Progress 09/01/18 to 08/31/23
Outputs
Target Audience:Our target audience included university researchers, growers, processors, distributors and the supportive agricultural industry including seed companies and those providing products for the control and mitigation of downy mildew and fusarium diseases of sweet basil. Our audience also includes extension specialists and county agents and educators involved in the basil and culinary herb commercial industry and master gardeners and horticulturalists. We also engage, mentor and train undergraduate and graduate students at Rutgers University and the University of Massachusetts in plant breeding and genetics, new crop development and plant pathology. Students were involved in undergraduate research for credit, and were engaged and mentored in lab, greenhouse and field research. Several graduate students were trained in plant biology, plant genetics and breeding and plant pathology and received their Ph.Ds working on this project. Others are still pursuing their advanced degrees on this project. We have communicated our results to a broad audience with stakeholders from commercial growers from New Jersey to Florida and around the country, seed companies, and national fresh produce and culinary herb distributors via trainings, field tours, workshops, national and consortium meetings, state meetings, involving conventional and organic growers, as together we sought to assist in providing solutions to address critical constraints facing basil production. During the course of this project, our outreach efforts have in in-person, as well as using Zoom or Webex (particularly during the covid pandemic). During the summer of 2022 and 2023 we hosted field days. Our science communication plans evolved to include documentation of the research process, engagement with the farming community, and the impact of the discoveries and results through storytelling using digital filmmaking to make the results more available to the public. Changes/Problems:We had been significantly slowed down due to the covid-19 pandemic. Original work was to explore theuse of steam for basil seed treatment to reduce downy mildew contamination but that work was suspended because the subcontractor was not able to procure diseased contaminated seeds to conduct the research during the covid-19 pandemic. Instead, we employed another strategy involving activated plasm to determine if that technology could be applied to clean contaminated basil seeds. What opportunities for training and professional development has the project provided?We mentored 5 Ph.D. graduate students and over 10 undergraduate science students. Students conducted field, greenhouse and lab research. Graduate students presented at professional scientific and industry conferences and meetings. Three Ph.D graduate finished their dissertations during this time period. This program also provided labs and demonstrations to students in plant breeding to demonstrate and teach methods to cross pollinate basil and approaches we use in plant breeding as well as other lab practicums and demonstrations in hydrodistillation, solvent extraction, headspace and GC/MS analysis. Students were trained in plant pathology, culturing fungal colonies, and experimental methods and in genetics, plant breeding, tissue culture and natural products chemistry.Undergraduates and graduate students were also trained and participated in science communication using videos to create science-in-action stories to share with growers, the industry and the public. How have the results been disseminated to communities of interest?Results have been presented at industry grower and trade show meetings in many states, directly to growers in the field during the growing season, and at national and international professional conferences. During the covid pandemic, we continued to present and share our results through remote zoom-based national consortia meetings and regional/state meetings. Over the course of this project, more than 40 presentations and extension workshops and extension articles were prepared and disseminated to communities of interest through publications in scientific journals, proceedings, workshops and grower and horticultural meetings (live and virtual and for organic and conventional growers), websites, articles in popular scientific journals and state agricultural newsletters and more. Some of our annual meetings had over 100 participants. Scientific presentations were given at national, regional, and local conferences. Monitoring of the movement of basil downy mildew was continued to be tracked by Cornell using: https://www.vegetables.cornell.edu/pestmanagement/disease-factsheets/basil-downy-mildew/ (this is a new website set up in 2020 that contains information originally posted at http://vegetablemdonline.ppath.cornell.edu/NewsArticles/BasilDowny.html); and, http://blogs.cornell.edu/livegpath/research/basil-downy-mildew/. Rutgers continued posting information on a Rutgers basil social media presence via an instagram account (@rutgersbasil) which during this project had over 2,500 followers. During the last year of this project, we completed a science-in-action documentary film, Fields of Devotion (see: https://fieldsofdevotion.rutgers.edu/) with a public launch in March, 2023 with over 100 attendees. From our FOD website: "Across America, small family farms are racing against climate change. Unpredictable weather and new diseases are destroying the very crops they depend upon. In New Jersey, when a devastating disease wipes out farmers' fields, growers turn to scientists for help. Fields of Devotion follows the unique relationship between farmers and scientists as they work together over a decade to develop disease and climate resistant food crops. Told from the perspective of the farmers and scientists in the field, Fields of Devotion shares the detailed science steps for developing disease resistant food crops and that farmers need. This is a story of hard work, collaboration and innovative solutions for a rapidly changing world". Since then, Fields of Devotion has been accepted into over a dozen film festivals nationally and internationally and has received many awards (See: https://fieldsofdevotion.rutgers.edu/news/news/) leading to far reaching dissemination of the science to the agricultural/farming community and public. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
Evaluating Available Cultivars to DM and FOB resistance: We evaluated commercially availablecultivars, for disease resistance, aroma and leaf characteristics in different locations. Rutgers DMR lines as well asProspera, and Amazel each exhibited DMR compared to other varieties in both area under the disease incidence progress curve and area under the disease severity progress curve (AUDSPC).Newly released sweet basil cultivarsreported as resistant showed significant DM. Susceptible lines differed in the severity in which sporulation occurred with the newer linesshowing less severe sporulation although all plants had BDM symptoms and sporulation. Field experiments were conductedwith the IR-4 in different locations and states thatevaluated new fungicides (organic and conventional). Use of disease resistant cultivars could reduce the number of total fungicide applications. Use of cold plasma as a sanitation treatment of plants and seeds were evaluated for FOB control. Cold plasma treatment before inoculation with FOB resulted in significantly less stunting.Cold plasma treatment of seed inoculated with FOB at the 1 x 103, (natural contamination rate), resulted in greater decontamination of seed compared to seed inoculated at the 1 x 106rate. A new and improved basil downy mildew map-based monitoring website was developed, maintained and improved withupdates posted onthe Cornell Vegetables webpage and the Basil Downy Mildew AgPestMonitor webpage. GWAS: We acquired 529 accessions from around the world which were thenselfed for genotyping. Three GWAS field studies were conducted in NJ and FL. and evaluated for 17 traits including BDM, blistering, cupping, flower corolla color, flowering time, glossiness, habit, height, inflorescence color, internode length, leaf anthocyanin intensity, leaf anthocyanin distribution, leaf greenness, leaf length, leaf width, leaf serration and stem color. We identified that 9.95% of our accessions were resistant to BDM and 3.62% were tolerant. Resistant accessions came from the following species:Ocimum americanumL. var.pilosum,O. americanum L. var. americanum,O. gratissimum L.and multiple subspecies,O. tenuiflorum L., Ocimum x africanum,O. viride, andO. labiatum. Tolerant accessions belonged to the following species:O. x citriodorum, O. basilicum L. var. purpurascens,O. basilicum L. var. basilicum,O. forskolei andO. americanum L. var. americanum. As new sources of resistance to BDM were identified, new improved DMR sweet basil varieties Obsession and Devotion were also over this project period being bred and evaluated to also enhance other traits. FOB Basil Breeding: Initial Cross: A highly resistant FOB basil was identified, selfed and crossed with SB17and then backcrossed for 5 generations; selfed for four generations. Final FOB inbred lines were completed and are now ready to be used incombinational breeding to stack these genes into sweet basil downy mildew resistant and chilling tolerant cultivars. Highthroughput UAV Phenotyping: The maiden dronevoyage of ourDJI Matrice 200 v2 UAV occurred in2021.Flightslasted for ca.15 minutes, taking up to 330 high resolution pictures. Initial data quality checks indicate high quality data with resolution up to .6in2/pixel. This approach appears promising forthe identification and phenotyping of basil diseases and traits such as anthocyanin content. On the ground, manual phenotyping of traits was conducted. Developing a nation-wide Screening of a Panel of Basils to Determine if there are Multiple Virulence types of DM in the USA: Growers and researchers began to observedifferential responses from new disease resistant and purported DM immune basils. We hypothesized that when sweet basils with known response to the BDM show vastly differential response to the ambient BDM, new DM races or virulence in the BDM may be the cause. We developed a panel screening of a known set of sweet basil varieties in a uniform manner and with a uniform scoring system to be used by growers and researchers to inform us as to whether we have more than one virulence type of BDM. This panel is available to other researchers. Basil resistance toP. belbahriiinfection: PCR amplification from the resulting genomic DNA showed that the top basil candidate gene for resistance toP. belbahariiinfection,a member of the nucleotide-binding leucine-rich repeat (NB-LRR) family denoted comp160460c0, was found in the resistant ornamental basil cultivar Mrihani but not in the susceptible Sweet Basil cultivar SB22. As no microsatellite markers existed forP. belbahriiour team identified transcriptome data for this pathogen on NCBI and using the program BatchPrimer3 (Tm = 60) identified ~255 putative microsatellites. From these ~255, 54 were chosen at random to evaluate for amplification and specificity to BDM. Currently only 24 have been evaluated.Our consortium has continued to collect and isolate BDM sporangia to build a large collection of isolates (n=234). P. belbahriisecreted effectors: In 2020 theP. belbahriigenome as well as transcriptomics data was published (Thines,et al.MPMI 33:742-753). Guided by that research, along with UMass researchers own sporangia transcriptomics data, work was conducted to identify polymorphisms in the genome and to separate haplotypes. Comparative transcriptomics betweensusceptibleand resistantbasil suggest that during infection the degree of heterozygosity for secreted effectors may be different than that observed in the sporangia transcriptomics. Basil Genomics: A major accomplishment of this project was to annotate the first pseudo-chromosome level genome for sweet basil. Genotyping-by-sequencing was first used on sweet basil only in 2015 and, breeding efforts have largely remained more traditional since genomic resources have been limited. In order to facilitate bringing basil into the modern genomic age a 2.26 Gbp chromosome-level genome assembly was generated for the sweet basil 'RUSB22' genome by Rutgers in concert with NRGene in 2019 that accounts for 75% of scaffolds. Twenty-six chromosomes were identified which contradicts the expected number of chromosomes in the basil karyotype (n=24). However, multiple published and unpublished linkage maps have identified 26 linkage groups suggesting some ambiguity within the basil genome. An initial genome annotation was completed chromosome-by-chromosome using the MAKER pipeline, a previously published O. basilicum trinity transcriptome, an Arabidopsis thaliana proteome and a Thymus vulgaris proteome. The initial annotation was then used to train SNAP, an ab initio gene prediction program software (AED > 0.25) and selecting for gene models with a length of >50 amino acids. A total of three iterative rounds of ab initio gene model prediction was completed using SNAP and the final genome annotation resulted in 47,649 number of genes on the pseudo-chromosomes proper and 9,956 on chr99, which holds the unplaced scaffolds. Functional annotation of these genes were accomplished using GOFeat and PANNZER2 to identify gene ontology while PlantiSMASH was used to identify 82 CD-clusters for secondary metabolites with eighteen of these related to terpene synthesis. The protein annotations identified for 'RUSB22' were used along with 82 other plant proteomes in the OrthoFinder pipeline to identify orthogroups and create a rooted species tree. All three Ocimum spp. accessions grouped together providing support for this annotation.?
