Source: MICHIGAN STATE UNIV submitted to
CUCCAP 2: HARNESSING GENOMIC RESOURCES FOR DISEASE RESISTANCE AND MANAGEMENT IN CUCURBIT CROPS – BRINGING THE TOOLS TO THE FIELD
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
NEW
Funding Source
Reporting Frequency
Annual
Accession No.
1023460
Grant No.
2020-51181-32139
Project No.
MICL08593
Proposal No.
2020-02596
Multistate No.
(N/A)
Program Code
SCRI
Project Start Date
Sep 1, 2020
Project End Date
Aug 31, 2024
Grant Year
2020
Project Director
Grumet, R.
Recipient Organization
MICHIGAN STATE UNIV
(N/A)
EAST LANSING,MI 48824
Performing Department
HORTICULTURE
Non Technical Summary
Producers and processors of cucurbit crops (watermelons, melons, cucumbers, winter and summer squashes) consistently identify diseases as their primary constraint. These diseases cause severe reductions in yield and quality, increased labor and expenses for disease control, negative environmental impacts from application of pesticides, loss of profitability, and potential outright loss of the crop in the field or at point of sale. The most cost-effective, environmentally desirable solution is disease-resistant cultivars deployed with effective integrated disease management strategies. To achieve this outcome, CucCAP2 will develop and deliver: advanced genomic, bioinformatic, and breeding tools; disease resistant materials; and disease management strategies and economic analyses for critical diseases threatening cucurbit production. Four crop teams (watermelon, melon, cucumber, squash) together with genomics/bioinformatics, and integrated disease management teams, will take an integrated research and extension/outreach approach to: develop novel bioinformatic, pan-genome and genetic mapping tools; utilize genomic approaches to identify, map, and develop markers for resistances to priority diseases identified by cucurbit industries; introduce and combine resistances in advanced breeding lines; and perform multi-location, multi-isolate trials of resistances to improve integrated disease management and assess economic impacts. This project will expand on the nation-wide, interdisciplinary collaborations established in CucCAP1, bringing together bioinformaticians, genomicists, geneticists, breeders, plant pathologists, and economists, to provide genomic tools for public and private breeders to accelerate breeding for disease resistance in cucurbit crops, and develop and provide readily accessible disease control information, disease management strategies, and estimates of economic net returns for cucurbit producers. This project also will benefit the larger scientific and private breeding and crop production communities by providing transdisciplinary STEM training for undergraduate, graduate students and post-doctoral researchers, including participants from Historically Black (HBCU) and Hispanic-Serving (HIS) universities.
Animal Health Component
0%
Research Effort Categories
Basic
30%
Applied
50%
Developmental
20%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2011420108010%
2011420108120%
2011421108010%
2011421108110%
2011429108010%
2011429108110%
2161420116010%
2161421116010%
2161429116010%
Goals / Objectives
The goals of the project are to: (1) Develop novel advanced bioinformatic, pan-genome, and genetic mapping tools for cucurbits; (2) Utilize genomic approaches to identify, map, and develop markers for resistances to priority diseases identified by cucurbit industries; (3)Introduce and pyramid resistances into advanced breeding lines; and (4) Perform multi-location, multi-isolate trials of resistances to improve integrated disease management and assess economic impacts. The project will also provide state-of-the-art, cross disciplinary plant breeding, molecular genetics, genomics, bioinformatics, plant pathology, and economics training to undergraduate, graduate, and post-doctoral trainees, preparing scientists to meet needs of the public and private sectors.Specific objectives are:Objective 1.Develop novel advanced bioinformatic, pan-genome, and genetic mapping tools for cucurbits. (A)Develophigh-resolution genotyping platforms for cucurbits - Re-sequence core collections for the four cucurbit crops; construct high-resolution genome-wide variome maps; construct pan-genomes for the cucurbit species. (B) Develop breeder-friendly web-based database to manage, store, distribute and analyzephenotype, genotype, and germplasm information. (C)Perform seed multiplication and sequencing analysis of core collections of the four species andassess genetic diversity to provide community resources for genome wide association studies (GWAS). (D)Maintain and enhance the Cucurbit Genomics Database (http://cucurbitgenomics.org/), providing publicly available tools to analyze and integrate genotype, phenotype, and pan-genome data.Objective 2. Utilize genomic approaches to identify, map, and develop markers for resistances to priority diseases identified by cucurbit industries. (A)Identify disease resistance associated quantitative trait loci (QTL) using standard QTL mapping, bulked-segregant analysis, or GWAS. (B) (Refine/fine map QTL using increased population sizes and denser sets of molecular markers. (C)Develop and verify markers for marker assisted selection.Objective 3.Introduce and pyramid/stack resistances into advanced breeding lines. (A)Perform marker assisted selection to introgress resistances into publicly available, elite germplasm selected for yield, fruit quality and current disease resistances; test performance of resulting lines in replicated greenhouse and/or field trials. (B)Perform genomic selection to maximize number of resistance alleles in cases of highly quantitative resistances and gene stacking to combine resistance to multiple diseases.Objective 4.Perform multi-location, multi-isolate trials of resistances to improve integrated disease management, assess economic impacts, and provide state-of-the-art disease control recommendations. (A)Provide up-to-date recommendations for disease control in cucurbit crops building on the centralized cucurbit disease website (https://cuccap.org/) developed under CucCAP1 to provide diagnostic resources, control recommendations disease alerts, and forecasting tools; and via direct extension activities. (B)Perform multi-location, multi-isolate trials and pathogen population analyses to evaluate breeding lines in combination with integrated disease control approaches. (C)Collect geographically diverse pathogen samples and develop markers to analyze pathogen populations to inform breeding and disease management. (D)Assess economic impacts of disease and gains from control tools, and valuation of crop attributes, using a partial budgeting approach and stated preference analyses.
