to stakeholders at several forums, including the January 2023National Potato Expo, the December 2022National Chip and Fry Processing programs of Potatoes USA, the December 2022USDA multi-state project NCCC215 (Potato Breeding & Genetics Technical Committee), the annual meeting of the Potato Association of America.Results have been presented at the North Plains Potato Growers' Association (NPPGA) and the Minnesota Area II Potato Research and Promotion Council (Area II) summer field days in Hoople, ND, Inkster, ND, Larimore, ND, and Becker, MN; the NPPGA and Area II joint research planning meeting in Alexandria MN, the winter NPPGA research reporting meeting in East Grand Forks, and the Area II short course.Results from yearly trials were reported during the February 2023NPPGA Research Reporting Conference, February 2023Michigan Winter Potato Conference and the February 2023Wisconsin Winter Potato conference in February.Additionally presentations were made at the Potato Association of America Meeting in Charlottetown Prince Edward Island in July 2023. Popular articles: Thompson, A. 2023. Larimore Processing Trial - 2022 Summary. Valley Potato Grower 88(301):16-22. Thompson, S. 2023. Crystal Fresh Market Trial - 2022 Summary. Valley Potato Grower 88(302):16-21. Specific Presentations were made as follows: Thompson, S. NDSU Potato Breeding 2022 Growing Season Summary. MN Area II Research Meeting. Alexandria, MN. November 14, 2022. Thompson, S. Hidden Gems. University of Minnesota Horticulture Department Seminar. November 30, 2022. (Invited) Thompson, S. NDSU Potato Breeding Program Update. NCCC215 Meeting. Chicago, IL. December 6, 2022. Thompson, S. Potato Breeding. AES 2-Minute Videos for ND Legislature. January 2023. (invited) Thompson, S. Potato Breeding and Cultivar Development. International Crops Expo. Potato Program. February 22, 2023. (invited) Panelist. Stump the Docs. International Crops Expo. Potato Program. February 23, 2023. (invited) Thompson, S. NDSU Potato Breeding Update. MN Area II Potato Shortcourse. March 7, 2023. (invited) Thompson, S. Buried Treasures. PLSC Graduate Student Symposium. March 18, 2023. (Invited) Thompson, S. Introduction and History of Potatoes. 2023 RDO Scout School. June 6, 2023. (Invited) Thompson, S. Plant Growth and Development. 2023 RDO Scout School. June 6, 2023. (Invited) Thompson, S. Potato Breeding at NDSU and Greenhouse Tour. RDO/Syngenta Intern Tour. July 18, 2023. Thompson, S. NDSU Potato Breeding Update. 2023 Minnesota Area II Potato Council Field Day. Becker, MN. July 18, 2023. NDSU Potato Breeding. Oakes Field Day. Oakes Research Extension Center. August 3, 2023. (Invited) Thompson, S. North Dakota Nutrition Council Webinar. August 9, 2023. (invited) NDSU Potato Breeding Program Update. Northland Potato Growers Association Field Day (Larimore/Inkster/Hoople sites). August 24, 2023. (Invited) Yusuf M., Miller M., Stefaniak T., and Shannon L. Genomic selection for quality traits using image based tools in potato. Potato Association of America Meeting July 2023, Charlottetown, PEI Agha I, and Shannon LM. Genotype-by-Environment interaction and local adaptation shape the National Chip Processing Trial. Gordon Research Seminar on Quantitative Genetics. February 2023, Ventura, CA Agha I, and Shannon LM. Genotype-by-Environment interaction and local adaptation shape the National Chip Processing Trial. Gordon Research Conference on Quantitative Genetics. February 2023, Ventura, CA Agha I, and Shannon LM. Genotype-by-Environment interaction and local adaptation shape the National Chip Processing Trial. Midwest Population Genetics Conference. August 2023, Ann Arbor, MI What do you plan to do during the next reporting period to accomplish the goals? In the fall we spend a majority of the time conducting evaluation and selection of the potato germplasm within the breeding program. That involves disease assessment for scab and late blight. We also conduct post-harvest analyses and store potato samples for processing analysis. The data is summarized and used to determine what material to advance as well as what material to consider for commercialization. In the winter crossing blocks are established to initiate the next cycle of the breeding program. DNA marker analysis and genotyping is also conducted in the post-harvest season. Winter is also the reporting season to the stakeholders as well new variety releases. There are also plans to expand our genomic selection models to encompass the russets and wider variety of traits.

