Source: MICHIGAN STATE UNIV submitted to NRP
POTATO BREEDING AND VARIETY DEVELOPMENT IN THE NORTH CENTRAL US: ENHANCING YIELD, QUALITY AND RESILIENCE WITH NEW TECHNOLOGIES, 2023-25
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
ACTIVE
Funding Source
SPECIAL GRANT
Reporting Frequency
Annual
Accession No.
1031249
Grant No.
2023-34141-41020
Cumulative Award Amt.
$2,284,747.00
Proposal No.
2023-05585
Multistate No.
(N/A)
Project Start Date
Sep 1, 2023
Project End Date
Aug 31, 2025
Grant Year
2024
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 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, a joint effort of the potato breeding and genetics programs at four North Central land-grant universities (UW, MSU, NDSU, UMN). There are three specific objectives detailed: 1) Generate segregating populations based on phenotypic and genomic selection of superior parents, 2) Identify superior clones based on marker-assisted selection for yield, quality and resilience to biotic and abiotic stress and 3) Commercialize new potato varieties in collaboration with industry stakeholders. 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
50%
Research Effort Categories
Basic
(N/A)
Applied
50%
Developmental
50%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
20113101081100%
Knowledge Area
201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
1310 - Potato;

Field Of Science
1081 - Breeding;
Goals / Objectives
1. Generate segregating populations based on phenotypic and genomic selection of superior parents.2. Identify superior clones based on marker-assisted selection for yield, quality and resilience to biotic and abiotic stress.3. Commercialize new potato varieties in collaboration with industry stakeholders.
Project Methods
Objective 1. Generate segregating populations based on phenotypic and genomic selection of superior parentsParent selection and the generation of true seeds are essential to the design of an efficient potato breeding program. Historically, potato clones were selected as parents after many years of testing, around the same time they were identified as candidates for commercialization. With genomic selection (GS), the breeding value of a clone can be predicted based on the performance of its ancestors across multiple years and locations--this is called the training population. GS allows for a much shorter breeding cycle (time from cross to cross) with similar prediction accuracy, creating more genetic gain per year. The potato breeding program at UW has been using GS since 2019 based on data in Wisconsin, and our goal for the next two years is to create a multi-location prediction model for the North Central Region.Separate training populations are being developed for three market categories: 1. Round whites for chip processing, 2. Russets (fresh market and processing), and 3. Reds (fresh market). Our training population is updated annually based on phenotypes collected during the FY3 stage of evaluation, which adds from 200 (reds) to 400 (chips) new genotypes to the training population annually. About 20% of the FY3 selections, which are only tested in their home state, advance to FY4 for testing across multiple states in the NC Region. GS models are being developed for many traits (depending on market type), including yield, tuber size, tuber shape, skin appearance, specific gravity, tuber dormancy, and fry color after 6 months of storage at 45F. The ability to estimate allele dosage is important for breeding value predictions. For genomic selection candidates at the FY2 stage, the SNP array is too expensive, so in 2020 we developed a genotyping service through DArT (Canberra, AUS) based on targeted amplicon sequencing at 2000 loci, which are a subset of the array SNPs chosen to get even coverage of all chromosomes and high rates of polymorphism. Software for imputing from the low-density panel to the higher density array has been developed by co-PD Endelman and shared through GitHub. More extensive validation of the methodology and training for all NC breeding programs is planned over the next two years.As our training population for GS expands, effective management of the phenotype and marker datasets is crucial. UMN led the development of a trait ontology that specifies the method of measuring a trait as well as the scale on which a trait is measured. Over the next two years we will refine the ontology such that it includes phenotyping practices from all four programs. We have chosen to use the Breedbase database because it has the capacity to store a variety of genotype and phenotype data, is well supported, and was designed