Source: UNIVERSITY OF CALIFORNIA, DAVIS submitted to NRP
NEXT-GENERATION DISEASE RESISTANCE BREEDING AND MANAGEMENT SOLUTIONS FOR STRAWBERRY
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
OTHER GRANTS
Reporting Frequency
Annual
Accession No.
1013142
Grant No.
2017-51181-26833
Cumulative Award Amt.
$4,494,490.00
Proposal No.
2017-03187
Multistate No.
(N/A)
Project Start Date
Sep 1, 2017
Project End Date
Aug 31, 2022
Grant Year
2017
Program Code
[SCRI]- Specialty Crop Research Initiative
Recipient Organization
UNIVERSITY OF CALIFORNIA, DAVIS
410 MRAK HALL
DAVIS,CA 95616-8671
Performing Department
Plant Sciences
Non Technical Summary
Between 1970 and 2016, strawberry growers heavily relied on the highly effective soil fumigant methyl bromide (MeBr) to control pathogens and weeds. When MeBr was banned by a global treaty to protect the ozone layer in 2005 and phased out over the next decade, growers had to turn to other alternatives. Coincidentally, two devastating soil-borne diseases (charcoal rot and Fusarium wilt) first appeared in 2005 and 2006 and another (Verticillium wilt) became more prevalent and troublesome in the aftermath of the MeBr phaseout, greatly increasing economic risks for growers in the US. The long-term goals of the proposed initiative are to reduce these risks and increase the sustainability of strawberry production across the US. This will be accomplished by identifying, monitoring, and managing pathogen threats; mining elite and wild genetic resources to identify natural sources of resistance to pathogens; and accelerating the development of commercial cultivars resistant to a broad spectrum of soil-borne and above-ground pathogens. This research specifically focuses on: developing a deeper understanding of economic and socioeconomic factors underlying rapidly evolving production systems; detecting, quantifying, and minimizing pathogen threats in strawberry production; developing deeper insights into genetic mechanisms underlying disease resistance; accelerating the development of disease resistant cultivars through the application of genomic technologies; and delivering cultivars with commercially viable levels of resistance to multiple soil-borne and above-ground pathogens. The proposed initiative is aligned with the mission of the SCRI to develop solutions to scientific problems that address critical stakeholder needs.
Animal Health Component
60%
Research Effort Categories
Basic
20%
Applied
60%
Developmental
20%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2011122108150%
2121122116030%
6011122209010%
8031122308010%
Knowledge Area
601 - Economics of Agricultural Production and Farm Management; 212 - Pathogens and Nematodes Affecting Plants; 803 - Sociological and Technological Change Affecting Individuals, Families, and Communities; 201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
1122 - Strawberry;

Field Of Science
2090 - Statistics, econometrics, and biometrics; 1160 - Pathology; 1081 - Breeding; 3080 - Sociology;
Goals / Objectives
The loss of methyl bromide as a chemical for controlling soil-borne pathogens, as well as increasing resistance of pathogens to fungicides, is severely limiting the effectiveness of chemical measures for managing disease pressure in strawberry. Our long-term goal is to increase the economic sustainability of strawberry fruit and nursery stock production under increasing pathogen pressure. The elimination of methyl bromide fumigation has threatened the economic outlook for strawberry growers and created an urgent need for the development and deployment of cultivars resistant to soil-borne and above-ground pathogens that cause losses in both fumigated and non-fumigated production systems.Objective #1. Understanding Economic Factors Affecting Stakeholders. Develop a more thorough understanding of the economic impacts of pathogens affecting nursery and fruit production to guide genomic and breeding efforts.Objective #2. Enhancing Genomic-Enabled Breeding Platforms. Expand genomic-enabled breeding resources and knowledge to accelerate the development and deployment of high-yielding cultivars resistant to multiple pathogens.Objective #3. Deploying Genetically Superior Cultivars. Expand cultivar testing for economically important pathogens and deliver commercial cultivars resistant to multiple pathogens.Objective #4. Predicting, Monitoring, and Preventing Losses Caused by Plant Pathogens. Determine how sources of resistance influence the capacity of plants to harbor asymptomatic infection of pathogens and the ability of cultivar selection to reduce the dissemination of pathogens from nursery to field production.Objective #5. Understanding Socioeconomic Factors Affecting Stakeholders. Build a long-term strategy for disease management and cultivar adoption in light of fumigant restrictions and socioeconomic challenges.
Project Methods
Standard breeding methods will be used to develop and evaluate cultivars. Progress will be evaluated by the number of cultivars selected for advanced testing, number of cultivars released, and strength of resistance to one or more diseases.Our genomic effort focuses on the development of DNA sequence resources and leveraging of the recently developed octoploid reference genome. Success will be measured by the successful development of a genotyping-by-sequencing pipeline, development of a haplotype mapping platform, development of robust, high-throughput, sub-genome specific assays for DNA variants linked to resistance genes, and development and application of a next-generation single nucleotide polymorphism genotyping array.Our genomic selection effort focusing on applying prediction methods to identify individuals in segregating populations for selection and advancement. Progress will be evaluated by the empirical estimation of the accuracy of predictions and by realized genetic gains (changes in disease resistance phenotypes).Standard economic and socio-economic analyses will be performed, including surveys of stakeholders to assess the relative importance of factors hypothesized to affect the economic impact of pathogens. This information will be used to evaluate the determinants of growers' views regarding relative importance and compare their views to the results of the economic analysis and calculate economic losses from pathogens at field and regional levels. Evaluating both field and regional losses is important for prioritizing breeding efforts; a disease that causes severe losses on affected fields but affects relatively little acreage and spreads slowly will be a very high priority for growers with affected fields. On the other hand, a disease that causes relatively modest losses but affects substantial acreage and spreads easily may not be the highest priority for any individual grower but from a regional perspective and the perspective of the land grant mission could be the highest priority.We will develop high-throughput methods that are simple, accurate, and inexpensive for detecting cryptic infections on nursery stock and for pathogen identification. A high-throughput detection system combining rapid DNA extraction and high-resolution melting (HRM) analysis for detection of cryptic infections of the anthracnose pathogen is under development.We will develop a statistically-sound sampling strategy for nurseries to detect cryptic infections and avoid shipment of transplants that initiate major disease outbreaks in grower fields. We will design a statistically based sampling strategy to detect a certain disease incidence with a specific confidence level. The levels of detection and confidence will be based on the pathogen carrying capacity of cultivars and the level of infection required to cause economic losses in fruit production fields.We will integrate pathogen detection methods with cultivar resistance information generated under Sub-Activity #3C and define cultivar-specific infection thresholds. We propose to use qPCR to quantify biomass of F. oxysporum f. sp. fragariae in strawberry crowns that have been inoculated using a root-dip procedure. This test will be applied to genotypes that are rated as resistant using the standard screen to identify heritable differences in the extent to which resistant genotypes support development of the pathogen. If successful, this will make it possible to develop cultivars less prone to colonization by the pathogen, which should enhance the durability of resistance. Colonization of V. dahliae and M. phaseolina will be assessed by a combination of traditional microbiological methods and qPCR. Protocols for the latter are undergoing validation in multiple laboratories.Even cultivars with moderate levels of resistance can be accepted and thrive with the reduced fungicide spray recommendations by the Strawberry Advisory System (SAS; http://agroclimate.org/tools/strawberry/; Pavan et al. 2011). SAS is currently being expanded to nurseries in CA and has proven to help nurseries and growers reduce fungicide applications without compromising yield (Mackenzie et al. 2012). Thus, moderate resistance, in some cases, might be sufficient when other tools such as SAS are available to manage the disease problem while remaining economical.Conduct a baseline written survey of growers in California and Florida. Growers will have a choice of completing on-line or by mail. We will compile contact information from California's Pesticide Use Reporting System and signed-on stakeholder groups such as the CSC and FSGA. The surveys will be available in English and Spanish, combine structured and select open-ended questions, the latter to explore non-hypothesized findings. Questions will focus on: (a) farm characteristics and location; (b) perspectives and experience with pathogen infestation; (c) factors affecting cultivar choice; (d) experience with and expectations for disease resistant cultivars; and (e) factors and conditions that would shape grower willingness to use disease-resistant cultivars along with alternative fumigants or reduce fumigation or shift to non-fumigated organic systems. Survey data will be analyzed quantitatively using multivariate regression analysis to identify factors associated with growers' interest in adopting disease resistant cultivars and examine whether respondents can be clustered into groups with common characteristics. Open-ended questions will be coded and analyzed with qualitative research methods, allowing the identification of additional (non-hypothesized) concerns and issues that bear on adoption. We will, in addition, perform a baseline analysis of fumigant use in major strawberry regions of CA and FL using data from California's Pesticide Use Reporting System and the FSGA and UF Cooperative Extension. The analysis will include acreage treated, fumigant products applied, and product and active ingredient application rates.Conduct ongoing observations at workshops, field trials, and other interactions with growers to attend to socioeconomic concerns affecting grower interest in disease resistant cultivars. Relevant interactions will be audio recorded and transcribed and observations will be recorded with field notes. These data will be coded and analyzed with qualitative research methods to support identification and grouping of key concerns.Hold focus groups with stakeholder groups in all major study regions to discuss obstacles to disease-resistant cultivar adoption and explore possible policies, practices and incentives to encourage adoption. Focus groups will be video recorded, transcribed, and analyzed with qualitative research software.Conduct an ending written survey of growers that ascertains interest and experience with new disease resistant cultivars and, drawing on data collected in step (d), tests interest in various policies, practices and incentives that encourage adoption. Survey data will be analyzed quantitatively to identify factors associated with growers' interest in adopting disease resistant cultivars and examine whether respondents can be clustered into groups with common characteristics. Open ended questions will be coded and analyzed with qualitative research methods to identify non-hypothesized findings. All findings will be compared to those from the baseline survey to ascertain changes in grower perspectives and concerns. We will, in addition, perform an ending analysis of fumigant use in major strawberry regions of CA and FL to ascertain degree of fumigant reduction, controlled for changes in acres in production. The analysis will include acreage treated, fumigant products applied, and product and active ingredient application rates.

