NE2231: Collaborative Potato Breeding and Variety Development Activities to Enhance Farm Sustainability in the Eastern US

(Multistate Research Project)

Status: Active

NE2231: Collaborative Potato Breeding and Variety Development Activities to Enhance Farm Sustainability in the Eastern US

Duration: 10/01/2022 to 09/30/2027

Administrative Advisor(s):


NIFA Reps:


Non-Technical Summary

Statement of Issues and Justification

Issue(s) and Justification:


 Needs as indicated by stakeholders – Potato growers and industry stakeholders consistently rank new high quality improved varieties for a wide range of fresh and processing markets as one of their greatest needs. New varieties are needed to meet continually changing environmental stresses, disease and insect damage, and evolving consumer demands. In this long-term project, stakeholders have always played a key role in defining the objectives of our potato breeding and variety development efforts. Indeed, potato variety development is impossible without active interaction between researchers, extension, and stakeholders. Our project is highly engaged with the U.S. potato industry and all eastern potato breeding programs utilize direct input from growers, processors, and industry groups (e.g., Potatoes USA, grower associations, processors, consumer groups, etc.) to guide research priorities and variety release. Our broad stakeholder support is significantly enhanced by our participation in Potatoes USA SNAC chipping trials, national chip (NCPT) and fry processing (NFPT) trials, as well as several USDA-NIFA-SCRI-funded projects, each of which have annual project meetings that bring researchers and industry stakeholders together in a structured format to share recent results, review progress and discuss ongoing short- and long-term industry needs, all of which results in a sense of shared purpose and responsibility. Growers in each state are introduced to new clones and varieties through various mechanisms such as presentations at extension and industry-sponsored meetings, research meetings, field days, demonstration trials, and web sites such as our searchable and quite popular project web site at (https://neproject.medius.re/). The final decision for recommending and releasing a new variety is based on grower and industry input.


Based on stakeholder input, several market needs, including for tablestock reds and whites, chipping-, and russet-types need to be addressed simultaneously by the eastern potato breeding programs. New red-skinned and specialty varieties are in high demand, and a premium-priced market exists for them. Novelty varieties (e.g., fingerlings, purple-skinned, and multi-colored-flesh types) are growing in popularity in the high-value, direct-sale market. Better-adapted novelty varieties would offer new marketing opportunities, especially for small-scale growers that specialize in direct sales to consumers. New varieties containing multiple resistances to insects, pathogens and stress would provide better performance without chemical inputs in the organic industry.


Two distinct marketing opportunities exist for chip potatoes in the Eastern region. Potato producers from the southern areas (e.g. FL, NC, VA, MD, NJ, and southeastern PA) sell their processing potatoes to chip factories directly following harvest. The variety requirements for these regions stress earliness, chip quality from the field, high tuber dry matter content, and tolerance to high temperatures during bulking. The cultivar Atlantic has dominated commercial production in these areas for many years; however, it is very susceptible to internal heat necrosis (IHN), a serious quality defect throughout many of the Eastern-coastal and Southeastern states.    Potatoes USA has made developing an improved potato variety to replace Atlantic a top priority.


Contrasted with the south, processing growers from the northern states (PA, NY, and ME) store most of their crop before it is sold. These growers need high yielding, high specific gravity varieties with low defect levels and the ability to process into chips or fries from long-term cold storage. Snowden has been the standard storage chipping variety in northern regions for about 25 years; however, NY’s Lamoka cultivar is now the top storage chipping variety in the US.  Snowden’s long-term success is due to its combination high yield potential and specific gravity with reliable chip color through mid-term storage; however, it has weaknesses (e.g., scab susceptibility, stem and vascular defects, taste panel concerns, and poor chip quality from long-term storage). The national potato industry continues to place developing an improved potato variety to replace Snowden (and now Lamoka) as a top priority.


Most of the russet- and French fry-type varieties developed in the western and mid-western states are poorly adapted to the East, as is the standard variety, Russet Burbank. A major goal is to develop russet varieties with high yield, improved disease resistance, uniform long tuber shape, high specific gravity, low internal and external defects, and acceptable fry color under Eastern growing conditions. This is critical for Maine’s French fry markets and could allow expansion of French fry processing into other Eastern states.  Due to production problems (e.g. yield consistency, external tuber defects, and disease susceptibility) and recent concerns about acrylamide levels in fries that are processed from Russet Burbank, the major French fry processors and the national potato industry has been increasingly searching for new varieties to replace Russet Burbank.  While Caribou Russet, a 2015 ME release, has been highly successful, our industry still needs new russet varieties with greater pest tolerance, longer storage potential, and better adaptation to the wide range of Eastern environments.


In all market sectors, disease- and insect-resistance that provide economical and environmentally sound alternatives to pesticide use are needed for the Eastern potato production system. Foliar fungicide applications for control of late blight (Phytophthora infestans) and early blight (Alternaria solani) account for approximately 80% of the pesticide active ingredient applied to Eastern potatoes during a typical growing season. These applications are costly to growers and may result in chronic environmental degradation and/or health problems for agricultural workers. Potato virus Y (PVY) has become more difficult to manage as new recombinant strains have been introduced from other production areas. Likewise, new challenges have developed in managing bacterial soft rot (Pectobacterium and Dickeya spp.) throughout the eastern region.  Golden nematode (Globodera rostochiensis) is highly destructive to the potato crop and its spread is controlled by quarantine regulations.  Once it becomes established in a production area (e.g. parts of NY, Canada, and Europe), potato production is impossible without varietal resistance.


Importance of work - This multidisciplinary regional research project helps potato growers at all scales supply high quality, highly nutritional products to consumers, while maintaining economically and environmentally sustainable production practices.  Specifically, we will provide farmers new potato varieties to solve production problems and meet consumers’ changing needs. These varieties will have improved yields, enhanced fresh market, processing or value-added traits, and better pest resistance resulting in reduced chemical inputs.