Project Methods
OBJECTIVE 1: Develop novel advanced bioinformatic, pan-genome, and genetic mapping tools for cucurbits. 1.1. Genomic and bioinformatic platforms for cucurbit crops. Processed resequencing data from the core collections will be mapped to reference genomes and used to construct high-resolution genome-wide variation maps (variome) comprising both SNPs and large structural variations (SVs) for each crop. The genotype (SNP/SV) matrix in each core collection will be recorded in commonly used genotyping file formats and made publicly available through the Cucurbit Genomics Database (CuGenDB; http://cucurbitgenomics.org). De novo assembly from PacBio HiFi circular consensus sequence (CCS) data will be combined with deep genome resequencing of 100 accessions selected from the core collections to capture maximal diversity and important traits for each species. PacBio HiFi reads will be assembled into contigs, pseudomolecules constructed genetic maps and syntenic information, and master reference genome derived from non-redundant sequences. Unaligned sequences will be anotated and a pan-genome constructed for each species by combining reference and non-reference sequences. We will develop an integrated, breeder-friendly database module to manage, store, distribute and analyze the phenotyping, genotyping, and germplasm information generated in CucCAP2. 1.2 Analysis of core collections of the four species for genome wide association studies (GWAS). Seeds of the core collections developed in CucCAP1 will be multiplied for distribution. The high-resolution variome data will be used to assess genetic diversity, define phylogenetic relationships, and population structure. GWAS analysis will be performed using the SNP/SV variation data; significantly associated regions will be examined for PAVs in the pan-genome; their patterns in the core collections will be analyzed to identify correlations with traits of interest.OBJECTIVE 2: Utilize genomic approaches to identify, map, and develop markers for resistances to priority diseases identified by the cucurbit industries. 2.1. Map resistance and identify QTL for key cucurbit diseases.For crop-disease combinations with known sources of resistance, but without identified QTL; for which new sources of resistance are being characterized; or for which QTL require verification and refinement, segregating populations will be phenotyped for disease response. Protocols will assure sufficient disease pressure for accurate differentiation between resistant (R) and susceptible (S) progeny. DNA for genotyping will be prepared from young leaf samples for QTL mapping or QTL-seq analysis. The core collections will be phenotyped for disease response to perform GWAS analysis using data and tools from obj 1. If broad QTL have been identified, new markers will be identified in the target interval and used to genotype large segregating populations to narrow the interval. 2.2. Develop and verify markers for marker assisted selection (MAS).Refined QTL will be used to develop high throughput, low cost molecular markers focusing efforts on major effect, robust QTL. New markers will be tested and validated in multiple segregating populations to verify usefulness across multiple genetic backgrounds and locations. Validated markers will be used to assist introgression of resistance into elite lines and facilitate pyramiding and stacking of resistance genes.Objective 3: Introduce and pyramid/stack resistances into advanced breeding lines. 3.1. Introgress resistance alleles into advanced breeding lines.Disease resistances will be introgressed into publicly available, elite germplasm selected for yield, fruit quality/industry standards/earliness/shipping quality, and current disease resistances Validated markers will expedite introgression of resistance loci into elite germplasm. Segregating progeny will be phenotyped, genotyped, and selected for individuals possessing desired combinations of disease resistance and fruit quality traits to backcross into elite germplasm. Performance of resulting lines will be evaluated in greenhouse and/or field trials. Advanced materials will be tested in multiple locations.3.2. Pyramid/stack resistances.Multi-locus marker-assisted selection (MAS) will be used to develop multi-disease resistant breeding lines by combining disease resistance genes from multiple sources.Gene pyramiding/stacking will utilize a breeding scheme of sequential marker-assisted backcrossing coupled with background selection (markers and morphological) to expedite accumulation of one copy of all target QTL and recovery of the genetic background in a single genotype. At the last backcrossing generation (BC3 or BC4) selected plants will be self-pollinated and homozygous plants fixed for all target resistance alleles will be identified. The resulting multiple-disease resistant breeding lines will be tested for resistances in controlled environments (growth chamber, greenhouse) and field trials and released to seed companies along with the corresponding markers for incorporation into the elite cultivars proprietary to each company. In cases where esistance is highly quantitative, we will apply genomic selection to a densely genotyped population using a strategy to maximize the number of resistance alleles available to optimize training model development. A subset of the training population will be used for cross-validation to assess model prediction accuracy.OBJECTIVE 4: Perform multi-location, multi-isolate trials to improve integrated disease management; assess economic impacts, and provide state-of-the-art disease control recommendations .4.1. Disease management information and recommendations. Multiple venues will be used to provide up-to-date recommendations for cucurbit crops including the centralized cucurbit disease website (https://cuccap.org/) developed under CucCAP1, field days, grower meetings, plant disease clinics, agent trainings, webinars, local and regional meetings. Information provided will include: diagnostic resources, control recommendations, links to plant disease clinics, crop production guides, disease fact sheets, disease alerts, and forecasting tools. 4.2. Multi-location, multi-isolate trials and pathogen population analyses. Trials will be performed in different states to evaluate new breeding lines, compare to commercially available tolerant varieties, and determine if integrated approaches can complement host tolerance. Evaluations will be done in research locations centered in production regions following local production practices. Pathogen population analyses of Phytophthora capsiciandPseudoperonospera cubensiswill be performed to characterize local isolates and ensure our breeding efforts are robust to pathogen diversity in different growing regions. Geographically diverse isolates collected from states withlosses on cucurbits will be genotyped, tested for virulence, and for association of SNP markers with virulence. 4.3. Economic impacts of disease and gains from control tools and valuation of crop attributes.A partial budgeting approach will be used to evaluate change in net returns that may result from new disease-resistant varieties and integrated disease control methods.Contemporary crop budgets will be developed for cucumber in MI and NC, watermelon in NC, and squash in MI and NY to use a baseline of comparison. Statedpreference analyses will be performed to identify attributes with the highest potential returns to improvements. Choice surveys will be developed to estimate growers' willingness-to-pay and likelihood to adopt new technologies.