Progress 09/01/17 to 08/31/22

Outputs
Target Audience:The target audiences for this research are: (a) private and public sector strawberry breeders, plant pathologists, scientists, and extension specialists; (b) strawberry growers, shippers, and packers and others engaged in producing and marketing strawberries; (c) academic scientists engaged in breeding and genomics of other species in the Rosaceae and other asexually propagated species; (d) graduate students, postdoctoral researchers, and academic scientists engaged in economics, sociology, plant pathology, horticulture, breeding, genetics, and genomics research. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Our initiative has provided significant training and professional development opportunities for graduate students, postdoctoral scholars, and research staff through hands-on training in greenhouse and field operations, planning, organizing, and overseeing field experiments, participating in breeding program activities and operations, on-farm research with fruit and nursery growers, and guest lectures in undergraduate and graduate classes. We estimate that our initiative contributed towards the training and mentoring of graduate students and postdoctoral resaerchers, 14 professional and technical staff. Approximately 30 undergraduate students gained experience through part-time research positions and internships. Our records show that 10 trainees secured positions in small fruit research and development. How have the results been disseminated to communities of interest?The results of our research initiative have been disseminated to communities of interest through: refereed journal publications, poster and oral presentations at national and international scientific meetings, the deposition of data and other materials in public databases and other open source repositories (e.g., the NCBI Short-Read Archive, the Rosaceae Genomics Database, and DRYAD), field days, stakeholder and industry organized meetings, on-farm experiements, one-on-one and small group interactions with fruit and nursery growers and stakeholders, progress reports to commodity groups and stakeholders, cultivar releases, the popular press and new releases, websites, and multimedia presentations. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? We released the first chromosome-scale assembly of the octoploid strawberry genome, resequenced the genomes of 143 germplasm accessions spanning global diversity, identified approximately 50M DNA variants among the resequenced individuals, developed and released 50K and 850K SNP genotyping arrays using DNA sequences anchored to the octoploid genome, and demonstrated the feasibility of applying genotyping-by-sequencing in the octoploid using whole-genome shotgun sequencing. The location of the FW1 Fusarium wilt resistance gene was pinpointed using GWAS and verified by high-density genetic mapping. DNA variants in linkage disequilibrium with FW1 were identified by whole-genome resequencing and SNP array genotyping. We completed the second year of screening 500-1,000 germplasm accessions for resistance to Fusarium wilt, Verticillium wilt, and Phytophthora crown rot, identified resistant cultivars and several strong sources of resistance to these pathogens to support breeding, and completed one generation of breeding to introduce favorable alleles for resistance to these pathogen into elite genetic backgrounds. We completed genomic selection studies in two different training populations for resistance to Verticillium wilt, identified and hybridized selection candidates, and initiated the next cycle of selection. We developed segregating populations to support breeding for resistance to Macrophomina, completed one cycle of recurrent phenotypic selection for resistance to Macrophomina, and identified and selected several highly resistant individuals for another cycle of recurrent selection. Screening for disease resistance has allowed the breeding programs to identify sources of resistance in commercial cultivars and advanced selections to major strawberry pathogens such as Colletotrichum acutatum, Colletotrichum gloeosporioides, Phytophthora cactorum, Macrophomina phaseolina, and Xanthomonas fragariae. Results were used to discover major locus for resistance that can be used in the future to develop markers to screen seedlings. One major locus was discovered and validated, Ca1, increasing resistance to anthracnose fruit rot and crown rot, both caused by Colletotrichum acutatum. Our host resistance studies show that a wide range of susceptibilities exist to Verticillium wilt, Macrophomina crown rot and anthracnose. Genotypes that show high levels of resistance to these pathogens were identified and are being used by growers (in the case of existing cultivars) and breeders (in the case of elite lines). In addition, awareness of host plant resistance as a means of managing soilborne pathogens is heightened among California growers. Deepened understanding of the socioeconomic factors affecting cultivar choice, e.g., most growers want high yielding varieties because of competition with other growers and because marketers pay them by volume produced, at the same time that they recognize that over-production contributes to low prices and risks losing their business. They also choose high yielding varieties to attract workers in the context of labor shortages, since workers are paid on piece rates and prefer to work on farms where berries are plentiful on the vine, but at the same time some recognize that some of that production could go to waste. Before UC's new cultivars were released few growers were seeking out disease resistant varieties because they had other means to deal with disease (e.g., continued allowability of fumigation). To support the development of high-throughput genotyping assays for marker-assisted selection, the QTL regions of Pc2, Ca1, Xf1, and Cg1 were narrowed down using transcriptome and genome sequencing data from cultivated strawberry varieties. Marker genotypes and sequencing data were used for developing sugenome specific markers (HRM and KASP) and applied for marker-assisted seedling selection. Three day-neutral and two short-day cultivars were released with strong resistance to one or more soil-borne pathogens, including Fusarium wilt, Verticillium wilt, and Macrophomina. We identified four novel genes on three chromosomes for resistance to the California race of Fusarium wilt. These were physically and genetically mapped and high-throughput genotyping assays were developed to accelerate their introduciton into modern cultivars through marker-assisted selection. We completed one cycle of selection for resistance to Verticillium wilt and Macrophomina, initiated the second cycle of selection, and identified several selection candidates with strong resistance to these pathogens. The latter were utilized as parents to develop segregating populations. A reliable molecular method to diagnose crown rot pathogens (Macrophomina, Colletotrichum and Phytophthora in the case of Florida) was developed and is now routinely employed in our diagnostic clinic, allowing results to be provided to growers within 24 hours, rather than 5-7 days. The HRM molecular method was evaluated for detection of pathogens in nursery transplants. However, it was shown to be most effective in detecting pathogens from symptomatic tissue rather than asymptomatic as is usually observed in nurseries. Sampling from asymptomatic plants at nurseries has turned out to be logistically and operationally challenging, in addition to the difficulty in the interpretation of results. To identify candidate genes for Pc2, Ca1, Xf1, and Mp1/2/3, the genome of major Florida cultivar (Florida Brilliance) was sequenced and assembled. Three loci were discovered and validated, Mp1, Mp2 and Mp3, increasing resistance to charcoal rot caused by Macrophomina phaseolina. The Ca1 locus and two previously discovered loci Xf1 and Pc2 were used in marker-assisted breeding for cross-combination selection and increasing resistance in seedling populations. Genomic selection methods for seedlings were developed and validated for foliar powdery mildew resistance. Two extended day-neutral (summer-plant) cultivars were released with strong resistance to Macrophomina and Verticillium wilt. We developed host different panels for resistance to California, Australian, Japanese, and Spanish races of the pathogen and identified multiple sources of resistance to each race. We hypothesized that these carry gene-for-gene resistance to these races. We initiated their introgression into modern cultivars and genetic studies to identify their locations and effects in the strawberry genome. We completed one cycle of selection for resistance to Verticillium wilt and Macrophomina, initiated the third cycle of selection, and identified several selection candidates with strong resistance to these pathogens. We developed high-throughput genotyping assays for DNA variants in linkage disequilibrium with five Fusarium wilt resistance genes (FW1, FW2, FW3, FW4, and FW5), completed a cycle of selection to introgress FW2, FW4, and FW5 into modern cultivars, and completed a cycle of population development to support genetic studies to identify genes that confer resistance to the Australian and Japanese races of the Fusarium wilt pathogen. We completed a genomic selection study of resistance to Phytopthora crown rot. We completed a study of the evolution of Fusarium oxysporum and showed that horizontal chromosome transfer is widespread in this pathogen and that pathogenicity can nevertheless evolve independently. We showed that a specific chromsome (chrY-frag) was absent in wilt-fragariae isolates, which suggested that multiple, distinct pathogenicity chromosomes can confer the same host specificity. Our research has provided knowledge on when plants become infected in the field and how water stress affects this process, which is important for designing and implementing management practices.