Impacts
What was accomplished under these goals? Release of superior varieties is a major impact of the potato breeding programs. Dakota Russet, released in 2012, bulks early and rapidly, has medium maturity, produces a uniform tuber size profile, processes consistently from 45F storage, is resistant to the sugar end disorder, and is moderately resistant to Verticillium wilt, pink rot, and Pythium leak. In 2022 this variety qualified for McDonald's fries which will increase its commercial impact. Dakota Russet reached the top 12 cultivars for certified seed potato production in North America in 2022. For 2023 certification applications it ranks 2ndin North Dakota.Significant certified seed acreagefor ND113207-1R (fresh market) and ND1241-1Y (fresh and chip processing) in MN and ND was planted. Dakota Dawn was featured in the NDseed catalog and was approved for release.Dakota Dawn PVP application is in progress. UMN released Polaris Gold (MN04844), a long season yellow with low internal defects. MSU released Dundee (MSZ242-13), a scab resistant chip processing variety. PVP is being applied for.PVP certificate was issued for the variety 'Plover Russet' (No. 20200152) and a new application was filed for Lakeview Russet. UW initiated foundation seed production of two specialty varieties: W15271-1R/Y and AW08112-4P/Y.12new advanced selections were establishedin tissue culture to enable the production of foundation seed. Variety development is the core function of the project. Across our four states, more than 1000 segregating populations with over 120,000 seedlings were generated in 2023. This leads to early generation evaluation of second, third- and fourth-year clones with increasing selection pressure taking into account disease testing, marker screening, agronomic performance and post-harvest storage testing. Over 500 lines were evaluated in in-state trials and over 200 lines were evaluated in multistate trials. These include lines for the chip processing selections from the four breeding programs that participate in the National Chip Processing Trial (NCPT), which is managed by Potatoes USA.MSU, NSDU and UW manage test sites. Fry processing selections entered the National Fry Processing Trial (NFPT), which is also managed by Potatoes USA, and for which NDSU and UW manage test sites. Disease and pest testing is integrated with the selection stages of the breeding programs. A key impact has been the recently identified source of LB resistance is on chromosome 11, on the same haplotype as the Ryadg gene for potato virus Y resistance. In collaboration with the USDA-ARS unit in Madison, WI, UW is in the process of identifying the underlying R gene using sequence capture (RenSeq) methods in both 2x and 4x populations descended from NY121. Recent variety releases from MSU, including Saginaw Chipper (2016) and Mackinaw (2018), contain this late blight and PVY resistance. Based on published reports of field late blight resistance in Palisade Russet (Novy et al. 2012) and Payette Russet (Novy et al. 2017), both clones have been used as parents for breeding in the NC breeding programs. We were able to determine that the source of resistance in Payette Russet is an R2 homolog (Karki et al. 2021). A haplotype-specific KASP marker for this gene was developed in 2021 and is now being used for marker-assisted selection.The Ryadg gene from S. tuberosum ssp. andigena and Rysto gene from S. stoloniferum are present in a number of elite parents used for crossing in the North Central region. In 2022over 800 clones have been screened for PVY resistancein the North Central region. Fifty-seven genotypes have been evaluated for resistance toDickeya dianthicolausing a petiole assay. Several selections exhibit tolerance including ND1412Y-5Russ and ND12241YB-2Russ. Progress in breeding for scab tolerance has been made by conducting phenotypic selection in dedicated scab fields. information is used in determining continuation in the breeding pipeline, parental selection, and in development of cultivar specific management guidelines. At MSU over 1,400 scab nursery plots were evaluated for scab resistance. Scab resistance is found across a wide range of germplasm at both 4x and 2x ploidy levels. 