Source: UNIVERSITY OF CALIFORNIA, DAVIS submitted to NRP
HARNESSING GENETIC AND GENOMIC RESOURCES TO DEVELOP STRAWBERRY CULTIVARS RESISTANT TO MULTIPLE FRUIT ROT DISEASES
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
ACTIVE
Funding Source
AFRI COMPETITIVE GRANT
Reporting Frequency
Annual
Accession No.
1032390
Grant No.
2024-67013-42591
Cumulative Award Amt.
$585,643.00
Proposal No.
2023-11100
Multistate No.
(N/A)
Project Start Date
Jun 1, 2024
Project End Date
May 31, 2028
Grant Year
2024
Program Code
[A1141]- Plant Health and Production and Plant Products: Plant Breeding for Agricultural Production
Recipient Organization
UNIVERSITY OF CALIFORNIA, DAVIS
410 MRAK HALL
DAVIS,CA 95616-8671
Performing Department
(N/A)
Non Technical Summary
Fruit rot diseases caused by several pathogens, namely Botrytis cinarea, Colletotrichum acutatum,and Neopestalotiopsis sp., are economically impactful in strawberry nurseries, fruiting fields, grocery stores, and homes worldwide, especially where warm and wet conditions provide the pathogen with the ideal environment to cause pre- and postharvest yield losses. Commercial strawberry varieties benefit from being resistant to multiple fruit rot diseases. Favorable alleles for disease resistances and bother traits may exist in wild relatives and are becoming more accessible through modern, data-driven breeding approaches informed by knowledge of genetic relationships and molecular diversity. The objectives of this proposal are aligned with the Farm Bill priority of plant health and production and plant products under the program area of Plant Breeding for Agricultural Production and specifically addresses breeding for "improved crop productivity, efficiency, quality, performance, and local adaptation to biotic and abiotic stress." Through the research outlined in this proposal we will expand our knowledge of genetic resistance to multiple fruit rot pathogens and develop tools to identify and select for QTL that underlie desirable variation. Specific objectives will address 1) the accessibility and availability of donors of genetic resistance that exist in public germplasm collections (USDA NCGR GRIN); 2) the relationship between fruit quality traits that affect consumer preference and the proclivity to be infected; 3) the development of breeding strategies that simultaneously improvement of fruit rot disease resistance that do not eliminate consumer-focused fruit quality; and 4) the need for the development of cost-effective,molecular marker tools for strawberry breeders.
Animal Health Component
75%
Research Effort Categories
Basic
25%
Applied
75%
Developmental
0%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2011122108050%
2021122108140%
7121122108110%
Knowledge Area
712 - Protect Food from Contamination by Pathogenic Microorganisms, Parasites, and Naturally Occurring Toxins; 201 - Plant Genome, Genetics, and Genetic Mechanisms; 202 - Plant Genetic Resources;

Subject Of Investigation
1122 - Strawberry;