Publications

  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Henry PM, Pincot DDA, Jenner B, Borrero C, Aviles M, Nam M-H, Knapp SJ, Gordon TR (2021) Horizontal chromosome transfer, convergent evolution, and host heterogeneity drive diversification in the global population of Fusarium oxysporum f. sp. fragariae. New Phytologist 230: 327340. https://doi.org/10.1111/nph.17141
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Pincot, DDA, Ledda M, Feldmann MJ, Hardigan MA, Poorten TP, Heffelfinger C, Dellaporta S, Cole CS, Knapp SJ (2021) Social network analysis of the genealogy of cultivated strawberry: retracing the wild roots of modern cultivars. G3: Genes | Genomes | Genetics 11: jkab015. https://doi.org/10.1093/g3journal/jkab015
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Hardigan MA, Lorant A, Pincot DDA, Feldmann MJ, Famula R, Acharya C, Lee Seonghee, Bassil NV, Whitaker VM, Cole GS, Knapp SJ (2021) Unraveling the complex hybrid ancestry and domestication history of cultivated strawberry. Molecular Biology & Evolution 38:2285-2305. https://doi.org/10.1093/molbev/msab024
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Petrasch S, Mesquida-Pesci SD, Pincot DDA, Feldmann MJ, Lopez CM, Famula R, Hardigan MA, Cole GS, Knapp SJ, Blanco-Ulate B (2021) Genomic prediction of strawberry resistance to postharvest fruit decay caused by the fungal pathogen Botrytis cinerea. G3: Genes | Genomes | Genetics jkab378
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Qiao Q, Edger PE, Qiong L, Lu J, Zhang Y, Cao Q, Yocca AE, Platts AE, Knapp SJ, Montagu MV, de Peer YV, Lei J, Zhang T (2021) Evolutionary history and pan-genome dynamics of strawberry (Fragaria spp.). Proceedings National Academy of Science 118: e2105431118. https://doi.org/10.1073/pnas.210543111
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Alger EI, Platts AE, Deb SK, Luo X, Ou S, Cao Y, Hummer KE, Xiong Z, Knapp SJ, Liu Z, McKain MR, Edger PP (2021) Chromosome-scale genome for a red-fruited, perpetual flowering and runnerless woodland strawberry (Fragaria vesca). Front. Genet. 12: 671371 https://doi.org/10.3389/fgene.2021.671371
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Bird K, Hardigan MA, Ragsdale AP, Knapp SJ, VanBuren R, Edger PE (2021) Diversification, spread, and admixture of octoploid strawberry in the Western Hemisphere. Amer. J Bot. 108: 2269-2281. https://doi.org/10.1002/ajb2.1776
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Pincot DDA, Feldmann MJ, Hardigan MA, Vachev MV, Henry PM, Gordon TR, Bjornson M, Rodriguez A, Cobo N, Cole GS, Coaker GL, Knapp SJ (2022) Novel Fusarium Wilt resistance genes uncovered in natural and cultivated strawberry populations are found on three non-homoeologous chromosomes. Theor. Appl. Genet. 135: 21212145. https://doi.org/10.1007/s00122-022-04102-2
  • Type: Journal Articles Status: Published Year Published: 2022 Citation: Jim�nez NP, Feldmann MJ, Famula RA, Pincot DDA, Bjornson M, Cole GS, Knapp SJ (2022) Harnessing underutilized gene bank diversity and genomic prediction of cross usefulness to enhance resistance to Phytophthora cactorum in strawberry. The Plant Genome
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Nelson JR, Verman S, Bassil NV, Finn CE, Hancock JF, Cole CS, Knapp SJ, Whitaker VM (2020) Discovery and validation of three loci increasing resistance to charcoal rot caused by Macrophomina phaseolina in octoploid strawberry. G3: Genes | Genomes | Genetics 11:jkab037. https://doi.org/10.1093/g3journal/jkab037
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Tapia RR, Barbey CR, Chandra S, Folta KM, Whitaker VM, Lee S. Evolution of the MLO gene families in octoploid strawberry (Fragaria� ananassa) and progenitor diploid species identified potential genes for strawberry powdery mildew resistance. Horticulture research. 2021 Dec 1;8.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Baggio JS, Cordova LG, Seijo TE, Noling JW, Whitaker VM, Peres NA. Cultivar Selection Is an Effective and Economic Strategy for Managing Charcoal Rot of Strawberry in Florida. Plant Disease. 2021 Aug 20;105(8):2071-7.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Marin MV, Seijo TE, Baggio JS, Whitaker VM, Peres NA. Resistance of strawberry cultivars and the effects of plant ontogenesis on Phytophthora cactorum and P. nicotianae causing crown rot. Plant Disease. 2022 Jul 8(ja).
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Tapia R, Abd-Elrahman A, Osorio L, Whitaker VM, Lee S. Combining canopy reflectance spectrometry and genome-wide prediction to increase response to selection for powdery mildew resistance in cultivated strawberry. Journal of Experimental Botany. 2022 Apr 6.
  • Type: Theses/Dissertations Status: Published Year Published: 2022 Citation: Koster, J. 2022. An integrated approach for controlling Verticillium wilt of strawberry. Masters Thesis. California Polytechnic State University. August
  • Type: Theses/Dissertations Status: Published Year Published: 2022 Citation: Wang, Y. 2022. Strawberry disease management improvement for Macrophomina root rot and Botrytis fruit rot. Masters Thesis. California Polytechnic State University. August
  • Type: Theses/Dissertations Status: Published Year Published: 2020 Citation: Omar A. Gonzalez-Benitez (2022) Host plant resistance in strawberries to anthracnose and colonization of crown and root tissue by Verticillium dahliae and Macrophomina phaseoline. Master's Thesis. California Polytechnic State University.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Wang, N.-Y., Gama, A.B., Marin, M.V., and Peres, N.A. 2021. Development of a multiplex high-throughput diagnostic assay for the detection of strawberry crown rot diseases using high-resolution melting analysis. Phytopathology 111: 1470- 1483. https://doi.org/10.1094/PHYTO-12-20-0556-R
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Marin, M.V., Seijo, T.E., Zuchelli, E., and Peres, N.A. 2022. Detection and characterization of quinone outside inhibitorresistant Phytophthora cactorum and P. nicotianae causing leather rot in Florida strawberry. Plant Disease 106:1203- 1208. https://doi.org/10.1094/PDIS-08-21-1658-RE