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

Outputs
Target Audience:Our target audiences are our key stakeholders: the cucurbit industries (growers, shippers, processors) who depend on high crop quality, disease resistant cultivars and effective integrated management strategies; the cucurbit breeding community (seed companies and public breeders) who must develop these cultivars; and the scientific community who develop knowledge to facilitate more effective plant breeding and disease control strategies, and train the next generation of agricultural scientists. In the past year we engaged stakeholders via: (a) our annual CucCAP stakeholder advisory board/project investigator meeting (held by zoom this year); (b) organizing or participating in field days, research 'open houses', extension workshops, agricultural expositions, and industry group meetings; (c) presentations at scientific meetings; (d) web-based communication, project newsletters (the CucCAP Chronicle), and cucurbit disease diagnostic and control information, through https://cuccap.org/; (e) expansion of cucurbit genomic and breeding databases, tools and bioinformatics platforms through http://cucurbitgenomics.org/; (f) sharing genetic and marker information and germplasm releases for cucurbit breeding; and (g) scientific and extension publications. We also interacted with stakeholders by sampling pathogens from cooperator farms, performing disease trials at off-campus university farms located within growercommunities and collaborative research with seed companies for disease trials, marker verification and seed multiplication. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?The CucCAP2 has project provided training opportunities for 8 post-docs and 11 graduate students (fully or partially supported by CucCAP) and 12 undergraduate students in the areas of plant breeding, genetics, genomics, bioinformatics, plant pathology, extension and agricultural economics. Training opportunities included thesis or dissertation research; participation in computational, laboratory, greenhouse or field based projects; contributions to scientific and/or extension publications; and opportunities to present findings to industry and scientific audiences. How have the results been disseminated to communities of interest?In the past year the CucCAP team collectively published 48 CucCAP-related refereed publications and 44 CucCAP-related extension publications, web-materials, or webinars. In addition we made 38 CucCAP-related presentations at scientific conferences, universities, and more than 31 CucCAP-related presentations in commodity-based venues. Establishment of the two cross-linked websites, http://cucurbitgenomics.org for bioinformatics and genomics, and https://cuccap.org/ for disease control information, have been a major route to disseminate information. Specific examples of interactions with the cucurbit industries, and scientific and breeding communities are listed below. A. Interaction with Cucurbit Industries. CucCAP team members have had extensive interaction with the cucurbit industries they serve through a variety of venues. These include presentations of CucCAP related work and participation in industry and grower meetings and field days such as: Pickle Packers International Conferences (multiple CucCAP participants and presentations) Agri-Food Canada (multiple CucCAP participants and presentations) BASF Farm Lane Society Meeting, MI Great Lakes Farm, Fruit and Vegetable EXPO (multiple CucCAP participants and presentations) Vegetable and Root Crop Field Day, MI Southeast Vegetable Meeting MI Watermelon Research and Development Group Meeting Mid-Atlantic Fruit and Vegetable Conference CREC Field Day, SC Southwest Indiana Melon Growers Meeting Clemson Hort Team Cucurbit Meeting Southeast Florida Extension Meeting Extension Field Day for Vegetable Growers in Miami-Dade County NC Watermelon Convention Eastern NC Certified Crop Advisor Training Western NY Vegetable Twilight Meeting CREC Field Day, SC Florida State Horticultural Society What do you plan to do during the next reporting period to accomplish the goals?Each CucCAP team will continue working on the CucCAP project objectives including: Obj 1. Genomic and bioinformatic tools. Development of version 2 of the cucurbit genomics database; seed multiplication and re-sequencing (~30X) of the core populations for each of the four crops; initiation of pan genome assemblies. Obj 2. Identify, map, and develop markers for resistances to important cucurbit diseases. Efforts will continue to develop segregating populations, phenotype disease responses, identify QTL, perform fine-mapping and develop markers for the 17 crop-disease combinations. Obj 3. Introduce and pyramid/stack resistances into advanced breeding lines. Efforts will continue, or be initiated, to introgress identified resistances from Obj 2 into advanced breeding lines with multiple resistances and desirable fruit quality. Obj 4. Perform multi-location, multi-isolate trials of resistances, assess economic impacts, and provide state-of-the-art disease control recommendations. We will continue to maintain, update and develop new disease diagnostic and control informational materials for the CucCAP website, produce extension publications and present face-to-face informational sessions for cucurbit disease management. A series of replicated multi-location trials to evaluate breeding lines in combination with integrated disease control strategies is planned for summer 2022. Efforts will be initiated to collect geographically diverse pathogen samples and develop markers to analyze pathogen populations. Additional updated crop budgets and costs of disease control estimates will be developed.