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Seidel, D.K., X. Morin, M. Staffen, R.D. Ludescher, J.E Simon and O. Schofield. Building a Collaborative, University Based Science-in-Action Video Storytelling Model that Translates Science for Public Engagement and Increases Scientists Relatability. Frontiers in Communication-Science and Environmental Comm. 7:1049648. doi: 10.3389/fcomm.2022.1049648
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Homa, K., Barney, W.P., C.A. Wyenandt, D.L. Ward and J.E. Simon. Range of susceptibility of selected sweet basil cultivars and lines to Fusarium oxysporum f. sp. basilici. Plant Health Progress: Published Online:25 May 2022https://doi.org/10.1094/PHP-05-21-0079-RS
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Zhang, X., Y.C. Low, M.A. Lawton, J.E. Simon and R. Di. CRISPR-editing of sweet basil (Ocimum basilicum L.) homoserine kinase gene for improved downy mildew disease resistance. Front. Genome Ed. 3:629769. doi: 10.3389/fgeed.2021.629769.
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
McGrath, M. T. and Downing, C. T. Evaluation of organic and IPM conventional fungicide programs for downy mildew in a resistant sweet basil cultivar, 2022. Plant Disease Management Reports 17:V057.
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
McGrath, M. T. and Downing, C. T. Evaluation of commercial and experimental cultivars of sweet basil resistant to downy mildew, 2022. Plant Disease Management Reports 17:V056.
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
McGrath, M. T. 2023. Efficacy of organic fungicides for downy mildew in field-grown sweet basil. Plant Disease 107:(Feb 2023 published as First Look article). https://doi.org/10.1094/PDIS-10-22-2424-RE
- Type:
Other
Status:
Published
Year Published:
2020
Citation:
Mattera III R, Brindisi L, McGrath M, Allen K, Homa K, Ma LJ, Wick R, Ben-Naim Y, Cohen Y, Raid RN, Hartman A, Wyenandt CA and Simon JE (2020). Nation-wide Screening of a Panel of Basils to Determine if there are Multiple Virulence types of Peronospora belbahrii in the USA (2020).
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
McGrath, M. T. and Downing, C. T. 2022. Evaluation of biopesticides for organic management of downy mildew in sweet basil, 2021. Plant Disease Management Reports 16:V093
|
Progress 09/01/21 to 08/31/22
Outputs
Target Audience:As our project involves the genetic and management improvement of sweet basil against downy mildew and fusarium diseases, our target audience includes university researchers, growers, processors, distributors and the supportive agricultural industry including seed companies and those providing products for the control and mitigation of these diseases. Our audience also includes extension specialists and agents involved in the basil and culinary herb commercial industry and master gardeners and horticulturalists. From the university perspective, we also engage, mentor and train undergraduate and graduate students at Rutgers University and the University of Massachusetts in plant breeding and genetics, new crop development and plant pathology. Students are involved in undergraduate research credits, for undergraduate honors theses and for hands-on practical experiential trainings. We have several graduate students being trained in plant biology, plant genetics and breeding and plant pathology whom are pursuing their advanced degrees working on this project. We have communicated our results to a broad audience with stakeholders from commercial growers from New Jersey to Florida and around the country, seed companies, and national fresh produce and culinary herb distributors as together we seek to solve critical constraints facing basil production. During this year, while operating under the Covid-19 pandemic, most of our outreach efforts have been held remotely using Zoom or Webex. During the summer of 2022were held field days. We continued to realign our plans to communicate and share our results to communicate our findings and science through storytelling using digital filmmaking and virtual workshops and conferences to accommodate those interested. Changes/Problems:No problems except slower progress due to covid19 pandemic related issues. However, in our work to develop a high throughput UAV/ phenotyping, we found technical issues with our done and breakdown of motherboard has resulted in loss of collection capability for the summer of 2022. What opportunities for training and professional development has the project provided?We mentored 5 Ph.D. graduate students and over 10 undergraduate science students. Students conducted field, greenhouse and lab research. Graduate students presented at professional scientific and industry conferences and meetings. One Ph.D graduate finished their dissertation during this time period. This program also provided labs and demonstrations to studentsin plant breeding to demonstrate and teach methods to cross pollinate basil and approaches we use in plant breeding as well as other lab practicums and demonstrations in hydrodistillation, solvent extraction, headspace and GC/MS analysis. Students were trained in plant pathology,culturing fungal colonies, and experimental methods How have the results been disseminated to communities of interest?Results have been presented at industry grower and trade show meetings in many states, directly to growers in the field during the growing season, and at national and international professional conferences. More than 10 presentations and extension workshops and extension articles were prepared and disseminated to communities of interest through publications in scientific journals, proceedings, workshops and grower and horticultural meetings (live and virtual and for organic and conventional growers), websites, articles in popular scientific journals and state agricultural newsletters and more. Researchers from our consortium and invited experts came together virtually, with our annual meeting hosted by Rutgers in December, 2021, for a full day meeting open to the public conducted via zoom in which over 120 participated. Scientific presentations were given at national, regional, and local conferences. Monitoring of the movement of basil downy mildew was continued to be tracked by Cornell using: https://www.vegetables.cornell.edu/pestmanagement/disease-factsheets/basil-downy-mildew/ (this is a new website set up in 2020 that contains information originally posted at http://vegetablemdonline.ppath.cornell.edu/NewsArticles/BasilDowny.html); and, http://blogs.cornell.edu/livegpath/research/basil-downy-mildew/. Rutgers continued posting information on aRutgers basil social media presence via an instagram account (@rutgersbasil) now with 2,653 followers. What do you plan to do during the next reporting period to accomplish the goals?We will continue to pursue the goals as originally stated in the project proposal and initiation. Specifically, Working on the genetics and completing the annotation of the genomic sequence of sweet basil; Work toward developing higher resolution linkage maps and aligning published transcriptomes to identify genetic markers associated with DM and FOB resistance and basil aroma volatiles; Develop gene-based SNP arrays for practical use in basil breeding; Continue a GWAS study phenotyping >300 basils; Complete the analysis of our RILS and phenotyping the basils in the GWAS; Work toward achieving two generations of gene stacking with our newly created FOB resistant sweet basil into our DMR sweet basils; Continued testing and evaluation of best management practices; Develop and examine new organic and conventional fungicides and programs with combinations of products and determine whether fungicide applications can be reduced with DMR basils; Continue and expand our basil DM monitoring online program; Focus on genetic identify and traditional panels for identification of new races; Validating putative R-genes, identifying pathogen effectors and developing PCR based molecular marker to aid in MAS. One of the greatest challenges is to understand whether we are witnessing new races or different responses to the same race of BDM and FOB. We hypothesize that sweet basils with known response to the BDM now show vastly differential response to the ambient BDM. We were not able to conduct in 2022 a panel screening of a known set of sweet basil varieties in a uniform manner and with a uniform scoring system will detect whether we have more than one virulence type of BDM. We hope to next growing season.