75 clones evaluated at four nitrogen levels for nitrogen use efficiency At MSU a diploid S. chacoense F5 RIL population has been developed to better understand the genetics of the resistance in a more inbred background. The best inbreds were crossed to the advanced diploid clones. Selections were made for beetle resistance and used in crosses for 2022. Additional sources of resistance are being exploited from S. commersonii and S. jamesii. Beetle trials in 2023 confirm that the resistance is being transmitted to the progeny. Genomic selection: Starting in 2016, UW-Madison began genotypingFY3 clones each year from the potato chip breeding program with thousands of SNP markers on a microarray. Phenotypes for total yield, tuber size (median weight), specific gravity, and fry color were collected at a single location. In 2021-2 UW completed validation of a new, mid-density (2K) genotyping platform for potato. UW updated and distributed genomic prediction models for the potato chip market.Genomic Selection model has now been developed for yield, specific gravity and shape in chipping potatoes, and color and shape in red potatoes. Diploid potato breeding: A yield trial in 2022confirmed that diploid selections with greater yield than the tetraploid check varieties Atlantic and Lamoka are now available for continued breeding.

Publications

  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Stefaniak TR, Miller J, Jones CR, Miller M, Harder MA, Schmitz Carely CA, Haagenson D, Thompson A, Michaels TE, Thill C, Shannon LM. (In Review). Polaris Gold: An Attractive, Yellow-fleshed Tablestock Cultivar with Chipping Potential. American Journal of Potato Research.
  • Type: Journal Articles Status: Published Year Published: 2022 Citation: Shelley, B., Pandey, B., Xue, W., Douches, D., Collins, P., Qu, X., ... & Clarke, C. (2022, November). Improvements to field detection and genomic characterization of Streptomyces species. In PHYTOPATHOLOGY (Vol. 112, No. 11, pp. 72-73).
  • Type: Journal Articles Status: Published Year Published: 2022 Citation: Schlachter, E. M., Dmytryszyn, C. M., Bloomingdale, C., Kurzer, D., VanAtta, K., Douches, D., ... & Willbur, J. F. (2022, November). Evaluation of varietal responses and peroxyacetic acid application for postharvest disease management in potato storages. In PHYTOPATHOLOGY (Vol. 112, No. 11, pp. 39-39).
  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Agha HI, Schroeder L, Eikholt D, Schmitz Carely CA, Cavendar-Bares J, Shannon LM (2023). Assessing the Effectiveness of Reflectance Spectroscopy Analysis to Determine Ploidy in Potato. American Journal of Potato Research.100, pages135141.
  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Miller MD, Schmitz Carley CA, Figueroa RA, Feldman MJ, Haagenson D, Shannon LM (2023). TubAR: an R package for quantifying tuber shape and skin traits from images. American Journal of Potato Research 100,5262.
  • Type: Journal Articles Status: Under Review Year Published: 2023 Citation: Feldman MJ, Park J, Miller N, Wakholi C, Greene K, Abbasi A, Rippner D, Navarre D, Schmitz Carley C, Shannon LM, Novy R. (In Review). A scalable, low-cost phenotyping strategy to assess tuber size, shape, and the colorimetric features of tuber skin and flesh in potato breeding populations. The Plant Phenome.
  • Type: Journal Articles Status: Under Review Year Published: 2023 Citation: Agha HI, De Jong WS, Douches DS, Endelman JB, Sathuvalli VR, Thompson AL, Vales MI, Yencho GC, Zotarelli L, Shannon LM (In Review). Genotype-by-Environment interaction and local adaptation shape the National Chip Processing Trial. Theoretical and Applied Genetics.