Potato ranks among the top three vegetable crops produced in FL, ME, NC, NY, OH, PA, and VA (USDA NASS 2020), while ME and NY maintain high-quality seed potato industries that supply much of the seed for eastern U.S. market needs. Cash farm receipts for eastern potatoes are approximately $500M annually (USDA NASS 2020) and multiplier effects in the state economies are many times this amount. Production occurs under a wide range of environmental conditions, ranging from the winter crop in southern FL, out-of-field marketed summer chipping and fresh market crops throughout the region to the fall storage crops of ME, NY, and PA. This creates diverse variety needs. Fresh market production remains a significant part of the industry (e.g. 20, 20, 25, 50, 60% of ME, FL, NC, OH, PA’s crops, respectively); even so, 43% of U.S. chip production occurs in the east (USDA NASS 2020). Processing, primarily for French fries, accounts for 60% of ME utilization (USDA NASS 2020). Markets range from high value, direct sales of specialty varieties to contracting with large, international processing companies. This span of conditions creates a tremendous diversity in variety needs and research aiding the Eastern potato industry impacts markets associated with over half of the US population.


The NE1731 project and its predecessors have a solid track record in producing new potato varieties that have been commercially accepted. As examples, the following recent releases from the eastern breeding programs were in the top 100 list of US certified seed production for 2020: Lamoka, Waneta, Caribou Russet, Lady Liberty, Lehigh, Reba, Hamlin Russet, Eva, Keuka Gold, Brodie, Andover, Pike, and Upstate Abundance.  Though adopted on a smaller scale, specialty varieties (e.g. Adirondack Blue, Adirondack Red, Peter Wilcox, Pinto Gold, and Strawberry Paw) provide very high net returns for small-scale growers with direct sales to consumers. We propose to continue our regional collaborative efforts to breed, select, and develop improved potato varieties to enhance marketing opportunities and reduce farm dependence on costly agricultural chemicals.


Technical feasibility of the research.


We propose to use well-established breeding, evaluation and extension techniques to develop and facilitate the adoption of new, improved potato varieties.  We already have a long track record of successful, stakeholder-driven research programs, and a fully-developed multisite regional trial network, and we expect to continue developing successful new potato varieties over the next five years. We have also added DNA-based markers to our selection efforts and are working to integrate new genomic selection models to enhance our research efforts.


We anticipate that the objectives for the revised project would be similar to our current NE1731 project objectives:


1) Conduct multidisciplinary conventional and molecular marker-assisted breeding, germplasm enhancement, and early-generation selection research to improve potato productivity and quality for important Eastern U.S. markets.


2) Use novel and improved potato germplasm to reduce the impact of economically important potato pests and abiotic stress in the Eastern US.


3) Evaluate yield, quality, and pest and abiotic stress resistances of preliminary and advanced potato breeding lines in experimental- and commercial-scale trials at multiple Eastern locations to aid industry adoption of new varieties.


4) Provide timely and relevant information to stakeholders through various means including the maintenance of a project website and a web-based potato variety performance database for use by researchers, extension, potato growers, and allied industry members.


The objectives and activities of related projects, such as USDA's Sturgeon Bay, WI potato germplasm collection program (introduction, preservation, distribution, and evaluation of Solanum species), NCCC-215 (potato genetics), and WRCC-27 (potato variety development) are complementary to this project. NE-1731 interacts with these projects through exchange of promising germplasm and research results. There is a need for good communication between regions to take advantage of widely-adapted germplasm.


Advances in potato genomics, reduced next generation sequencing costs, and the development of quantitative genetic algorithms specific for polyploids have recently come together to make the use of genomic selection (GS) more feasible in potato.  GS enables breeders to select earlier in the breeding cycle, while more precisely estimating the potential breeding value of parents. Hence, GS can shorten the breeding cycle and accelerate genetic gain (Cobb et al., 2019). This predictive ability helps breeders make better crosses that have the potential to yield a greater frequency of favorable progeny for a given trait. GS can also improve efficiency by enabling breeders to advance clones for further evaluation based solely on their composite genotype at a large number of loci at an earlier stage in the breeding process, i.e. by genotyping a large number of early-generation clones (at a lower relative cost) prior to evaluation of a smaller number of clones in the field in more detail (at a higher relative cost). Our breeding programs are in the process of integrating GS into our research programs and this process will likely improve efficiency over the coming years.


Advantages of a collaborative, multistate research project - This project addresses the needs of the Eastern potato industry (small- and large-scale growers, marketers, processors) through a collaborative process of potato breeding, selection, evaluation, and variety release. It is a highly collaborative project involving seven states and five breeding programs.  Our project’s overall goal is to develop high-yielding, disease-resistant, and stress-tolerant potato varieties for fresh market, specialty, and processing markets.  This effort is aimed at enhancing farmers’ ability to provide a safe and nutritious supply of potatoes to consumers in an environmentally sustainable manner that enhances profits and rural America.  Within this context, it is important to recognize that the Eastern US region is not only linked geographically, but is also closely linked through potato seed sales (from northern production areas), production (north and south), and product marketing (north and south). Thus, regional communication among scientists, farmers and industry members is a critical aspect of variety development.


Our project design encourages collaboration, pooling of regional resources. Hybridization and selection are conducted within the region’s five breeding programs (FL, ME, NC, NY, USDA-ARS). Potato germplasm is exchanged throughout the region as well as nationally.  This allows us to gain benefit from plant materials that would not occur if each program worked independently. The major potato breeding programs and seed potato production areas are largely located in the North (NY and ME).  If early selection occurred only in the northern production areas, most of the genetic variation would be lost before the material entered trials in the SE (FL, NC, VA).  Early-generation selection of breeding materials under SE conditions improves the utilization of our breeding materials and increases the probability and speed of selecting new potato varieties that are adapted to the SE. Two to four selection cycles are conducted by each breeding program at their field sites; however, the diverse environments provided by regional cooperators are increasingly used to supplement the selection process via simultaneous early-generation selection in multiple environments.  This facilitates selection of both broadly and specifically-adapted plant materials for diverse eastern environments. 


As superior progeny are identified, they are evaluated for other traits under a wider range of environmental conditions. To accomplish this, selected clones are entered into the eastern regional potato variety trials to subject them to diverse growing conditions and learn more about their strengths and weaknesses, geographical adaptation, yield stability, and durability of pest and disease resistance.  The most promising lines are entered into commercial-scale demonstration trials to begin the final assessment for commercial potential. 


