Source: MICHIGAN STATE UNIV submitted to
CUCCAP: LEVERAGING APPLIED GENOMICS TO INCREASE DISEASE RESISTANCE IN CUCURBIT CROPS
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
NEW
Funding Source
OTHER GRANTS
Reporting Frequency
Annual
Accession No.
1007605
Grant No.
2015-51181-24285
Project No.
MICL05092
Proposal No.
2015-09260
Multistate No.
(N/A)
Program Code
SCRI
Project Start Date
Sep 1, 2015
Project End Date
Aug 31, 2019
Grant Year
2015
Project Director
Grumet, R.
Recipient Organization
MICHIGAN STATE UNIV
(N/A)
EAST LANSING,MI 48824
Performing Department
Department of Horticulture
Non Technical Summary
The Cucurbitaceae family includes many high-value, flavorful, and nutritious crops, consumed as vegetables and fruits in the American diet. U.S. production of watermelons, melons, cucumbers, squash, and pumpkins contributes an average of $1.65 billion farm gate value per year (USDA-NASS, 2009-2013). To maintain robust, internationally competitive cucurbit industries, growers, shippers, and processors must provide high quality products produced in an economically viable and environmentally sustainable manner. Cucurbit growers, shippers and processors consistently identify fungal/oomycete pathogens and insect-transmitted viral diseases as their major production constraints. These diseases cause severe reductions in fruit 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 and environmentally desirable solution to these problems is disease-resistant cultivars. Resistant cultivars reduce production costs and application of potentially environmentally damaging fungicides and insecticides used to combat insect-transmitted diseases, while increasing yields and improving product quality. Acceptance and value of new resistant cultivars depends on a combination of yield and ease of production for the producer, and price and desirability for the consumer. This makes it imperative that breeding programs effectively combine multiple critical disease resistances without sacrificing yield or quality. Cucurbit breeders are faced with challenges to find new sources of resistance, identify genetic loci conferring resistance, efficiently incorporate new resistances into elite cultivars, and combine resistances to multiple diseases, while retaining superior productivity and fruit quality.CucCAP will create a collaborative, national initiative to develop and deliver breeder-friendly genomic tools for accelerated development of cultivars with resistances to critical diseases threatening production of cucurbit crops. Rapid advances in genomic technology and recent sequencing of the four cucurbit species make cucurbit crops ideally poised for genomics-assisted breeding. This project will undertake an integrated research and extension approach to: (1) Develop genomic approaches and tools for accelerated crop improvement of cucurbit species; (2) Use these tools to perform genomic-assisted breeding to facilitate efficient introgression of disease resistance into commercially valuable cucurbit cultivars; and (3) Perform economic impact analyses with respect to cost of production and disease control, and provide readily accessible information to facilitate disease control.We will develop sustainable genomic and bioinformatic web-based platforms for genotyping by sequencing, sequence data processing and analysis, breeding data information management, and genome wide association studies; map resistance loci and develop markers for introgression of resistances to key cucurbit diseases; develop models to define, parameterize, simulate and analyze costs of cucurbit production and disease control; and develop a centralized cucurbit disease website providing readily accessible information in English and Spanish for disease diagnosis and control.The results of this project will contribute to stronger cucurbit industries by helping to deliver superior cultivars with genetic resistance against major diseases. It will aid the cucurbit breeding community by developing breeder-friendly databases and molecular markers for efficient trait selection, and it will benefit the larger scientific community by producing undergraduate and graduate students and post-doctoral researchers who have received state of the art, trans-disciplinary STEM training, 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
2011420108130%
2011421108115%
2011429108115%
2011420108020%
2011421108010%
2011429108010%
Knowledge Area
201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
1429 - Cucurbits, other; 1420 - Melons; 1421 - Cucumber;

Field Of Science
1080 - Genetics; 1081 - Breeding;
Goals / Objectives
Infection by fungal/oomycete pathogens and insect-transmitted viral diseases are major production constraints for cucurbit (watermelon, melon, cucumber, and squash) crops causing severe reductions in yield, loss of fruit quality, increased labor and expense for control, and negative environmental impacts from application of pesticides. The most cost-effective and environmentally desirable solution to these problems is disease-resistant cultivars. This project, which responds to the legislatively mandated focus area: "Research in plant breeding, genetics and genomics to improve crop characteristics", brings together the community of U.S. public cucurbit breeders and geneticists with plant pathologists, genomicists, economists and extension specialists to leverage applied genomics for improved disease resistance in cucurbit crops.The goals and objectives of this project are:1. Develop genomic approaches and tools for cucurbit species.- Develop genomic and bioinformatic platforms for: genotyping by sequencing (GBS); sequence data processing and analysis; and genotype, phenotype and QTL databases- Perform GBS analysis of PI collections and core populations of the four species to provide a community resource for genome wide association studies (GWAS) for current and future traits of interest- Provide access to cucurbit genomics tools and databases via the International Cucurbit Genome Initiative (ICuGI) website, and by genomics and bioinformatics workshops open to all members of the cucurbit scientific and breeding communities2. Perform genomic-assisted breeding to introgress disease resistance into cucurbit cultivars.- Utilize genomic approaches to map resistance loci for key cucurbit diseases- Develop and verify molecular markers for efficient trait selection and gene pyramiding- Introgress resistances into advanced breeding lines- Provide web-based and face to face information via field trials, extension venues, and scientific meetings regarding breeding materials, markers, and breeding progress3. Perform economic impact analyses of cost of production and disease control and provide readily accessible information to facilitate disease control.- Define, parameterize, simulate, and validate production variables based on cucurbit production crop budgets- Use a risk-based simulation model to analyze economic potential of the disease resistant cucurbit cultivars- Develop a centralized cucurbit disease website, including content in English and Spanish, providing information about diagnostics and links to disease clinics; disease control recommendations; disease alerts and links to forecasting toolsThis project will also provide trans-disciplinary training (genetics, genomics, plant breeding, and plant pathology) to prepare undergraduate students, graduate students and post-doctoral researchers for the scientific and plant breeding communities.
Project Methods
MethodsObj. 1 . Develop genomic approaches and tools for cucurbit species1.1. Develop genomic and bioinformatic platforms for cucurbit crops. GBS will be performed via Illumina HiSeq using barcoded libraries of samples in a 96-well plate format. SNP calling will be performed using the TASSEL-GBS pipeline. The genotype matrix will be recorded in commonly used genotyping file formats (e.g., VCF). The identified SNPs from each population will be filtered based on minor allele frequency, missing data points and deviation from Hardy-Weinberg equilibrium. High-quality SNPs will be used for population genetics and GWAS analysis. We will develop an integrated, breeder-friendly, publically available database to manage, store, distribute and analyze the data generated by building on the existing International Cucurbit Genomics Initiative (ICuGI) database and website. Genotype, phenotype, and experimental metadata from this project, along with transcriptome sequence, annotation, marker data, and genetic maps of the four cucurbit species currently available in the database, can be queried, analyzed and visualized through a set of user-friendly interfaces and genome browser portals. GWAS analysis tools will be implemented by building upon open source packages (EMMAX and GenABEL). Syntenic genome regions between different cucurbit species will be identified using MCScanX, and a genome synteny browser will be implemented in ICuGI using GBrowse syn. A Cucurbit Gene Registry will be established at ICuGI to facilitate guidance for naming genes.1.2. Perform GBS analysis of PI collections, establish core populations of the four species, provide community resource for genome wide association studies (GWAS). Diversity in the cucurbit germplasm collections will be genotyped by GBS for 1000-1600 accessions of each crop. Automated, high-throughput DNA extraction in 96-well format will be performed using a coding system for sample identity. A set of 384 accessions that best represent diversity of each species at the genome level will be selected using the methods of MSTRAT, Powercore and Core Hunter II. Intra-accession diversity will be managed by self-pollination to create a more uniform seed stock. Parents for the self-seed stock will be re-genotyped by GBS. SNPs obtained from the PI collections will be used to assess genetic diversity, define phylogenetic relationships, population structure, and characterize the rate of LD decay. QTL will be identified using the compressed mixed linear model (MLM) implemented in TASSEL 4.0, efficient mixed-model association (EMMA) implemented in R package EMMAX, and linear regression model in GenABEL.Obj. 2. Perform genomic-assisted breeding to introgress alleles for disease resistance2.1. Map resistances to key cucurbit diseases. Genetic populations segregating for cucurbit crop-disease combinations will be phenotyped for disease response. DNA prepared from the 10-20% most resistant and most susceptible individuals will be bar-coded for GBS, and identified SNPs assigned a position on the integrated map. MapQTL 6 will be used to analyze association of SNPs with phenotype and perform interval mapping to determine QTL linked with resistance. For crop-disease combinations where disease resistance screening has been performed on large numbers of PIs, data sets will be used to perform GWAS for disease resistance QTL. 2.2. Marker development and verification for marker assisted selection (MAS). QTL regions that explain a significant portion of variation and appear to be robust [i.e., observed across environments, seasons, genetic backgrounds, or independent approaches] will be used to develop molecular markers for the KASP (Kompetitive Allele Specific PCR, LGC Genomics) high-throughput assay system. If the QTL regions are too large, we will increase size of the segregating populations and/or identify new markers in the target interval based on re-sequence data of the parental lines.2.3. Introgress resistance alleles into advanced breeding lines. Breeding for resistances of each of the priority diseases is currently underway by CucCAP team members. Disease resistances will be introgressed into publically available, elite germplasm selected for yield, fruit quality, industry standards, and current disease resistances. Breeding strategies are determined based on knowledge of the pathogens, sources of resistance, cross compatibility between sources of resistance and cultivated materials, inheritance of resistance, availability of breeding populations, and state of breeding progress with regard to introgression of resistance, identification of QTL, and marker development. In most cases, introgression of resistance into cultivated types will go hand-in-hand with QTL analysis and marker development. Validated markers can be used to introgress resistance loci into elite germplasm. Performance of resulting lines will be evaluated in appropriate greenhouse and/or field trials. Advanced materials will be tested in multiple locations.Obj 3. Perform economic impact analyses of cost of production and disease control, and provide readily accessible information to facilitate disease control.3.1 Perform economic impact analysis of cost of production and disease control. Enterprise crop budgets will be used to build a risk based simulation model to analyze scenarios of disease control in cucurbit production. Farm panels representing each of the cucurbit products in three locations will develop consensus estimates of inputs, costs, and yields to provide data for input into farm-level simulations. The simulation model will define, parameterize, simulate, and validate variables and evaluate the economic effect of disease resistant cultivars with respect to chemical use, labor and other inputs. These values will be used to calculate production, receipts, costs, cash flows, and other financial statements. We will stochastically sample the probability distributions to generate empirical estimates of probability distributions for unobservable key output variables (e.g., net present value, annual cash flows). Potential economic impacts of new cultivars will be estimated using input-output models. Results of the representative farm models (micro level) will be the input to estimate impacts at the macro/industry level. Total economic impacts will be evaluated using input-output models to estimate economic multipliers generated by the IMPLAN Pro social accounting software and associated databases. Economic impact estimates will be provided for output, employment, value added, labor income, and indirect business taxes.3.2 Provide readily accessible information to facilitate disease control. We will develop a CucCAP Cucurbit Disease Extension Website to provide information for cucurbit disease diagnosis and control. The website will include: A) Project information and events [objectives, team members, links to ICuGI genomics and breeding databases, events calendar (field days, grower meetings, research meetings), electronic newsletters]; economic analysis of disease impacts and controls; links to state, regional, and national cucurbit commodity organizations, and B) Diagnostic and disease control resources [disease fact sheets, disease alerts, and links to plant disease clinics, production guides including disease control recommendations, and disease forecasting tools]. We will also engage extension agents and agricultural consultants via collaborations with Plant Disease Clinics, field days, grower meetings and webinars. Modern disease fact sheets including pathogen biology, diagnostic guides, and symptom and pathogen pictures at the macro and micro level will be prepared in English and Spanish for the prioritized cucurbit diseases.