  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Endelman JB (2023) Fully efficient, two-stage analysis of multi-environment trials with directional dominance and multi-trait genomic selection. Theoretical & Applied Genetics 136:65. doi:10.1007/s00122-023-04298-x
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Endelman JB (2023) Genomics-assisted breeding of potato. University of Florida Plant Science Symposium. January 30, 2023.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Endelman JB (2023) New trends in fresh market potato variety development. Wisconsin Fresh Fruit & Vegetable Conference. January 31, 2023.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Endelman JB (2023) Potato Breeding and Genetics. UW Extension/WPVGA Grower Education Conference. February 9, 2023.
  • Type: Conference Papers and Presentations Status: Awaiting Publication Year Published: 2023 Citation: Song L, Endelman JB (2023). Exploring the potential of genomic selection for diploid potato. 107th Annual Meeting of the Potato Association of America. July 24, 2023.
  • Type: Other Status: Published Year Published: 2023 Citation: Thompson, S. 2023. Potato breeding and cultivar development for the Northern Plains Region  2022 Summary. Minnesota Area II Potato Research and Promotion Council and Northland Potato Growers Association 2022 Research Reports. On-line.


Progress 09/01/21 to 08/31/22

Outputs
Target Audience:Potato breeding and genetics community and the state/national potato industries (growers, processors and marketers). Changes/Problems: Covid restrictions limited activities with students and others, and increased travel costs to sites for harvesting, etc. It limited in-person meetings and grower interaction at annual meetings/conferences as events were cancelled or held virtually including NCCC215, the NPPGA Research Reporting Conference (February 2021).Significant drought impacted potato production in 2021 in the Northern Plains; yields for producers and research trials/breeding program certified seed production were much reduced. What opportunities for training and professional development has the project provided?Heather Tuttle a masters student in the Bioinformatics and Computational Biology Programhas been funded on this project. Additionally two undergraduate interns and 4 undergrad lab assistants have been funded on this project. NC PIs, staff and graduate studentsparticipated in the SCRI Polyploid Workshop. Yusef Muyideen (graduate student at UMN) came to NDSU program July 13, 2021 and provided training for the cut-stem technique for mass pollination for haploid extraction. At the University of Wisconsin two undergraduates, three graduate students, and a postdoc have gained experience with potato breeding and variety development. At Michigan State University two undergraduates and 2 graduate students gained experience within the potato breeding and genetics field program. At NDSU one undergraduate student and five graduate students have gained experiences in agronomic and convention breeding efforts.The NDSUproject supports activities used as examples and in teaching PLSC425/625 Potato Science; 26 students completed the course (21 undergraduate, 5 graduate) as well asactivities used in training summer interns (RDO/Syngenta Internship Program); spring/summer 2022. How have the results been disseminated to communities of interest?Results have been presented at the North Plains Potato Growers' Association (NPPGA) and the Minnesota Area II Potato Research and Promotion Council (Area II) field days in Hoople, ND, Inkster, ND, Larimore, ND, and Becker, MN; the NPPGA and Area II joint research planning meeting in Alexandria MN; the NPPGA research reporting meeting in East Grand Forks; and the Area II short course. Additionally presentations were made by PIs and graduate students at the NCCC215Breeding and Genetics Technical Committee meeting in Chicago IL and at the Potato Association of America Meetingto an audience of plant breeders and geneticists. Results from 2021trials were reported duringthe NPPGA Research Reporting Conference, Michigan Winter Potato Conferenceand the Wisconsin Winter Potato conference in February 2022. Three articles were published in the Valley Potato Grower as follows: Thompson, S. 2022. Crystal Fresh Market Trial - 2021 Summary. Valley Potato Grower (April issue) 87(293):16-22. Thompson, A. 2022. 2021 Hoople Chip Processing Trial Summary. Valley Potato Grower 87(294):10-15. Robinson, A., D. Haggenson, and A. Thompson. 