Importantly, the NE-1731 project has developed a uniform potato germplasm evaluation and selection system, which takes advantage of the diverse environmental and pest incidence conditions of the Eastern region.  All seed is produced at a single site in Maine, to eliminate the substantial impact of seed source on clone performance, and evaluation methods are standardized across the trial network.  Each year the project evaluates about 30 potato clones across the Northeast and compares performance to 11 existing varieties.  The 30 clones tested each year represent the very best advanced plant material from our breeding programs. The project also provides a mechanism for screening regional selections for specific characteristics at a single location (e.g., early blight and late blight resistance in PA; golden nematode resistance in NY; common scab and viruses in ME) and multiple locations (e.g., chip quality in ME, NY, OH, PA, NC, FL; internal heat necrosis resistance in NC, VA, FL, PA, NY). This collaborative evaluation system makes efficient use of scientific expertise available in the region, and results in more efficient release and adoption of new potato varieties than would occur without the project. Research results documenting the performance of our potato clones/lines/selections at each trial location is now available on our Variety Data Management (VDM) website (https://neproject.medius.re/). The analytical and search capabilities of the VDM site are superior to those of our previous database which, in turn, was a model for U.S. potato variety development programs.


Likely impacts of successfully completing the work.


Our new varieties have had significant positive impacts on local and national potato growers, processors, and consumers.  Nationally, varieties produced by our long-term project were grown on 7316 seed acres during 2020 with an approximate seed value of $26M and potential ware production value of $220M.  New potato variety adoption in the U.S. comes from many different sources; nevertheless, five of the top 20 recently introduced varieties in the U.S. were developed as part of our collective eastern efforts.


Building on our successful track record, this regional potato breeding and trial network proposes to continue producing new potato varieties for the fresh, processing, and specialty potato markets in the East.  These new varieties will improve grower profitability by increasing yields, enhancing market quality, and/or decreasing costs associated with pests or climatic stress. In terms of potential economic impacts, farm gate receipts for eastern potato production exceed $500M annually, therefore the impact of a successful new potato cultivar can mean many millions of dollars to the industry over time. Potatoes can cost more than $3000 per acre to produce and devastating diseases such as soft rot, pink rot and/or late blight can totally destroy the crop.  Resistant varieties greatly decrease the risk of losses and, in the case of late blight resistance, can reduce production costs by reducing the number of chemical sprays applied to protect the crop from the pest.  Similarly, new stress-tolerant varieties can reduce losses due to climate change induced stresses (heat, drought, flooding, etc).


NE-1731 productivity extends to research, as well, as our scientists publish peer-reviewed articles in scientific journals, develop new management practices, and create disease/pest resistant potato germplasm that is utilized as parental material throughout North America.  Each year the NE-1731 team also leverages regional funding to attract additional funding from the federal government and potato industry.  In 2021, NE-1731 scientists shared $510,104 in funding via the potato special grant (administered by USDA-NIFA), and attracted an additional $373,739 from industry stakeholders.


Some example outcomes that are expected for the next five-year period:



  1. New potato varieties with improved disease and insect resistance, improved processing or fresh market characteristics, and enhanced nutritional quality will be released, providing growers with better marketing opportunities and/or improved resistance to pests.

  2. Adoption of new, high quality, pest resistant varieties will occur, leading to increased profitability, greater worker safety, and reduced pesticide load in the environment and diet.

  3. Our multi-site evaluation and selection process will result in the release of new, broadly adapted potato varieties that will be stress tolerant and suitable for use in a changing climate.

  4. DNA-based markers for disease resistance and genomic selection tools for complex traits will be increasingly important in our breeding efforts and will result in improved selection efficiency.

  5. Web-based and traditional conduits for the distribution of timely and readily available potato variety production information to growers, processors, and consumers will be further strengthened.

Related, Current and Previous Work

The NE-1731 Project and its predecessors have played a central role in Eastern potato variety development for many years. Appendix 1 summarizes the seventeen (seven fresh market, seven chipping and three russet/long-tuber types) potato varieties released from 2007 to 2021.


 By way of example - Caribou Russet was released by ME during 2015 for fry processing and russet fresh market. It is being rapidly adopted due to high yields, scab and verticillium resistance, and excellent consumer quality. Certified seed acreage rose to 1475 acres (#16 in the US) during 2021. Caribou Russet’s cash farm value to ME seed growers was ~$5.2 M during 2021 and the estimated cash farm value when this seed crop is planted, grown, and sold in 2022 is ~$47.9M. It is also being evaluated and adopted in many other countries around the world. 


 Adoption and seed multiplication takes considerable time in the potato industry, in part because vegetative multiplication is slow, and in part because growers need several years before they can determine whether a promising new variety will work for them (many agronomic practices need to be adjusted for any new variety to achieve optimal performance). Thus, impacts occur over a long time period. Despite these limitations, recent Eastern releases were grown on 3127 ME and NY seed acres during 2021 with a seed value of ~$10.9M. The resulting seed crop has the potential to plant 31,274 acres in 2022 with a ware value estimated at $101.6M. Nationally, varieties released by our long-term project since 2007 were grown on 7369 seed acres during 2021 with an approximate seed value of $25.8M and potential ware production value of $239.4M. Several varieties developed though our collective efforts are in the top 100 U.S. varieties based on seed acreage, including (acres, rank): Lamoka (3108, 8), Waneta (1511, 15), Caribou Russet (1476, 16), Lady Liberty (629, 31), Lehigh (283, 48), Reba (126, 71), Hamlin Russet (90, 81), Eva (88, 83), and Genesee (73, 92). 


 NE-1731 productivity extends to research as well: over the past five years NE-1731 scientists have published 48 peer-reviewed articles. Each year the NE-1731 team also leverages regional funding to attract additional funding from the federal government and potato industry. During the last five years, NE-1731 scientists shared funding included $2.38M from the USDA-NIFA Special Grant for Potato Breeding Research and attracted an additional $1.54M from industry stakeholders.


 The objectives and activities of related projects, such as NCCC-215 (potato genetics), and WRCC-27 (potato variety development) are complementary to this project. NE-1731 scientists interact with these projects through exchange of promising germplasm, meeting participation, and sharing trial results as well as peer-reviewed research. There is a need for good communication between regions to take advantage of widely adapted germplasm and share knowledge and NE breeders routinely attend the annual NCCC-215 meeting in Chicago.