Progress 09/01/16 to 08/31/17

Outputs
Target Audience:The overarching objective of the CucCAP project is to leverage applied genomics for improvement of disease resistance of cucurbit crops. Therefore, the target audiences for the CucCAP project are: - the cucurbit industries, i.e., growers, shippers, processors, commodity organizations, pest management company representatives for watermelon, melon, cucumber and squash; - the cucurbit breeding community (seed companies and public breeders); - the academic community developing knowledge leading to improved varieties. We have engaged our stakeholders via interaction with the project advisory board, web-based communication, collaborative research, research and extension publications, organizing and participating in industry and grower-focused meetings and events, and scientific conferences. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?This project provides numerous training opportunities for undergraduate students, graduate students and postdoctoral researchers in the areas of plant breeding and genetics, plant pathology, bioinformatics, horticulture, and agricultural economics. Training opportunities include 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?A. Dissemination of information and 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 including: California Melon Research Board, San Diego, CA; Certified Crop Advisor Training, Smithfield NC; Commerical Vegetable Grower Symposium, Henderson NC; CucCAP Project Meeting, Charleston SC; Cucurbit Field Day, Cleveland NC; Extension Conference Raleigh NC; Extension Specialist Breakfast Meeting via Zoom videoconference, East Lansing MI; Field Day University of Wisconsin Hancock Agricultural Research Station. WI; Gadsden Tomato Forum, Quincy, FL; Great Lakes Fruit, Vegetable and Farm Market Expo, Grand Rapids, MI; NC Watermelon Convention, Wrightsville Beach NC; NCSU Masters Symposium, Raleigh NC; Pickle Packers International Annual Meeting, Charleston SC; Pickle Packers International Spring Meeting, Chicago IL; Pickling Cucumber Commodity Meeting, Grand Rapids MI; Southeast Vegetable and Fruit Expo, Myrtle Beach NC; Southwest Hort Days, Benton Harbor, MI; Syngenta Meeting, East Lansing, MI; UPRM Expo HORT, Lajas, PR; Vegetable Growers' Meeting, East Aurora, NY; Watermelon Research and Development Group meeting. Mobile AL; Wisconsin Fresh Fruit and Vegetable Conference, Wisconsin Dells, WI. Information also has been communicated to our stakeholders through development of our new website (https://cuccap.org/) including development and posting of cucurbit disease fact sheets, team member websites, extension articles and bulletins, disease management reports, contributions to production guides, and webinars. The extension team members also provide on-line reports of disease occurrences, and diagnostic and disease management assistance. B. Interaction with cucurbit scientific and breeding communities.The CucCAP project had extensive interaction with the broader scientific and breeding communities through active participation in national and international scientific conferences; seminar presentations; and collaborative research with industry partners. CucCAP team members have attended and presented CucCAP related work at the: American Society for Horticultural Science; American Society for Horticultural Science, Southern Region; American Society for Phytopathology; CROPS Conference, Hudson Alpha, Huntsville, Alabama; National Association of Plant Breeders Conference, University of California, Davis-CA; Pickling Cucumber Improvement Committee; Plant and Animal Genome Conference San Diego CA; Secretary of Agriculture, Sonny Purdue; SolCuc, Joint International Solanaceae and Cucurbitaceae Conference, Valencia, Spain; Watermelon Research and Development Working Group; Western Regional Seed Physiology Research Group, Davis CA PI's also presented seminars related to CucCAP work in a variety of venues including: China Agricultural University, Beijing China; Cornell University; Department of Plant Pathology, University of Georgia Athens, GA; Institute of Plant Breeding, Genetics and Genomics, UGA; Nanjing Agricultural University; Texas A&M University We have also engaged in research with numerous seed companies including: Abbott & Cobb, Bayer Crop Science, Bejo, DP Seeds, Enza Zaden, Hazera, Highmark Seed, HM Clause, Hollar Seeds, Johnny's Selected Seed, K&B Development, Origene Seeds, Rijk Zwaan, Rupp Seed, Sakata, Seedway, Seminis Vegetable Seed/Monsanto, Siegers, Syngenta, United Genetics, US AgriSeeds What do you plan to do during the next reporting period to accomplish the goals?Obj. 1. Develop genomic approaches and tools for cucurbit species. -- Complete genotyping of PI collections for the Cucurbita species (C. pepo, C. maxima, C. moschata) using the GBS platform and the SNP calling from the GBS data. -- Collect historical phenotypic data for the genotyped cucurbit accessions, resolve population structure and identity by descent for use in GWAS for various cucurbit collections, testing and optimize suitable GWAS models for cucurbits and identify appropriate methods to validate GWAS results, and perform GWAS to identify genome regions tightly linked to interesting traits, mainly disease resistances. -- Establish molecular-informed core populations four all the four cucurbit crops and initiate genome resequencing of these core collections (a total ~1,600 accessions, with each sequenced to 10-15X coverage), to provide a useful community resource for GWAS. -- Continue database development, with focuses on developing breeder-friendly tools and interfaces that can efficiently store, visualize and analyze phenotypic, genotypic and QTL information for cucurbit species. Obj. 2. Perform genomic-assisted breeding to introgress disease resistance into cucurbit cultivars. Watermelon -- Resistance to Fusarium oxysporum - race 2. DNA will be isolated from F2 parents of the USVL-252FR x PI 244019-PRSV-R(S3) F2:3 families for GBS analysis, genetic mapping and identification of QTL associated with FW race 2 resistance. DNA will be isolated for the USVL246-FR2 x C.l. var. citroides PI582114 RIL population and submitted for GBS. Race 1. KASP markers will be validated in collaboration with the HM.Clause team (Davis, CA) using advanced populations segregating for FW race 1 resistance. We will continue narrowing QTL for Fon race 1 and 2 through KASP, additional GBS analysis, and phenotyping of the RIL population. Back-crossing and further selection of USVL246-FR2 an USVL252-FR2 lines will continue. -- Powdery mildew (PM) - Perform GBS analysis for F2 USVL531-MDR x USVL677-PMS. Rescreen selected F4 families to confirm resistance to powdery mildew and assess fruit quality and advance to F5 and F6. Initiate inheritance studies of segregating populations from cross of USVL003-MDR x USVL677-PMS. Release selections from crosses of three additional PM resistant lines that reasonable flesh color and brix. -- Phytophthora fruit rot. Continue to develop RIL population from USVL531-MDR x USVL677-PMS. Generate F2:3 populations for further evaluation. Phenotype populations from USVL003-MDR x USVL677-PMS. -- Gummy stem blight (GSB) - DNA will be prepared from a GSB RIL population for GBS. Selected resistant RILs with good fruit quality will be carried forward. Map resistance in PI 482276 (R) x Crimson Sweet (S) population. Phenotype PI 526233(R) x Sugar Baby(S). Validate markers in BC1F2 population. -- Papaya ringspot virus (PRSV) - F2 and BC1 populations derived from the cross USVL-252FR x PI 244019-PRSV-R(S3) will be evaluated for PRSV-resistance and further analyzed using GBS procedure for identification of QTL associated with the resistance. -- Cucumber green mottle mosaic virus. Advance most promising C. colocynthis line to S3. Generate F2, BC1 seeds. Melon: -- Fusarium wilt and Powdery Mildew Resistances. RILs of MR-1 (multi-resistant) x Ananas Yokneam (MR1xAY) will be used for QTL analysis. Begin Fusarium wilt race 2, and powdery mildew race 2 tests. -- CYSDV and powdery mildew resistances. Phenotype F2:3 Top Mark x PI 313970 families for resistance to CYSDV and powdery mildew in field tests. -- CMV resistance. Increase advanced CMV-resistant lines (western U.S. shipping type cantaloupe and honeydew). Assess for resistance in controlled-inoculation greenhouse tests and for adaptation and fruit quality in field tests at three locations in AZ and CA. -- CMV resistance. Use 3' RNAseq to look for common introgressions shared by CMV-resistant types. These shared regions, derived from sources of resistance, are presumed to contain the loci conferring resistance. Cucumber -- Downy mildew (DM) resistance. - QTL identification. Continue marker-assisted backcrossing in Gy14 genetic background to develop NILs carrying different combinations of dm4.1, dm5.2, and dm5.3 QTLs from WI7120 and PI 197088. Narrow down the QTL region (1.5 LOD interval) of target QTL regions through fine genetic mapping and GWAS. Start to pyramid major-effect QTL for DM resistance from both WI7120 and PI 197088 resistance sources. Perform growth chamber and field evaluation of DM resistance of the NILs and introgression lines. Phenotype DM resistance in cucumber natural populations for future GWAS analysis. Breeding. Selected populations developed from crossing the DM resistant PI 197088 with one of three elite fruit quality lines Gy14, NC-25, and Poinsett 76, and from S9-S14 PI197088 X Coolgreen-derived RIL population will be grown in the greenhouse to be selfed this winter. Hybrid progeny of Poinsett 76 X PI 605996 will be selfed to S3 and backcrossed to resistant and susceptible parents for evaluation in 2018 field trials. -- Phythophthora fruit rot resistance. - Young fruit resistance. Perform replicated trial of PI 104983-derived families in P. capsici infested field in NY. Prepare DNA from F2 progeny exhibiting extremes of resistance/susceptibility to initiate QTLseq analysis. Plant functional panel in the field and phenotype for resistance to P. capsici and initiate GWAS analysis for resistance to P. capsici. - Age-related resistance (ARR). Perform QTL seq analysis for ARR from F2 populations of GY14 X Poinsett and GY14 X Vlaspik. Compare results of transcriptomic and metabolomic analysis of peels from ARR+ and ARR- cultivars with QTL seq analysis. Perform RNAseq time course analysis of 8 and 16 day old fruit for infection process. Squash/pumpkin -- Potyvirus resistance. Virus resistant squash breeding lines derived from crosses between the resistant parents ('Nigerian Local' and 'Menina') and two susceptible genotypes ('Taína Dorada' and 'Verde Luz') will be increased, screened and genotyped by GBS or RNA-seq. -- Phytophthora resistance. Create F2:3 populations from C. moschata accessions PI 211996, PI 483347, and PI 634693 selected for resistance to Phytophthora root rot and cross with a powdery mildew resistant bush butternut. F3 families will be field-tested for resistance to Phytophthora. Obj. 3 Perform economic impact analyses of cost of production and disease control and provide readily accessible information to facilitate disease control. Define, parameterize, simulate, and validate production variables based on cucurbit production crop budgets. Identify the number of representative farms to be developed depending on geographic location, common production practices, and marketing windows, among others variables. Develop representative farms in Florida and Texas and schedule development of northeast representative farms. Develop a centralized cucurbit disease website. Populate the website with news posts, especially during the growing season. Report research highlights from professional meetings. Integrate video interviews of CucCAP researchers. Continue to translate factsheets into Spanish.Continued updating, reporting, and maintaining the website so that it is current and useful with the goal of expanding numbers of end users.