2022. Andy's Advice: Storage Trial Results for the North Dakota Fresh Market Potato Trials. Valley Potato Grower 87(294):16-19. In the Red River Valley specific presentations were made as follows: Thompson, S. Upcoming NDSU red and yellow clones. Tater Talk hosted by Dr. Andy Robinson. December 1, 2021. NPPGA East Grand Forks, MN. (Invited) Thompson, S. Genetic Improvement and Potato Cultivar Development for the Northern Plains. Northern Plains Potato Growers Association Research Reporting Conference. February 15, 2022. (invited) Thompson, S. Tuber Storage Quality: Sugars and Starch. International Crops Expo. Potato Program. February 17, 2022. (invited) Thompson, S. Genetic Improvement and Potato Cultivar Development for the Northern Plains. MN Area II Potato Shortcourse. February 22, 2022. (invited) Thompson, S. Let's Talk Potatoes. North Dakota Nutrition Council Webinar. April 27, 2022 (invited) Additionally, results will be discussed at our upcoming Annual Field Days in the summer of2022.Other scientific talks utilizing data collected with the support of this project were made to international audiences of plant breeders. What do you plan to do during the next reporting period to accomplish the goals?We will complete the the 2022 field studies, conduct post harvest assessments, summarize data for variety release and conduct the genomics analysis.We will continue evaluations for agronomic performance, disease resistance and insect resistanceand crossing as described above to generate the next round of germplasm for selection. UMN is considering the release of MN13142 a long storing russet and MN07112 a purple specialty variety. MSU is considering a fast track clone identified in the NCPT.Diploid breeding efforts will continue to increase as parental germplasm is developed. We will also continue to create a genomic selection model appropriate to our germplasm for chips and fresh market potatoes. NDSUhybridized parental genotypes (63 parents including named cultivars, wild species-hybrids and advancing selections) in the 2022 greenhouse to obtain true potato seed; creation of new segregating families for disease, pest and stress resistances and quality attributes important to ND and Northern Plains producers; 1344 pollinations were made resulting in more than 150 new segregating families. NDSU also planted field trials and certified seed production at seven locations in 2022 across western Minnesota and North Dakota, evaluation advancing selections for potential release and segregating populations for phenotyping and genetic analysis in the next reporting period.

Impacts
What was accomplished under these goals? Impact varieties: Manistee has been a key long-term storage chip potato that has had impact for the growers in the region with over 700 acres of certified seed. Being able to store until July is a market advantage. Petoskey was recently released in 2020 and is offering scab resistance, high solids and storability until June. Mackinaw, with almost 200 acres of certified seed was also released and PVP protected. It offers high solids, storage until July and resistance to scab, late blight and PVY. The tuber size profile of Mackinaw is also of value to the processors. Saginaw Chipper and PVP-protected Huron Chipper are finding commercial potential in the Pacific Northwest. Blackberry was released and PVP protected. It has a deep purple-fleshed specialty potato that has fresh market potential but also is being used in chip processing in Michigan. Dakota Russet, released in 2012, bulks early and rapidly, has medium maturity, produces a uniform tuber size profile, processes consistently from 45F storage, is resistant to the sugar end disorder, and is moderately resistant to Verticillium wilt, pink rot, and Pythium leak. It recently qualified for McDonald's fries which will increase its commercial impact. Dakota Ruby, released in 2014, has exceptional red skin color and snowy white flesh; attributes include a very uniform and high tuber set, resulting in high yield of A and B sized tubers. It is grown in several states for the fresh market. Dakota Dawnwas approved for released(March 2022). UMN released Polaris Gold (MN04844), a long season yellow with low internal defects. UW initiated foundation seed production of a new fresh market russet variety, W13008-1rus and alsoestablished 5 advanced selections (FY6) in tissue culture after completingtheir antiviral treatment. Variety development scheme: Across our four states, more than 1000 segregating populations with over 120,000 seedlings were generated for 2021. Over 1,500 year 2 selections and400 year 3 selections were evaluated. After 3 to 4 years of field evaluation within each state, each clone is entered in the appropriate regional or national trials. Over 200lines were evaluated in multistate trials. Chip processing