 The Potatoes USA and SNAC International National Chip Processing Trials (NCPT) and National Fry Processing Trials (NFPT), which are nationwide initiatives supported and driven by potato industry stakeholders, coordinate the development of new chip and French fry varieties. Both started in 2010 and are directed at speeding the development of improved varieties for these markets, while assuring that germplasm is widely evaluated at the national level. NE-1731 scientists contribute clones to these trials and host trial sites in NY, NC, ME and FL.  The NCPT and NFPT collaborative breeding trials have proven useful in three important respects. First, they allow originating breeders to identify broadly adapted clones much earlier than was possible before. Second, they provide publicity to the best clones – when a good clone is identified, the entire processing industry knows about it, not just the scientists in the region that developed it. Third, they provide a rapid mechanism to increase seed at scale for future trialing and possible rapid commercialization.


 To address specific Southern chipping industry needs Potatoes USA established the Early Generation Southern Selection Trial (EGSS) during 2017. This two-year screening trial acts as a precursor to the NCPT. Breeding programs have been encouraged to submit clones for evaluation earlier in their program selection schemes to reduce loss of genetic variation with the intention of identifying material more suitable for the elevated temperatures in the Southern US. NC was selected as the screening location for EGSS. Clones surviving evaluation in this trial are sent on to the NCPT for broader national screening the following year.


 The incorporation of disease resistance into varieties with desirable horticultural characteristics is of immense importance. The breeders in the NE-1731 Project have succeeded in incorporating disease resistance into many of the recently released varieties and clones now being tested. Priority disease and pest resistance breeding goals for our region continue to include resistances to: late blight, common scab, golden nematode, and potato virus Y. Although progress has been made in developing and introducing new varieties with combined disease resistance, favorable horticultural traits and desirable processing qualities, large-scale commercial adoption is hampered by marketing and seed production constraints. Our project intends to continue its focus on enhancing disease/pest resistance of potato while continuing to meet the diverse marketing needs of the Eastern fresh market (e.g., whites, reds, russets, organic and specialty varieties, etc.) and processing (French fries and chipping from field and/or storage) industries. We are also developing additional information and programs to enhance commercialization of new varieties (e.g., web-based information, variety profiles, licensing procedures, etc.).


 Fresh Market and Specialty Varieties. Excellent appearance and cooking quality are essential for fresh market success. Resistance to common scab and other diseases that cause external blemishes is extremely important. Resistance to mechanical damage during handling is critical. Unique tuber skin and flesh color (e.g., red, purple, yellow, etc.) can enhance appeal and marketing opportunities. Methods for breeding for improved yellow-flesh characteristics have been developed (Haynes et al., 1994; Haynes et al., 1996). Yellow-flesh intensity is highly heritable in the diploid hybrid phu-stn population, indicating that intense yellow-flesh color can be developed in this population (Haynes, 2000). Total carotenoid content of yellow-fleshed diploid phu-stn clones ranged from 3 to 13 times of that found in the yellow-fleshed variety Yukon Gold (Lu et al., 2001). Flavor and sensory components of cooked potato can be compared with various analytical methods (e.g., Oruna-Concha et al., 2001; Jensen et al., 1999; Ulrich, et al., 2000; Vainionopaa et al., 2000); however, these methods have not effectively substituted for sensory evaluation. Our project routinely conducts sensory evaluation of advanced potato selections to assure that new releases meet the markets’ rigorous quality demands. Potatoes are naturally nutritious and rich in vitamin C; however, introgression of yellow-fleshed diploid phu-stn hybrids into S. tubersosum will increase tuber concentrations of carotenoids, and other phytonutrients that would be highly beneficial to human health. Improving the nutritional quality of potato is a long-term goal. Over the past 15 years, 10 fresh market and specialty varieties have been released by this project (Appendix 1). Continued improvement is needed in the quality and pest resistance of potato varieties available to Eastern growers so that marketing opportunities can be expanded, and production can be more profitable, while minimizing negative environment impacts.


 Chipping and French Fry Processing. Selection of clones that maintain processing quality during cool temperature storage is a high priority and is a viable approach towards reducing sprout inhibitor and energy use. Adapted French fry processing clones are being selected from crosses conducted in ME and other states. New chipping varieties with high yields, high tuber dry matter, reduced susceptibility to bruising, and resistance to IHN are being developed by all Eastern breeding programs. Our research has shown that there is no significant correlation between susceptibility to IHN and either total yield or specific gravity in commercial potato germplasm (Henninger et al., 2000). Research by McCord et al. (2011a, b), Schumann et al. (2017) and da Silva et al. (2021) identified quantitative trait loci (QTL) linked to IHN in a population developed from a cross between Atlantic and B1829-5. Over the past 15 years, eight chipping and/or French fry processing varieties have been released by this project (Appendix 1). The varieties Lady Liberty, Lamoka, and Waneta have been successful in the chip processing marketplace, while Caribou Russet has been useful for fry processing and russet fresh market. Early indications are that Hamlin Russet will also be useful for fry processing.


 Potato Diseases Constraining Eastern Production. Bacterial and fungal diseases such as late blight, early blight, scab (common, acid, and powdery), verticillium wilt, rhizoctonia (stem canker and black scurf), silver scurf, pink rot, soft rot (e.g. Pectobacterium and Dickeya spp.), dry rot (Fusarium spp.) and virus diseases (leafroll, potato viruses X and Y, corky ring spot) reduce the yield and quality of the Eastern potato crop. All currently available potato varieties are susceptible to one or more of these diseases. Resistance to fungicides previously used for disease control [e.g., mefenoxam resistance to pink rot (Fitzpatrick and Lambert, 2006 and 2010)] makes development of improved genetic resistance particularly important.  Breeding and selection for improved disease resistance is a major focal area for the Eastern potato breeding programs and NE-1731. The impacts provided by successful development of high yielding, high quality and pest-resistant potato varieties are tremendous for Eastern growers (e.g., reduced costs, fewer losses, lower risk, etc.) and the public (e.g., less pesticide use, higher quality, etc.).