Impacts
What was accomplished under these goals?
Objective 1) Field studies were conducted in Florida and New York building upon results from previous experiments. One goal is to determine if downy mildew can be effectively managed with an organic fungicide program applied on a preventive schedule to a DMR basil variety (Rutgers Passion DMR). This integrated management approach was used because several past experiments demonstrated that BDM cannot be effectively managed with organic fungicides applied to a susceptible variety or a DMR variety with low level of resistance (Eleonora). The organic fungicide program is Regalia (extract of giant knotweed) plus Stargus (Bacillus amyloliquefaciens) applied in alternation with EcoSwing (extract ofSwinglea glutinosa) plus Badge X2 (copper). The second goal is to determine if downy mildew can be effectively managed with a conventional fungicide program applied on an IPM schedule (started after symptoms found) to Rutgers Passion DMR. Past experiments have demonstrated that effective control of downy mildew on a susceptible variety necessitates applying fungicides on a preventive schedule. The conventional fungicide program is Orondis Ultra applied in alternation with Ranman plus K-Phite and with Presidio plus K-Phite (3 way alternation). Developing an online map-based DM monitoring system to provide growers important information on seasonal DM epidemics which will allow them to better time fungicide application dates; The new basil downy mildew map-based monitoring website developed during Year 2 was maintained and improved. Main activity in maintaining the website is verifying reports from people not on the Expert list for reporting. Objective 2) Identifying genetic diversity in P. belbahrii and F. oxysporum f. sp. basilici across the US to help identify the population structure of each pathogen; we hypothesize that there may be variability in each population which would potentially lead to new race development in each pathogen; Due to complications with COVID-19 resulting in limited access to lab facilities a lot of the planned work with GBS and genetic diversity analysis of P. belbahrii and FOB has stalled. Collections of DM have continued as we continue to grow our collection but protocols for DNA extraction and GBS have not been completed although this work is beginning again. A GWAS study was successful - conducted in southern New Jersey with over 300 basils allowing us to continue our phenotyping and this builds upon two prior ones we conducted in other locations. To validateputative R-genes, identifying pathogen effectors and developing PCR-based molecular marker to aid in MAS comparative transcriptomics was performed to identify candidate resistance genes and potential mechanisms for BDM resistance; RNA samples from BDM- infected MRI and SB22 plants were harvested at 4 time points during the first 3 days of infection to differentiate interactions in resistant and susceptible plants. Three categories of genes uniquely induced in resistant MRI upon pathogen challenge were identified: nucleotide-binding leucine rich repeat proteins (NLRs), multi-functional receptor-like kinases (RLKs), and secondary metabolic enzymes; validation of the top resistance candidate NLR gene confirmed its unique presence in MRI as well as in two of four resistant MRIxSB22 F2 progeny. In MRI, pathogen challenge also upregulated transcripts in the salicylic acid synthesis pathway, suggesting its role in BDM resistance, and demonstrating the application of using comparative transcriptomics to identify resistance genes and mechanisms in non-model crops for marker-assisted breeding approaches. We made progress in developing higher resolution linkage maps and aligning published transcriptomes to identify genetic markers associated with DM and FOB resistance and basil aroma volatiles. These maps should provide strong QTL and eQTL for DM/FOB resistance and aroma volatiles allowing the development of gene-based SNP arrays for practical use in basil breeding. We also made significant progress in the O. basilicum Genome Sequence project.Annotation of the SB22 genome has begun following the MAKER pipeline. The genome was repeat masked to eliminate repetitive regions from being annotated. MAKER allows for multiple iterations of gene modelling using ab initio predictors. The SNAP gene prediction program was used to train the gene models (AED > 0.25). Only gene models with a length of >50 amino acids were used to avoid junk gene models. An approximate number of 57896 genes were identified throughout the genome with Chromosome 1 having approximately 2860 genes. As of date of submission about 33343 have been found to have Gene Ontology with at least one other gene in multiple databases (NCBI, uniprot, nterPro, KEGG, Pfam, and SEED). QTL associated to DMR were found on chromosome 2 but further annotation and exploration is needed to identify the gene controlling resistance.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Zhang, X., Y.C. Low, M.A. Lawton, J.E. Simon and R. Di. 2021. CRISPR-editing of sweet basil (Ocimum basilicum L.) homoserine kinase gene for improved downy mildew disease resistance. Front. Genome Ed. 3:629769. doi: 10.3389/fgeed.2021.629769
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2021
Citation:
Gaur A, Brindisi L, Barret A, Mattera R and Simon JE. (2021, August). Phenotypic Traits of Basil. Poster presentation at the Project SUPER Research Symposium, New Brunswick, Virtual.
- Type:
Theses/Dissertations
Status:
Published
Year Published:
2022
Citation:
Allen, Kelly S. â¿¿Investigation of basil downy mildew pathogen survival, new pathotype development and sources of quantitative disease resistanceâ¿. Doctoral dissertation. PhD awarded September 2022.
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
McGrath, M. T. and Downing, C. T. 2022. Evaluation of an experimental and commercial cultivars of sweet basil resistant to downy mildew, 2021. Plant Disease Management Reports 16:V092.
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
McGrath, M. T. and Downing, C. T. 2022. Evaluation of conventional fungicides for downy mildew in sweet basil, 2021. Plant Disease Management Reports 16:V094.
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Patel, J.S., Wyenandt, C.A. and McGrath, M.T., 2021. Effective downy mildew management in basil using resistant varieties, environment modifications, and fungicides. Plant Health Progress, 22(3), pp.226-234.
- Type:
Journal Articles
Status:
Submitted
Year Published:
2022
Citation:
Allen, Kelly S., Gregory A. DeIulio, Robert Pyne, Jacob Maman, Li Guo, Robert L. Wick, James Simon, Anne Gershenson, and Li-Jun Ma.2022 â¿¿Identification of novel basil downy mildew resistance genes using de novo comparative transcriptomicsâ¿. BioRxiv, 2022.05.23.491563.
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Homa, K., Barney, W.P., C.A. Wyenandt, D.L. Ward and J.E. Simon. 2022 Range of susceptibility of selected sweet basil cultivars and lines to Fusarium oxysporum f. sp. basilici. Plant Health Progress: Published Online:25 May 2022 https://doi.org/10.1094/PHP-05-21-0079-RS
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2022
Citation:
Mattera, R, Simon, JE (January 2022). Annotating the Pseudo-Chromosome Level Genome Assembly of Ocimum basilicum â¿¿SB22â¿¿ with the MAKER pipeline. Poster presented at Plant and Animal Genome Conference 29, San Diego, CA.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2021
Citation:
Jarral M, Brindisi L, Barret A, Mattera R and Simon JE. (2021, September). Breeding Basil for commercially and botanically favored traits. Poster presentation at the Project SUPER poster symposium, Virtual.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2022
Citation:
Sullivan, Sean, Kelly S. Allen, Ma LJ (May 2022). â¿¿iCons: Understanding Emerging Races of Basil Downy Mildew (Peronospora belbahrii)â¿. Poster session presented atâ¿UMass Integrated Concentration in Science (iCons) Senior Exposition & Celebration, Amherst, MA.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2022
Citation:
Allen, Kelly S., Gregory A. DeIulio, Robert Pyne, Jacob Maman, Li Guo, Robert L. Wick, James Simon, Anne Gershenson, and Li-Jun Ma (August 2022). â¿¿Investigation of basil downy mildew quantitative disease resistance and identification of new Peronospora belbahrii pathotypesâ¿. Poster session presented at: APS Plant Health 2022, Pittsburgh,Pennsylvania
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2022
Citation:
Allen, Kelly S. and Li-Jun Ma (August 2022). â¿¿Basil Downy Mildew: Resistance is NOT futile!â¿. Presentation given at the 2022 UMass Crop and Animal Research Tour & Field Day
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Martÿnez-Soto D, Yu H, Allen KS, Ma LJ. Differential colonization of the plant vasculature between endophytic versus pathogenic Fusarium oxysporum strains. Mol Plant Microbe Interact. 2022 Oct 24. doi: 10.1094/MPMI-08-22-0166-SC. Epub ahead of print. PMID: 36279112.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2022
Citation:
Brindisi L, Mattera R, Barrett A, Styles T, Amer I, Karunaratne K, Dager E, Bombardiere J, Wyenandt CA, Homa K, Barney WP, Oâ¿¿Brien R, Tepper B, Di R, Lawton M and Simon JE. (2022, January). Updates on basil research in developing disease resistance and improved new varieties. Oral talk at the NJ Agricultural Convention & Trade Show, Atlantic City, New Jersey.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2021
Citation:
Brindisi L, Oâ¿¿Brien R, Lyu W, Tepper B and Simon JE. (2021, November). Relationship between descriptive sensory and chemical profiles of basil (Ocimum basilicum L.). Invited oral talk for the Department of Architecture and Environmental Design at Temple University, Philadelphia, Pennsylvania.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2021
Citation:
Brindisi L, Oâ¿¿Brien R, Lyu W, Tepper B and Simon JE. (2021, August). Breeding Sweet Basil for Taste, Flavor and Aroma. Oral talk at the Annual Meeting of American Society for Horticultural Science, Denver, Colorado.