Impacts
What was accomplished under these goals? 1. Develop genomic and bioinformatic platforms for cucurbit crops. (a) Genotyping by sequencing (GBS) of USDA plant introduction (PI) collections of cucumber, watermelon, melon and squash. DNA preparation and GBS has been completed for cucumber (n=1564), melon (n=2077) and watermelon (n=1365). Squash is underway (829 Cucurbita pepo, 191 C. moschata and 177 C. maxima completed). SNPs have been called from the GBS data for cucumber, melon and watermelon with 114,338, 89,377 and 62,258 raw SNPs respectively, and 23,828, 27,846 and 25,930 after filtering (missing rate < 0.5; minor allele frequency > 0.01). (b) Establishment of core germplasm collections. SNPs from GBS data were used to develop core collections for cucumber, melon and watermelon (~300 accessions capturing >98% genetic diversity) using the GenoCore program (https://www.ncbi.nlm.nih.gov/pubmed/28727806). Functional panels for genome resequencing combining genotypic core collections and economically valuable traits are being established by the crop teams in consultation with industry partners. (c) Development of the Cucurbit Genomics Database. The database for cucurbit sequence information (Cucurbit Genomics Database; http://www.cucurbitgenomics.org), initially established through International Cucurbit Genome Initiative (ICuGI) website was redesigned using the GMOD Tripal system and Chado database schema. Novel interfaces and functions are being developed to provide breeder-friendly databases for genomic, genotypic, phenotypic and QTL information. Genome syntenies among the species have been identified and a genome syntenty browser will be implemented. Public RNA-Seq datasets downloaded from NCBI were processed and expression profiles derived and stored in the database. Interfaces and tools to visualize and analyze the expression profiles have been implemented. The new database was released to the public in May 2017. (d) Additional genomics resource development. We have generated reference genomes for Cucurbita maxima, C. moschata and Lagenaria siceraria; all are publicly available through the Cucurbit Genomics Database. Obj. 2. Perform genomic-assisted breeding to introgress disease resistance into cucurbit cultivars. Watermelon: Fusarium wilt (FW) - Race 2. F2:3 families (220) of USVL-252FR x PI 244019-PRSV-R(S3) were constructed and evaluated for resistance. Phenotyping indicates possible normal distribution of resistance. A second population (F7 - F8 single seed descent lines of USVL246-FR2 x C.l. var. citroides PI582114) was produced, DNA isolated and sequenced, and QTL-seq performed on 180 of the F2 plants. FW Race 1. SNPs on chromosome 1 putatively associated with race 1 resistance were converted to Kompetitive Allele Specific PCR (KASP) primers; several were tightly linked to resistance. Papaya ringspot virus (PRSV-W) - F2 and BC1 populations derived from the cross USVL-252FR x PI 244019-PRSV-R(S3) were constructed. Seeds of the Fon race 1 and 2 resistant lines USVL246 and USVL252 were disseminated to seed companies and researchers and crossed with cultivated watermelons. Powdery mildew (PM) - We have developed USVL531-MDR, resistant to PM and Phytophthora fruit rot (PFR); seed has been provided to two companies. Resistance appears to be dominant. RNAseq was performed on resistant and susceptible lines. Fruit from F2 plants with PM resistance and desirable color and brix have been advanced to F4. Progeny test on 23 red fleshed F4 lines identified several homozygous for resistance. Crosses of 3 additional PM resistant lines were performed to develop populations for inheritance studies. PFR - Several germplasm lines derived from USVL531-MDR were developed with high levels of resistance. F3 families (n=400) were screened and 186 self-pollinated to F2:3. RNAseq experiments were performed for resistant and susceptible genotypes. Gummy stem blight (GSB) - A GSB population was developed by intercrossing the most resistant accessions of Citrullus, and crossing with elite cultivars (I4F1I4S1); 300 RILs and 20 controls were evaluated for GBS resistance and fruit quality in the greenhouse and field. A PCR-based marker test was developed to distinguish field isolates of GSB. PI 482276 x Crimson Sweet lines were phenotyped in the growth chamber and field and highly resistant lines selected. Cucumber green mottle mosaic virus. Initial screening of USDA watermelon germplasm was completed and several potentially tolerant lines selected. Single plant selections were made and S2 seed generated from one line. Melon: Powdery Mildew - MR-1 was crossed with 'Hale's Best Jumbo', 'Top Mark', and 12 highly susceptible Chinese heirloom melon lines. Cucurbit yellow stunting disorder virus (CYSDV) - Resistant field selections were backcrossed and selfed for testing. Cucumber mosaic virus (CMV) - Advanced resistant lines, including 25 unique genotypes spanning domesticated sources, 'Top Mark', 'Honeydew' and Eastern 339 types, were increased to assess resistance, adaptation, and fruit quality and in CA and AZ. Cucumber: Downy mildew - Comparative QTL analysis was performed in F2:3 (PI 330628 source) and RIL (PI 197088 source) populations identifying 4 and 11 DM resistance QTL, respectively; three were in common. QTL mapping of dm1 was also performed in Gy14× 9930 RIL population. Marker-assisted introgression of major QTL, dm4.1, dm5.2 and dm5.3 into an elite pickling cucumber inbred is underway. Populations derived from PI 197088 X elite fruit quality lines Gy14 (8 cultigens), NC-25 (13 cultigens), and Poinsett 76 (16 cultigens) were evaluated in replicated field trials and selected for resistance, quality and yield. A S9-S14 PI197088 X Coolgreen-derived RIL population (n=132) was evaluated in replicated field trials; 2 cultigens were selected for high resistance, 2 for elite fruit quality. PFR - S6 families derived PI 109483 with young fruit resistance to PFR were released and seed provided to several breeding companies. Crosses to introgress into pickling line Gy14 are underway (BC2); F2 of Gy14 X MSU109483-53 (n=400) was screened to initiate QTL analysis. Squash: Powdery mildew - identification of a marker for resistance was completed and published. Viruses - A similar mapping approach to Pm-0 is underway to identify regions for resistances to CMV and three cucurbit potyviruses. Phenotyping and DNA analysis is in progress. Resistances are being incorporated into several tropical pumpkin breeding lines. F2 populations were phenotyped by ELISA and symptom development. Phytophthora - F2 populations generated between bush butternuts and resistant accessions were phenotyped for resistance to P. capsici in the field. Obj. 3 Perform economic impact analyses of cost of production and disease control and provide readily accessible information to facilitate disease control. A. Economic analysis: Macro and micro economic variables (interest rates, input costs, production windows, existing crop budgets) were collected and 11 representative farms developed (watermelon - 3 CA, 3 FL, 1 TX; melon - 3 CA, 1 TX). All California farms were updated, validated and analyzed. B. Readily accessible information to facilitate disease control. The CucCAP website (http://CucCAP.org) was created and launched March 2017; 69 pages have been created providing cucurbit disease resources, information postings, and links to http://cucurbitgenomics.org/ and multiple extension websites. A newsletter (The CucCAP Chronical) is distributed monthly. Fact sheets have been developed to provide information for downy mildew, powdery mildew, Phytophthora, fusarium wilt, and gummy stem blight; 6 have been translated into Spanish. The extension team is also involved in consulting, conference calls, diagnostics, disease management recommendations, field days, demonstration plots, and publication of extension articles, bulletins, disease management reports, and production guides.