Objectives

  1. 1) Conduct multidisciplinary conventional and marker-assisted breeding, germplasm enhancement, and early-generation selection research to improve potato productivity and quality for important Eastern U.S. markets.
  2. 2) Use novel and improved potato germplasm to reduce the impact of economically important potato pests and abiotic stress in the Eastern US.
  3. 3) Evaluate yield, quality, pest resistance, and abiotic stress tolerance of preliminary and advanced potato breeding lines in experimental- and commercial-scale trials at multiple Eastern locations to aid industry adoption of new varieties.
  4. 4) Provide timely and relevant information to stakeholders through various means including the maintenance of a project website and a web-based potato variety performance database for use by researchers, extension, potato growers, and allied industry members.

Methods

<p>&nbsp;</p> <p><strong>Objective 1: </strong><strong>Conduct multidisciplinary conventional and marker-assisted breeding, germplasm enhancement, and early-generation selection research to improve potato productivity and quality for important Eastern US markets. </strong></p> <p>&nbsp;</p> <p><strong>1a. Collaborative Potato Breeding, Selection, and Variety Development in the Eastern US. </strong>&nbsp;</p> <p>Initial crossing and germplasm improvement will be conducted within the ME, NY, NC, FL and USDA-ARS breeding programs (see Figure in Appendix 2). Parents, including wild or cultivated diploid germplasm, are selected for desirable yield, quality, and pest and abiotic stress resistance traits, as well as male and female fertility. Initial selection is done by each breeding program at their field sites. The diverse environments provided by regional cooperators are used to supplement the early-selection process and improve regional adaptation. For example, materials from the ME and USDA-ARS programs are screened in NC and FL for internal heat necrosis (IHN) resistance and materials from USDA-ARS are screened in PA for common scab resistance. Each program tests lines for 5 to 8 years and at multiple eastern sites to evaluate yield, quality, disease resistance, and other agronomic characteristics. Promising clones are entered into national trials (e.g. EGSS, NCPT, NFPT) and the Eastern regional potato variety trials.</p> <p>&nbsp;</p> <p><strong>1b. Integrate genomic selection for improved potato productivity, quality, and heat tolerance into our breeding programs.</strong> &nbsp;Our goal is to calibrate genomic selection (GS) models and establish proof of concept studies using this new technology for the selection of potato varieties with good marketability and resilience to environmental stress, pests, and diseases. GS enables breeders to make more precise and early estimates of potential breeding value of parents thus shortening the breeding cycle and speeding genetic gain (Cobb et al., 2019, Gemenet et al. 2020). Before genomic selection can begin in eastern potato programs, we first need to create &ldquo;training populations&rdquo; by genotyping and phenotyping several hundred clones from each program. Data collected from these training populations allows GS prediction models to be built. In each year of this project, the FL, ME and NC breeding programs will collect yield, specific gravity, fry color, tuber shape, internal defect, and other agronomic trait data from ~200 3<sup>rd</sup>&ndash;year clones per program per year. NY will collect similar phenotypic data on up to 150 clones per year. ME will focus on russets and chipping types. NY and NC will focus on chippers while NC and FL will phenotype a common set of training materials in both environments. We also plan to utilize multi-site phenotypic data from our eastern trial network for the development of site-specific models. These trial sites will provide greater heat stress exposure than the originating ME and NY breeding programs (e.g. all 3<sup>rd</sup>-year ME chipping clones are selected under relatively cool northern ME conditions, but will also be screened under heat stress in FL and NC; most 3<sup>rd</sup>-year ME russet clones will be screened under heat stress conditions in NC and PA; NC will also screen NY 3<sup>rd</sup>-year clones for heat tolerance). For each breeding program, we will combine the phenotypic data collected in this proposal with genotype data from the same elite clones to develop prediction models. Predictive models that incorporate additive and non-additive effects will be evaluated using a dosage model that take into account potato&rsquo;s polyploid nature. We will estimate the prediction accuracy of previously developed additive models (Meuwissen et al., 2001; Resende et al., 2012; Endelman et al., 2018, Gemenet et al., 2020) and evaluate whether including non-additive effects will improve clonal prediction. Next, we will also train a GS model with the semiparametric Reproducing Kernel Hilbert Space, which can capture non-additive effects implicitly or explicitly (Gianola and Van Kaam, 2008). Predictive ability, accuracy, and bias will be compared among methods. In addition to the calibration of single-trait models with data from each breeding program, we will also evaluate the performance of joint models that combine multi-trait analysis and/or that combines phenotype from multiple breeding programs during the model calibration. Altogether, this aim will allow us to begin predicting phenotypes and selecting parents for future crosses that will more rapidly advance breeding progress for complex traits such as yield, market quality, and heat tolerance.</p> <p>&nbsp;</p> <p><strong>1c. Improving the chip quality and long-term cold storage processing genetic base. </strong>Improved chip and fry processing are high priority industry traits. A multi-site, parallel-selection approach will be used by the ME, NY, NC and USDA-ARS programs to identify chipping clones for the mid-Atlantic and SE states. Potatoes USA sponsors the NCPT and the EGSS programs to rapidly identify chipping clones and speed their commercial testing. Our breeding programs provide chipping candidates for evaluation in both trials with FL, NC, and NY serving as eastern NCPT screening locations and NC serving as the initial EGSS screening site. Promising NCPT clones advance to the industry-funded SNAC trials where advanced chipping clones are tested for three years across 11 states. The most promising NCPT, SNAC, and NFPT clones are fast tracked into industry-funded seed propagation and commercialization trials. Clones developed by our four breeding programs are major components to these national, industry-driven efforts.</p> <p>&nbsp;</p> <p>ME uses its own russet germplasm plus USDA-ARS-Idaho, CO, and ND seedling tubers to develop russet types that are adapted to the East. Yield, appearance, tuber length and size, specific gravity, internal quality, French fry color (from 7 and 10<sup>o</sup>C storage and reconditioned from 4<sup>o</sup>C storage), French fry texture, and disease reaction are used to further select the lines prior to NE-1731 and commercial evaluation. The most promising fry processing candidates are entered into the industry funded NFPT which tests promising French fry clones at six locations (ME, WI, ND, ID, OR, WA). NFPT is used extensively by the large-scale national fry processors to identify candidate French fry processing varieties. &nbsp;</p> <p>&nbsp;</p> <p><strong>1d. Improving the genetic base of fresh market and specialty potatoes. </strong>High-yielding, disease-resistant, fresh market lines will be intercrossed to produce seedling populations that will allow selection of superior fresh market varieties. Foremost among the selection attributes will be appearance (smooth skin texture, freedom from blemishes, and desirable color), tuber shape, yield, cooking quality (satisfactory texture, freedom from internal defects, after cooking darkening and sloughing), and disease resistance (see Objective #2).