Impacts
What was accomplished under these goals? Our objectives are: (1) Develop advanced bioinformatic, pan-genome, and genetic mapping tools to facilitate more effective breeding of high quality, disease resistant cucurbit crops. (2) Identify and map resistances, and develop markers to facilitate breeding for resistances, to priority diseases identified by watermelon, melon, cucumber and squash industries. (3) Introduce and combine resistances to provide advanced breeding lines for public and private breeders. (4) Perform multi-location, multi-isolate trials of resistances to improve integrated disease management, assess economic impacts, and provide state-of-the-art disease control recommendations. Progress toward each of these goals is described below. Obj 1. Genomic and bioinformatic tools.(A) Develop high-resolution genotyping platforms. Re-sequence core collections for the four cucurbit crops; construct high-resolution genome-wide variome maps; construct pan-genomes for the cucurbit species. Long read sequencing and reference genome assembly was performed for 11 cucumber accessions. Resequencing was performed for 414 accessions of watermelon and watermelon relatives. (B) Maintain and enhance the Cucurbit Genomics Database (http://cucurbitgenomics.org/) and develop breeder-friendly web-based database to manage, store,distribute, and analyze phenotype, genotype, and germplasm information. Development of version 2 is in progress to allow for much more efficient data upload and analysis of the extensive sequencing data currently being produced. (C)Perform seed multiplication and sequencing analysis of core collections of the four sepcies; assess genetic diversity to provide community resources for GWAS. Accessions of the core populations for each of the four crops have been self-pollinated for one or more generations to provide starting material for seed increase by collaborating companies. The melon core collection was phenotyped for 33 vegetative, flower, and fruit characteristics. Obj 2. Identify, map, and develop markers for resistances to important cucurbit diseases. (A) Identify disease resistance associated quantitative trait loci (QTL).Watermelon: Resistance screening was performed for watermelon and/or watermelon relatives for resistance to downy mildew and powdery mildew. A population was developed map QTL for resistance to gummy stem blight. QTL were identified for resistance to downy mildew, Papaya ringspot virus, powdery mildew, and Phytophthora fruit rot. Crosses were made to initiate development of a MAGIC population. Melon: A mapping population was phenotyped to identify QTL for powdery mildew. Two QTL were identified for resistance to Cucurbit yellow stunting disorder virus. Cucumber: The core collection was phenotyped for resistance to Phytophthora fruit rot and a set of inbred lines was screened for resistance to Cucumber green mottle mosaic virus. A segregating population was phentoyped to map QTL for resistance to downy mildew introgressed from Cucumis hystrix. Squash: The Cucurbita pepo reference genome was used to develop a library of probes for mapping resistance. Families of C. pepo were phenotyped for resistance to Phytophthora crown rot and a resistance QTL identified. (B, C) Refine/fine map QTL using increased population sizes and denser sets of molecular markers; develop and verify markders for marker assisted selection. Watermelon: KASP markers were developed for resistance to Fusarium race 2, powdery mildew, gummy stem blight, and Zucchini yellow mosaic virus, and Papaya ringspot virus. Melon: markers were developed for fusarium race 1, race 2 and powdery mildew. Cucumber: Two QTL for resistance to Phytophthora fruit rot were verified; fine mapping for QTL for resistance to downy mildew and Phytophthora fruit rot is in progress. Squash: A KASP marker was developed for resistance to Phytophthora crown rot. Obj 3. Introduce and pyramid/stack resistances into advanced breeding lines. (A) Marker assisted selection to introgress resistances; test performance of resulting lines in replicated greenhouse and/or field trials. Melon: A breeding line was developed with resistance to downy mildew and powdery mildew. Cucumber: Breeding lines carrying two QTL for resistance to downy mildew resistance have been developed. Squash: Introgression of resistance to Phytophthora crown rot into commercial Cucurbita pepo types has been initiated;interspecific crosses were made to transfer resistance to Phytophthora fruit rot from C. moschata into C. maxima. An allele for powdery mildew resistance was transferred into processing pie pumpkin. (B) Genomic selection to maximize resistance alleles for highly quantitative resistances. This work will come later in the project. Obj 4. Perform multi-location, multi-isolate trials of resistances, assess economic impacts, and provide state-of-the-art disease control recommendations. (A) Recommendations for disease control. CucCAP website: Cucurbit disease factsheets, production manuals, and integrated pest management resources for the Northeast, Southeast and the Midwest are maintained and updated. Notices of regional commodity meetings and Extension education sessions, weekly reports from The Cucurbit Downy Mildew Forecast and Melcast along with 77 Integrated Crop and Disease Management were posted. Other disease control information: NC,SC. Diagnostics and disease management recommendations for 76 cucurbit samples (NC); cultivar and management recommendations through oral presentations; and development of disease management resources, NC Agricultural and Chemicals Manual and the Southeastern US Vegetable Crop Handbook. NY: Disease alerts through email, weekly publications, and social media; ~50 individual cucurbit disease recommendations; 25 diagnoses; disease control recommendations to extension educators, two field days, virtual talks at NY and MN expos. MI: Dedicated downy mildew page (weekly spore trapping data, fact sheets, information on identifying, monitoring, managing, and testing, links to other cucurbit diseases; >1000 visits/downloads summer 2021). (B) Multi-location, multi-isolate trials to evaluate breeding lines in combination with integrated disease control. Watermelon-powdery mildew: Replicated experiments in SC and NC. Significant differences were observed among varieties; the CucCAP breeding line USVL608-PMR performed well in both locations. Watermelon-Fusarium. Replicated studies in SC and NC. No Fusarium wilt symptoms were detected in plants grafted onto Carolina Strongback rootstocks (breeding material developed by the USVL). Cucumber-downy mildew. Replicated trials in MI and NC. Resistant PI197088 used as a breeding source had significantly less disease compared to all other lines tested. Squash-powdery mildew. Replicated trials in NY and MI. Significant differences for disease and yield were observed among commercial cultivars. Squash- Phytophthora crown rot. Replicated trials in MI. Four cultivars demonstrated a greater level of resistance in two seasons. Combining fungicides and genetic resistance: Three fungicide programs and different application intervals were compared for downy mildew control on cucumbers, melons, squash, and pumpkins in MI. Fungicides were evaluation for control of powdery mildew in squash and pumpkins in NY and MI. (C) Collect geographically diverse pathogen samples and develop markers to analyze pathogen populations to inform breeding and disease management. This objective is planned for later in the project. (D) Assess economic impacts of disease and gains from control tools, and valuation of crop attributes. Updated crop budgets are being developed for cucumber in MI and NC, watermelon in NC, and squash in MI and NY. Costs of disease control and yield losses are being determined for cucumber/downy mildew in MI. Data suggest that combined efforts of fungicides, application programs, spore trapping, and disease forecasting are effective in keeping losses from increasing.