Publications

  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Dhillon, N.P.S., S. Phethin, S. Sanguansil, and J.D. McCreight. 2017. Early staminate flowering monoecious lines have potential as pollenizers for gynoecious hybrid bitter gourd cultivars Pak. J. Agri. Sci. 54:2733. 10.21162/PAKJAS/17.4354
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Grumet R, Colle M. 2017. Cucumber (Cucumis sativus) breeding line with young fruit resistance to infection by Phytophthora capsici. HortScience. 52:922-924.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Holdsworth WL, LaPlant KE, Bell DC, Jahn MM, Mazourek M. 2016. Cultivar-Based Introgression Mapping Reveals Wild Species-Derived Pm-0, the Major Powdery Mildew Resistance Locus in Squash. PLoS One 11:e0167715
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Krasnow, C.S., and Hausbeck, M.K. 2017. Characteristics of resistance to Phytophthora root and crown rot in Cucurbita pepo L. Plant Disease 101:659-665.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Krasnow, C.S., and Hausbeck, M.K. 2016. Evaluation of winter squash and pumpkin cultivars for age-related resistance to Phytophthora capsici fruit rot. HortScience 51:1251-1255.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Krasnow, C.S., and Hausbeck, M.K. 2017. Evaluation of winter squash cultivars for resistance to Phytophthora root rot, 2015. Plant Disease Management Reports 11:V028. Online.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Kousik C. S., Ji P., Egel D., and Quesada-Ocampo L. M. (2017) Fungicide rotation schemes for managing Phytophthora fruit rot of watermelon across Southeastern United States. Plant Health Progress 18: 28-34.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Levi, A., A.M. Simmons, L. Massey, J. Coffey, W.P. Wechter, R.L. Jarret, Y. Tadmor, P. Nimmakayala, and U.K. Reddy. 2017. Genetic diversity in the desert watermelon Citrullus colocynthis and its relationship with Citrullus species as determined by high-frequency oligonucleotides-targeting active gene markers J. Amer. Soc. Hort. Sci. 142(1):4756.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Mansfeld BN, Colle M, Kang Y, Jones AD, Grumet R 2017. Transcriptomic and metabolomic analyses of cucumber fruit peels reveal a developmental increase in terpenoid glycosides associated with age-related resistance to Phytophthora capsici. Horticulture Research. 4:17022
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: McCreight, J.D., W.M. Wintermantel, and E.T. Natwick. 2017. Host plant resistance in melon to sweetpotato whitefly in California and Arizona. Acta Hort. 1151:237244.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: McCreight, J.D., W.M. Wintermantel, E.T. Natwick, J.W. Sinclair, K.M. Crosby, and M.L. G�mez-Guillam�n. 2017. Recessive resistance to Cucurbit yellow stunting disorder virus in melon TGR 1551. Acta Hort. 1151:101107.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Palma, Marco A., Luis A. Ribera, and Ronald D. Knutson. 2016. The Era of the Functional Consumer. Journal of Food Products Marketing. 2:5, 555-570, DOI:10.1080/10454446.2015.1121425
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Pan YP, Qu SP, Bo KL, Gao ML, Haider KR, Weng Y (2017) QTL mapping of domestication and diversifying selection related traits in round-fruited semi-wild Xishuangbanna cucumber (Cucumis sativus L. var. xishuangbannanesis). Theor Appl Genet 130:1531-1548
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Rahman A.P, Miles T. D., Martin F. N., and Quesada-Ocampo L. M. (2017) Molecular approaches for development of biosurveillance tools for the cucurbit downy mildew pathogen Pseudoperonospora cubensis. Canadian Journal of Plant Pathology: 39:282-296.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Rennberger, G., Kousik, C.S., and Keinath, A.P. 2017. First report of powdery mildew on Cucumis zambianus, Cucurbita digitata and Melothria scabra caused by Podosphaera xanthii. Plant Disease "First Look" http://apsjournals.apsnet.org/doi/pdf/10.1094/PDIS-06-17-0916-PDN Posted on 09/06/2017.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Schultheis, J.R., A.C. Thornton, and W. B. Thompson. 2016. Evaluating pickling cucumber plant populations to maximize yield for once-over mechanical harvest in the southeastern United States. Acta Horticulturae. 1123:69-78.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Sun H, Wu S, Zhang G, Jiao C, Guo S, Ren Y, Zhang J, Zhang H, Gong G, Jia Z, Zhang F, Tian J, Lucas WJ, Doyle JJ, Li H, Fei Z, Xu Y (2017) Karyotype stability and unbiased fractionation in the paleo-allotetraploid Cucurbita genomes. Molecular Plant, http://www.cell.com/molecular-plant/abstract/S1674-2052(17)30266-6
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Thomas A., Carbone I., Choe K., Quesada-Ocampo L. M., and Ojiambo P. (2017) Resurgence of cucurbit downy mildew in the United States: Insights from comparative genomic analysis of Pseudoperonospora cubensis. Ecology and Evolution: 7:6231-6246.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Wallace E. and Quesada-Ocampo L. M. (2017) Analysis of microsatellites from the transcriptome of downy mildew pathogens and their application for characterization of Pseudoperonospora populations. PeerJ 5:e3266.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Wang, Y., K. VandenLangenberg, T. C. Wehner, P. A. G. Kraan, J. Suelmann, X. Zheng, K. Owens, and Y. Weng. 2016. QTL mapping for downy mildew resistance in cucumber inbred line WI7120 (PI 330628). Theor. Appl. Genet. 129:14931505.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Webster, C.G., Turechek, W.W., Li, W., Kousik, C.S. and Adkins, S. 2017. Development and evaluation of ELISA and qRT-PCR for identification of Squash vein yellowing virus in cucurbits. Plant Disease 101:178-185. 2017.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Wintermantel, W.M., Gilbertson, R.L., Natwick, E.T., McCreight, J.D. 2017. Emergence and epidemiology of Cucurbit yellow stunting disorder virus in the American Desert Southwest, and development of host plant resistance in melon. Virus Res. 2017 Jun 18. pii: S0168-1702(17)30154-5. doi: 10.1016/j.virusres.2017.06.004.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Wu S, Shamimuzzaman M, Sun H, Salse J, Sui X, Wilder A, Wu Z, Levi A, Xu Y, Ling K-S, Fei Z (2017) The bottle gourd genome provides insights into Cucurbitaceae evolution and facilitates mapping of a Papaya ringspot virus resistance locus. Plant J DOI: 10.1111/tpj.13722
  • Type: Book Chapters Status: Published Year Published: 2017 Citation: Adkins, S.T., and Kousik, C.S. 2017. Cucumber vein yellowing virus. Compendium of Cucurbit Diseases. American Phytopathological Society. 2017:143-144.
  • Type: Book Chapters Status: Published Year Published: 2017 Citation: Adkins, S.T., Turechek, W., Roberts, P.D., Webb, S.E., Baker, C.A., and Kousik, C.S., 2017. Squash vein yellowing virus. Compendium of Cucurbit Diseases. American Phytopathological Society. 2017:149-151.
  • Type: Book Chapters Status: Published Year Published: 2017 Citation: Bai Y, Zhang Z, Fei Z. 2017. Databases and bioinformatics for cucurbit species. In: Grumet R, Katzir N, Garcia-Mas J, editors. Genetics and genomics of the Cucurbitaceae. New York: Springer Intl Pub p.253-268
  • Type: Book Chapters Status: Published Year Published: 2017 Citation: Grumet R, Colle M. 2017. Genomic analysis of cucurbit fruit growth. In: Grumet R, Katzir N, Garcia-Mas J (eds). Genetics and Genomics of the Cucurbitaceae. Springer Publishing. P. 321-344
  • Type: Book Chapters Status: Published Year Published: 2017 Citation: Grumet R, Garcia-Mas J, Katzir N. 2017. Cucurbit genetics and genomics: A look to the future. In: Grumet R, Katzir N, Garcia-Mas J (eds). Genetics and Genomics of the Cucurbitaceae. Springer Publishing. P. 409-416.
  • Type: Book Chapters Status: Published Year Published: 2017 Citation: Hausbeck, M.K. 2017. Phytophthora crown and root rot. Pages 43-45 in: Compendium of Cucurbit Diseases and Pests, 2nd ed. Keinath, A.P, Wintermantel, W.M., and Zitter, T.A., eds. APS Press, Minneapolis, MN.
  • Type: Book Chapters Status: Published Year Published: 2017 Citation: Levi A, Jarret R, Kousik S, Wechter WP, NImmakayala P, Reddy U. 2017. Genetic Resources of Watermelon. In: Grumet R, Katzir N, Garcia-Mas J (eds). Genetics and Genomics of the Cucurbitaceae. Springer Publishing.p. 87-110
  • Type: Book Chapters Status: Published Year Published: 2017 Citation: McCreight JD. 2017. Cultivation and uses of cucurbits. In: Grumet R, Katzir N, Garcia-Mas J (eds). Genetics and Genomics of the Cucurbitaceae. Springer Publishing. P. 1-12
  • Type: Book Chapters Status: Published Year Published: 2017 Citation: McCreight, J.D. 2017. Botany and culture, p. 19. In: A.P. Keinath, W.M. Wintermantel, and T.A. Zitter (eds.). Compendium of cucurbit diseases and insect pests, 2nd ed. APS Press, St. Paul, Minn.
  • Type: Book Chapters Status: Published Year Published: 2017 Citation: McCreight, J.D. and A.P. Keinath. 2017. Crown blight of melons and crown decline of watermelon, p. 185186. In: A. Keinath, W.M. Wintermantel, and T.A. Zitter (eds.). Compendium of cucurbit diseases and insect pests, 2nd ed. APS Press, St. Paul, Minn.