- Type:
Websites
Status:
Published
Year Published:
2022
Citation:
Up-dated content about BDM and its management plus research results at two websites:
https://www.vegetables.cornell.edu/pest-management/disease-factsheets/basil-downy-mildew/ (this is a new website set up in 2020 that contains information originally posted at http://vegetablemdonline.ppath.cornell.edu/NewsArticles/BasilDowny.html)
http://blogs.cornell.edu/livegpath/research/basil-downy-mildew/
Posted news updates at the Cornell Vegetables webpage and the Basil Downy Mildew AgPestMonitor webpage.
- Type:
Other
Status:
Published
Year Published:
2022
Citation:
Rutgers basil social media presence: Instagram account (@rutgersbasil) with 2,653 followers
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Mattera III, Robert, Lara Brindisi, Robert Pyne, Yariv Ben Naim, Yigal Cohen, C. Andrew Wyenandt and James Simon. 2022 The history of breeding for basil downy mildew resistance in sweet basil (Ocimum basilicum). Invited presentation at: All-Africa Summit on Diversifying Food Systems with African Traditional Vegetables to Increase Health, Nutrition, and Wealth. J. Medicinally Active Plants (11):3:13. Conference held Arusha, Tanzania, January 25-28, 2021. https://scholarworks.umass.edu/jmap/vol11/iss3/1
|
Progress 09/01/20 to 08/31/21
Outputs
Target Audience:As our project involves the genetic and management improvement of sweet basil against downy mildew and fusarium diseases, our target audience includes university researchers, growers, processors, distributors and the supportive agricultural industry including seed companies and those providing products for the control and mitigation of these diseases. Our audience also includes extension specialists and agents involved in the basil and culinary herb commercial industry and master gardeners and horticulturalists. From the university perspective, we also engage, mentor and train undergraduate and graduate students at Rutgers University and the University of Massachusetts in plant breeding and genetics, new crop development and plant pathology. Students are involved inundergraduate research credits, for undergraduate honors theses and for hands-on practical experiential trainings. We have several graduate students being trained in plant biology, plant genetics and breeding and plant pathology whom are pursuing their advanced degrees working on this project. We have communicated our results to a broad audience with stakeholders from commercial growers from New Jersey to Florida and around the country, seed companies, and national fresh produce and culinary herb distributors as together we seek to solvecritical constraints facingbasil production. During this year, while operating under the Covid-19 pandemic, most of our outreach efforts have been held remotely using Zoom or Webex and only during the summer of 2021 were we able to begin holding traditional field tours and meetings while maintaining social distancing and our repsective university guidelines for meetings. This program is heavily oriented to meeting market and consumer demand by evaulating all available germplasm and new varieties with downy mildew and/or fusarium wilt resistnace and to communicate improved control and IPM strategies to growers to mitigate the impact of these diseases impacting this crop. Due to the pandemic that began in 2020, we continue to realigned our plans to communicate and share our results to communicate our findings and science through storytelling using digital filmmaking and virtual workshops and conferences to accommodate those interested. Changes/Problems:COVID-19 restrictions on in-person gatherings resulted in the cancellation of the Rutgers Annual Basil Taste Test again in 2021. Furthermore COVID-19 restrictions prevented the ability to further train basil taste panels. Work toward identifying the compounds associated with taste and flavor are underway but slowed down due in part to pandemic early in the year. In Florida, atotal of ten field trials were planted for basil downy mildew fungicide testing during this period. Due to primarily environmental reasons, none of these were fruitful. Four trials planted at the Everglades Research and Education Center (EREC) during October 2020 were flooded out due to repeated excessive rainfalls during the month of November. Two trials replanted during December had to be terminated due to a fatal frost during January 2021, and four trials conducted at C & B Farms during fall 2020 were terminated by the cooperator because of the unanticipated threat to commercial production. To make up for these set backs, we turned to basil trials conducted in large concrete planters, and comparable trials conducted against a related downy mildew, Hyaloperonospora parasitica, on baby leaf kale. Past experience has shown that this downy mildew responds to fungicides in a manner similar to Peronospora belbahrii. We have not been able to evaluatenew steam seed treatment methods for reducing DM seed infestation and as such shifted to explore the potential of cold plasma in reducing disease on basil seeds. We also have not yet been able to develop a rapid molecular assay for pathogen viability on seed, thus decreasing disease outbreaks. What opportunities for training and professional development has the project provided?This project has provided training and professional development for two PhD students at UMASS; fivePhD students at Rutgers and more than 10 undergraduatestudents at Rutgers, UFand UMass. This project has involved Rutgers PhD students Robert Mattera, Alex Barrettand Lara Brindisi (DMR plant breeding and genetics), Kathryn Homa (fusarium wilt breeding and genetics and new technologies to disinfect seeds from fusarium), Ariane Vasilatis (plant biology and aroma chemistry) and UMass PhD students, Kelly S. Allen (genetics of the DM pathogen) and Jacob Maman (genetics of the fusarium pathogen). Homa and Vasilaites each successully defended their dissertation projects in 2021 receivingtheir doctoral degrees. Lab, greenhouse and field research opportunities were re-opened with relaxation of the prior covid restrictions allowing undergraduates to be involved. This program also provided labs and demonstrations to students at Rutgers in plant breeding to demonstrate and teach methods to cross pollinate basil and approaches we use in plant breeding as well as other lab practicums and demonstrations in hydrodistillation, solvent extraction, headspace and GC/MS analysis. The pandemic continued to impact negatively progress andreduced the access and ability to do as many trainings as would have occurred. How have the results been disseminated to communities of interest?More than 30 presentations and extension workshops and extension articles were prepared and disseminated to communities of interest through publications in scientific journals, proceedings, workshops and grower and horticultural meetings (live and virtual and for organic and conventional growers), websites, articles in popular scientific journals and state agricultural newsletters and more. Researchers from our consortium and invited experts came together virtually, with our annual meeting hosted by UMass in December, 2020, for a full 2-day meeting open to the public conducted via zoom in which over 100 participated.Scientific presentations were given at national, regional, and local conferences. Monitoring of the movement of basil downy mildew was continued to be tracked with the lead of Cornell using: https://www.vegetables.cornell.edu/pest-management/disease-factsheets/basil-downy-mildew/ (this is a new website set up in 2020 that contains information originally posted at http://vegetablemdonline.ppath.cornell.edu/NewsArticles/BasilDowny.html); and,http://blogs.cornell.edu/livegpath/research/basil-downy-mildew/. News updates were posted online and electronically to growers and the industry largely using the Cornell Vegetables webpage and the Basil Downy Mildew AgPestMonitor webpage and the NJ Rutgers Pest Advisory Newsletter. During this year and due to the pandemic, additional planned field tours and grower meetings were postponed and we hope to restart such activities when its safe. What do you plan to do during the next reporting period to accomplish the goals?We will continue to pursue the goals as originally stated in the project proposal and initiation. Specifically,(i) working on the genetics and completing the annotation of the genomic sequence of sweet basil; (ii) work toward developing higher resolution linkage maps and aligning published transcriptomes to identify genetic markers associated with DM and FOB resistance and basil aroma volatiles; (iii) develop gene-based SNP arrays for practical use in basil breeding; (iv) continuea GWAS studyphenotyping >300 basils; (v) complete the analysis of our RILS and phenotyping the basils in the GWAS; (vi) work toward achiecing two generations of gene stacking with our newly created FOB resistant sweet basil into our DMR sweet basils; (v) continued testing and evaluation of best management practices; (vi) develop and examine new organic and conventional fungicides and programs with combinations of products and determine whether fungicide applications can be reduced with DMR basils; (vii) continue and expand our basil DM monitoring online program; (viii) focus on genetic identify and traditional panels for identification of new races; (ix) validating putative R-genes, identifying pathogen effectors and developing PCRbased molecular marker to aid in MAS. One of the greatest challenges we are facing is to test, screen and collectively gather data as to whether we are witnessing new races or different responses to the same race of BDM and FOB. We hypothesize that sweet basils with known response to the BDM now ashow vastly differential response to the ambient BDM.Using a panel screening of a known set of sweet basil varieties in a uniform manner and with a uniform scoring system will detect whether we have more than one virulence type of BDM.