selections participate in the National Chip Processing Trial (NCPT), which is managed by Potatoes USA, and for which Douches, Thompson, and Endelman manage test sites. In 2021, there were 66 clones entered in the NCPT from the North Central Region breeders. Fry processing selections entered the National Fry Processing Trial (NFPT), which is also managed by Potatoes USA, and for which NDSU and UWmanage test sites. Late blight: Another recently identified source of LB resistance is on chromosome 11, on the same haplotype as the Ryadg gene for potato virus Y resistance. In collaboration with the USDA-ARS unit in Madison, WI, we are in the process of identifying the underlying R gene using sequence capture (RenSeq) methods in both 2x and 4x populations descended from NY121. Recent variety releases from MSU, including Saginaw Chipper (2016) and Mackinaw (2018), contain this resistance. Based on published reports of field resistance in Palisade Russet (Novy et al. 2012) and Payette Russet (Novy et al. 2017), both clones have been used as parents for breeding. In 2020, we were able to determine that the source of resistance in Payette Russet is an R2 homolog (Karki et al. 2021). A haplotype-specific KASP marker for this gene was developed and is now being used for marker-assisted selection. Other pests: Progress in breeding for scab tolerance has been made by conducting phenotypic selection in dedicated scab fields. Genotypes across market types were evaluated for common scab in a scab screening trial conducted by NDSU.information is used in determining continuation in the breeding pipeline, parental selection, and in development of cultivar specific management guidelines. At MSU both tetraploid and diploid advanced breeding lines were evaluated for scab resistance. Resistance is found across a wide range of selections at both ploidy levels. At MSU scab resistance is a priority so advancement is dependent upon resistance. UMN evaluated 16 advanced clones in newly developed verticillium wilt nursery and is developing a scab nursery from future screening. The Ryadg gene from S. tuberosum ssp. andigena and Rysto gene from S. stoloniferum are present in a number of elite parents used for crossing in the North Central region. In 2021 over 1000 clones have been screened for PVY resistance using molecular markers in the North Central region. Furthermore, Intertek offers a KASP-based assay to screen for the PVY resistance markers. The NC breeders are utilizing this high-throughput and cost-effective assay to characterize early generation breeding lines. At MSU a diploid S. chacoense F5 RIL population has been developed to better understand the genetics of the resistance in a more inbred background. The best inbreds were crossed to the advanced diploid clones. Selections were made for beetle resistance and used in crosses for 2022. Genomic selection: Starting in 2016, UW-Madison began genotyping 120 FY3 clones per year from the potato chip breeding program with thousands of SNP markers on a microarray. Phenotypes for total yield, tuber size (median weight), specific gravity, and fry color were collected at a single location. The same data were collected for clones from the National Chip Processing Trial (at the same location) to generate a training set of 600 clones for GS (Endelman et al. 2018). Genomic- estimated breeding values (GEBV) for non-phenotyped clones had expected accuracies of 0.5-0.7, depending on the relationship between the clone and training set. When phenotypes for the selection candidates were included (i.e., genome- wide marker-assisted selection), the expected in 2019 at UW-Madison, in conjunction with data for other phenotypes and markers linked to disease resistance. Compared to historical practice, in which clones were not typically selected for crossing until after FY5, this represents a reduction of two years for the breeding cycle. Completed validation of a new, mid-density (2K) genotyping platform for potato. UW updated and distributed genomic prediction models for the potato chip market. Diploid potato breeding: With support from an AFRI Award 2014-67013-22434, MSU and UW-Madison have generated over 80 female-fertile dihaploids from elite tetraploid chip processing, table and russet clones. These dihaploid founders were crossed to self-compatible diploid germplasm to initiate recurrent selection for tuber traits, plant maturity, and self-fertility. The transmission of Sli was appraised in a diploid germplasm to introgress SC while simultaneously improving agronomic traits. A yield trial in 2021 identifed diploid selections with greater yield than the tetraploid check varieties Atlantic and Lamoka.