Publications

  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Parada-Rojas, C.H., Granke, L.L., Naegele, R.P, Hansen, Z., Hausbeck, M.K., Kousik S., McGrath M. T., Smart C., and Quesada-Ocampo L. M. (2021) A Diagnostic Guide for Phytophthora capsici Infecting Vegetable Crops. Plant Health Progress: PHP-02-21-0027-FI.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Rahman A., Standish J.R., DArcangelo K. N., and Quesada-Ocampo L. M. (2021) Clade-specific biosurveillance of Pseudoperonospora cubensis using spore traps for precision disease management of cucurbit downy mildew. Phytopathology 111: 312-320.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: . Renner SS, Wu S, Perez-Escobar OA, Silber MV, Fei Z, Chomickie G (2021) A chromosome-level genome of a Kordofan melon illuminates the origin of domesticated watermelons. Proc Natl Acad Sci USA 118:e2101486118
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: . Salcedo, A., Hausbeck, M., Pigg, S., and Quesada-Ocampo, L.M. (2020) Diagnostic guide for cucurbit downy mildew. Plant Health Progress 21:166-172.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Salcedo A., Purayannur S., Standish J. R., Miles T., Thiessen L., and Quesada-Ocampo L. M. (2021) Fantastic downy mildew pathogens and how to find them: Advances in detection and diagnostics. Plants 10: 435
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Seda-Mart�nez, W., L. Wessel-Beaver, A. Linares-Ram�rez and J.C.V. Rodrigues. 2021. Virus quantification, flowering, yield, and fruit quality in tropical pumpkin (Cucurbita moschata Duchesne) genotypes susceptible or resistant to two potyviruses. HortScience 56(2):https://doi.org/10.21273/HORTSCI15525-20.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Sorokina, M., Mccaffrey, K.S., Ordovas, J.M., Deaton, E.E., Ma, G., Perkins-Veazie, P.M., Steinbeck, C., Levi, A., Parnell, L.D. 2021. A catalog of natural products occurring in watermelon - Citrullus lanatus. Frontiers in Nutrition. 8:602. https://doi.org/10.3389/fnut.2021.729822
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Stajich, JE, Vu, AL, Judelson, H, Vogel, GM, Gore, MA, Carlson, MO, Devitt, N, Jacobi, J, Mudge, J, Lamour, K, and Smart, CD (2021) High quality reference genome for the oomycete vegetable pathogen Phytophthora capsici strain LT1534. Microbiology Resource Announcements Volume 10 Issue 21.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Tamang, P., K. Ando, W.M. Wintermantel, and J.D. McCreight. 2021. QTL mapping of Cucurbit yellow stunting disorder virus resistance in melon accession PI 313970. HortScience 56:424430. doi: https://doi.org/10.21273/HORTSCI15495-20.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Toporek, S. M., Branham, S. E., Katawczik, M. M., Keinath, A. P., and Wechter, W. P. (2021) QTL mapping of resistance to Pseudoperonospora cubensis clade 1, mating type A2, in Cucumis melo. Theoret. Appl. Genet. 134:25772586.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Vogel, GM, Gore, MA, and Smart CD (2021) Genome-wide association study in New York Phytophthora capsici isolates reveals loci involved in mating type and mefenoxam sensitivity. Phytopathology https://doi.org/10.1094/PHYTO-04-20-0112-FI
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Vogel, GM, LaPlant, KE, Mazourek, M, Gore, MA and Smart, CD (2021) A combined BSA-Seq and linkage mapping approach identifies genomic regions associated with Phytophthora root and crown rot resistance in squash. Theoretical and Applied Genetics 134:1015-103. https://doi.org/10.1007/s00122-020-03747-1
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Wang X, Ando K, Wu S, Reddy UK, Tamang P, Bao K, Hammar SA, Grumet R, McCreight JD, Fei Z (2021) Genetic characterization of melon accessions in the U.S. National Plant Germplasm System and construction of a melon core collection. Molecular Horticulture 1:11
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Weng, Y., Garcia-Mas, J., Levi, A., Luan, F. 2020. Editorial: translational research for cucurbit molecular breeding: traits, markers, and genes. Frontiers in Plant Science. 11. Article 615346. https://doi.org/10.3389/fpls.2020.615346
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Zhang C, Mansfeld BN, Lin YC, Grumet R (2021) Quantitative high-throughput, real-time bioassay for plant pathogen growth in vivo. Frontiers Plant Sci 12:637190.
  • Type: Book Chapters Status: Published Year Published: 2021 Citation: DArcangelo K., Quesada-Ocampo L. M., and Hausbeck M. K. (2021) Diseases of cucurbits: Cucurbit downy mildew. In: Handbook of Vegetable and Herb Diseases. Editors: Elmer W., McGrath M. T., and McGovern R. Springer.
  • Type: Book Chapters Status: Published Year Published: 2021 Citation: Keinath, A. P. (2021). Diseases of cucurbits: anthracnose. In: Handbook of Vegetable and Herb Diseases. Editors: Elmer W., McGrath M. T., and McGovern R. Springer.