  • Type: Book Chapters Status: Published Year Published: 2017 Citation: Naegele RP, Wehner TC. 2017. Genetic Resources of Cucumber. In: Grumet R, Katzir N, Garcia-Mas J (eds). Genetics and Genomics of the Cucurbitaceae. Springer Publishing. P. 61-86
  • Type: Book Chapters Status: Published Year Published: 2017 Citation: Nimmakayala P, Saminathan T, Abburi VL, Yadav LK, Tomason Y, Levi A, Weng Y, Reddy UK. 2017. Comparative Genomics of the Cucurbitaceae. In: Grumet R, Katzir N, Garcia-Mas J (eds). Genetics and Genomics of the Cucurbitaceae. Springer Publishing. P. 229-240
  • Type: Book Chapters Status: Published Year Published: 2017 Citation: Quesada-Ocampo L. M., Ed, (2017) Disease control for commercial vegetables. North Carolina Agricultural and Chemicals Manual.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Fei Z. 2017. Cucurbit Genomics Database Workshop. SolCuc. Valencia, Spain. September 2017 https://pag.confex.com/pag/xxv/meetingapp.cgi/Paper/25600
  • Type: Book Chapters Status: Published Year Published: 2017 Citation: Weng Y. 2017. The cucumber genome. In: Grumet R, Katzir N, Garcia-Mas J (eds). Genetics and Genomics of the Cucurbitaceae. Springer Publishing. P. 199-210
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Alzohairy, S.A., Hammerschmidt, R., and Hausbeck, M.K. 2017. Characterization of the structural basis of winter squash fruit age-related resistance to Phytophthora capsici. American Phytopathological Society Annual Meeting, San Antonio, TX 526-P
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Colle M, Mansfeld B, Grumet R. 2017. Genome-wide SNP discovery and identification of age-related resistance loci in cucumber by QTL-seq. PAG XXV. https://pag.confex.com/pag/xxv/webprogram/paper24399.html.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Guo S, Sun H, Ren Y, Zhang J, Tian S, Gong G, Zhang H, Fei Z, Xu Y. 2017. Genome variation elucidates evolution and domestication of fruit ripening and quality traits in watermelon. PAG. January, 2017. https://pag.confex.com/pag/xxv/meetingapp.cgi/Paper/25600
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Gimode, W.R. and C.E. McGregor. 2017. Fine Mapping of a Major Flowering Time Quantitative Trait Locus in Watermelon Using Single Nucleotide Polymorphisms. CROPS 2017, Hudson Alpha, Huntsville, Alabama.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Gimode, W.R., J. Clevenger and C.E. McGregor. 2017. Fine Mapping of a Major Flowering Time Quantitative Trait Locus in Watermelon. NAPB 2017, University of California, Davis-CA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Kaur, N., Chen, W., Fei, Z. and Wintermantel, W.M. Transcriptome changes occurred in the whitefly, B. tabaci MEAM1 in response to feeding on melon infected with the crinivirus, CYSDV, 3rd Hemipteran-Plant Interactions Symposium, Madrid. Spain. June 4-8, 2017.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Kousik, C.S., Ikerd, J.L. and Mandal, M.K. 2017. Long term monitoring of cucurbit powdery mildew (Podosphaera xanthii) races in Charleston, South Carolina. Presented at the Annual meeting of the American Phytopathological Society, San Antonio, TX August 2017. 503-P
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Krasnow, C.S., and Hausbeck, M.K. 2016. Age-related resistance of Cucurbita spp. fruit to Phytophthora capsici. Abstr. Phytopathology 106 (Suppl.):S1.5.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Miranda-V�lez, M, L. Wessel-Beaver, Jose C. Verle-Rodrigues and W. Seda-Mart�nez. 2016. Effect of leaf position on the assessment of resistance to Papaya ringspot virus and Zucchini yellow mosaic virus in tropical pumpkin. Proceedings of the 41st meeting of the Sociedad Puertorrique�a de Ciencias Agr�colas, November 18, 2016, Corozal, Puerto Rico. p. 57.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Mandal, M.K., Suren, H. and Kousik, C.S. 2017. Transcriptomic profiling of watermelon-powdery mildew (Podosphaera xanthii) interactions. Presented at the Annual meeting of the American Phytopathological Society, San Antonio, TX August 2017. 361-P
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Mandal, M.K., Ikerd, J.L., Wallace, E.C., Rebbeca, G., Turechek, W., Quesada-Ocampo, L.M. and Kousik, C.S. 2017. Population biology of the downy mildew pathogen on tolerant and susceptible cucumber in the southeastern United States. American Phytopathological Society, San Antonio, TX August 2017. 563-P
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Mantooth, K.L., Ikerd, J.L., Mandal, M.K. and Kousik, C.S. 2017. Potential sources of resistance to Phytophthora crown rot in Cucurbita maxima and Cucurbita moschata. American Phytopathological Society, San Antonio, TX August 2017. 291-P
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Natwick, E.T, Wintermantel, W. M., Gilbertson, R.L., Blanco, S.G., and McCreight, J.D.2017. Evaluation of Potential New Sources of Melon Host Plant Resistance to the Whitefly, Bemisia tabaci. 3rd Hemipteran-Plant Interactions Symposium, Madrid. Spain.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Perkins-Veazie, P., J.R. Schultheis, G. Ma, and T. Birdsell. 2016. Carotenoid content of butternut squash cultivars following harvest and storage. HortScience. 51(9):S358
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Rahman A., Martin F., Shands A., Miles T., and Quesada-Ocampo L. M. 2017.Using comparative genomics to develop biosurveillance tools for the cucurbit downy mildew pathogen Pseudoperonospora cubensis. Oomycete Molecular Genetics Network Meeting, Pacific Grove, CA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Branham S, Levi A, Farnham M, Wechter P. 2017. Quantitative Trait Loci Mapping of Resistance to Fusarium oxysporum f. sp. niveum race 2 in Citrullus lanatus var. Citroides using Genotyping-by-Sequencing (GBS). PAG XXV. https://pag.confex.com/pag/xxv/meetingapp.cgi/Paper/25554
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Wechter P, Branham S, Levi A. 2017. 66-P: GBS-SNP-based linkage mapping and QTL associated with resistance to race 1 Fusarium wilt in Cucumis melo. American Phytopathological Society. 266-P
  • Type: Other Status: Published Year Published: 2017 Citation: Adams M. L. and Quesada-Ocampo L. M. (2017) Evaluation of cultivars and fungicides for control of downy mildew on cucumber, Clinton 2015. Plant Disease Management Reports 11: V160.
  • Type: Other Status: Published Year Published: 2017 Citation: Adams M. L. and Quesada-Ocampo L. M. (2017) Evaluation of cultivars and fungicides for control of downy mildew on cucumber, Clinton 2014. Plant Disease Management Reports 11: V161.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Schultheis, J.R. and W.B. Thompson. 2016. Watermelon yield and fruit size response to grafted versus non-grafted transplants in plasticulture and bare ground production systems. HortScience. 51(9):S38 (abstr.)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Schultheis, J.R. and W.B. Thompson. 2016. Watermelon cultivar yield and quality results, North Carolina, 2015. HortScience. 51(9):S37 (abstr.)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Seda-Mart�nez, W., M. Miranda-V�lez, L. Wessel-Beaver and A. M. Linares-Ramirez. 2017. Approaches to Phenotyping PRSV and ZYMV Resistance in Tropical Pumpkin. HortScience 45(8):S234.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Vogel, G. LaPlant, K. Reeves, E., Mazourek, M., Gore, M., Smart, CD. 2017. Evaluation of Cucurbita pepo breeding lines with reduced susceptibility to root and crown rot caused by Phytophthora capsici. American Phytopathological Society, San Antonio TX August 237-P
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Daley J, Branham SE, Hassell R, Levi A, Wechter P. 2017. Mapping Resistance to Alternaria Cucumerina in Muskmelon, Plant and Animal Genome meeting, San Diego, CA, January 14-18, 2017. https://pag.confex.com/pag/xxv/meetingapp.cgi/Paper/25467
  • Type: Other Status: Published Year Published: 2017 Citation: Adams M. L., Noel N. A., and Quesada-Ocampo L. M. (2017) Evaluation of fungicides for control of anthracnose on cucumber, Cleveland 2016. Plant Disease Management Reports 11: V099.
  • Type: Other Status: Published Year Published: 2017 Citation: Adams M. L., Parada C. H., and Quesada-Ocampo L. M. (2017) Evaluation of fungicides for control of Phytophthora fruit rot of watermelon, Kinston 2016. Plant Disease Management Reports 11: V111.
  • Type: Other Status: Published Year Published: 2017 Citation: Adams M. L. and Quesada-Ocampo L. M. (2017) Evaluation of fungicides for control of downy mildew on cucumber, Clayton 2016. Plant Disease Management Reports 11: V100.
  • Type: Other Status: Published Year Published: 2017 Citation: Adams M. L. and Quesada-Ocampo L. M. (2017) Evaluation of fungicides for control of powdery mildew of winter squash, Cleveland 2016. Plant Disease Management Reports 11: V112.
  • Type: Other Status: Published Year Published: 2017 Citation: Adams M. L. and Quesada-Ocampo L. M. (2017) Evaluation of fungicides for control of downy mildew on cucumber, Kinston II 2016. Plant Disease Management Reports 11: V096.
  • Type: Other Status: Published Year Published: 2017 Citation: Adams M. L. and Quesada-Ocampo L. M. (2017) Evaluation of fungicides and cultivars for control of downy mildew on cucumber, Kinston 2016. Plant Disease Management Reports 11: V097.
  • Type: Other Status: Published Year Published: 2017 Citation: Adams M. L. and Quesada-Ocampo L. M. (2017) Evaluation of cultivars and fungicides for control of downy mildew on cucumber, Clinton 2016. Plant Disease Management Reports 11: V098.
  • Type: Other Status: Published Year Published: 2016 Citation: Hausbeck, M.K., Krasnow, C.S., and Linderman, S.D. 2016. Managing Phytophthora on winter squash and pumpkin. Online at https://veggies.msu.edu/extension-publications/#FactSheets.
  • Type: Other Status: Published Year Published: 2016 Citation: Hausbeck, M.K., and Linderman, S.D. 2016. Managing Phytophthora on summer squash and zucchini. Online at https://veggies.msu.edu/extension-publications/#FactSheets
  • Type: Other Status: Published Year Published: 2016 Citation: Hausbeck, M.K., and Linderman, S.D. 2016. Managing Phytophthora on cucumber. Online at https://veggies.msu.edu/extension-publications/#FactSheets
  • Type: Other Status: Published Year Published: 2016 Citation: Hausbeck, M.K., and Linderman, S.D. 2016. Managing Phytophthora on cantaloupe, muskmelon and watermelon. Online at https://veggies.msu.edu/wp-content/uploads/2017/05/FS_Managing-Phytophthora-on-Melon.pdf
  • Type: Other Status: Published Year Published: 2017 Citation: Miller N., Adams M. L., and Quesada-Ocampo L. M. (2017) Evaluation of fungicides for Fusarium wilt of watermelon, 2016. Plant Disease Management Reports 11: V135.
  • Type: Other Status: Published Year Published: 2017 Citation: Miller N., Adams M. L., and Quesada-Ocampo L. M. (2017) Evaluation of fungicides for control of Fusarium wilt of watermelon, Salisbury, NC, 2015. Plant Disease Management Reports 11: V134.
  • Type: Other Status: Published Year Published: 2017 Citation: No�l N.A. and Quesada-Ocampo L. M. (2017) Tolerance of watermelon lines to cucurbit anthracnose, 2016. Plant Disease Management Reports 11: V062.