Publications

  • Type: Journal Articles Status: Under Review Year Published: 2022 Citation: Miller MD, Schmitz Carley CA, Figueroa RA, Feldman MJ, Haagenson D, Shannon LM (In Review). TubAR: an R package for quantifying tuber shape and skin traits from images. American Journal of Potato Research
  • Type: Journal Articles Status: Under Review Year Published: 2022 Citation: Agha HI, Schroeder L, Eikholt D, Schmitz Carely CA, Cavendar-Bares J, Shannon LM (In Review). Assessing the Effectiveness of Reflectance Spectroscopy Analysis to Determine Ploidy in Potato. American Journal of Potato Research.
  • Type: Journal Articles Status: Under Review Year Published: 2022 Citation: Stefaniak TR, Miller J, Jones CR, Miller M, Harder MA, Schmitz Carely CA, Haagenson D, Thompson A, Michaels TE, Thill C, Shannon LM. (In Review). Polaris Gold: An Attractive, Yellow-fleshed Tablestock Cultivar with Chipping Potential. American Journal of Potato Research.
  • Type: Journal Articles Status: Published Year Published: 2022 Citation: Hoopes G, Meng X, Hamilton JP, Achakkagari, SR, Guesdes FAF, Bolger ME, Coombs JJ, Esselink D, Kaiser NR, Kodde L, Kyriakidou M, Lavrijssen B, van Lieshout N, Shereda R, Tuttle HK, Vaillancourt B, Wood JC, de Boer JM, Bourke PM, Douches D, van Eck HJ, Ellis D, Feldman MJ, Gardner KM, Hopman JCP, Jiang J, de Jong WS, Kuhl JC, Novy RG, Oome S, Sathuvalli V, Tan EH, Ursem RA, Vales MI, Vining K, Visser, RGF, Vossen J, Yencho GC, Anglin NL, Bachem CWB, Endelman JB, Shannon LM, Str�mvik M, Tai HH, Usadel B, Buell CR, Finkers R. (2022). Phased, chromosome-scale genome assemblies of tetraploid potato reveals a complex genome, transcriptome, and proteome landscape that underpin phenotypic diversity. Molecular Plant. 15(3):520-536.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Busse JS, Jansky SH, Agha HI, Schmitz Carley CA, Shannon LM, Bethke PC. (2021). A high throughput method for generating dihaploids from tetraploid potato. American Journal of Potato Research. 98(4): 304-314.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Kaiser, N.R., Jansky, S., Coombs, J.J. et al. Assessing the Contribution of Sli to Self-Compatibility in North American Diploid Potato Germplasm Using KASP" Markers. Am. J. Potato Res. 98, 114 (2021). https://doi.org/10.1007/s12230-021-09826-3
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Otieno, S. A., Coombs, J., & Douches, D. S. (2021). Frequency of Polyploids of Solanum tuberosum Dihaploids in 2X-2X Crosses. Journal of Agriculture and Crops, 7(2), 76-80.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Bamberg, J., Kielar, A., del Rio, A., & Douches, D. (2021). Making Hybrids with the Wild Potato Solanum jamesii. American Journal of Potato Research, 1-7.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2021 Citation: Endelman JB. Genomic selection in potato. International Potato e-Conference. ICAR-Central Potato Research Institute, Shimla, India. November 23, 2021.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Endelman JB. Fully efficient, two-stage analysis for genomic selection and GWAS. Plant and Animal Genome XXIX, Jan. 8, 2022.