Progress 09/01/20 to 08/31/21

Outputs
Target Audience:The target audiences for this research are: (a) private and public sector strawberry breeders, plant pathologists, scientists, and extension specialists; (b) strawberry growers, shippers, and packers and others engaged in producing and marketing strawberries; (c) academic scientists engaged in breeding and genomics of other species in the Rosaceae and other asexually propagated species; (d) graduate students, postdoctoral researchers, and academic scientists engaged in economics, sociology, plant pathology, horticulture, breeding, genetics, and genomics research. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Nothing Reported How have the results been disseminated to communities of interest? Nothing Reported What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Significant progress was made in transferring alleles for resistance to Macrophomina from exotic to elite germplasm. This work spanned six years, pre-dating the SCRI. We showed that strong resistance to the pathogen was extremely rare in elite and exotic germplasm; however, genetic variation from resistant exoitc donors were crossed with susceptible or weakly resistant modern cultivars todevelop a base population for recurrent selection. We observed a normal phenotypic distribution in the first cycle of selection with individuals spanning the range from highly resistant to highly susceptible. The population was greatly enriched for resistance relative to the elite founders. We observed a complete reversal in the second cycle of selection: > 70% of the individuals were resistant. This population has yielded hybrids that are being advanced for possible commercial release.

Publications


    Progress 09/01/19 to 08/31/20

    Outputs
    Target Audience:The target audiences for this research are: (a) private and public sector strawberry breeders, plant pathologists, scientists, and extension specialists; (b) strawberry growers, shippers, and packers and others engaged in producing and marketing strawberries; (c) academic scientists engaged in breeding and genomics of other species in the Rosaceae and other asexually propagated species; (d) graduate students, postdoctoral researchers, and academic scientists engaged in economics, sociology, plant pathology, horticulture, breeding, genetics, and genomics research. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?As in previous years, our initiative has provided significant training and professional development opportunities for graduate students, postdoctoral scholars, and research staff through hands-on training in greenhouse and field operations, planning, organizing, and overseeing field experiments, participating in breeding program activities and operations, on-farm research with fruit and nursery growers, and guest lectures in undergraduate and graduate classes. How have the results been disseminated to communities of interest?As in previous years, the results of our research initiative have been disseminated to communities of interest through:refereed journal publications, poster and oral presentations at national and international scientific meetings, the deposition of data and other materials in public databases and other open source repositories (e.g., the NCBI Short-Read Archive, the Rosaceae Genomics Database, and DRYAD), field days, stakeholder and industry organized meetings, on-farm experiements, one-on-one and small group interactions with fruit and nursery growers and stakeholders, progress reports to commodity groups and stakeholders, cultivar releases, the popular press and new releases, websites, and multimedia presentations. What do you plan to do during the next reporting period to accomplish the goals?We plan to complete the identification and fine scale mapping of genes conferring resistance to a broad spectrum of pathogens, advance the development and release of disease resistant cultivars, develop the information and physical resources needed to apply genome-informed approaches in strawberry breeding, complete one cycle of breeding, select individuals for advanced testing, and complete advanced testing in artificially inoculated disease screening trials.

    Impacts
    What was accomplished under these goals? To identify candidate genes for Pc2, Ca1, Xf1, and Mp1/2/3, the genome of major Florida cultivar (Florida Brilliance) was sequenced and assembled. Three loci were discovered and validated, Mp1, Mp2 and Mp3, increasing resistance to charcoal rot caused by Macrophomina phaseolina. The Ca1 locus and two previously discovered loci Xf1 and Pc2 were used in marker-assisted breeding for cross-combination selection and increasing resistance in seedling populations. Genomic selection methods for seedlings were developed and validated for foliar powdery mildew resistance. Two extended day-neutral (summer-plant) cultivars were released with strong resistance to Macrophomina and Verticillium wilt. We developed host different panels for resistance to California, Australian, Japanese, and Spanish races of the pathogen and identified multiple sources of resistance to each race. We hypothesized that these carry gene-for-gene resistance to these races. We initiated their introgression into modern cultivars and genetic studies to identify their locations and effects in the strawberry genome. We completed one cycle of selection for resistance to Verticillium wilt and Macrophomina, initiated the third cycle of selection, and identified several selection candidates with strong resistance to these pathogens. We proposed a logical chromosome nomenclature for the octoploid and created databases to facilitate cross-referencing coordinates for physically and genetically mapped loci. We developed haplotype-phased chromosome genome assemblies for the strawberry cultivar Royal Royce. This genome corrects local assembly errors found in earlier genomes, was validated by high-density de novo genetic mapping, and furnishes a reference grade standard for downstream genome-informed biological and agricultural research in the genus, the rose family, and plants more broadly. With this genome in hand, we reanalyzed DNA variants genome wide, aligned octoploid genome-anchored SNPs on previously developed arrays to the newly developed reference, and developed databases to interconnect information across studies and platforms. Finally, we completed the development of a medium-density SNP genotyping platform and initiated the development of a second medium-density SNP genotyping platform to support large-scale applications of genomic selection in breeding programs. We developed high-throughput genotyping assays for DNA variants in linkage disequilibrium with five Fusarium wilt resistance genes (FW1, FW2, FW3, FW4, and FW5), completed a cycle of selection to introgress FW2, FW4, and FW5 into modern cultivars, and completed a cycle of population development to support genetic studies to identify genes that confer resistance to the Australian and Japanese races of the Fusarium wilt pathogen. We completed a genomic selection study of resistance to Phytopthora crown rot. We completed a study of the evolution of Fusarium oxysporum and showed that horizontal chromosome transfer is widespread in this pathogen and that pathogenicity can nevertheless evolve independently. We showed that a specific chromsome (chrY-frag) was absent in wilt-fragariae isolates, which suggested that multiple, distinct pathogenicity chromosomes can confer the same host specificity. Our research has provided knowledge on when plants become infected in the field and how water stress affects this process, which is important for designing and implementing management practices.