  • Type: Book Chapters Status: Published Year Published: 2021 Citation: Mazourek M, Hernandez C, Fabrizio J. 2021. Reconsidering Approaches to Selection in Winter Squash Improvement: Improved Quality and Breeding Efficiency. In: Plant Breeding Reviews, Volume 44. (Ed: Goldman I). John Wiley & Sons, Inc. p. 247-272.
  • Type: Book Chapters Status: Published Year Published: 2021 Citation: Parada-Rojas C. H., Quesada-Ocampo L. M., and Hausbeck M. K. (2021) Diseases of cucurbits: Phytophthora blight. In: Handbook of Vegetable and Herb Diseases. Editors: Elmer W., McGrath M. T., and McGovern R. Springer.
  • Type: Book Chapters Status: Published Year Published: 2021 Citation: Rennberger, G., and Keinath, A. P. (2021) Diseases of cucurbits: gummy stem blight. In: Handbook of Vegetable and Herb Diseases. Editors: Elmer W., McGrath M. T., and McGovern R. Springer.
  • Type: Book Chapters Status: Published Year Published: 2021 Citation: Salcedo A., Parada-Rojas C. H., Guerrero R., Stahr M., DArcangelo K.N., McGregor C., Kousik C., Wehner T., and Quesada-Ocampo L. M. (2021) The NLR family of disease resistance genes in cultivated watermelon and other cucurbits: opportunities and challenges. Chapter 3. In: The Watermelon Genome. Editors: Dutta S. K. and Reddy U. Springer.
  • Type: Other Status: Published Year Published: 2020 Citation: Adams M. L., Collins H., and Quesada-Ocampo L. M. 2020. Evaluation of fungicides for control of downy mildew on cucumber, Kinston II, 2019. Plant Disease Management Reports 14:V106.
  • Type: Other Status: Published Year Published: 2020 Citation: Adams M. L., Collins H., and Quesada-Ocampo L. M. 2020. Evaluation of fungicides for control of downy mildew on cucumber, Kinston III, 2019. Plant Disease Management Reports 14:V105.
  • Type: Other Status: Published Year Published: 2020 Citation: Bello, J. C., Engfehr, C.L. and Hausbeck, M.K. (2020) Evaluation of alternating programs of fungicides for control of downy mildew on pickling cucumber, 2019. Plant Disease Management Reports 14:V163.
  • Type: Other Status: Published Year Published: 2021 Citation: Egel, D.S., Foster, R., Maynard, E., Weller, S., Babadoost, M., Nair, A., Rivard, C., Kennelly, M., Hausbeck, M., Szendrei, Z., Hutchison, B., Orshinsky, A., Eaton, T., Welty, C., Miller, S., eds. 2016-21. Midwest Vegetable Production Guide for Commercial Growers. Michigan State University Extension Bulletin 0312.
  • Type: Other Status: Published Year Published: 2021 Citation: Hausbeck, M. 2021. Downy mildew confirmed on cucumbers in four Michigan counties: Grower are urged to implement an aggressive fungicide program immediately. MSU Extension News for Agriculture-Vegetables: 23 Jul.
  • Type: Other Status: Published Year Published: 2021 Citation: Hausbeck, M. and Kenny, G. 2021. Cucumber downy mildew disease confirmed in Michigan: First detection in 2021 made in Saginaw County. MSU Extension News for Agriculture-Vegetables: 16 Jul.
  • Type: Other Status: Published Year Published: 2021 Citation: Hausbeck, M., Peterson, A., and Higgins, D. 2021. First cucurbit downy mildew spores identified in air samples in Allegan County: Growers are urged to scout early plantings of cucumber and melon for downy mildew. MSU Extension News for Agriculture-Vegetables: 27 Jun.
  • Type: Other Status: Published Year Published: 2021 Citation: Hausbeck, M.K. 2021. Managing cucurbit downy mildew. Fact Sheet.
  • Type: Other Status: Published Year Published: 2020 Citation: Hausbeck, M.K. Krasnow, C., and Linderman, S.D. 2020. Managing Phytophthora on Winter Squash and Pumpkin. Fact Sheet.
  • Type: Other Status: Published Year Published: 2020 Citation: Hausbeck, M.K. and Linderman, S.D. 2020. Managing Phytophthora on Summer Squash and Zucchini. Fact Sheet.
  • Type: Book Chapters Status: Published Year Published: 2021 Citation: Toporek, S. M., and Keinath, A. P. (2021). Diseases of cucurbits: Pythium damping-off and root and stem rot. In: Handbook of Vegetable and Herb Diseases. Editors: Elmer W., McGrath M. T., and McGovern R. Springer.
  • Type: Other Status: Published Year Published: 2020 Citation: Adams M. L., Collins H., and Quesada-Ocampo L. M. 2020. Evaluation of fungicides for control of downy mildew on cucumber, Clayton, 2019. Plant Disease Management Reports 14:V116.
  • Type: Other Status: Published Year Published: 2020 Citation: Adams M. L., Collins H., and Quesada-Ocampo L. M. 2020. Evaluation of cultivars in combination with fungicides for control of downy mildew and yield effects on cucumber, Clinton, 2019. Plant Disease Management Reports 14:V117.
  • Type: Other Status: Published Year Published: 2020 Citation: Adams M. L., Collins H., and Quesada-Ocampo L. M. 2020. Evaluation of fungicides and cultivars for control of downy mildew on cucumber, Kinston 2019. Plant Disease Management Reports 14:V107.