  • Type: Other Status: Published Year Published: 2017 Citation: Wessel-Beaver, L. and A.M. Linares-Ramirez. 2017.Dos virus importantes en la Calabaza: Mosaico Amarillo de la clabaza (ZYMV) y Mancha Anular de la Papaya (PRSV). UPRM EEA-Lajas Publication 003. Factsheet


Progress 09/01/15 to 08/31/16

Outputs
Target Audience:The overarching objective of the CucCAP project is to leverage applied genomics for improvement of disease resistance of cucurbit crops. Therefore, the target audiences for the CucCAP project are: - the cucurbit industries, i.e., growers, shippers, processors, commodity organizations, pest management company representatives for watermelon, melon, cucumber and squash; - the cucurbit breeding community (seed companies and public breeders); - the academic community developing knowledge leading to improved varieties. We have engaged our stakeholders via interaction with the project advisory board, web-based communication, collaborative research, research and extension publications, organizing and participating in industry and grower-focused meetings and events, and scientific conferences. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?This project provides numerous training opportunities for undergraduate students, graduate students and postdoctoral researchers in the areas of plant breeding and genetics, plant pathology, bioinformatics, horticulture, and agricultural economics. Training opportunities include 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?A. Dissemination of information and 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 including: UCCE Fall Desert Crops Workshop, El Centro, CA; California Melon Research Board, San Diego, CA; Proceedings of the Lower Mainland Horticultural Improvement Association/Pacific Agriculture Show; Pickle Packers International Annual Meeting, Fort Worth, TX; Pickle Packers International Spring Meeting. Raleigh, NC, Apr. Great Lakes Fruit, Vegetable and Farm Market Expo, Grand Rapids, MI, Pickling Cucumber Commodity Meeting, Grand Rapids MI; Vine Crops Twilight Meeting, Byron Center, MI; Extension Specialist Breakfast Meeting via Zoom videoconference, East Lansing, MI; Southwest Hort Days, Benton Harbor, MI; Bay Area Growers Extension Meeting, Bay City, MI; The downy mildew report, Syngenta Meeting, Lansing, MI Field Day University of Wisconsin Hancock Agricultural Research Station. Indiana Horticultural Congress, Indianapolis, IN. Empire State Producers Expo.; Western NY Vegetable Growers Meeting; Western NY Field Days. Portland NY; Twilight meeting, Eden Valley, NY. Crop Consultant Meeting, Syracuse NY; Southeast Regional Fruit & Vegetable Conference, Savannah, GA; NC Watermelon Convention. Wrightsville Beach, NC; Annual Southeast Vegetable and Fruit Expo. Myrtle Beach, SC; US Vegetable Laboratory Open House, Charleston SC Georgia Watermelon Association, St. Simmons, GA. Watermelon Research and Development Group meeting. San Antonio, TX. Information also has been communicated to our stakeholders through websites, extension articles and bulletins, disease management reports, contributions to production guides, and webinars. The extension team members also provide on-line reports of disease occurrences, and diagnostic and disease management assistance. On line resources include websites: www.veggies.msu.edu http://cucurbitbreeding.com/cucumber-breeding/downy-mildew-resistance/ and a new CucCAP website that is currently under development: (https://cucurbits.ces.ncsu.edu/) and cucurbit disease fact sheets: Anthracnose of cucurbits: http://content.ces.ncsu.edu/anthracnose-of-cucurbits Cucurbit downy mildew: http://content.ces.ncsu.edu/cucurbit-downy-mildew Cucurbit powdery mildew: http://content.ces.ncsu.edu/cucurbit-powdery-mildew Fusarium wilt of watermelon: http://content.ces.ncsu.edu/fusarium-wilt-of-watermelon Gummy stem blight of cucurbits: http://content.ces.ncsu.edu/gummy-stem-blight-and-phoma-blight-on-cucurbits B. Interaction with cucurbit scientific and breeding communities. The CucCAP project had extensive interaction with the broader scientific and breeding communities through active participation in national and international scientific conferences; seminar presentations; and collaborative research with industry partners. CucCAP team members have attended and presented CucCAP related work at the: Plant and Animal Genome Conference American Society for Phytopathology Cucurbitaceae 2016: XIth Eucarpia Meeting on Genetics and Breeding of Cucurbitaceae American Society for Plant Biology American Society for Horticultural Science International Congress of Entomology Entomological Society of America International Soilborne Oomycete Conference International Whitefly Symposium International Plant Virus Epidemiology Symposium Brazilian Virology Congress PI's also presented seminars related to CucCAP work in a variety of venues including: Dept. of Plant Biology, Cornell University Plant Pathology, Penn State University College of Horticulture, Shandong Agric. Univ. April College of Food Science and Engineering, Hefei University of Technology Rijk Zwaan Seed Company, Netherlands U.S. Vegetable Laboratory, Charleston, SC. Department of Plant, Soil and Microbial Science, Michigan State Univ. Department of Biochemistry, NC State A primary venue for dissemination of the genomic work of the project is the International Cucurbit Genomics Initiative (ICuGI) website (http://www.icugi.org) which is currently being updated by the bioinformatics team. CucCAP team members also conduct collaborative cucurbit research with researchers in several vegetable seed companies including: Axia Vegetable Seeds, HM Clause, Rijk Zwan, Sakata Seeds, Syngenta Collaborative efforts include development of genetic materials and sharing of genetic maps and molecular markers. What do you plan to do during the next reporting period to accomplish the goals?Obj. 1. Develop genomic approaches and tools for cucurbit species. Develop genomic and bioinformatic platforms for cucurbit crops. Continue database development. Release newly designed ICuGI database (http://www.icugi.org). GBS of cucurbit species, establish molecular-informed core populations. Complete DNA isolation and genotyping of PI collections for the four cucurbit species using the GBS platform and the SNP calling from the GBS data. Perform SNP analysis for watermelon, melon, cucumber and squash PI collections. Resolve population structure and identity by descent for use in GWAS for various cucurbit collections, testing and optimize suitable GWAS models for cucurbits and identify appropriate methods to validate GWAS results. Use GBS data to design core collections for the four crops. Obj. 2. Perform genomic-assisted breeding to introgress disease resistance into cucurbit cultivars. Watermelon -- Resistance to Fusarium oxysporum races 1 and 2. Perform inheritance studies and GBS analyses for populations generated from USVL246-FR2 and the susceptible Clc parent PI 542114 (Pop 46-14), and Pop 52-17 and Pop 52-19. Screen genetic populations from [Calhoun Gray (R) x Sugar Baby (S); or Calhoun Gray (R) x Black Diamond (S)] to identify QTL. Validate markers using 500 F2 plants segregating for FW race 1 resistance. -- Gummy stem blight. Continue phenotyping of the WmGsb in the greenhouse and the field (NC). Initiate analysis for GBS resistance-associated SNPs using genome-wide association studies (GWAS) with the USDA watermelon germplasm collection. Complete development of three mapping populations for GSB resistance and initiate phenotyping for resistance. -- Phytophthora fruit rot of watermelon. Complete analysis of inheritance of resistance to Phytophthora fruit rot in the segregating population derived from the cross of USVL531-MDR x PI 269677. -- Powdery mildew. Prepare samples from the population segregating for resistance to powdery mildew for DNA extraction and analysis by GBS. -- Papaya ringspot virus (PRSV). Evaluate genetic populations of PRSV-susceptible Clc parent USVL252-FR2 crossed with the PRSV-resistant Clc parents PI 244017 (Pop 52-17) or PI 244019 (Pop 52-19) for PRSV-resistance. Perform GBS for identification of SNPs and QTL associated with the resistance. -- Cucumber green mottle mosaic virus (CGMMC). Repeat screening for CGMMV resistance with selected promising accessions and produce seed from selected resistant plants. Develop F1, F2, BC1S, and BC1R populations for the genetic of inheritance study. Initiate genome-wide association study (GWAS) to identify putative SNPs associated with CGMMV resistance. Melon -- Fusarium and powdery mildew resistance. RILs of MR-1 (multi-resistant) x Ananas Yokneam (MR1xAY) will be used for GBS to identify SNPs for QTL analysis. Begin Fusarium assays for Race 1 and 2, repeat Powdery mildew tests, and begin QTL analysis and mapping of Powdery mildew resistance. -- CYSDV resistance. Test selected selfed lines for resistance to CYSDV. -- CMV resistance. Increase advanced CMV-resistant lines (western U.S. shipping type cantaloupe, and honeydew). Assess for resistance in controlled-inoculation greenhouse tests and for adaptation and fruit quality in field tests at three locations in AZ and CA. Cucumber -- Downy mildew (DM) resistance. - QTL identification. Continue marker-assisted backcrossing in Gy14 genetic background to develop NILs carrying different combinations of dm2.1, dm4.1 and dm5.1 QTLs from WI7120. Narrow down the QTL region (1.5 LOD interval) of target QTL regions through fine genetic mapping and GWAS. Start to pyramid major-effect QTL for DM resistance from both WI7120 and PI 197088 resistance sources. Perform growth chamber and field evaluation of DM resistance of the NILs (WI, NC). - Phenotype DM resistance in cucumber natural populations for subsequent GWAS analysis. - Develop inbred pickling and slicing cucumber populations selected for yield, earliness, quality and resistance to DM. Develop a new population derived from PI 605996 (HR) x 'Poinsett 76' to provide new sources of high resistance to downy mildew. Self pollinate F2 progeny and field test S1 lines for high resistance to natural disease incidence in NC. -- Phythophthora fruit rot resistance. - Young fruit resistance. Perform replicated trial of PI 104983-derived families in P. capsici infested field in NY. Produce F2 progeny from PI-derived resistant lines x GY14, phenotype for response to P. capsici and initiate QTL analysis. Initiate GWAS analysis for resistance to P. capsici. - Age-related resistance (ARR). Perform QTL seq analysis for ARR from F2 populations of GY14 X Poinsett and GY14 X Vlaspik. Compare results of transcriptomic and metabolomic analysis of peels from ARR+ and ARR- cultivars with QTL seq analysis to help identify genomic regions of greater interest. Squash/pumpkin -- Potyvirus resistance. Perform inheritance studies of virus resistance on F2 populations from crosses between the resistant parents ('Nigerian Local' and 'Menina') and two susceptible genotypes ('Taína Dorada' and 'Verde Luz'). Continue introgression of resistance into tropical pumpkin genotypes 'Soler' and 'TP411'. Prepare DNA samples for SNP analysis. -- Phytophthora resistance. Create F2:3 populations from C. moschata accessions PI 211996, PI 483347, and PI 634693 selected for resistance to Phytophthora root rot and cross with a powdery mildew resistant bush butternut. Map resistance and validate QTL from the initial F2:3 populations. Obj. 3 Perform economic impact analyses of cost of production and disease control and provide readily accessible information to facilitate disease control. Define, parameterize, simulate, and validate production variables based on cucurbit production crop budgets. Identify the number of representative farms to be developed depending on geographic location, common production practices, and marketing windows, among others variables. Identify facilitators to develop representative farms in Northeast region. Develop and validate representative farms in Northeast region. Develop a centralized cucurbit disease website. Populate the CucCAP website (https://cucurbits.ces.ncsu.edu/) to provide project information and events, diagnostic resources and disease control recommendations, disease alerts and forecasting tools. Disease control information. Translate into Spanish factsheets for anthracnose, powdery and downy mildew of watermelon currently prepared and posted in English. Produce additional crop-disease fact sheets.