    Publications

    • Type: Journal Articles Status: Published Year Published: 2020 Citation: Guthman, J and Zurawski, E (2020) If I need to put more armor on, I cant carry more guns: the collective action problem of breeding for productivity in the California strawberry industry. International Journal of Sociology of Agriculture and Food 26 (1): 69-88
    • Type: Journal Articles Status: Published Year Published: 2020 Citation: Guthman, J. (2020) Strawberry growers are unlikely to forgo soil fumigation with disease-resistant cultivars alone. California Agriculture 74(3):138-143. https://doi.org/10.3733/ca.2020a0021
    • Type: Theses/Dissertations Status: Published Year Published: 2020 Citation: Gonzalez-Benitez, O.A. 2020. Host plant resistance in strawberries to anthracnose and colonization of crown and root tissue by Verticillium dahliae and Macrophomina phaseolina. MS Thesis, California Polytechnic State University, San Luis Obispo, June.
    • Type: Theses/Dissertations Status: Published Year Published: 2019 Citation: Winslow, J. 2019. Evaluation of host resistance and the utilization of organic amendments to manage Macrophomina crown rot of strawberry in California. MS Thesis, California Polytechnic State University, San Luis Obispo, June.
    • Type: Theses/Dissertations Status: Published Year Published: 2020 Citation: Boyd, E. 2020. The strawberry rhizosphere microbiome: role on plant health and nutrition. MS Thesis, California Polytechnic State University, San Luis Obispo, March.
    • Type: Journal Articles Status: Published Year Published: 2020 Citation: Hon T, Mars K, Young G, Tsai Y-C, Karalius J, Landolin J, Maurer N, Kudrna D, Hardigan MA, Steiner C, Knapp SJ, Ware D, Shapiro B, Peluso P, Rank D (2020) Highly accurate long-read HiFi sequencing data for five complex genomes. Nature Scientific Data 7: 399. https://doi.org/10.1038/s41597-020-00743-4
    • Type: Journal Articles Status: Published Year Published: 2020 Citation: Casttillejo C, Waurich V, Wagner H, Ramos R, Oiza N, Munoz P, Trivino JC, Caruana J, Liu Z, Cobo N, Hardigan MA, Knapp SJ, Vallarino JG, Osorio S, Martin-Pizarro C, Pose D, Toivainen T, Hytonen T, Oh Y, Barbey CR, Whitaker VM, Lee S, Olbricht K, Sanchez-Sevilla JF, Amaya I (2020) Allelic variation of MYB10 is the major force controlling natural variation of skin and flesh color in strawberry (Fragaria spp.) fruit. The Plant Cell 32: 3723-3749. DOI: 10.1105/tpc.20.00474.
    • Type: Journal Articles Status: Published Year Published: 2020 Citation: Pincot DDA, Hardigan MA, Cole GS, Famula R, Henry PA, Gorden TR, Knapp SJ (2020) Accuracy of genomic selection and long-term genetic gain for resistance to Verticillium wilt in strawberry. The Plant Genome: e20054. https://doi.org/10.1002/tpg2.20054.
    • Type: Journal Articles Status: Published Year Published: 2020 Citation: Feldmann MJ, Hardigan MA, Famula RA, L�pez CM, Tabb A, Cole GS, Knapp SJ (2020) Multi-dimensional machine learning approaches for fruit shape recognition and phenotyping in strawberry. GigaScience 9. https://doi.org/10.1093/gigascience/giaa030
    • Type: Journal Articles Status: Published Year Published: 2020 Citation: Hardigan MA, Feldmann MJ, Lorant A, Bird KA, Famula R, Acharya C, Cole GS, Edger PP, Knapp SJ (2020) Genome synteny has been conserved among the octoploid progenitors of cultivated strawberry over millions of years of evolution. Frontiers Plant Sci 10:1789. https://doi.org/10.3389/fpls.2019.01789
    • Type: Journal Articles Status: Published Year Published: 2020 Citation: TYPE: Journal Article Edger PP, McKain MR, Yocca AE, Knapp SJ, Qiao Q, Zhang T (2020) Reply to: Revisiting the origin of octoploid strawberry. Nat Genet 52:57. https://doi.org/10.1038/s41588-019-0544-2
    • Type: Theses/Dissertations Status: Published Year Published: 2020 Citation: Pincot DDA (2020) The Genealogy of Strawberry and Host Resistance in Strawberry-Vascular Wilt Pathosystems. Ph.D. Dissertation, University of California, Davis.
    • Type: Theses/Dissertations Status: Published Year Published: 2020 Citation: Petrasch S (2020) Genetics of Strawberry Postharvest Fruit Quality and Resistance to Necrotrophic Fungi. Ph.D. Dissertation, University of California, Davis.
    • Type: Theses/Dissertations Status: Published Year Published: 2020 Citation: Feldmann MJ (2020) A Quantitative Analysis of Complex Agronomic Traits in Garden Strawberry (Fragaria � ananassa). Ph.D. Dissertation, University of California, Davis.
    • Type: Theses/Dissertations Status: Published Year Published: 2020 Citation: Henry PM (2020) The Ecology and Epidemiology of Fusarium oxysporum f. sp. fragariae and Xanthomonas fragariae in California . Ph.D. Dissertation, University of California, Davis.
    • Type: Journal Articles Status: Published Year Published: 2020 Citation: Whitaker V, Knapp SJ, Hardigan M, Edger P, Slovin J, Bassil N, Hyt�nen T, Mackenzie K, Lee S, Jung S, Main D, Barbey C, Verma S (2020) A roadmap for research in octoploid strawberry. Horticulture Research 7: 33. https://doi.org/10.1038/s41438-020-0252-1
    • Type: Journal Articles Status: Published Year Published: 2020 Citation: Salinas N, Fan Z, Peres NA, Lee S, Whitaker VM. 2020 FaRCa1 confers moderate resistance to the root necrosis form of strawberry anthracnose caused by Colletotrichum acutatum. HortScience 55:693-698.
    • Type: Journal Articles Status: Published Year Published: 2020 Citation: Barbey, C. R., Hogshead, M. H., Schwartz, A. E., Mourad, N., Verma, S., Lee, S., Whitaker, V. M. and Folta, K. M. 2020. The genetics of differential gene expression related to fruit traits in strawberry (Fragaria �ananassa). Frontiers in Genetics 10: 1317
    • Type: Journal Articles Status: Published Year Published: 2020 Citation: Oh, Y., Chandra S. and Lee, S. 2020. Development of subgenome-specific markers for high-throughput marker-assisted selection of bacterial angular leaf spot resistance in allo-octoploid strawberry. International Journal of Fruit Science 1-13
    • Type: Journal Articles Status: Published Year Published: 2020 Citation: Baggio, J.S., Ruschel, R.G., Noling, J., and Peres, N.A. 2020. Physical, cultural, and chemical alternatives for integrated management of charcoal rot of strawberry. Plant Disease https://apsjournals.apsnet.org/doi/pdf/10.1094/PDIS-04-20-0917-RE
    • Type: Journal Articles Status: Published Year Published: 2020 Citation: Henry PM, Haugland M, Lopez L, Munji M, Watson DC, Gordon TR. 2020. The potential for Fusarium oxysporum f. sp. fragariae, cause of Fusarium wilt of strawberry, to colonize organic matter in soil and persist through anaerobic soil disinfestation. Plant Pathology 69:1218-1226. doi: 10.1111/ppa.13225
    • Type: Journal Articles Status: Published Year Published: 2020 Citation: Seijo, T.E., Whitaker, V.M., and Peres, N.A. 2020. Evaluation of strawberry cultivars and advanced breeding selections for resistance to anthracnose fruit rot, Botrytis fruit rot, and powdery mildew, 2019-2020. Plant Disease Management Reports 14: (online). PF085. DOI:10.1094/PDMR14. The American Phytopathological Society, St. Paul, MN.
    • Type: Journal Articles Status: Published Year Published: 2020 Citation: Seijo, T.E., Marin, M.V., Whitaker, V.M., and Peres, N.A. 2020. Evaluation of strawberry cultivars and advanced breeding selections for resistance to Phytophthora crown rot caused by Phytophthora cactorum, 2019-2020. Plant Disease Management Reports 14: (online). PF086. DOI:10.1094/PDMR14. The American Phytopathological Society, St. Paul, MN.
    • Type: Journal Articles Status: Published Year Published: 2020 Citation: Seijo, T.E., Rebello, C.S., Whitaker, V.M., and Peres, N.A. 2020. Evaluation of strawberry cultivars and advanced breeding selections for resistance to Colletotrichum crown rot caused by Colletotrichum gloeosporioides, 2019-2020. Plant Disease Management Reports 14: (online). PF087. DOI:10.1094/PDMR14. The American Phytopathological Society, St. Paul, MN.
    • Type: Journal Articles Status: Published Year Published: 2020 Citation: Seijo, T.E., Whitaker, V.M., and Peres, N.A. 2020. Evaluation of strawberry cultivars and advanced breeding selections for resistance to charcoal rot by Macrophomina phaseolina, 2019-2020. Plant Disease Management Reports 14: (online). PF088. DOI:10.1094/PDMR14. The American Phytopathological Society, St. Paul, MN.
    • Type: Journal Articles Status: Published Year Published: 2020 Citation: Suguinoshita Rebello, C., Wang, N.Y., Baggio, J.S., and Peres, N.A. 2020. Detection and identification of Neopestalotiopsis species from strawberry using a high-resolution melting (HRM) assay. Phytopathology S2:63.
    • Type: Journal Articles Status: Published Year Published: 2020 Citation: Wang, N.Y., Gama, A.B., Marin, M., and Peres, N.A. 2020. Development of a multiplex high-throughput diagnostic assay for the detection of strawberry crown rot diseases using high-resolution melting analysis. Phytopathology S2:101.
    • Type: Journal Articles Status: Published Year Published: 2020 Citation: Oliveira, M., Wang, N.Y., and Peres, N.A. 2020. Use of high-resolution melting analysis to identify species in the Colletotrichum gloeosporioides species complex from strawberry. Phytopathology S2:114.
    • Type: Journal Articles Status: Published Year Published: 2020 Citation: Holmes, G.J., Mansouripour, S. M. and Hewavitharana, S. 2020. Strawberries at the crossroads: Management of soilborne diseases in California without methyl bromide. Phytopathology 110:956-968. https://doi.org/10.1094/PHYTO-11-19-0406-IA
    • Type: Journal Articles Status: Published Year Published: 2020 Citation: Lazcano, C., Boyd, E., Holmes, G., Hewavitharana, S, Pasulka, A. and Ivors, K.2021. The rhizosphere microbiome plays a role in the resistance to soil-borne pathogens and nutrient uptake of strawberry cultivars under field conditions. Sci Rep 11:3188. https://doi.org/10.1038/s41598-021-82768-2