</p> <p><strong>&nbsp;</strong></p> <p><span style="text-decoration: underline;">Yellow-Fleshed Potatoes</span> - USDA-ARS is developing yellow- and orange-flesh diploid potatoes for the &lsquo;baby&rsquo; or creamer potato market. A primary objective is to lengthen tuber dormancy so they can be stored for several months without sprouting. All eastern breeding programs continue to include novel, yellow-fleshed clones in their crossing programs with the goal of developing yellow-fleshed potato varieties with improved market quality, pest resistance, and tolerance to environmental stress.</p> <p>&nbsp;</p> <p><span style="text-decoration: underline;">Red-, Purple-Skinned, and Other High-Value Novel-Colored Potatoes</span> - The genetic base of red-skinned and other high-value, novel-colored potatoes will be improved through crosses and backcrosses between tetraploid and diploid lines with solid or patterned red or purple skin. Red- and purple-skinned clones will also be intercrossed with yellow-flesh clones to develop a population of colored-skin, yellow-flesh lines. Crosses will be made between tetraploid<em> tuberosum</em> and diploid <em>phu-stn</em> lines to add increased color variation and nutritional quality.</p> <p>&nbsp;</p> <p><strong>1e. Development of diploid inbred lines to facilitate breeding and genetic studies. </strong>In an initial survey of self-incompatibility in <em>phu-stn</em> diploid population, 17 of 42 clones were found to be self-compatible. The USDA-ARS team will identify more self-compatible clones from this population. Additionally, USDA-ARS has acquired self-compatible diploids from Michigan State University, the University of Wisconsin, and true seed from H. De Jong (AAFC Fredericton, now retired) via the USDA-ARS Potato Genebank. Crosses among well-adapted, self-compatible clones will be undertaken to combine favorable gene combinations for development of elite inbred lines.&nbsp;Additionally, UMaine has advanced 18 novel primary dihaploids from 8 elite tetraploid varieties, and will continue to extract novel primary dihaploids. UMaine and USDA-ARS will assess these dihaploids for fertility while crossing them with selected diploid germplasm that restores self-compatibility to enable diploid potato breeding and genetic studies.</p> <p>&nbsp;</p> <p><strong>Objective 2: </strong><strong>Use novel and improved potato germplasm to reduce the impact of economically important potato pests and abiotic stress in the Eastern US</strong></p> <p>&nbsp;</p> <p><strong><span style="text-decoration: underline;">2a.</span> Improve potato resistance to significant pests in the East. </strong><span style="text-decoration: underline;">Late Blight</span> &ndash; Screening for late blight resistance within NE-1731 is conducted in the field and greenhouse using natural infection and/or artificial inoculation. The most promising late blight resistant selections undergo further evaluation in PA, the key late blight screening site for NE-1731.</p> <p>&nbsp;</p> <p>A tetraploid population was developed from clone B0692-4, which has shown excellent to late blight resistance, by crossing with a susceptible clone. Late blight resistance of this population was evaluated in field trials in PA and the population was further genotyped with the SolCAP Infinium SNP array. QTL/genes associated with resistance have been identified, and SNPs linked to these resistance loci will be converted into simpler molecular markers for future selection efforts (da Silva et al., 2021).</p> <p>&nbsp;</p> <p>With the development of high throughput SNP genotyping and next-generation sequencing technologies, genome-wide association studies (GWAS) have become a powerful tool for decoding genotype-phenotype association and exploring the genetic architecture of complex traits in crops. The USDA-ARS maintains a collection of 250 old and modern tetraploid potato varieties. These potato varieties were evaluated for resistance to late blight for two years in field trials in PA, genotyped with the SolCAP SNP chip, and candidate resistance genes identified by GWAS. Candidate genes were cloned from a resistant cultivar and transferred by <em>Agrobacterium</em> to a susceptible cultivar. If any of these candidate genes confers resistance in greenhouse and/or field trials, we will develop markers diagnostic for resistance alleles to facilitate selection in applied breeding programs.</p> <p>&nbsp;</p> <p><span style="text-decoration: underline;">Scab resistant germplasm -</span> Our breeding programs extensively utilize common scab resistant parent material and select for resistance in inoculated and/or naturally infected field experiments. Clones are tested over multiple years because of environmental effects on disease incidence and severity. PA provides a centralized screening site for early-generation materials from USDA-ARS, while ME and NY conduct their own early-generation screening.</p> <p>&nbsp;</p> <p>As with late blight, we have evaluated a collection of tetraploid potato varieties for resistance to common scab in field trials in PA. Candidate genes associated by GWAS with resistance to common scab have been transformed into susceptible potato by <em>Agrobacterium</em>. The susceptibility of the transgenic plants to common scab is being evaluated in greenhouse experiments at USDA-ARS Beltsville and in field trials in PA. If any of these candidate genes confers resistance, we will develop markers diagnostic for resistance alleles.</p> <p>&nbsp;</p> <p><span style="text-decoration: underline;">Dry rot, pink rot, and softrot resistant germplasm -</span> Fusarium dry rot (<em>Fusarium</em> spp.), pink rot (<em>Phytophthora erythroseptic</em>a) and soft rot (<em>Pectobacterium</em> and <em>Dickeya</em> spp.) resistance screening will be conducted using field (pink rot, Fitzpatrick and Lambert, 2010) or laboratory-based (soft rot and dry rot, J. Hao, unpublished) techniques with the goal of identifying advanced clones and parents with improved resistance.&nbsp; Breeding populations will then be developed to allow further study of resistance and development of SNP-based markers.&nbsp;&nbsp;</p> <p>&nbsp;</p> <p><span style="text-decoration: underline;">Golden Nematode - </span>Breeding efforts in NY have emphasized resistance to golden nematode Ro1; however, resistance to race Ro2 is also a priority. The NY program developed Ro2 resistance by selecting for adaptation within a collection of South American tetraploids and subsequent work has incorporated additional resistance sources from Europe to broaden the genetic base and provide resistance to <em>G. pallida</em>. Our other programs also use parental materials with nematode resistance. Progeny from crosses using resistant parents will be evaluated for resistance to both races of the golden nematode at the USDA-ARS in NY.&nbsp; Marker-assisted selection for golden nematode resistance (H1 marker; Galek et al. 2011) will be used to supplement traditional screening methods and provide earlier detection of resistant clones within selected breeding families. NY also has the ability to test for resistance to <em>G. pallida</em> in vitro.