Impacts
What was accomplished under these goals?
Obj 1) Field studies in NY and NJ evaluated the current state of resistance of DMR sweet basils. We observed very high and early disease pressure and that resistance is beginning to breaking down in many DMR resistant varieties. Results confirm the concurrent need for breeding to identify additional resistance genes, determine if and how the pathogen has changed, all making IPM management strategies even more critical. A basil downy mildew residue and efficacy study was initiated in 2021 at IR-4 for fluoxapiprolin; study; and at IR-4, PR 12633 picarbutrazox / basil (GLP residue and efficacy studies continued. Range of organic control products were again evaluated. Results show a lack of effective control. Steam seed treatments appear not to be of strong commercial interest, so our attention shifted to exploring alternative novel technologies such as cold plasma treatments againt fusarium wilt. Results indicate potential but far greater research is needed. Cold plasma treatment before inoculation with FOB resulted in significantly less stunting and numerically lower AUDPC values suggesting a plant growth or defense response; damage was observed as wilting and browning of plant tissue upon contact with the cold plasma jet. Obj 2) We initiated our first GWAS study with 433 basil assessions from Ocimum americanum L. var. pilosum, O. americanum L. var. americanum, O. gratissimum L.and multiple subspecies, O. tenuiflorum L. Ocimum x africanum, O. viride, and O. labiatum. Tolerant accessions belonged to the following species: Ocimum x citriodorum Vis., O. basilicum L. var. purpurascens Benth., O. basilicum L. var. basilicum, O. forskolei Benth. and O. americanum L. var. americanum. Manual phenotyping of traits were recored and highthroughput UAV Phenotyping accomplished with drone voyage of our DJI Matrice 200 v2 UAV. Based on a metatranscriptomics study, a candidate resistant gene was identified which is predicted to encode a nucleotide-binding leucine-rich repeat (NB-LRR) protein. The NB-LRR protein family contains the majority of disease resistance proteins, which are involved in recognizing specific microbial effectors and conferring resistance. We cloned and sequenced the PCR products amplified from the DMR parents genomic DNA. Sequencing results identified four recognizable alleles. In parallel, progress in annotating the sweet basil SB22 genome has begun following the WQ-MAKER pipeline. The genome was repeat masked to eliminate repetitive regions from being annotated. MAKER allows for multiple iterations of gene modelling and upon the first pass of AUGUSTUS and SNAP training chromosome 1 was found to have approximately 2860 genes Significant progress was made in developing new sources and improved breeding lines for FOB. Cytology and flow cytometry studies conducted to determining if meiosis was proceeding normally and results help explain altered segregation patterns during breeding process. A final series of 7 advanced FOB lines have been selected and several will now be used for breeding int our DMR sweet basils for gene stacking for multiple disease resistance.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Patel, J.S., Wyenandt, C.A., and M.T. Mcgrath. 2021. Effective downy mildew management in basil using resistant varieties, environmental modifications and fungicides. Plant Health Progress. https://doi.org/10.1094/PHP-02-21-0041-FI
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Patel, M., Lee, R., Merchant, E.V., Juliani, H.R., Simon, J.E., and B.J. Tepper (2021). Descriptive aroma profiles of fresh sweet basil cultivars (Ocimum spp.): Relationship to volatile chemical composition. J. Food Science 1-12.https://doi.org/10.1111/1750-3841.15797
- Type:
Other
Status:
Published
Year Published:
2021
Citation:
Raid, R. N., L. Rodrigues, E. Cooper; P. Watanabe; A. Hartman; G. Sandoya. 2021.Evaluation of various rates of potassium phosphite for management of downy mildew on baby leaf kale, 2021. APS Press, Plant Disease Management Reports 15: V118.
- Type:
Other
Status:
Other
Year Published:
2021
Citation:
Raid, R. N., L. Rodrigues, E. Cooper; P. Watanabe; A. Hartman; G. Sandoya. 2021. Evaluation of systemic acquired resistance inducers for management of downy mildew on baby leaf kale, 2021. APS Press, Plant Disease Management Reports 15: V119.
- Type:
Other
Status:
Published
Year Published:
2021
Citation:
Raid, R. N., L. Rodrigues, E. Cooper; P. Watanabe; A. Hartman; G. Sandoya. 2021. A comparison of single or double applications of three different fungicides for management of downy mildew on baby leaf kale, 2021. APS Press, Plant Disease Management Reports 15: V120.
- Type:
Other
Status:
Published
Year Published:
2021
Citation:
Raid, R. N., L. Rodrigues, E. Cooper; P. Watanabe; A. Hartman; G. Sandoya. 2021. A comparison of single applications of oxathiapiprolin and fluoxapiprolin at three different rates for management of downy mildew on baby leaf kale, 2021. APS Press, Plant Disease Management Reports 15: V121.
- Type:
Other
Status:
Published
Year Published:
2021
Citation:
Raid, R. N., L. Rodrigues, E. Cooper; P. Watanabe; A. Hartman; G. Sandoya. 2021. Evaluation of assorted fungicides for management of downy mildew on baby leaf kale, 2021. APS Press, Plant Disease Management Reports 15: V122
- Type:
Theses/Dissertations
Status:
Awaiting Publication
Year Published:
2021
Citation:
Homa, K. Breeding Ocimum basilicum for Resistance to Fusarium oxysporum f. sp. basilici and Alternative Control Strategies (2021). Rutgers, The State University of New Jersey. Ph.D. Dissertation, Sept. 2021. 298 pp.
- Type:
Websites
Status:
Published
Year Published:
2020
Citation:
2020. Simon, J., A. Wyenandt, R. Raid, M. McGrath and K. Homa. A plant breeding breakthrough: downy mildew resistant sweet basil. American Vegetable Grower, June, 2020: Online: https://www.growingproduce.com/vegetables/a-breeding-breakthrough-downy-mildew-resistant-sweet-basil/
- Type:
Websites
Status:
Published
Year Published:
2020
Citation:
2020. Wyenandt, A., K. Homa and J.E. Simon. Options for controlling basil downy mildew in the field. Plant Pest Advisory Board, Feb 01, 2020: https://plant-pest-advisory.rutgers.edu/options-for-controlling-basil-downy-mildew-in-the-field/
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Brindisi, L. C.A. Wyenandt, V. Arora, D. Kenigsbuch, N. Dudai, I. Gonda and J.E. Simon (2021). A rapid screening approach to identify chilling tolerant sweet basil (Ocimum basilicum L.). J Medicinally Active Plants 1177:1-10.
- Type:
Journal Articles
Status:
Under Review
Year Published:
2021
Citation:
Homa, K., Barney, W. P., Wyenandt, C. A., Ward, D. L., Simon, J. E. (Submitted for review) Range of Susceptibility of Sweet Basil Cultivars and Lines to Fusarium oxysporum f. sp. basilici. Plant Health Progress
- Type:
Other
Status:
Published
Year Published:
2020
Citation:
Wyenandt, C.A., and J.E. Simon. 2020. Evaluation of biopesticide and conventional fungicides for management of downy mildew in sweet basil, 2019. Plant Disease Management Reports. No. 14:V175
- Type:
Other
Status:
Published
Year Published:
2021
Citation:
McGrath, M. T. and Downing, C. T. 2021. Evaluation of commercial cultivars of sweet basil resistant to downy mildew, 2020. Plant Disease Management Reports 15:V069.
- Type:
Other
Status:
Published
Year Published:
2021
Citation:
McGrath, M. T. and Downing, C. T. 2021. Evaluation of conventional and organic biopesticides applied with organic coppers for downy mildew in sweet basil, 2020. Plant Disease Management Reports 15:V077.
- Type:
Websites
Status:
Published
Year Published:
2020
Citation:
2020. Wyenandt, A. and J.E. Simon. Controlling basil downy mildew in the greenhouse. Plant Pest Advisory Board, January 22, 2020: https://plant-pest-advisory.rutgers.edu/controlling-basil-downy-mildew-in-the-greenhouse/
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2021
Citation:
Cooper, E., Watanabe, P., and Raid, R. N. 2021. Evaluation of various rates of potassium phosphite for management of downy mildew on baby leaf kale. American Society of Plant Biologist (ASPB) Southern Regional Annual Conference. (Virtual on April 18, 2021).
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2021
Citation:
Gaur A, Brindisi L, Barret A, Mattera R and Simon JE. (2021, August). Phenotypic Traits of Basil. Poster presentation at the Project SUPER Research Symposium, New Brunswick, New Jersey.