    Progress 09/01/18 to 08/31/19

    Outputs
    Target Audience:The target audiences for this research are: (a) private and public sector strawberry breeders, plant pathologists, scientists, and extension specialists; (b) strawberry growers, shippers, and packers and others engaged in producing and marketing strawberries; (c) academic scientists engaged in breeding and genomics of other species in the Rosaceae and other asexually propagated species; (d) graduate students, postdoctoral researchers, and academic scientists engaged in economics, sociology, plant pathology, horticulture, breeding, genetics, and genomics research. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?As in the previous year, our initiative has provided significant training and professional development opportunities for graduate students, postdoctoral scholars, and research staff through hands-on training in greenhouse and field operations, planning, organizing, and overseeing field experiments, participating in breeding program activities and operations, on-farm research with fruit and nursery growers, and guest lectures in undergraduate and graduate classes. How have the results been disseminated to communities of interest?As in the previous year, the results of our research initiative have been disseminated to communities of interest through:refereed journal publications, poster and oral presentations at national and international scientific meetings, the deposition of data and other materials in public databases and other open source repositories (e.g., the NCBI Short-Read Archive, the Rosaceae Genomics Database, and DRYAD), field days, stakeholder and industry organized meetings, on-farm experiements, one-on-one and small group interactions with fruit and nursery growers and stakeholders, progress reports to commodity groups and stakeholders, cultivar releases, the popular press and new releases, websites, and multimedia presentations. What do you plan to do during the next reporting period to accomplish the goals?We expect to continue ongoing studies and statistical analyses and develop and publish additional papers describing the results of our studies. We will continue to extend information to the scientific community and stakeholders through open source publications, field days, interactions with growers, and participation in scientific and cooperative extension meetings.

    Impacts
    What was accomplished under these goals? To support the development of high-throughput genotyping assays for marker-assisted selection, the QTL regions of Pc2, Ca1, Xf1, and Cg1 were narrowed down using transcriptome and genome sequencing data from cultivated strawberry varieties. Marker genotypes and sequencing data were used for developing sugenome specific markers (HRM and KASP) and applied for marker-assisted seedling selection. Three day-neutral and two short-day cultivars were released with strong resistance to one or more soil-borne pathogens, including Fusarium wilt, Verticillium wilt, and Macrophomina. We identified four novel genes on three chromosomes for resistance to the California race of Fusarium wilt. These were physically and genetically mapped and high-throughput genotyping assays were developed to accelerate their introduciton into modern cultivars through marker-assisted selection. We completed one cycle of selection for resistance to Verticillium wilt and Macrophomina, initiated the second cycle of selection, and identified several selection candidates with strong resistance to these pathogens. The latter were utilized as parents to develop segregating populations. Disease surveys at both high and low elevation nurseries did not detect significant levels of disease. Statistical approaches to achieve high levels of confidence in monitoring are unrealistic for regulators or nurseries to employ because this requires the collection of many thousands of plants. Detection techniques for the four major soilborne pathogens (Verticillium, Macrophomina, Fusarium and Phytophthora) were optimized and are now employed in routine disease diagnostics. A quick and reliable molecular method to diagnose crown rot pathogens (Macrophomina, Colletotrichum and Phytophthora in the case of Florida) was developed and is now routinely employed in our diagnostic clinic, allowing results to be provided to growers within 24 hours, rather than 5-7 days. The HRM molecular method was evaluated for detection of pathogens in nursery transplants. However, it was shown to be most effective in detecting pathogens from symptomatic tissue rather than asymptomatic as is usually observed in nurseries. Sampling from asymptomatic plants at nurseries has turned out to be logistically and operationally challenging, in addition to the difficulty in the interpretation of results. Our research has provided knowledge on when plants become infected in the field and how water stress affects this process, which is important for designing and implementing management practices.