with clonal crops in mind. It can be used for drone and lightbox imagery, trial design, tracking crosses and pedigrees, marker data, barcoding and inventory for both seed and tissue culture, and clone metadata. Our goal is to have all programs utilizing the database by the end of the current project.Objective 2. Identify superior clones based on marker-assisted selection for yield, quality and resilience to biotic and abiotic stress. The NC breeding programs have well established programs with a track record of identifying superior clones. True potato seed will be sown in greenhouses and harvested to generate seedling tubers for the first field year (FY1). Between 150,000 and 200,000 unique clones will be evaluated as single plants, over 95% of which will be culled based on visual selection for tuber type and maturity. Between 3,500 and 5,000 clones will be evaluated in FY2 as a single plot with 4, 8, or 12 plants (depending on program). In addition to the traits used in FY1, tuber size and number are considered during visual selection at harvest in FY2, and for processing types, specific gravity is measured post-harvest.We have experience using genetic markers in FY2, and use of this selection method will expand in 2023-25 due to the development of more haplotype-specific markers for key traits. High-throughput genotyping platforms, either in our labs or through service providers, will be used to efficiently screen thousands of clones. DNA is extracted from tuber core samples collected at harvest or planting time, which improves logistical efficiency. A number of the markers are well established, including 5 R genes for virus resistance, 3 R genes for late blight resistance, and one R gene for nematode resistance. We are also pioneering marker-assisted selection for the potato maturity geneCDF1, at which there are 3 known alleles for early maturity. We have designed KASP markers specific to the 7 bp insertions that characterize theCDF1.2andCDF1.4alleles, and the large 865 bp insertion inCDF1.3generates a null marker phenotype.Based on the phenotype and marker data, between 800 and 1000 clones advance to FY3 in the NC region. FY3 marks the beginning of more intensive data collection for clones at locations representative of commercial production (as opposed to seed production). This data is used to update the genomic prediction model (Objective 1) and contributes to more accurate selection. Two main experimental designs are used in FY3 in the NC region. The more traditional approach is an augmented design with repeated checks per incomplete block. Alternatively, programs are combining the FY3 and FY4 clones into a single trial, using the FY4 entries as partially replicated entries to improve estimation of standard errors and spatial variability. Each plot contains 15-20 plants. Besides total yield, the size distribution of each clone is measured using specialized grading lines, which facilitates the prediction of marketable yield. Internal defects caused by abiotic and biotic stresses are evaluated on 10-20 tubers per plot at harvest. Specific gravity is measured for chip and russet clones at harvest based on the underwater weight method, using a 2-3 kg sample. Skin appearance is assessed visually and at some locations based on quantitative analysis of images taken in an Ortery Photosimile 200 Lightbox.?Objective 3. Commercialize new potato varieties in collaboration with industry stakeholders.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.A second aspect of translating our research into commercial acreage is the production of virus-free mother plantlets and foundation seed for new varieties. The Douches Lab at MSU has performed its own virus eradication for 20 years, typically after Year 3. At UW, new breeding lines go through virus eradication after FY5, using the "standard" combination of antiviral media, elevated temperatures, and a 4 hr light/4 hr dark cycle. UMN and NDSU follow similar protocols. MSU has had good success with novel virus removal procedures based on cryotherapy, which is faster than the standard approach but sometimes fails to remove PVS. In the past two years MSU has removed virus from 15 infected lines and UMN has removed virus from 30 lines. The NDSU and MSU clone banks contain an excess of 1,500 virus free genotypes. The production of certified minitubers and foundation seed occurs in all four states, although each has a unique approach. Producers request minitubers for evaluation or commercialization purposes under Material Transfer Agreements through the UW, UMN, NDSU Research Foundation, and MSU Technologies.?