- Type:
Websites
Status:
Published
Year Published:
2020
Citation:
2020. Wyenandt, A. and J.E. Simon. Rutgers downy mildew resistant sweet basils available around the world; Research efforts continue. Rutgers Cooperative Extension Service. Plant Pest Advisory Board, January 12,2020: https://plant-pest-advisory.rutgers.edu/an-introduction-to-rutgers-downy-mildew-resistant-sweet-basils-2/
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2021
Citation:
Jarral M, Brindisi L, Barret A, Mattera R and Simon JE. (2021, September). Breeding Basil for commercially and botanically favored traits. Poster presentation at the Project Super poster symposium, New Brunswick, New Jersey
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2021
Citation:
Watanabe, P. , Cooper, E., and Raid, R. N. 2021. Evaluation of Systemic Acquired Resistance (SAR) Inducers for Management of Downy Mildew (DM) on Baby Leaf Kale. American Society of Plant Biologist (ASPB) Southern Regional Annual Conference. (Virtual on April 18, 2021).
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2021
Citation:
Kelly S. Allen (April 2021). Dominican College Science Seminar: Building Healthier Crops Using Plant Disease Resistance; virtual: https://www.youtube.com/watch?v=ykXpKw6Mw7I.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2021
Citation:
Kelly S. Allen, Gregory A. DeIulio, Robert Pyne, Jacob Maman, Li- Guo, Robert L. Wick, James Simon, Anne Gershenson, Li-Jun Ma (August 2021). Basil downy mildew quantitative resistance gene candidates identified using comparative transcriptomics. APS Annual Meeting; virtual poster session.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2020
Citation:
Maman, J. Identification of a Fusarium isolate that bypasses resistance in the sweet basil cultivar Newton. Oral session presented at: 2020 USDA NIFA Basil Workshop; virtual, December 2020.
through zoom.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2021
Citation:
Brindisi L, O⿿Brien R, Lyu W, Tepper B and Simon JE. (2021, August). Breeding Sweet Basil for Taste, Flavor and Aroma. Oral talk at the Annual Meeting of American Society for Horticultural Science, Denver, Colorado.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2020
Citation:
Brindisi L, Wyenandt CA, Di R and Simon JE. (2020, December). Challenges and progress in breeding basil for chilling tolerance. Oral talk at the USDA NIFA Basil Workshop, Virtual.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2020
Citation:
Brindisi L, Vasilatis AA, Mattera R, Tepper B, Wyenandt CA, Juliani R and Simon JE. (2020, January). The Sweet Basil Bouquet. Oral talk at the Plant Science Symposium, Rutgers the State University of New Jersey, New Brunswick, New Jersey
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2020
Citation:
Homa, K., Barney, W.P., Davis, W.P., Guerrero, D., Berger, M.J., Lopez, J.L., Wyenandt, C.A., Salvi, D., Karwe, M.V. and Simon, J.E. (2020). Cold Plasma Treatment Strategies for the Control of Fusarium oxysporum f. sp. basilici in Sweet Basil. In: USDA NIFA Basil Workshop (presentation)
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2020
Citation:
Homa, K. (2020). The IR-4 Project: New Pesticide Projects and Current Registrations for Basil. In: USDA NIFA Basil Workshop (presentation)
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2020
Citation:
Homa, K., Wyenandt, C.A., and Simon, J.E. (2020). Breeding for Fusarium oxysporum f. sp. basilici Resistance in Sweet Basil. In: USDA NIFA Basil Workshop (presentation)
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2021
Citation:
Li-Jun Ma (May 2021). Comparative fungal genomics. Invited seminar, School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, VA.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2020
Citation:
Li-Jun Ma (November 2020). Genome compartmentalization and fungal pathogenesis. Invited seminar, Department of Genetics and Biochemistry, Clemson University, SC
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2020
Citation:
Rob Wick (December 2020). Reflections on Fusarium Wilt Disease on Sweet Basil. Oral session presented at: 2020 USDA NIFA Basil Workshop; virtual through zoom, December, 2020.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2020
Citation:
Kelly S. Allen. Developing molecular markers for BDM resistance. Oral session presented at: 2020 USDA NIFA Basil Workshop; virtual through zoom, December 2020.
|
Progress 09/01/19 to 08/31/20
Outputs
Target Audience:As our project involves the genetic and management improvement of sweet basil against downy mildew and fusarium diseases, our target audience includes university researchers, growers, processors, distributors and te allied agricultural industry including seed companies and those providing products for the control and mitigation of these diseases. Our audience also includes extension specialists and agents involved in the basil and culinary herb commercial industry and master gardeners and horticulturalists. From the university perspective, we also engage, mentor and train undergraduate and graduate students at Rutgers University and the University of Massachusetts in plant breeding and genetics and new crop development. We specifically involve students for undergraduate research credits, for undergraduate honors theses. We have several graduate students being trained in plant biology, plant genetics and breeding and plant pathology whom are pursuing their advanced degrees working on this project. We have communicated our results to a broad audience with stakeholders from commercial growers from New Jersey to Florida and around the country, seed companies, and national fresh produce and culinary herb distributors as together we seek to solve their critical constraints in basil production. Prior to Covid-19 and the pandemic, stakeholders have been engaged via a series of meetings and field tours of the new Rutgers DM resistant basils in Florida and New Jersey, with growers representing over 5,000 acres of the annually produced field sweet basil for fresh market and processing. This program is heavily oriented to meeting market and consumer demand by the introduction of industry acceptable and desired improved germplasm and new cultivars, improved scouting and monitoring, and improved best practices in the management of the diseases impacting this crop. Due to the pandemic that began in 2020, we have realigned our plans to communicate and share our results to communicate our findings through storytelling using digital filmmaking and virtual workshops and conferences to accommodate those interested. Changes/Problems:The covid-19 pandemic did slow down several activities. From March- September, many of our university consortium labs were closed and/or under strict 'back-to-lab rules and regulations' to ensure work was conducted safely. We were not able to hire new staff and/or students, many of the planned field studies were established late or not conducted. The pandemic impacted seriously the scheduled work. Yet, despite, the team members also were able to make significant progress over the entire reporting period as shown in this progress report. Additional studies in Year 3 are planned to compensate for the reduced and slowed down studies originally scheduled for Year 2. The GWAS studies for example were not able to be conducted in New Jersey and in Florida as planned so will be done in Year 3. What opportunities for training and professional development has the project provided?This project has provided training and professional development for several graduate and undergraduate students at both Rutgers and UMass. This project has involved Rutgers PhD students Robert Mattera and Lara Brindisi (DMR plant breeding and genetics), Kathryn Homa (fusarium wilt breeding and genetics and new technologies to disinfect seeds from fusarium), Ariane Vasilatis (plant biology and aroma chemistry) and UMass PhD students, Kelly S. Allen (genetics of the DM pathogen) and Jacob Maman (genetics of the fusarium pathogen). Project provided opportunities for Alex Barrett to conduct his undergraduate honors thesis research on basil and additional opportunities for undergraduates when labs and greenhouses were opened prior to the pandemic. This program also provided labs and demonstrations to students at Rutgers in plant breeding to demonstrate and teach methods to cross pollinate basil and approaches we use in plant breeding as well as other lab practicums and demonstrations in hydrodistillation, solvent extraction, headspace and GC/MS analysis. The pandemic this year in 2020, reduced the access and ability to do as many trainings as would have occurred both at Rutgers and UMass. How have the results been disseminated to communities of interest?More than 20 presentations and extension workshops and extension articles were prepared and disseminated to communities of interest through publications in scientific journals, proceedings, workshops and grower and horticultural meetings (live and virtual and for organic and conventional growers), in popular scientific journals and state agricultural newsletters and national trade magazines and in other extension oriented outlets that share information about plant diseases and control options. Researchers from our consortium and invited experts came together in Belle Glade, Florida for our annual basil workshop and research meeting for 2 days of oral presentations, posters and field tours at the UF Everglades Research and Education Center, Belle Glade, FL., and a commercial basil farm. Scientific presentations were given at the national American Phytopathological Society, American Society for Horticultural Science, and other forums. Monitoring of the movement of basil downy mildew was tracked using: https://www.vegetables.cornell.edu/pest-management/disease-factsheets/basil-downy-mildew/ . This is a new website was developed and rolled out in 2020 and contains information originally posted at http://vegetablemdonline.ppath.cornell.edu/NewsArticles/BasilDowny.html) http://blogs.cornell.edu/livegpath/research/basil-downy-mildew/. During this year and due to the pandemic, additional planned field tours and grower meetings were postponed and we hope to restart such activities when its safe. What do you plan to do during the next reporting period to accomplish the goals?We will continue to pursue the goals as originally stated in the project proposal and initiation. Specifically a few highlights include (i) working on the genetics and genomic sequence of sweet basil; (ii) work toward developing higher resolution linkage maps and aligning published transcriptomes to identify genetic markers associated with DM and FOB resistance and basil aroma volatiles; (iii) develop gene-based SNP arrays for practical use in basil breeding; (iv) conduct a GWAS study at field locations phenotyping >300 basils; (v) complete the analysis of our RILS; (vi) gene stacking with our newly created FOB resistant sweet basil into our DMR sweet basils; (v) continued testing and evaluation of best management practices; (vi) develop and examine new organic and conventional fungicides and programs with combinations of products and determine whether fungicide applications can be reduced with DMR basils; (vii) continue and expand our basil DM monitoring online program; (viii) focus on disease free seed and seed quality and cleaning seeds; (ix) focus on genetic identify and traditional panels for identification of new races; (x) validating putative R-genes, identifying pathogen effectors and developing PCR-based molecular marker to aid in MAS. One of the greatest challenges is to test, screen and collectively gather data as to whether we are witnessing new races or different responses to the same race of BDM and FOB. We hypothesize that sweet basils with known response to the BDM now appear to show vastly differential response to the ambient BDM. This could suggest that we may be witnessing a change in the plant response, new DM races or virulence in the BDM. Using a panel screening of a known set of sweet basil varieties in a uniform manner and with a uniform scoring system will detect whether we have more than one virulence type of BDM. We prepared a protocol for such screening and basil seed packets have been distributed to multiple locations. Due to covid-19 we could not roll it out in 2020. In Year 3, we will do same for FOB screening.