Impacts
What was accomplished under these goals? 1. Develop genomic and bioinformatic platforms for cucurbit crops. The development of genomic and bioinformatics platforms for cucurbit crops will enable plant breeders to access the most up-to-date and efficient approaches to crop improvement for watermelon, melon, cucumber and squash. These tools will help identify genomic regions associated with resistance to key cucurbit diseases, and ultimately, provide molecular markers by which breeders can facilitate transfer of resistances to high yielding varieties with superior fruit quality. To this end, the bioinformatics team has evaluated and compared performance of software that enables identification of SNPs (single nucleotide polymorphisms that serve as molecular markers for breeders) for output and accuracy to establish appropriate parameters for sequence data (genotyping by sequencing-GBS) analysis. The database for cucurbit sequence information, initially established through International Cucurbit Genome Initiative (ICuGI; (http://www.icugi.org) website is being updated using the GMOD Tripal system and Chado database schema and novel interfaces and functions are being developed to provide a breeder-friendly database for genomic, genotypic, phenotypic and QTL information. Genome syntenies between watermelon, melon and cucumber have been identified and a genome syntenty browser will be implemented in the database. These genomic and bioinformatics platforms, coupled with DNA sequence analyses, will allow perform genetic analyses of the plant introduction (PI) collections. The resultant data and analyses will provide a community resource for genome wide association studies (GWAS) for current and future traits of interest. A partially automated facility and optimized protocols for high throughput DNA preparation were established to allow us to assay 1000-1600 PI accessions from the USDA collections for each crop. DNA preparation was completed for the cucumber PI collection and is underway for the watermelon collection. GBS of initial cucumber samples provided high quality sequence data and identified thousands of SNPs well distributed over the 7 chromosomes. Overall, in this first year, we have made good progress toward our short term (1-2 year objectives) of: 1. Establishing state of the art, genotyping by sequencing (GBS) and data analysis platforms for cucurbit species; and 2. Obtaining GBS sequence data for 1000-1600 PIs for each of the four cucurbit crops. Completion of these goals will allow us to develop new tools for public and private cucurbit breeding programs to enhance genomic and breeding capacity. Obj. 2. Perform genomic-assisted breeding to introgress disease resistance into cucurbit cultivars. Cucurbit growers and processors consistently identify diseases as major constraints causing severe reductions in yield, loss of fruit quality, increased labor and expense for control, and negative environmental impacts from application of pesticides. As the most cost-effective and environmentally desirable solution is disease-resistant cultivars, breeding for resistance is a major focus of this project. The priority diseases, as identified by the cucurbit industries, vary with crop, and the associated breeding projects are at various stages of development. Watermelon: Fusarium, Alternaria, powdery mildew - An F7 RIL population has been produced and DNA isolated for GBS QTL analysis. Additional lines with high resistance to Fon race 1 and 2 are being used to initiate inheritance studies. Gummy stem blight - Several mapping populations with resistance from C. amarus and C. lanatus accessions are under development. Phytophthora fruit rot and powdery mildew - Inheritance studies were conducted on segregating F2 and BC1 populations derived from the cross of USVL531-MDR x PI 269677. Leaf samples were collected for GBS and selected individuals were self-pollinated. Papaya ringspot virus - Progeny populations are under development. Cucumber green mottle mosaic virus - 1600 accessions were screened for resistance; several have been selected for further evaluation and seed production. Melon: Powdery mildew - RIL lines were tested for resistance in the greenhouse (SC) and field in SC, CA and AZ. CYSDV - Backcrossed resistant field selections and selfed for testing. CMV - Advanced resistant lines were increased to assess resistance, adaptation and fruit quality and tested in CA and AZ. Cucumber: Downy mildew - Analysis of F2:3 (PI 330628 source) and RIL populations (Coolgreen source) identified 5 and 6 QTL, respectively; three in common between the sources. The data provide the starting point for fine mapping of major-effect QTL. Introgression of three major QTL has been initiated into an elite pickling cucumber inbred. Initial crosses have been made between Gy14 and plants carrying dm2.1, dm4.1 and dm5.1. Advanced populations derived from Coolgreen are being evaluated to combine resistance with high fruit quality, yield, and good agronomic traits. Phytophthora fruit rot - Individuals from PI 104983 were self-pollinated to stabilize resistance; progeny were tested for response to multiple isolates. Crosses were made to initiate introgression into pickling line GY14 and analysis of inheritance. Squash: Powdery mildew - GWAS-based mapping of major resistance gene Pm-0 and subsequent refinement via GBS with additional PIs identified a 76.4 kb region associated with resistance. Two molecular markers were created, that in testing to date, predict powdery mildew resistance derived from C. okeechobeensisin Cucurbita pepo with 100% accuracy. Viruses - A similar mapping approach to Pm-0 is underway to identify regions for resistances to cucumber mosaic virus and three cucurbit potyviruses. Phenotyping and DNA analysis is in progress. Resistances are being incorporated into several tropical pumpkin breeding lines with the intent to develop advanced breeding lines. F2 populations are being phenotyped by ELISA and symptom development. Phytophthora - Field testing is performed on a dedicated P. capsici farm to test breeding lines and determine best management practices. Several PI accessions have been identified as possible sources of resistance and will be used for crossing. During the first year we made good progress in meeting our short term (1-2 year) goals of developing germplasm lines with resistance to Fusarium r.1,2, Phytophthora, powdery mildew, and PRSV in watermelon; CYSDV in melon, and Phytophthora in cucumber. Identification of QTL for downy mildew in cucumber and a definition of markers for powdery mildew resistance in squash are an important steps toward more efficient marker-assisted breeding. Obj. 3 Perform economic impact analyses of cost of production and disease control and provide readily accessible information to facilitate disease control. Economic analysis: Macro and micro economic variables were collected to develop the economic model, such as interest rates, input costs, production windows and existing crop budgets. Eleven representative farms were developed (watermelon - 3 CA, 3 FL, 1 TX; melon - 3 CA, 1 TX). These accomplishments are making good progress toward the short term goal to develop representative farms for economic analyses for three locations for each of the four commodities. Readily accessible information to facilitate disease control. A draft, centralized cucurbit disease website has been created (https://cucurbits.ces.ncsu.edu/) and web manager position recently hired. The website will link to ICuGI and extension websites in MI, NC, and NY. Fact sheets have been developed to provide information to growers for cucurbit downy mildew and powdery mildew, and fusarium wilt and gummy stem blight of watermelon. The extension team also has been actively involved in consulting, conference calls, field days and demonstration plots as well as publication of extension articles and bulletins, disease management reports, and contributions to production guides.

Publications

  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Levi, A., J. Coffey, L.M. Massey, N. Guner, E. Oren, Y. Tadmor, and K.S. Ling. 2016. Resistance to papaya ringspot virus-watermelon strain (PRSV-W) in the desert watermelon Citrullus colocynthis. HortScience 51:47.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Meru, G. and C. McGregor. 2016. Genotyping by sequencing for SNP discovery and genetic mapping of resistance to race 1 of Fusarium oxysporum in watermelon. Scientia Horticulturae 209: 31-40.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Naegele R. P., Quesada-Ocampo L. M., Kurjan J. D, Saude C., and Hausbeck M. K. (2016) Regional and temporal population structure of Pseudoperonospora cubensis in Michigan and Ontario. Phytopathology 106: 372-379.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Nimmakayala, P., Y. Tomason, V.L. Abburi, T. Saminathan, A.G.A. Rodr�guez, V.G. Vajja, G. Salazar, G. Panicker, A. Levi, W.P. Wechter, J.D. McCreight, R. Grumet, A. Korol, Y. Ronin, and U.K. Reddy. 2016. Genome-Wide Differentiation of Various Melon Horticultural Groups for Use in GWAS for Fruit Firmness and Construction of a High Resolution Genetic Map. Frontiers in Plant Science 22 September 2016 http://dx.doi.org/10.3389/fpls.2016.01437
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Niu, X. X. Zhao, K. Ling, A. Levi, Y. Sun, M. Fan. 2016. The FonSIX6 gene acts as an avirulence effector in the Fusarium oxysporum f. sp. niveum - watermelon pathosystem. Nature Scientific Reports 6:28146 DOI: 10.1038/srep28146
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Sabanadzovic, S., R. Valverde, J.D. McCreight, W.M. Wintermantel, and N. Aboughanem-Sabanadzovic. 2016. Cucumis melo endornavirus: Genome organization, host range and co-divergence with the host. Virus Research 214:4958
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Summers, C.F., Gulliford, C.M., Carlson, C.H., Lillis, J.A., Carlson, M.O., Cadle-Davidson, L., Gent, D.H., and Smart, C.D. (2015) Identification of genetic variation between obligate plant pathogens Pseudoperonospora cubensis and P. humuli using RNA sequencing and genotyping-by-sequencing. PLoS ONE 10(11): eD143665. DOI: 1D.1371/journal.pone.D143665
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Summers, C.F., Adair, N., Gent, D.H., McGrath, M.T., and Smart, C.D. (2015) Pseudoperonospora cubensis and P. humuli detection using species-specific probes and high definition melt curve analysis. Canadian Journal of Plant Pathology 37:315-330. DOI: 10.1080/07060661.2015.1053989
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Thies, J.A., J.J. Ariss, C.S. Kousik, R.L. Hassell, and A. Levi. 2016. Resistance to Southern Root-knot Nematode (Meloidogyne incognita) in Wild Watermelon (Citrullus lanatus var. citroides) Populations. Journal of Nematology 48:1419.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Wallace E., Adams M., and Quesada-Ocampo L. M. (2015) First report of downy mildew on buffalo gourd (Cucurbita foetidissima) caused by Pseudoperonospora cubensis in North Carolina. Plant Disease 99: 1861.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Wechter, W.P., McMillan, M.M., Farnham, M.W., and Levi, A. 2016. Watermelon germplasm lines USVL246-FR2 and USVL252-FR2 tolerant to Fusarium oxysporum f. sp. niveum race 2. HortScience 51:1065-1067.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Wintermantel, W.M., Gilbertson, R.L., McCreight, J.D., and Natwick, E.T. 2015. Host-specific relationship between virus titer and whitefly transmission of Cucurbit yellow stunting disorder virus. Plant Disease 100: 92-98. http://dx.doi.org/10.1094/PDIS-11-14-1119-RE