&nbsp;</p> <p>&nbsp;</p> <p><span style="text-decoration: underline;">Virus &ndash; </span>All four breeding programs will continue to include virus-resistant clones as parents.&nbsp; Marker-assisted selection for potato virus Y resistance (Whitworth et al., 2009; <em>Ry<sub>adg</sub></em>, RYSC3, Kasai et al., 2000; <em>Ry<sub>sto</sub></em>, YES3, Song and Schwarzfischer 2008; <em>Ry<sub>chc</sub></em>) will be used to supplement traditional screening methods and provide earlier detection of resistant clones. We will attempt to clone the <em>Ry<sub>adg</sub></em> gene using sequence capture followed by long-read sequencing to potentially provide a mechanistic understanding and additional molecular markers for this resistance trait.</p> <p>&nbsp;</p> <p><strong>2b. Improve the genetic base of potatoes for resistance to heat stress</strong>. Potato plants subjected to heat stress have lower tuber yield and quality (e.g., tubers may form in chains, have internal heat necrosis, and/or heat sprouting). Potato production in the south and mid-Atlantic states frequently experiences high temperatures during the late tuber bulking. USDA-ARS and FL will screen 125 named varieties for heat tolerance by comparing tuber yield and quality traits from early-season and late-season plantings.</p> <p>&nbsp;</p> <p><strong>2c. Improve the genetic base of potatoes for nitrogen uptake efficiency (NUE). </strong>Commercial potatoes currently take up only 33 to 53% of applied nitrogen. The rest is lost to denitrification and nitrate leaching.&nbsp;One strategy for improving NUE is to introgress high NUE traits from wild species. FL and USDA-ARS have identified improved NUE in <em>chc</em> and crosses have been made to transfer NUE into a <em>phu-stn </em>population. A mapping population has been generated between a <em>phu-stn </em>clone with poor NUE and a <em>chc </em>clone with superior NUE.&nbsp;This population will be phenotyped for NUE by measuring yield and quality traits at USDA-ARS (ME) and FL under high and low N regimes and genotyped using the potato SNP array.&nbsp;Loci and&nbsp;SNPs linked to NUE will be identified and used as markers for future breeding to improve NUE.</p> <p>&nbsp;</p> <p><strong>Objective 3. Evaluate yield, quality, pest resistance, and abiotic stress tolerance of preliminary and advanced potato breeding lines in experimental- and commercial-scale trials at multiple Eastern locations to aid industry adoption of new varieties.</strong></p> <p>&nbsp;</p> <p><strong>3a. Evaluation of Promising Selections for Early Maturity, Quality, and Storage Potential. </strong></p> <p><span style="text-decoration: underline;">Seed Increase for Standardized Regional Variety Trials</span> - Advanced selections will be placed in the NE-1731 Project seed nursery at the University of Maine Aroostook Research Farm in Presque Isle, ME to provide a uniform seed source for the project. The seed will be tested according to Maine seed certification regulations. This common seed source is a vital component for valid research and modeling of environmental characteristics, since performance of a clone varies widely according to the seed crop&rsquo;s quality, growing, and storage conditions.</p> <p>&nbsp;</p> <p><span style="text-decoration: underline;">Regional Variety Trial Procedures - </span>All tablestock, processing and specialty market selections will be evaluated in replicated field trials in multiple locations (FL, ME, NY, NC, OH, PA, VA) using standardized NE-1731 evaluation techniques and descriptors. These techniques include observations on agronomic as well as internal and external quality data. Bruise susceptibility (Hunter and Reeves 1983; Pavek et al. 1985), and storage characteristics will also be measured (ME). Appropriate industry standards (e.g. Atlantic, Snowden, Russet Burbank) are included at each test site. Five standard varieties will be grown at all NE-1731 test sites to provide data for modeling environments and genotype x environment interactions.</p> <p>&nbsp;</p> <p><span style="text-decoration: underline;">Processing from Storage</span><strong> - </strong>Samples of NE-1731 selections will be stored at two temperatures (typically 7.2 and 10C). Weight loss will be measured to help select clones that do not require the use of chemical sprout suppression. Chip or fry color will be measured with an Agtron instrument or with USDA Chip or Fry Color Charts following storage for two to six months (ME, NY, PA, USDA). &nbsp;</p> <p>&nbsp;</p> <p><strong>3b. Evaluate Promising Selections for Resistance to Potato Diseases.</strong></p> <p>All breeding lines will be evaluated under uniform conditions for resistance/susceptibility to major potato diseases. This assessment provides comparative information to help breeding programs, researchers, and the industry decide on the merits of new clones. Regional disease screening will be conducted for <strong>golden nematode resistance</strong> (USDA-ARS NY), <strong>late and early blight </strong>(PA), <strong>common scab</strong> (ME), <strong>potato virus Y</strong> &ndash; PVY (ME), <strong>potato leaf roll virus</strong> &ndash; PLRV (ME), and <strong>corky ring spot &ndash; CRS</strong> (FL). Additional disease resistance screening is done by the respective programs to screen their breeding materials for disease susceptibility including <strong>late and early blight </strong>(USDA-ARS, ME), <strong>common scab</strong> (USDA-ARS, ME, NY), <strong>Verticillium wilt</strong> (ME), <strong>pink rot</strong> (ME), <strong>Fusarium dry rot</strong> (ME), <strong>bacterial soft rot</strong> (ME), <strong>potato virus Y</strong> &ndash; PVY (ME, NY), and <strong>potato leaf roll virus</strong> - PLRV (ME). To insure they do not mask symptoms, all selections not showing PVY or PLRV symptoms will be tested for pathogen presence using ELISA (ME).&nbsp;</p> <p>&nbsp;</p> <p><strong>3c. Evaluate promising selections for sensory and nutritional quality.</strong></p> <p>NE-1731 clones and advanced ME breeding clones will be evaluated for boiling and baking quality by consumer panels (ME). Test lines will be compared to appropriate industry standards.&nbsp; Only lines with acceptable total glycoalkaloid (TGA) content will be evaluated (Asano et al., 1996; Baker et al., 1991; Friedman and McDonald, 1997). A hedonic scale (Peryam and Pilgrim, 1957) will be used for each of the baked attributes. Sloughing and graying of boiled tubers will be subjectively evaluated using sensory panels. The boiled potato evaluations will employ a 15-point intensity scale. After cooking darkening of boiled selections will also be evaluated objectively using a LabScan XE Hunter Lab Colorimeter (Hunter Associates Laboratory, Reston, VA).&nbsp;</p> <p>&nbsp;</p> <p><strong>Objective 4. Provide timely and relevant information to stakeholders through various means including the maintenance of a project website and a web-based potato variety performance database for use by researchers, extension, potato growers, and allied industry members.</strong></p> <p><strong>&nbsp;</strong></p> <p>Project cooperators will present project information to stakeholders through presentations, printed media, trade shows, and websites to inform them of promising selections and new variety releases. Modeled on the early efforts of the NC State University potato database, Medius.re has developed a long-term database for NE-1731 trials to facilitate data analysis and encourage collaboration among NE-1731 participants. Web interfaces to this database allow access for all project participants and are updated and improved as needed and new ideas emerge.</p>