Impacts
What was accomplished under these goals?
Obj. 1. 1a: Basil varieties were grown at multiple field locations and evaluated for basil downy mildew resistance, yield and multiple other agronomic traits. The Rutgers DMR basils were found to be consumer and market acceptable. 1b: Fungicide trials were conducted on university field stations in NJ and NY and in FL on a commercial basil production farm during fall/winter for evaluation of BDM management. In FL, studies were conducted and completed to: (i) Evaluate post-emergence oxalthiopiprolin applications at different rates for longevity of downy mildew control; (ii) Evaluate fungicides of varying modes-of-action for inclusion in comprehensive basil downy mildew management programs; (iii) Examine efficacy of systemic acquired resistant inducers (SARs) in combination with potassium phosphite for basil downy mildew control; and (iv) Evaluate organic and biopesticides alone and in combination with host-plant resistance for management of basil downy mildew. Results demonstrated that our recommendations can successfully prevent devastating downy mildew outbreaks from occurring. Several studies needed to be terminated prematurely due to covid-19 and other were postponed. In NY, at the Cornel LIHREC, a field experiment was conducted to evaluate new organic fungicides applied to a DMR basil variety (Rutgers Passion DMR). This integrated management approach is being used because several past experiments demonstrated that BDM cannot be effectively managed with organic fungicides applied to a susceptible variety or a DMR variety with low level of resistance (Eleonora). 1c: The evaluation of new steam seed treatment were not conducted in Year 2 but Cornell grew plants of a susceptible basil variety (DiGenova) to obtain seed expected to be contaminated with the BDM pathogen. Seeds were collected are will be used in steam seed treatment studies in Year 3 or 4. The development of a molecular assay for pathogen viability is progressing at UMass. 1d: Monitoring of the movement of basil downy mildew was tracked using an online live map: https://www.vegetables.cornell.edu/pest-management/disease-factsheets/basil-downy-mildew/. This is a new website was developed and rolled out in2020. Obj. 2. 2a: Due to COVID-19 complications and delays we have not begun testing high-throughput drone-based phenotyping systems but drone and imaging equipment and software purchased. To lay the groundwork for a genome-wide association mapping study (GWAS) in the Ocimum genus for Years 3 and 4, we acquired over 560 new basils from around the world. We have begun selfing each line to ensure cultivar purity for next year's studies. The Rutgers team obtained backcross 5 of second generation of selfed seed to develop new and improved FOB varieties. Field screening of these backcross lines in field was conducted and currently growth chambers and inoculum screens are being used for final FOB breeding selections that will then be crossed into basil DMR lines. 2b: UMass team successfully developed a DNA extraction protocol that yields DNA with sufficient quality and concentration to use GBS to explore the genetic diversity of FOB. We have also identified common restriction enzyme sites in fungi and Oomycetes for the restriction digest stage of our GBS protocol. Collectively, our consortium has continued to collect and isolate BDM sporangia to build a large collection of isolates (n=234). 2c) We are validating putative R-genes, identifying pathogen effectors and developing PCR-based molecular marker to aid in MAS. Plasmids containing putative effectors tagged with green fluorescent protein (GFP) to facilitate fluorescence microscopy investigations of effector molecular mechanisms have been constructed. The UMass team is working to: (i) functionally validate basil resistance genes that based on comparative transcriptomics data, are predicted to increase resistance to Peronospora belbahrii infection; (ii) investigate the genetic diversity of P. belbahrii, how this diversity affects transcription during infection of resistant and susceptible hosts and to validate the function and role of putative secreted effectors in pathonogenesis; (iii) use comparative transcriptomics to investigate the genetic diversity of Fusarium oxysporum f. sp. basilici (FoB) strains and strain pathogenicity towards resistant and susceptible hosts. 2d: Recombinant Inbred Lines were evaluated in Florida in early 2019. Disease resistance, aroma profile, flower color, phenology, leaf shape, leaf ruffling, leaf cupping and internode length were scored. DNA was isolated from all 113 lines and put through a ddRADseq GBS pipeline. Forty-eight libraries each were barcoded and pooled into three Basil-sets, which were processed and then used to call approximately 1200 SNPs in our mapping population. Following a series of QC checks and the STACKS ref_map command we generated 6000 high quality SNPs. We are now in the process of constructing a linkage map from these SNPs and have generated a linkage map that is agreement with our research. Genome Sequencing basil: Using Illumina Hi-seq to generate short reads and Pac-Bio sequencing to generate long reads we were able to sequence the genome of RUSB22 and this resulted in over 43,000 scaffolds. We are now refining the basil genome from a scaffold-level assembly to a pseudo-chromosome level assembly. BUSCO analysis was also completed.
Publications
- Type:
Journal Articles
Status:
Awaiting Publication
Year Published:
2020
Citation:
Homa, K., W.P. Barney, W.P. Davis, D. Guerrero, M.J. Berger, J.L. Lopez, C.A. Wyenandt and J.E. Simon. Cold plasma treatment strategies for the control of Fusarium oxysporum f. sp. basilici in sweet basil. HortSci: https://doi.org/10.21273/HORTSCI15338-20.
- Type:
Other
Status:
Published
Year Published:
2020
Citation:
Simon, J.E. 2020. A breakthrough in the war against basil downy mildew. Scientia: https://doi.org/10.33548/SCIENTIA540
- Type:
Other
Status:
Published
Year Published:
2020
Citation:
Simon, J., A. Wyenandt, R. Raid, M. McGrath and K. Homa. 2020. A plant breeding breakthrough: downy mildew resistant sweet basil. American Vegetable Grower, June, 2020:10-11.
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
McGrath M.T. 2020. Efficacy of conventional fungicides for downy mildew in field-grown sweet basil in the US. Plant Disease: May 2020 on-line at https://doi.org/10.1094/PDIS-11-19-2382-RE
- Type:
Other
Status:
Published
Year Published:
2020
Citation:
McGrath M. and Sexton Z.F. 2020. Evaluation of commercial cultivars of sweet basil resistant to downy mildew, 2019. Plant Disease Management Reports 14:V071.
- Type:
Other
Status:
Published
Year Published:
2020
Citation:
McGrath M.T. and Sexton, Z.F. 2020. Evaluation of organic fungicides for downy mildew in sweet basil, 2019. Plant Disease Management Reports 14:V083.
- Type:
Other
Status:
Published
Year Published:
2020
Citation:
Standish, J.R., Raid, R.N., Pigg, S., and Quesada-Ocampo, L.M. 2020. A diagnostic guide for basil downy mildew. Plant Health Progress 21:77-81. https://doi.org/10.1094/php-09-19-0062-DG
- Type:
Other
Status:
Published
Year Published:
2020
Citation:
Raid, R.N., Hartman, A., and Reis, K. 2020. Evaluation of the fungicide picarbutrazox for control of downy mildew on sweet basil. Plant Disease Management Reports 14:V039.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2020
Citation:
Simon, J., A. Wyenandt, R. Mattera III, K. Homa, A.J. Noto, L. Brindisi and W.P. Barney. 2020. From management to genetic resistance: new discoveries in controlling basil downy mildew and fusarium wilt, 3 pp. Proc of the New Jersey Vegetables Growers Association, Feb 03-05, 2020. Atlantic City, NJ.