  • Type: Other Status: Published Year Published: 2020 Citation: Hausbeck, M.K., Linderman, S.D., and Higgins, D.S. 2020. Managing cucurbit downy mildew. Fact Sheet.
  • Type: Other Status: Published Year Published: 2020 Citation: Hausbeck, M.K., Linderman, S.D., and Higgins, D.S. 2020. Monitoring cucurbit downy mildew. Fact Sheet.
  • Type: Other Status: Published Year Published: 2020 Citation: Higgins, D., Engfehr, C.L. and Hausbeck, M.K. 2020. Evaluation of fungicides for control of powdery mildew on pumpkin, 2019. Plant Disease Management Reports 14:V201.
  • Type: Other Status: Published Year Published: 2020 Citation: Higgins, D.S., Engfehr, C.L., and Hausbeck, M.K. 2020. Evaluation of fungicides for control of powdery mildew on squash, 2019. Plant Disease Management Reports 14:V202.
  • Type: Other Status: Published Year Published: 2021 Citation: Keinath, A.P., DuBose, V. B., and Zardus, S. H. 2021. Evaluation of several fungicides to manage foliar and fruit anthracnose on seedless watermelon, 2020. Plant Dis. Manag. Rep. 15:V089.
  • Type: Other Status: Published Year Published: 2021 Citation: Keinath, A.P., and Miller, G. A. Revised 2021. Watermelon Fungicide Guide for 2021. Land-Grant Press by Clemson Extension, LGP 1001.
  • Type: Other Status: Published Year Published: 2020 Citation: Kenny, G.E., Engfehr, C.L., and Hausbeck, M.K. 2020. Evaluation of 9 alternating programs of fungicides for control of downy mildew on pickling cucumbers, 2019. Plant Disease Management Reports 14:V216.
  • Type: Other Status: Published Year Published: 2020 Citation: 30. Kenny, G.E., Engfehr, C.L. and Hausbeck, M.K. 2020. Evaluation of single product treatments for control of downy mildew on pickling cucumbers, 2019. Plant Disease Management Reports 14:V183.
  • Type: Other Status: Published Year Published: 2020 Citation: Lukasko, N.T., Engfehr, C.L. and Hausbeck, M.K. 2020. Evaluation of fungicides for the control of powdery mildew on butternut squash, 2019. Plant Disease Management Reports 14:V159.
  • Type: Other Status: Published Year Published: 2021 Citation: Quesada-Ocampo L.M., Meadows I., and Gorny A. 2021. Disease control for commercial vegetables. North Carolina Agricultural and Chemicals Manual. Basil, cucurbits, hop, lettuce, endive, sweetpotato, and fungicide resistance tables (Contributed 11 tables total).
  • Type: Other Status: Published Year Published: 2021 Citation: 36. Schultheis, J.R., K.D. Starke, and M.D. Collins. 2021. 2020 Zucchini squash cultigen evaluations. Dept. of Horticultural Science. North Carolina State University. Hort. Series No. 237, 35 pp. https://cucurbits.ces.ncsu.edu/about-cucurbits/growing-cucurbits/variety-trials/2020-zucchini-squash-cultivar-evaluations/
  • Type: Other Status: Published Year Published: 2021 Citation: Smart, C.D. 2021. Phytophthora of cucurbit crops Disease fact sheet https://www.vegetables.cornell.edu/pest-management/disease-factsheets/phytophthora-blight/
  • Type: Other Status: Published Year Published: 2021 Citation: Smart, C.D. 2021. Cucurbit Downy Mildew Disease fact sheet https://www.vegetables.cornell.edu/crops/cucurbits/downy-mildew/
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Alzohairy, S.A., Hammerschmidt, R., and Hausbeck, M.K. (2021) Antifungal Activity in Winter Squash Fruit Peel in Relation to Age Related Resistance to Phytophthora capsici. Physiological and Molecular Plant Pathology 114:101603
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Acharya B, Mackasmiel L, Taheri A, Ondzighi-Assoume CA, Weng Y, Dumenyo CK (2021) Identification of bacterial wilt (Erwinia tracheiphila) resistances in USDA melon collection. Plants 10: 1972
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Alzohairy, S.A., Hammerschmidt, R., and Hausbeck, M.K. (2020) Changes in winter squash fruit exocarp structure associated with age-related resistance to Phytophthora capsici. Phytopathology 110(2):447-455
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Bello Rodriguez, J.C., Hausbeck, M., and Sakalidis, M.L. (2021) Application of target enrichment sequencing for population genetic analyses of the obligate plant pathogens Pseudoperonospora cubensis and P. humuli in Michigan. Molecular Plant-Microbiome Interactions https://doi.org/10.1094/MPMI-11-20-0329-TA
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Bello Rodriguez, J.C., Sakalidis, M.L., Perla, D., and Hausbeck, M.K. (2021) Detection of airborne sporangia of Pseudoperonospora cubensis and P. humuli in Michigan using Burkard spore traps couple to qPCR. Plant Disease 105(5):1373-1381.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Branham, S.E., Kousik, C.S., Mandal, M.K., Wechter, W.P. 2021. QTL mapping of resistance to powdery mildew race 1 in a recombinant inbred line population of melon. Plant Disease (First Look). https://doi.org/10.1094/PDIS-12-20-2643-RE
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Branham, S., Daley, J., Levi, A., Hassell, R., Wechter, W.P. 2020. QTL mapping and marker development for tolerance to sulfur phytotoxicity in melon (Cucumis melo). Frontiers in Plant Science. 11:1097-1105. https://doi.org/10.3389/fpls.2020.01097
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Garcia-Lozano, M., Natarajan, P., Levi, A., Katam, R., Nimmakayala, P., Reddy, U. 2021. Altered chromatin confirmation and transcriptional regulation in watermelon following genome doubling. Plant Journal. https://doi.org/10.1111/tpj.15256