    Publications

    • Type: Journal Articles Status: Published Year Published: 2019 Citation: Henry PM, Pastrana AM, Leveau JHJ, and Gordon TR. 2019. Persistence of Fusarium oxysporum f. sp. fragariae in soil through asymptomatic colonization of rotation crops. Phytopathology 109:770-779. doi: 10.1094/PHYTO-11-18-0418-R
    • Type: Journal Articles Status: Published Year Published: 2019 Citation: Barbey C, Lee S, Verma S, Bird KA, Yocca AE, Edger PP, Knapp SJ, Whitaker VM, Folta K (2019) Disease resistance genetics and genomics in octoploid strawberry. G3: Genes|Genomes|Genetics 9:3315-3332. https://doi.org/10.1534/g3.119.400597
    • Type: Journal Articles Status: Published Year Published: 2019 Citation: Salinas N, Verma S, Peres NA, Whitaker VM. 2019. FaRCa1: A major subgenome-specific locus conferring resistance to Colletotrichum acutatum in strawberry. Theoretical and Applied Genetics 132:1109-1120
    • Type: Journal Articles Status: Published Year Published: 2019 Citation: Oh Y, Zurn JD, Bassil N, Edger PP, Knapp SJ, Whitaker VM, Lee S (2019) The strawberry DNA testing handbook. HortScience 54:2267-2270
    • Type: Journal Articles Status: Published Year Published: 2019 Citation: Baggio, J.S., Cordova, L.G., and Peres, N.A. 2019. Sources of inoculum and survival of Macrophomina phaseolina in Florida strawberry fields. Plant Disease 103: 2417-2424. https://doi.org/10.1094/PDIS-03-19-0510-RE
    • Type: Journal Articles Status: Published Year Published: 2019 Citation: Seijo, T.E., Whitaker, V., and Peres, N.A. 2019. Strawberry cultivars have differing susceptibility to the two major Colletotrichum pathogens, C. acutatum and C. gloeosporioides. Phytopathology 109: S2.94.
    • Type: Journal Articles Status: Published Year Published: 2019 Citation: Marin, M., Seijo, T.E., Whitaker, V., and Peres, N.A. 2019. Resistance of strawberry cultivars to crown rot caused by Phytophthora cactorum and P. nicotianae. Phytopathology 109: S2.94.
    • Type: Theses/Dissertations Status: Published Year Published: 2019 Citation: Winslow, J. 2019. Evaluation of host resistance and the utilization of organic amendments to manage Macrophomina crown rot of strawberry in California. MS Thesis, California Polytechnic State University, San Luis Obispo, June.
    • Type: Journal Articles Status: Published Year Published: 2019 Citation: Barbey, C. R., Lee, S., Verma, S., Whitaker, V. M., Bird, K. A., Yocca, A. E., Edger, P. P., Knapp, S. J. and Folta, K. M. 2019. Genome characterization of disease resistance genes in strawberry. G3: GENES, GENOMES, GENETICS 9 (10), 3315-3332
    • Type: Theses/Dissertations Status: Published Year Published: 2019 Citation: Boyd, E. 2020. The strawberry rhizosphere microbiome: role on plant health and nutrition. MS Thesis, California Polytechnic State University, San Luis Obispo, March.
    • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Pedroncelli, L, Biscaro A, and Putman AI. 2020. The role of irrigation in disease development and management of Macrophomina charcoal rot on strawberries (Abstr.). Phytopathology 110:S2.56
    • Type: Journal Articles Status: Published Year Published: 2019 Citation: Edger PP, Poorten TJ, VanBuren R, Hardigan MA, Colle M, McKain MR, Smith RD, Teresi S, Nelson ADL, Wai CM, Alger EI, Bird KA, Yocca AE, Pumplin N, Ou S, Ben- Zvi G, Brodt A, Baruch K, Swale T, Shiue L, Acharya CB, Cole GS, Mower JP, Childs KL, Jiang N, Lyons E, Freeling M, Puzey JR, Knapp SJ (2019) Origin and evolution of the octoploid strawberry genome. Nature Genetics 51:541547. doi: 10.1038/ s41588-019-0356-4
    • Type: Journal Articles Status: Published Year Published: 2019 Citation: Petrasch S, Knapp SJ, van Kan JAL, Blanco-Ulate B (2019) Grey mould of strawberry, a devastating disease caused by the ubiquitous necrotrophic fungal pathogen Botrytis cinerea. Mol. Plant Path. 20:877-892.


    Progress 09/01/17 to 08/31/18

    Outputs
    Target Audience:The target audiences for this research are: (a) private and public sector strawberry breeders, plant pathologists, scientists, and extension specialists; (b) strawberry growers, shippers, and packers and others engaged in producing and marketing strawberries; (c) academic scientists engaged in breeding and genomics of other species in the Rosaceae and other asexually propagated species; (d) graduate students, postdoctoral researchers, and academic scientists engaged in economics, sociology, plant pathology, horticulture, breeding, genetics, and genomics research. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Our initiative has provided significant training and professional development opportunities for graduate students, postdoctoral scholars, and research staff through hands-on training in greenhouse and field operations, planning, organizing, and overseeing field experiments, participating in breeding program activities and operations, on-farm research with fruit and nursery growers, and guest lectures in undergraduate and graduate classes. How have the results been disseminated to communities of interest?The results of our research initiative have been disseminated to communities of interest through: refereed journal publications, poster and oral presentations at national and international scientific meetings, the deposition of data and other materials in public databases and other open source repositories (e.g., the NCBI Short-Read Archive, the Rosaceae Genomics Database, and DRYAD), field days, stakeholder and industry organized meetings, on-farm experiements, one-on-one and small group interactions with fruit and nursery growers and stakeholders, progress reports to commodity groups and stakeholders, cultivar releases, the popular press and new releases, websites, and multimedia presentations. What do you plan to do during the next reporting period to accomplish the goals?We plan to complete the identification and fine scale mapping of genes conferring resistance to a broad spectrum of pathogens, advance the development and release of disease resistant cultivars, develop the information and physical resources needed to apply genome-informed approaches in strawberry breeding, complete one cycle of breeding, select individuals for advanced testing, and complete advanced testing in artificially inoculated disease screening trials.

    Impacts
    What was accomplished under these goals? We released the first chromosome-scale assembly of the octoploid strawberry genome, resequenced the genomes of 143 germplasm accessions spanning global diversity, identified approximately 50M DNA variants among the resequenced individuals, developed and released 50K and 850K SNP genotyping arrays using DNA sequences anchored to the octoploid genome, and demonstrated the feasibility of applying genotyping-by-sequencing in the octoploid using whole-genome shotgun sequencing. The location of the FW1 Fusarium wilt resistance gene was pinpointed using GWAS and verified by high-density genetic mapping. DNA variants in linkage disequilibrium with FW1 were identified by whole-genome resequencing and SNP array genotyping. We completed the second year of screening 500-1,000 germplasm accessions for resistance to Fusarium wilt, Verticillium wilt, and Phytophthora crown rot, identified resistant cultivars and several strong sources of resistance to these pathogens to support breeding, and completed one generation of breeding to introduce favorable alleles for resistance to these pathogen into elite genetic backgrounds. We completed genomic selection studies in two different training populations for resistance to Verticillium wilt, identified and hybridized selection candidates, and initiated the next cycle of selection. We developed segregating populations to support breeding for resistance to Macrophomina, completed one cycle of recurrent phenotypic selection for resistance to Macrophomina, and identified and selected several highly resistant individuals for another cycle of recurrent selection. Screening for disease resistance has allowed the breeding programs to identify sources of resistance in commercial cultivars and advanced selections to major strawberry pathogens such as Colletotrichum acutatum, Colletotrichum gloeosporioides, Phytophthora cactorum, Macrophomina phaseolina, and Xanthomonas fragariae. Results were used to discover major locus for resistance that can be used in the future to develop markers to screen seedlings. One major locus was discovered and validated, Ca1, increasing resistance to anthracnose fruit rot and crown rot, both caused by Colletotrichum acutatum. Our host resistance studies show that a wide range of susceptibilities exist to Verticillium wilt, Macrophomina crown rot and anthracnose. Genotypes that show high levels of resistance to these pathogens were identified and are being used by growers (in the case of existing cultivars) and breeders (in the case of elite lines). In addition, awareness of host plant resistance as a means of managing soilborne pathogens is heightened among California growers. Deepened understanding of the socioeconomic factors affecting cultivar choice, e.g., most growers want high yielding varieties because of competition with other growers and because marketers pay them by volume produced, at the same time that they recognize that over-production contributes to low prices and risks losing their business. They also choose high yielding varieties to attract workers in the context of labor shortages, since workers are paid on piece rates and prefer to work on farms where berries are plentiful on the vine, but at the same time some recognize that some of that production could go to waste. Before UC's new cultivars were released few growers were seeking out disease resistant varieties because they had other means to deal with disease (e.g., continued allowability of fumigation).