- Type:
Other
Status:
Published
Year Published:
2020
Citation:
Wyenandt, C.A., and J.E. Simon. 2020. Evaluation of biopesticide and conventional fungicides for management of downy mildew in sweet basil, 2019. Plant Disease Management Rept. 14:V175.
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Progress 09/01/18 to 08/31/19
Outputs
Target Audience:The targeted audience is the commercial industry- growers, buyers, processors and distributors and the allied agricultural industry including seed companies and those providing products for the control and mitigation of these diseases. Other beneficiaries include master gardeners and horticulturalists as well as the research community from academia and the public and private sector. This project will improve stakeholder management of sweet basil downy mildew and fusarium wilt diseases in organic and conventional production systems by evaluating conventional and organic fungicide regimes, developing a new seed testing protocol to detect viable seed infestation, validate a new steam treatment method to prevent the spread of the pathogens via seed, and develop an online map-based monitoring system of disease occurrence to mitigate grower risk with an understanding of the economic impact gained by using market acceptable disease resistant basils. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?This project has provided training and professional development for several graduate and many undergraduate students at both Rutgers and UMass. This project has involved Rutgers PhD students Robert Mattera and Lara Brindisi (DMR plant breeding and genetics), Kathryn Homa (fusarium wilt resistance and breeding) Ariane Vasilatis (plant biology and aroma chemistry) and UMass PhD students Kelly S. Allen (genetics of the pathogen). Project provided the flatform for Kelly Allen to receive the Lotta M. Crabtree Research Fellowship in Production Agriculture, Spring 2019. This project also facilitated the funding of Molecular characterization of plant-microbe interactions, providing for an undergraduate summer research fellowship/internship, funded by the UMass CAFE Summer Scholars Program. How have the results been disseminated to communities of interest?Results were shared with growers, master gardeners, seed company's and distributors and buyers by communicating progress from this project at a wide variety of research and demonstrations at each university to stakeholder group meetings with wholesaler/retailers and producers including workshops/trainings, field days and grower participatory/collaborative evaluation of new disease resistant sweet basils production and yield performance. A new Instagram (rutgersbasil) which tracks our field studies to the new and improved basil downy mildew monitoring site at Cornell (See: http://vegetablemdonline.ppath.cornell.edu/NewsArticles/BasilDowny.html and http://blogs.cornell.edu/livegpath/research/basil-downy-mildew/. Public presentations at field days at Rutgers (southern and northern agricultural centers), UF Belle Glade station and the Long Island Cornell research agricultural station as well as winter and spring presentations to the New Jersey Organic Farmers Association, the New Jersey Vegetable Growers Association and the Florida Vegetable Growers Association all were part of a larger holistic effort to disseminate our findings to communities of interest. In this first year 8 presentations were made to growers and the industry, 5 to master and home gardeners and the public and 3 at scientific meetings. What do you plan to do during the next reporting period to accomplish the goals?We will continue with the methods and goals as originally stated in the initiation
Impacts
What was accomplished under these goals?
Obj 1. Fields trials in Florida, New Jersey and New York were established to evaluate DMR sweet basils; and FOB resistance only in Jersey. From NY, results indicated that BDM was first seen at LIHREC on 8/16. As of 8/28 symptoms had only been found in the susceptible variety and Eleonora. In New Jersey, basil downy mildew field research trials were established at RAREC to examine the level of DMR resistance in 5 DMR resistant lines: Rutgers Obsession DMR, Rutgers Devotion DMR, and Rutgers Thunderstruck DMR Rutgers Passion DMR and cv. Prospera compared with a another new sweet basil release, cv. Newton that has FOB resistance only. All lines were harvested at regular intervals to determine fresh-market yield as well as scored for the presence and onset of DMR infection. A subset of leaves from selected harvest are being analyzed for aroma and essential oils analysis and a subset of plants were not harvested and allowed to go to seed that has been collected from uncut plots and tested using PCR techniques to detect for the presence of BDM on seed, while also being shipped to High Mowing Organic Seed to evaluate a new potential seed treatment method. Field trials were established to compare an organic vs. conventional fungicide program to evaluate their potential control of BDM using Rutgers Obsession DMR, Rutgers Devotion DMR, and Rutgers Thunderstruck DMR lines and a commercial variety 'Nufar' or 'DiGenova'. Data currently being analyzed to determine if the presence of DMR resistance can help keep DMR pressure low enough to potentially improve control with some biopesticide fungicide treatments. Adequate control of BDM evaluating numerous biopesticides with susceptible sweet basil varieties have yet to provide effective control of BDM for a number of years. An organic trial was also established to determine the efficacy of 14 biopesticide treatments at various rates and spray applications using Rutgers Devotion DMR. A new herbicide trial was also done to evaluate number or registered and unregistered herbicide treatments to help improve weed control in commercially seeded basil fields. As there are few registered pre- and post emergent herbicides registered for BDM control finding potential active ingredients that can effectively control-damaging weeds is extremely important in basil production as it would improve the disease management of the crop. An online map-based DM monitoring system to provide growers important information on seasonal DM epidemics, which will allow them to better time fungicide application dates, was expanded and operational (web-site listed under products). Obj. 2. Relative to DRM resistance, 113 F8 recombinant inbred lines from the MRI x SB22 cross were sown in the greenhouse and subsequently transplanted in two field locations across the US (North and South New Jersey). All lines were transplanted in triplicate blocks and randomized. This same population was also transplanted in Florida. Disease resistance, aroma profile, flower color, phenology, leaf shape, leaf ruffling, leaf cupping and internode length were all evaluated. Aroma profiling was evaluated by drying freshly collected plant material and then grinding 100mg. This ground plant material was then placed in a GC headspace vial and run on the Shimadzu TQ8600 GC-MS with autosampler and SPME fiber. DNA was isolated from all 113 lines and put through the ddRADseq GBS pipeline. Forty-eight libraries each were barcoded and pooled into three Basil-sets that were sent to the company Genewiz for Illumina Hi-seq NGS. Data analysis is underway. Relative to Fob resistance, we completed the backcross 4th generation of FOB basil (9 lines; 900 seed); screening currently underway. Currently making crosses back to SB17 parent for each backcross generation to better understand/confirm disease resistance ratios. Identifying genetic diversity in P. belbahrii and F. oxysporum f. sp. basilici across the US to help identify the population structure of each pathogen; as there may be variability in each population which would potentially lead to new race development in each pathogen. As no microsatellite markers exist for P. belbahrii our team identified transcriptome data for this pathogen on NCBI and using the program BatchPrimer3 (Tm = 60) identified ~255 putative microsatellites. From these ~255, 54 were chosen at random to evaluate for amplification and specificity to BDM and 24 have been evaluated. We continue to collect and isolate BDM sporangia to build a large collection of isolates (n=234). The UMass team is currently working to functionally validate putative basil resistance genes that were predicted from the comparative transcriptomic analysis described in the grant proposal. Work to functionally validate putative pathogen effector genes, to establish a gene-cloning pipeline to express each putative gene in bacterial expression systems was initiated. We are also collecting active Peronospora belbahrii isolates to deliver to the Rutgers team for population genetic analyses.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Patel. N., Kobayashi., D., Noto, A.J., Baldwin, A.C., Simon, J.E., and Wyenandt, C.A. 2019. First report of Pseudomonas chicorii causing bacterial leaf spot on sweet basil (Ocimum basilicum) in New Jersey. Plant Dis. (First Look) https://doi.org/10.1094/PDIS-04-19-0895-PDN
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Wyenandt, C.A., Maimone, L.R., Homa, K., Madeiras, A.M., Wick, R.L., and J.E. Simon. 2018. Detection of downy mildew on seed of basil following field infection in southern New Jersey. HortTechnology 28:637-641.
- Type:
Other
Status:
Awaiting Publication
Year Published:
2019
Citation:
2019. Simon, J.E., C.A. Wyenandt, R. Raid, M. McGrath and K. Homa. Breeding for downy mildew resistance in sweet basil A success story though the war continues. American Vegetable Grower. (accepted).
- Type:
Book Chapters
Status:
Published
Year Published:
2018
Citation:
Zhang Y, Guo L and Ma L-J. 2018. A computational protocol to analyze meta-transcriptomic data capturing fungal-host interactions. In Methods in Molecular Biology. Eds: Ma WB and Wolpert T. Springer pp 207-233
- Type:
Websites
Status:
Published
Year Published:
2019
Citation:
http://vegetablemdonline.ppath.cornell.edu/NewsArticles/BasilDowny.html
http://blogs.cornell.edu/livegpath/research/basil-downy-mildew/
- Type:
Other
Status:
Published
Year Published:
2019
Citation:
New tools for managing basil downy mildew. 2019 Suffolk Ag News. Vol 103. No. 2. p 20-21. Prepared by M. McGrath.
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