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, data analysis, etc. which provides practical training in potato breeding. Additionally presentations were made by PIs and graduate students at the NCCC215 Breeding and Genetics Technical Committee meeting in Chicago IL and at the Potato Association of America Meeting to an audience of plant breeders and geneticists as well as industry winter potato conferences. 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 research reports, winter research conferences and summer field days. Information about new varieties, advanced breeding linesand breeding technologies has been presented to stakeholders at several forums, including the National Potato Expo, the National Chip and Fry Processing programs of Potatoes USA, the USDA multi-state project NCCC215 (Potato Breeding & Genetics Technical Committee), the annual meeting of the Potato Association of America. Specifically, results from yearly trials were reported during the NPPGA Research Reporting Conference, Michigan Winter Potato Conference and the Wisconsin Winter Potato conference in February. Additionally, results will be discussed at our upcoming Annual Field Days in the summer. What do you plan to do during the next reporting period to accomplish the goals?There are no changes made to the project milestones and deliverables. The activities for the three objectives are on course. We will follow the plan of work described in the proposal.

Impacts
What was accomplished under these goals? Objective 1. The NC regionpotato breeding and genetics programs areactively producing new germplasm and advanced seedlings that are improved for long-term storage chipping, and resistance to scab, late blight, and Colorado potato beetle. Atthe University of Wisconsin (UW), theirgenomic 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.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. The NC regionis now placing more emphasis on the diploid breeding effort because of the advantages the breeding system brings when we introduce the ability to self-pollinate a line. Features of diploid breeding include 1) a simpler genetic system than current breeding methods, 2) tremendous genetic diversity for economic traits, 3) minimal crossing barriers to cultivated potato, 4) the ability to reduce genetic load (or poor combinations) through selfing and 5) the ability to create true breeding lines like wheat, soybeans and dry beans. We are also using some self-compatible lines that derive their self-compatibility from S. chacoense that have fertility and vigor. These lines have been crossed to the over 50 dihaploids from cultivated potatoso we can develop self-compatible inbred diploid lines. Objective 2. MSU prioritizes scab resistance and PVY resistance in our chip-processing selections. MSU evaluated scab resistance at a highly infected site at the Montcalm Research Center with 63 advanced selections and 240 early generation selections (including diploid lines) being classified as resistant to scab. 13 advanced breeding lines positive for the Ryadg or Rychc DNA marker were validated as resistant to PVY in a field trial. The most promising advanced chip-processing lines are MSAA217-3 (early bulking with high specific gravity), MSBB058-1 (scab resistant) that are advanced in the NCPT trials (10 sites nationally). MSBB636- 11, MSDD244-05, MSDD247-07, MSDD247-11, and MSEE031- 3 all combine high specific gravity, earlier maturity and lower blackspot bruising as well as scab and PVY resistance. Promising tablestock lines include MSCC553-1R which is scab and PVY resistant. We are excited about MSFF031-6 as a high yielding scab and PVY resistant round white and MSGG039-11Y as a PVY resistant yellow table line. At UW after completing the 2023 field trials in late September, results were compiled and used to advance clones through the breeding program. 218 chip and russet clones advanced to the preliminary yield trial (FY3), which was planted April 23 for the 2024 season. 36 clones advanced to our replicated yield trial (FY4), including 22 in the North Central Regional Trial. 18 clones entered the National Chip Processing Trial as Tier 1 entries, and 7 returned as Tier 2 entries. Three clones were selected by the Potatoes USA National Chip Committee to advance from the NCPT to the SCAC trial. Two russet clones entered the National Fry Processing Trial as Tier 1 entries. Genetic marker screening was used to advance clones with resistance to several pests, including potato virus Y (PVY), golden nematode (GN), potato wart, and late blight. 130 of the 218 FY3 clones have a genetic marker for PVY resistance, and 101 clones have the genetic marker for GN resistance. At UMN, in the summer of 2024 we grew 25,000 FY1 potatoes and selected ~1% for further consideration. We simultaneously grew out 232 FY2 clones and selected 20% for further consideration. We evaluated 376 FY3 clones in preliminary yield trials. In addition to traditional phenotyping (yield, size profile, specific gravity, shape, color, skinning, and fry quality) we genotyped FY3 using a combination of genome wide markers and known markers for disease resistance including PVY and verticillium wilt and collected multispectral drone images at six points during the summer. Multispectral drone imaging and conventional phenotyping were also carried out on 115 more advanced clones in replicated trials, these clones had already been genotyped.NDSUplaces emphasis on incorporating PVY resistance across market types. More than 450 breeding selections were submitted for genotyping. Marker analysis has identified resistance in selections verified by field/greenhouse screening. Promising advancing selections include ND13220C-3, a chip processing selection and entry in the 2024 national SNAC trial. ND1241-1Y (a timely consideration, based on increasing importance of yellows for the fresh market in the Red River Valley; Objective 3. 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.The Potatoes USA-funded National Chip Processing Trial (NCPT) is an effort to synergize the strengths of the public breeding programs in the U.S. to identify improved chip-processing varieties for the industry. Cooperating breeding programs include the USDA (Idaho and Maryland) and land grant universities (Colorado, Maine, Michigan, Minnesota, North Carolina, North Dakota, New York, Oregon, Wisconsin and Texas). The coordinated breeding effort (led by MSU) includes early-stage evaluation of key traits (yield, specific gravity, chip color, chip defects and shape) from coordinated trials in 10 locations. Since the inception of the trial in 2010, over 1,000 different potato entries, including reference varieties, have been evaluated. The data for all the lines tested are summarized on a searchable, centralized database housed at Medius (https://potatoesusa.medius.re). The NCPT is also a feeder for the national SNAC International trials. We are using the NCPT trials to more effectively identify promising new selections.Highlights for 2023 included Dakota Russet reaching the top 10 cultivars for certified seed potato production in the US. Certified seed potatoes were produced for ND7519-1, ND7799c, ND113207-1R, ND1241-1Y, and ND13220C-3 in ND and MN in 2023. ND13220C-3 will be an entry in the 2024 national SNAC trial.

Publications

  • 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
  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Shelley, B., Pandey, B., Sarwar, A., Douches, D., Qu, X., Pasche, J. and Clarke, C.R., 2023. The role of soil abundance of TxtAB in potato common scab disease severity. Phytopathology.
  • Type: Journal Articles Status: Published Year Published: 2024 Citation: Agha HI, Endelman JB, Chittwood-Brown J, Clough M, Coombs J, De Jong WS, Douches DS, Higgins C, Holm D, Novy R, Resende MFR, Sathuvalli V, Thompson AL, Yencho GC, Zotarelli L, Shannon LM. (2024). Genotype-by-Environment interactions and local adaptation shape selection in the United States National Chip Processing Trial. Theoretical and Applied Genetics. 137(5)
  • 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: 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. Preprint available at https://www.biorxiv.org/content/10.1101/2024.02.12.579978v2