Field Of Science
1081 - Breeding; 1080 - Genetics;
Goals / Objectives
The proposal expands on the research themes the UC Davis Strawberry Breeding Program has focused on for the past eight years: improving disease resistance of strawberry cultivars to multiple pathogens. This proposal will facilitate research and initiate breeding for resistance to three relevant fruit-rotting pathogens, specifically Neopestalotiopsis sp., Colletotrichum acutatum, and Botrytis cinerea. This project comprises four main objectives:Objective #1: To significantly increase the knowledge of disease resistance donors, cultivars, and genetic solutions for multiple rot resistance (MRR) to Neopestalotiopsis sp., Colletotrichum acutatum, and Botrytis cinerea through in-field screening and genome-wide association. To achieve this goal we will (a) assess the frequency of resistance vs susceptibility to Neopestalotiopsis sp., Colletotrichum acutatum, and Botrytis cinerea in a large diversity panel and bi-parental breeding populations, (b) identifying quantitative trait loci (QTL) associated with favorable alleles, if present, and (c) developing cost-efficient, haplotype-specific molecular markers for marker-assisted selection (MAS) for the discovered QTL.Objective #2: To maintain superior productivity and improve quality during disease resistance improvement by accounting for genetic covariance between disease resistance and fruit quality to enhance the value of new cultivars. We will improve the productivity and profitability of strawberry cultivars by (a) measuring the genetic covariance between key fruit quality traits, including size, sugar:acid ratio, anthocyanins, vitamin C, firmness, and multiple disease resistance; (b) developing early, non-destructive phenomic tools for predicting fruit resistance and susceptibility using near-infrared spectroscopy (NIRs) and hyperspectral imaging; (c) developing and deploying phenomic breeding strategies that incorporate information on multiple trait covariances contributing to commercial value.Objective #3: To improve the ability of strawberry breeders to incorporate stacked disease resistance through genome and marker-informed breeding strategies. We will improve the rate of genetic gain for expensive-to-measure traits by (a) improving breeding practices through the implementation of multi-trait genomic selection (GS) with phenomics and correlated fruit traits and (b) conducting simulations with empirical validation to build internal and external confidence in data-driven decision making and predictive frameworks.Objective #4: To increase the accessibility to high-quality germplasm resources to public and private programs. We will disseminate information regarding beneficial alleles in available germplasm and improve the accessibility of high-value donors by (a) updating available data in the USDA GRIN and NCGR system and (b) extending knowledge of beneficial alleles to public and private partners.Our long-term goals are 1) to provide the genetic resources and breeding formulas to stakeholders, 2) to release cultivars with high yield, excellent shelf life, resistance to soil-borne diseases, resistance to fruit rot diseases, and preferred fruit quality, and 3) to release germplasm accessions with high concentrations of favorable alleles to deliver value to a diverse set of stakeholders in CA, the US, and around the world.One of our goals is to train the next-generation of problem solvers. Our trainees include undergraduate and graduate students and postdoctoral scholars in horticulture, plant breeding, genomics, bioinformatics, molecular biology, and plant pathology. Trainees will have the opportunity to extend knowledge and interact with diverse stakeholder communities through field days, workshops, on-farm research, cooperative extension and scientific meetings, and one-on-one and small group activities.We expect the proposed initiative to improve the lives of farmers and rural communities by preventing losses to diseases that adversely affect strawberry production. The solutions we deliver are expected to reduce production risk, improve disease diagnosis, prevention, and management, decrease pesticide usage, facilitate the transition from fumigant-dependent to alternative production systems, and enable the expansion of organic production. One of the goals of this research will be the development and deployment of cultivars with unmatched resistance to a broad spectrum of diseases.
Project Methods
The primary efforts associated with our initiative include the delivery of science-based knowledge through: (a) formal classroom and laboratory instruction; (b) informal laboratory and field research and development activities: (c) experiment design and planning, field experiment preparation, maintenance, and management; (d) greenhouse and laboratory experiment design and analysis; (e) workshops on genome-informed breeding and genome-editing; and (f) grower education, extension, and outreach programs.One of the primary methods for evaluating the impact of our work on growers (one of the intended audiences) will be the adoption of disease resistant cultivars, e.g., with over half of the acres in California planted to NPT and anthracnosesusceptible cultivars, we can directly estimate how our work increases the acreage planted toresistant cultivars from industry planting surveys. Similar metrics will be collected for the other diseases we are investigating.Our impact on the scientific community (one of the other intended audiences) will be evaluated by documenting: (a) the number and impact of peer-reviewed publications (measured by accesses and citations); (b) the quality and quantity of open-source data deposited in public databases and downloads from open-source data repositories; (c) direct feedback at scientific meetings and workshops; and (d) direct interactions with scientists in the broader scientific community.

Progress 06/01/24 to 05/31/25

Outputs
Target Audience:The target audience for our research is the CA, US, and worldwide strawberry industries, including nurseries, fruit growers, packer-shippers, retailers, and breeding organizations. We work closely with the California Strawberry Commission, the North American Strawberry Growers Association, the International Strawberry Symposium, and the California Strawberry Plant Growers Association to deliver science-based knowledge through formal presentations and annual conferences, commission and focus group research meetings, and breeding program field days. We will also use our existing partnerships with Global Plant Genetics and Fresa Fortaleza LLC (international variety licensing groups) to distribute our findings to global growers, shippers, and retailers. Because of the rapid spread of Neopestalotiopsis throughout the east coast USA and Canada, our target audience also included the University of Florida Strawberry Breeding Program, NovaFruit and EzGrow Nurseries in Canada, The USDA ARS strawberyr breeding program in Maryland, and North Carolina State University strawberry breeding program. All of these groups have shown strong interest in our reseach and research outputs. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? This research project has allowed my group to participate in the education and training of four scientists at four different career stages: undergraduate, masters, pre-doctoral, and post-doctoral. Paul Skillin, a PhD student sponsored by this award, has presented a 3 public outreach events and has prepared brochures for 1. Paul Skillin has trained an undergraduate researcher, Ryan Chiang,to use NIR and to perform phenomic prediction. Ryan prepared and presented a research poster at the UC Davis Undergraduate Research Conference in 2025. Paul is expected to take his qualifying exam in December 2025. Under typical circumstances I would expect Paul to advance to candidacy and apply for pre-doctoral fellowships. We will keep our eyes out for those opportunities. Dr. Barbara Blanco hired a MS student, Carlos Carachure, who is working closely with Paul to support this research, but also independently to study howNeopestalotiopsisinfects strawberry fruit. Dr. Shai Torgeman, a postdoctoral scholar at UC Davis,is working closely with Paul Skillin to support his research on Colletotrchum acutatum, to support multi-tasking, training, and education. Dr. Shai Torgenman is funded by a Vaadia-BARD postdoctoral fellowship. In practice, nearly every member of my lab (~25 people ranging from high school students, undergraduates, MS and PhD students, postdoctoral scholars, and staff members) have participated in thisexperiment and the accomplishments of this award. How have the results been disseminated to communities of interest?Results have been communicated through grower presentations hosted by UC Davis and the California Strawberry Commission reaching ~60-80 growers, PCAs, breeders, sales representatives in the CA strawberry industry;in field day reports supporting UC Davis Strawberry varieties reaching ~ 50-100 people x 4 events per year;in scientific outreach events coordinated by UC Davis Strawberry Breeding Program targeted towards students, staff, and scientists are UC Davis reaching ~25-50 scientists per year. At the end of the second year of this experiment, we will begin preparing multiple scientific articles for peer review publication andpresentation at scienctific conferences. What do you plan to do during the next reporting period to accomplish the goals?We anticipate that we will have 100% of the data produced for this project by the end of Year 2 of this award, and will be well on the way to completing several peer reviewed publications. Weanticipate that we will have designed and developed, and be in the processes of validating either marker assisted selection or genomic selection in the UC Davis Strawberry Breeding Program. The project team are currently developing plans for years 3-4, which will allow us to finalize analyses and publications, but also start the following foundational and applied research projects to understand mode of infection of these pathogens, but also to create more resilient plant products for strawberry growers in CA and the US.