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Withers S., Gongora-Castillo E., Gent D., Thomas A., Ojiambo P., and Quesada-Ocampo L. M. (2016) Using next-generation sequencing to develop molecular diagnostics for Pseudoperonospora cubensis, the cucurbit downy mildew pathogen. Phytopathology 106: 1105-1116.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Alzohairy, S., and Hausbeck, M. 2015. Transcriptomic profiling of Cucurbita species to characterize the age-related resistance against Phytophthora capsici. Page 19 in: Proceedings of the 1st International Soilborne Oomycete Conference, Duck Key, FL, 8-10 Dec. Abstract.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: VandenLangenberg, K. and T. C. Wehner. 2016. Downy mildew disease progress in resistant and susceptible cucumbers tested in the field at different growth stages. HortScience 51: 984-988.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Wallace E., Choi Y. J., Thines M., and Quesada-Ocampo L. M. (2016) First report of Plasmopara aff. australis on Luffa cylindrica in the United States. Plant Disease 100: 537.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Grumet, R. 2016. Introduction to CucCAP - developing genomic resources for the cucurbit community. Plant and Animal Genome Conference. San Diego, CA. https://pag.confex.com/pag/xxiv/webprogram/Paper18951.html
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Hausbeck, M.K., and Cook, A. 2015. The downy mildew report. Pages 9-14 in: Pickling Cucumber Session Summaries, Great Lakes Fruit, Vegetable and Farm Market Expo, Grand Rapids, MI, Dec. Online.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Hausbeck, M. 2015. Rots and blights of vegetables. Pages 71-79 in: Proceedings of the Lower Mainland Horticultural Improvement Association/Pacific Agriculture Show Horticultural Growers Short Course, Field Vegetables Session, Abbotsford, BC.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Grumet, R., Z. Fei, A. Levi, J.D. McCreight, M. Mazourek, M. Palma, J. Schultheis, Y. Weng, M. Hausbeck, S. Kousik, K.-S. Ling, C. McGregor, L. Quesada-Ocampo, A.L. Ramirez, U. Reddy, L. Ribera, C. Smart, P. Wechter, T. Wehner, L. Wessel-Beaver, and W. Wintermantel. 2016. CucCAP - Developing genomic resources for the cucurbit community, p. 222226. In: E.U. Kozik, and H.S. Paris (eds.). Cucurbitaceae 2016, XIth Eucarpia Meeting on Genetics and Breeding of Cucurbitaceae, Warsaw, Poland.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Krasnow, C., and Hausbeck, M. 2015. Using directed fungicide applications to manage Phytophthora fruit rot of processing squash. Page 23 in: Proceedings of the 1st International Soilborne Oomycete Conference, Duck Key, FL, 8-10 Dec. Abstract.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Kousik C.S., Egel D., Ji P., and Quesada-Ocampo L. M. (2016) Fungicide rotation schemes and Melcast for managing Phytophthora fruit rot of watermelon in Southeastern United States. Phytopathology. abstract.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Lebeda, A., E. K?�stkov�, B. Sedl�kov�, and J.D. McCreight. 2016 Initiative for international cooperation of researchers and breeders related to determination and denomination of cucurbit powdery mildew races, p. 148152. In: E.U. Kozik, and H.S. Paris (eds.). Cucurbitaceae 2016, XIth Eucarpia Meeting on Genetics and Breeding of Cucurbitaceae, Warsaw, Poland.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Levi, A., A. Simmons, K. Ling, Y. Tadmor, P. Nimmakayala, and U.K. Reddy. 2016. Utilizing Genetic Diversity in the Desert Watermelon Citrullus colocynthis for Enhancing Watermelon Cultivars for Resistance to Biotic and Abiotic Stress. p. 105-108. In E.U. Kozik and H.S. Paris (eds). Cucurbitaceae 2016, XIth EUCARPIA Meeting on Genetics and Breeding of Cucurbitaceae, Warsaw, Poland.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Mazourek M, Holdsworth WL, Hernandez C, LaPlant KE. 2016. Making up for lost time in Cucurbita molecular breeding." Plant and Animal Genome Conference. San Diego, CA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: McCreight, J.D., W.M. Wintermantel, and E.T. Natwick. 2016. Expression of Host Plant Resistance in Melon to Sweetpotato Whitefly in the Desert Southwest United States. XXV International Congress of Entomology, Orlando, FL, Sep. abstract
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: McCreight, J.D., W.M. Wintermantel, and E.T. Natwick. 2015. Evaluations of melon germplasm reported to exhibit host plant resistance to sweetpotato whitefly. Entomological Society of America, Annual Meeting, Minneapolis, MN, Nov. abstract
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: McCreight, J.D., W.M. Wintermantel, and E.T. Natwick. 2016. New Sources of Resistance to CYSDV in Melon, p. 6165. In: E.U. Kozik, and H.S. Paris (eds.). Cucurbitaceae 2016, XIth Eucarpia Meeting on Genetics and Breeding of Cucurbitaceae, Warsaw, Poland.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Miller N. F. and Quesada-Ocampo L. M. (2016) Evaluation of fungicides for management of Fusarium wilt of watermelon. Phytopathology. Abstract
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Noel N. and Quesada-Ocampo L. M. (2016) Fungicide resistance and host susceptibility of Colletotrichum orbiculare infecting cucurbit crops in North Carolina. Phytopathology. Abstract
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Rahman A. and Quesada-Ocampo L. M. (2016) Early detection and quantification of Pseudoperonospora cubensis airborne sporangia using real-time PCR. Phytopathology. Abstract
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Wallace E. C. and Quesada-Ocampo L. M. (2016) Pseudoperonospora cubensis on commercial and non-commercial cucurbits in North Carolina: population structure determine by simple sequence repeats (SSRs). Phytopathology. abstract
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Wessel-Beaver, L. and J. C. V. Rodrigues. 2016. Sources of variation in ELISA tests used to quantify ZYMV and PRSV resistance in Cucurbita moschata. In: Cucurbitaceae 2016, Proceedings of the XIth Eucarpia meeting on genetics and breeding of Cucurbitaceae (E. Kozik and H. Paris, eds)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Wintermantel WM, J.D. McCreight, and E.T. Natwick. 2016. Epidemiology of Cucurbit yellow stunting disorder virus (CYSDV) and associated whitefly-transmitted viruses in the US Southwest and development of CYSDV resistant melon. Paper presentation at 2nd International Whitefly Symposium, February 14-19, Arusha, Tanzania. abstract
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Wintermantel WM, J.D. McCreight, and E.T. Natwick. 2016. Reservoir hosts of Cucurbit yellow stunting disorder virus and development of resistant melon. 13th International Plant Virus Epidemiology Symposium. Avignon, France, June 6-10, 2016. abstract
  • Type: Book Chapters Status: Published Year Published: 2016 Citation: Quesada-Ocampo L. M., Ed, (2016) Disease control for commercial vegetables. North Carolina Agricultural and Chemicals Manual.
  • Type: Book Chapters Status: Published Year Published: 2015 Citation: Kemble J., Quesada-Ocampo L. M., Lewis Ivey M., Jennings K. M., and Walgenbach J. F., Eds. (2015). Southeastern Vegetable Extension Workers. Southeastern US 2015 Vegetable Crop Handbook
  • Type: Other Status: Published Year Published: 2016 Citation: Adams M. L., Noel N. A., and Quesada-Ocampo L. M. (2016) Evaluation of fungicides for control of downy mildew on cucumber, Clayton 2015. Plant Disease Management Report. 10: V084.
  • Type: Other Status: Published Year Published: 2016 Citation: Adams M. L. and Quesada-Ocampo L. M. (2016) Evaluation of fungicides for control of powdery mildew of winter squash, Cleveland 2015. Plant Disease Management Report. 10: V076.
  • Type: Other Status: Published Year Published: 2016 Citation: Adams M. L. and Quesada-Ocampo L. M. (2016) Evaluation of fungicides for control of downy mildew on cucumber, Cleveland 2015. Plant Disease Management Report. 10: V085
  • Type: Other Status: Published Year Published: 2016 Citation: Adams M. L. and Quesada-Ocampo L. M. (2016) Evaluation of fungicides for control of downy mildew on cucumber, Kinston 2015. Plant Disease Management Report. 10: V086
  • Type: Other Status: Published Year Published: 2016 Citation: Quesada-Ocampo L. M. Watermelon downy mildew reported in North Carolina. Extension Plant Pathology Portal. June 17, 2016.
  • Type: Other Status: Published Year Published: 2016 Citation: Quesada-Ocampo L. M. Cucumber downy mildew reported in North Carolina. Extension Plant Pathology Portal. June 1, 2016
  • Type: Other Status: Published Year Published: 2016 Citation: Quesada-Ocampo L. M. Keep an eye out for gummy stem blight in watermelons. Extension Plant Pathology Portal. May 5, 2016
  • Type: Other Status: Published Year Published: 2016 Citation: Lange, H.W., Smart, C.D. and Seaman, A.J. 2016. Evaluation of fungicides allowed for organic production on downy mildew of cucumber, 2015. Plant Disease Management Report. Vol. 10
  • Type: Other Status: Published Year Published: 2016 Citation: Anthracnose of cucurbits: http://content.ces.ncsu.edu/anthracnose-of-cucurbits
  • Type: Other Status: Published Year Published: 2016 Citation: Cucurbit downy mildew: http://content.ces.ncsu.edu/cucurbit-downy-mildew
  • Type: Other Status: Published Year Published: 2016 Citation: Cucurbit powdery mildew: http://content.ces.ncsu.edu/cucurbit-powdery-mildew
  • Type: Other Status: Published Year Published: 2016 Citation: Fusarium wilt of watermelon: http://content.ces.ncsu.edu/fusarium-wilt-of-watermelon
  • Type: Other Status: Published Year Published: 2016 Citation: Hausbeck, M. 2016. Downy mildew spends a decade damaging cucumbers. Vegetable Grower News 50(5):16-17.
  • Type: Other Status: Published Year Published: 2016 Citation: Krasnow, C., Hausbeck, M., Bryant, A., Morrison, W.R. III, Werling, B., Quinn, N., Szendrei, Z., and Buchanan, A. 2015. Diseases and insects in Michigan cucurbits and their management. Michigan State University Extension Bulletin E3276.
  • Type: Other Status: Published Year Published: 2016 Citation: Gummy stem blight of cucurbits: http://content.ces.ncsu.edu/gummy-stem-blight-and-phoma-blight-on-cucurbits
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Cohen, Y., K. M. VandenLangenberg, T. C. Wehner, P. S. Ojiambo, M. Hausbeck, L. M. Quesada-Ocampo, A. Lebeda, H. Sierotzki, and U. Gisi. 2015. Resurgence of Pseudoperonospora cubensis: the causal agent of cucurbit downy mildew. Phytophathology 105: 998-1012.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Ando K, Carr KM, Colle M, Mansfeld BN, Grumet R. 2015. Exocarp properties and transcriptomic analysis of cucumber (Cucumis sativus) fruit expressing resistance to Phytophthora capsici. PloS One 10: e0142133, doi:10.1371/journal.pone.0142133
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Branham, S.E. A. Levi, M.W. Farnham and W.P. Wechter. 2016. A GBS SNP based linkage map and quantitative trait loci (QTL) associated with resistance to Fusarium oxysporum f. sp. Niveum race 2 identified in Citrullus lanatus var. citroides. Theor Appl Genet DOI 10.1007/s00122-016-2813-0
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