Measurement of Progress and Results

Outputs

  • Output 1: Potato families that segregate for key quality, stress resistance, and disease tolerance traits will be developed and used to improve genome wide, marker-based selection strategies for key quality, stress tolerance, and disease resistance traits.
  • Output 2: The germplasm pool of high specific gravity, stress tolerant, disease-resistant and/or nutritionally-enhanced clones available for breeding purposes in the US will be broadened.
  • Output 3: Our collective potato breeding efforts will result in new varieties, such as Lamoka and Caribou Russet, with favorable characteristics for chip, fry processing, and/or fresh market utilization.
  • Output 4: Potato breeders and allied scientists will effectively communicate research results through meetings, websites, and published reports and will design improved regional breeding and selection strategies to more efficiently develop varieties for adaption to specific production areas as well as wide geographic areas.
  • Output 5: A project website and a web-based potato variety performance database for use by researchers, Extension, potato growers, and allied industry members will be refined, updated, and maintained to facilitate communication, information exchange and data analysis.

Outcomes or Projected Impacts

  • Outcome 1: New potato varieties with improved disease resistance, resistance to abiotic stresses, improved processing or fresh market characteristics, and enhanced nutritional quality will be commercially evaluated and released, providing growers with better marketing opportunities, great profits, and/or improved resistance to diseases.
  • Outcome 2: Farmers will learn how to successfully grow newly released potato varieties in different climates and for different uses.
  • Outcome 3: Adoption of new, high quality, pest resistant varieties will occur, leading to increased profitability, greater worker safety, improved human nutrition, and reduced pesticide load.
  • Outcome 4: Strengthened communication and interactions among potato scientists located in the eastern U.S. and elsewhere will lead to greater productivity and collaboration.
  • Outcome 5: Web-based and traditional conduits for the distribution of timely and readily available potato variety production information to growers, allied industry members and consumers will be further developed and strengthened.
  • Outcome 6: Rural communities dependent upon Eastern potato production will benefit from the economic and environmental sustainability provided by adoption of improved new varieties.

Milestones

(2022):Incorporate disease and insect resistances, abiotic stress resistances, improved processing characteristics, and enhanced nutritional quality, from diverse diploid and tetraploid potato species into high quality, adapted potato germplasm (S. tuberosum) (2022-2027, on-going activity)

(2022):Develop potato families that segregate for key quality, stress resistance, and pest tolerance traits and use them to improve marker-based selection strategies for key quality, stress tolerance, and pest resistance traits (2022-2027, on-going activity)

(2024):Evaluate our new plant materials in state, regional, and national potato variety trials leading to commercial evaluation and adoption of the most promising clones.

Projected Participation

View Appendix E: Participation

Outreach Plan

The NE-1731 Regional Potato Variety Development Project currently conducts outreach activities in all participating states using techniques ranging from face-to-face presentations at grower and scientific meetings to providing web-based content for industry members and consumers. Typical outreach activities include:



  1. Publication of project results in the NE-1731 annual publication, scientific journals, etc.

  2. Development of applied publications and Extension materials targeted to growers in each participating state or province.

  3. Multiple formal and informal presentations, demonstrations, trade show booths, and field days targeted to growers and industry in each participating state or province.

  4. Providing web-based project information via the NE-1731 project website to enhance access to research results, variety profiles, variety summaries, and photographs (http://potatoes.ncsu.edu/NE.html).

Organization/Governance

The regional technical committee is composed of all participating cooperators (see Appendix E), an administrative advisor (currently Dr. Mark Hutton) appointed by the Northeast Agricultural Experiment Station Directors, and a NIFA Representative (Tom Bewick). The technical committee meets at least once each year to discuss progress of the research, review procedures, coordinate research and plan future research activities.


 


The regional technical committee will elect an executive committee composed of a chair, vice-chair, and secretary. A succession of officers will be maintained so that the vice-chair becomes chair, the secretary becomes vice-chair, and a new secretary is elected each year. The responsibilities of the executive committee members are as outlined in the Guidelines for Multistate Research Activities. The chair will preside at all meetings of the technical committee and is responsible for organizing the agenda of the annual meeting. The vice-chair will prepare the annual report for the project. The secretary will prepare the minutes of the annual meeting and any special meetings. The administrative advisor is responsible for distributing the minutes and submitting the annual report and minutes to the NIFA representative and other interested parties. Participation by Agriculture Canada, the Provinces of Quebec and New Brunswick, Maine Department of Agriculture, Cooperative Extension, and Industry representatives is at the invitation of the Technical Committee with the approval of the Administrative Advisor.

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Attachments

Land Grant Participating States/Institutions

ME, NC, NY, OH, PA, VA

Non Land Grant Participating States/Institutions

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