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Chanda, B., Shamimuzzaman, M., Gilliard, A., and Ling, K.-S. 2021. Effectiveness of disinfectants against the spread of tobamoviruses: Tomato brown rugose fruit virus and Cucumber green mottle mosaic virus. Virology Journal 18:7 https://doi.org/10.1186/s1298502001479-8
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Crandall, S.G., Ramon, M.L., Burkhardt, A.K., Bello, J.C., Adair, N., Gent, D.H., Hausbeck, M.K., Quesada-Ocampo, L.M., and Martin, F.N. (2021) A multiplex TaqMan qPCR assay for detection and quantification of clade 1 and clade 2 isolates of Pseudoperonospora cubensis and Pseudoperonospora humuli. Plant Disease https://apsjournals.apsnet.org/doi/10.1094/PDIS-11-20-2339-RE
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: DArcangelo K. N., Adams M. L., Kerns J. P., and Quesada-Ocampo L. M. (2021) Assessment of fungicide product applications and program approaches for control of downy mildew on pickling cucumber in North Carolina. Crop Protection 140: 105412
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Grumet R, McCreight JD, McGregor C, Weng Y, Mazourek M, Reitsma K, Labate J, Davis A, Fei Z (2021) Genetic resources and vulnerabilities of major cucurbit crops. Genes 12:1222
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Gimode, W., Bao, K., Fei, F. & C. McGregor (2020) QTL associated with gummy stem blight resistance in watermelon. Theoretical and Applied Genetics 134(2), 573-584. https://doi.org/10.1007/s00122-020-03715-9
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Govindasamy, R., Arumugam, S., Gao, G., Hausbeck, M.K., Wyenandt, A., and Simon, J. (2021) Downy Mildew Impacts and Control Measure on Cucurbits in the United States. Journal of the American Society of Farm Managers and Rural Appraisers 2021:78-88
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Hausbeck, M.K., Krasnow, C.S., and Linderman, S.D. (2020) Methyl bromide alternatives for Phytophthora capsici on Michigans cucurbit crops. Acta Horticulturae 1270:307-314.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Jeon, S., Krasnow, C.S., Bhalsod, G.D., Harlan, B.R., Hausbeck, M.K., Safferman, S.I., and Zhang, W. (2020) Control of Phytophthora capsici diseases in greenhouse squash by fast-flow filtration. Acta Horticulturae 1296:32
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Karki, K., Coolong, T., Kousik, C.S., Petkar, A., Myers, B.K., Hajihassani, A., Mandal, M., Dutta, B. 2021. The Transcriptomic Profile of Watermelon Is Affected by Zinc in the Presence of Fusarium oxysporum f. sp. niveum and Meloidogyne incognita. Pathogens 2021, 10, 796. https://doi.org/10.3390/pathogens10070796
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Katuuramu, D.N., Wechter, W.P., Washington, M., Horry, M.I., Cutulle, M.A., Jarret, R.L., Levi, A. 2020. Phenotypic diversity for root traits and identification of superior germplasm for root breeding in watermelon. HortScience. 55(8):12-72-1279. https://doi.org/10.21273/HORTSCI15093-20
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Kavalappara, S.R., Milner, H., Sparks, A., McGregor, C., Wintermantel, W.M. & S. Bag (2021) First report of cucurbit chlorotic yellows virus in association with other whitefly-transmitted viruses in squash (Cucurbita pepo) in Georgia. Plant Disease https://doi.org/10.1094/PDIS-11-20-2429-PDN
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Kousik, C.S., Ikerd, J.L., Wechter, W.P., Branham, S.E., Turechek, W.W. 2021. Broad resistance to post-harvest fruit rot in USVL watermelon germplasm lines to isolates of Phytophthora capsici from across USA. Plant Disease (First Look). https://doi.org/10.1094/PDIS-11-20-2480-RE
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Kousik, C.S., Vogel, G., Ikerd, J.L., Mandal, M.K., Mazourek, M., Smart, C.D. and Turechek, W.W. 2021. New Sources of Resistance in Winter Squash (Cucurbita moschata) to Phytophthora Crown Rot and Their Relationship to Cultivated Squash. Plant Health Progress https://doi.org/10.1094/PHP-02-21-0047-FI
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Mandal, M.K., Suren, H. and Kousik, C.S. 2020. Elucidation of resistance signaling and identification of powdery mildew resistant mapping loci (ClaPMR2) during watermelon-Podosphaera xanthii interaction using RNA-Seq and whole-genome resequencing approach. Scientific Reports 10, 14038 (2020). https://doi.org/10.1038/s41598-020-70932-z
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Mondal S, Jenkins Hladky LL, Melanson RA, Singh R, Sikora E, Wintermantel WM. First report of cucurbit yellow stunting disorder virus and cucurbit chlorotic yellows virus in cucurbit crops in Alabama. Plant Dis. 2021 Jun 28. doi: 10.1094/PDIS-05-21-0922-PDN.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Mondal S, Jenkins Hladky LL, Fashing PL, McCreight JD, Turini TA, Wintermantel WM. First report of cucurbit yellow stunting disorder virus and cucurbit chlorotic yellows virus in melon in the Central Valley of California. Plant Dis. 2021 May 19. doi: 10.1094/PDIS-01-21-0184-PDN.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Michael, V.N.*; Fu, Y.; Shrestha, S.; Meru, G. 2021. A Novel QTL for Resistance to Phytophthora Crown Rot in Squash. Plants 10:2115. https://doi.org/10.3390/ plants10102115