    Publications

    • Type: Journal Articles Status: Published Year Published: 2017 Citation: Edger P, VanBuren R, Colle M, Poorten T, Man Wai C, Niederhuth C, Alger EI, Ou Shujun, Acharya C, Wang Jie, Callow P, McKain M, Shi J, Collier C, Xiong Z, Mower J, Slovin J, Hyt�nen T, Jiang N, Childs K, Knapp SJ (2017) Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity. Gigascience 7:1-7. doi: 10.1093/gigascience/gix124.
    • Type: Journal Articles Status: Under Review Year Published: 2018 Citation: Petrasch S, Knapp SJ, va Kan JAL, Blanco-Ulate B (2018) Gray mold of strawberry, a devastating disease caused by the ubiquitous necrotrophic fungal pathogen Botrytis cinerea. Mol. Plant Path. (submitted).
    • Type: Journal Articles Status: Published Year Published: 2018 Citation: Hardigan MA, Poorten TJ, Acharya C, Cole GS, Hummer K, Bassil N, Edger PP, Knapp SJ (2018) Domestication of temperate and coastal hybrids with distinct ancestral gene selection in octoploid strawberry. The Plant Genome 11:1-11. doi:10.3835/plantgenome2018.07.0049
    • Type: Journal Articles Status: Published Year Published: 2018 Citation: Pincot DD, Poorten TJ, Hardigan MA, Harshman JM, Acharya CB, Cole GS, Gordon TR, Stueven M, Edger PP, Knapp SJ (2018) Genome-wide association mapping uncovers Fw1, a dominant gene conferring resistance to Fusarium wilt in strawberry. G3: Genes|Genomes|Genetics 8:1817-1828. doi: 10.1534/g3.118.200129.
    • Type: Journal Articles Status: Accepted Year Published: 2018 Citation: Noh Y-H, Oh Y, Mangandi J, Verma S, Zurn JD, Lu Y-T, Fan Z, Bassil N, Peres N, Cole GS, Acharya C, Famula R, Knapp SJ, Whitaker VM, Lee S (2018) High-throughput marker assays for FaRPc2-mediated resistance to Phytopthora crown rot in octoploid strawberry. Molecular Breeding (in press).
    • Type: Journal Articles Status: Published Year Published: 2018 Citation: Forcelini BB, Lee S, Oliveira MS, Peres N (2018) Development of high-throughput SNP genotyping assays for rapid detection of strawberry colletotrichum species and the G143A mutation. Phytopathology (doi.org/10.1094/PHYTO-04-18-0128-R)
    • Type: Journal Articles Status: Published Year Published: 2018 Citation: Anciro A, Mangandi J, Verma S, Peres N, Whitaker VM, Lee S (2018) FaRCg1: a quantitative trait locus conferring resistance to Colletotrichum crown rot caused by Colletotrichum gloeosporioides in octoploid strawberry. Theoretical and Applied Genetics (doi: 10.1007/s00122-018-3145-z)
    • Type: Journal Articles Status: Submitted Year Published: 2018 Citation: Pastrana AM, Watson DC, Gordon TR. 2018. Transmission of Fusarium oxysporum f. sp. fragariae through stolons to strawberry plants. Plant Disease (submitted).
    • Type: Conference Papers and Presentations Status: Submitted Year Published: 2018 Citation: Winslow, J., Mazzola, M., Holmes, G., and Ivors, K. 2018. Integrating host resistance and organic amendments in a non-chemical approach to managing Macrophomina crown rot in strawberries. Phytopathology
    • Type: Journal Articles Status: Published Year Published: 2017 Citation: Henry PM, Kirkpatrick S, Islas CM, Yoshisato J, Koike ST, Daugovish O, Gordon TR. 2017. The population of Fusarium oxysporum f sp. fragariae, cause of Fusarium wilt of strawberry, in California. Plant disease. 101:550-556. doi:10.1094/PDIS-07-16-1058-RE
    • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Mansouripour, S.M., Winslow, J, Gomez-Soto, B, Liu, B. and Holmes, G. 2018. Two year summary of host plant resistance in strawberry to Macrophomina crown rot and Verticillium wilt. Pages 14-1 to 14-3 In MBAO: Fumigation and Alternatives for Production, Storage and Trade Conference, Orlando, FL. 12-14 Nov.
    • Type: Other Status: Published Year Published: 2018 Citation: Holmes, G.J., Ivors, K.L., Liu, B., Mansouripour, S.M. 2018. Evaluating strawberry cultivars for resistance to Verticillium wilt, field ratings from 2018. Calif. Strawberry Commission Annual Research Reports.
    • Type: Other Status: Published Year Published: 2018 Citation: Holmes, G.J., Hewavitharana, S.S., Gonzalez-Benitez, O.A. 2018. Evaluation of strawberry genotypes for susceptibility to anthracnose crown rot, field ratings from 2019. Pp. 59-65 In: California Strawberry Commission Annual Production Research Reports 2018.
    • Type: Other Status: Published Year Published: 2018 Citation: Holmes, G.J., Ivors, K.L., Liu, B., Mansouripour, S.M. 2018. Evaluating strawberry cultivars for resistance to Verticillium wilt, field ratings from 2018. Pp. 81-87 In: California Strawberry Commission Annual Production Research Report 2018.
    • Type: Other Status: Published Year Published: 2018 Citation: Holmes, G.J., Liu, B., Mansouripour, S.M. 2018. Evaluating strawberry cultivars for resistance to Verticillium wilt, field ratings from 2019. Pp. 89-95 In: California Strawberry Commission Annual Production Research Report 2018.
    • Type: Other Status: Published Year Published: 2018 Citation: Ivors, K.L., Holmes, G.J., Liu, B., Mansouripour, S.M. 2018. Investigating treatments for the management of Macrophomina on Californias Central Coast, field ratings from 2018. Pp. 67-73 In: California Strawberry Commission Annual Production Research Report 2018.
    • Type: Other Status: Published Year Published: 2018 Citation: Holmes, G.J., Liu, B., Mansouripour, S.M. 2018. Investigating treatments for the management of Macrophomina on Californias Central Coast, field ratings from 2019. Pp. 75-79 In: California Strawberry Commission Annual Production Research Report 2018.