Impacts
What was accomplished under these goals? Under Objective #1: We have completed 1 of 2 years of phenotypic evaluations of 440 genotypes of strawberry and evaluated detached fruits inoculated withNeopestalotiopsis sp.,Colletotrichum acutatum, andBotrytis cinerea.In order to accomplish these activities, we have partnered with Crown Nursery, a private strawberry plant nursery, to propagate clonal plant material in their high elevation nursery in MacDoel, CA.This resulted in nearly 9,000-12,000 fruit screen per disease in year 1. Dr. Barbara Blanco's expertise was essential in setting up the experiment designs, and access to space in the Mann Lab postharvest research facility at UC Davis. We are now partially through year 2 of this experiment, which will yield a similar size data set appropriate for dissecting the common genetic architecture of MRR, if present in octoploid strawberry. All 440 genotypes screened in this experiment have been genotyped with the FanaSNP 50K genotyping array for conducting GWAS and genomic prediction experiments. In collaboration with the University of Florida, we are also combining in-field whole plant resistance data to examine common inheritance of resistances using detached fruit and in-field assays. Under Objective #2:We have completed year 1 of 2 for fruit quality evaluations and have assayed fruit for size, sugar:acid ratio, anthocyanins, firmness, NIR, and VIS-NIR spectroscopy. Preliminary results suggest that firmness is a strong predictor of general resistance in strawberry fruit against fruit rot pathogens. This important covariate will need to be addressed in genetic analyses. Ryan Chiang, an undergraduate researcher advised by Paul Skillin, has started to examine the efficacy of different predictive models, including machine learning and AI models, to estimate the severity of disease progression and to estimate fruit quality parameters from rapid, non-destructive NIR. Under Objective #3:All 440 genotypes screened in this experiment have been genotyped with the FanaSNP 50K genotyping array for conducting GWAS and genomic prediction experiments. When the second year of data are collected and processed, we will immediately be able to conduct genetic mapping, genomic prediction, and marker design experiments for validation and deployment into the UC Davis breeding program. We will use multi-variate models that are able to capture embedded information from correlation of multiple traits to improve the genetic analyses. Under Objective #4:We have begun extending knowledge of beneficial alleles to public and private partnersbreeding strawberry in the US and EU. In year 1, we have primarily focused on in person communications while we are completingour experiments and will shift to posters and presentations at scientific conferences, project director meetings, and grower out reach events, when we have completed our primary projects. Once our second year of data are completed, we will summarize these and provide these to the USDA NCGR databases to increase the value of the national germplasm collections.

Publications

  • Type: Other Status: Other Year Published: 2025 Citation: Skillin PH, Bjornson ML, Feldmman MJ. Brochure handout for the American Phytopathology Society on "Fruit Rot Pathogens in Strawberry".
  • Type: Conference Papers and Presentations Status: Other Year Published: 2024 Citation: Paul Skillin. "Fruit Rot Pathogens and Disease Resistance in Strawberry". UC Davis Strawberry Breeding Program Disease Field Day.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2025 Citation: Paul Skillin. "Updates on Fruit Rot Pathogens and Disease Resistance in Strawberry". UC Davis Strawberry Breeding Program Disease Field Day.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2024 Citation: Paul Skillin. "Fruit Rot Pathogens and Disease Resistance in Strawberry". Fresh Forward Community Outreach Symposium.