Source: Agricultural Research Service submitted to NRP
EVALUATION AND BREEDING OF DIVERSE HEMP GERMPLASM FOR DISEASE RESISTANCE
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
ACTIVE
Funding Source
Reporting Frequency
Annual
Accession No.
1031217
Grant No.
2023-38624-40847
Cumulative Award Amt.
$722,166.00
Proposal No.
2023-04713
Multistate No.
(N/A)
Project Start Date
Sep 1, 2023
Project End Date
Aug 31, 2027
Grant Year
2023
Program Code
[HW]- Supplemental and Alternative Crops
Recipient Organization
Agricultural Research Service
600 E. Mermaid Lane Rm 2023
Glenside,PA 19038-8551
Performing Department
(N/A)
Non Technical Summary
Hemp (Cannabis sativa L.) is grown for essential oil, seed, and fiber production. Germplasm with superior agronomic performance combined with disease resistance is required to improve hemp yields and product quality. This project will focus on the evaluation of genetically and geographically diverse hemp genetic resources from the USDA ARS Plant Genetic Resources Unit Hemp Germplasm Repository for resistance to four diseases important to hemp industry. At least 100 hemp accessions will be tested yearly in randomized, replicated and inoculated field trials for: 1) Fusarium head blight, 2) powdery mildew, 3) Septoria leaf spot, and 4) downy mildew. Fusarium head blight tolerance will be evaluated in field trials in Lexington, KY. Powdery mildew, Septoria leaf spot, and downy mildew resistance will be tested in Geneva, NY. High-quality data obtained from these evaluations will be entered into GRIN-Global, a publicly accessible database. Resistant accessions identified during evaluations will be used in crosses to develop regulatory compliant, publicly available, stable, and disease-resistant industrial hemp germplasm in three important market classes. Additionally, germplasm identified during this work will be incorporated into downstream mapping populations to support the discovery of candidate resistance genes. Extension and outreach activities including field days, videos, and webinars will be used to inform the hemp community of the research findings.
Animal Health Component
100%
Research Effort Categories
Basic
0%
Applied
100%
Developmental
0%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2121730116060%
2011730108120%
2021730108020%
Goals / Objectives
The specific goals of the project are to:Evaluate diverse hemp germplasm for resistance to four important diseases of hemp including: a) Fusarium head blight, b) Powdery mildew, c) Septoria leaf spot, and d) downy mildew.Use molecular markers to genetically map resistance loci to these four diseases.Develop resistant pre-breeding lines that are publicly available.
Project Methods
Obj. 1. Evaluate diverse hemp germplasm for resistance to four important diseases of hempAccessions that are deemed to be regulatory compliant with a total THC content at or below 0.3% as described in the 2021 Hemp Final Rule (USDA-AMS 2021) will be evaluated in the disease trials. The same set of 400 accessions will be used in screening for each of the four diseases. Each year 100 new accessions will be evaluated. Accessions that show some level of resistance the first year they are evaluated will be evaluated a second year to verify resistance. Cuttings or seeds of resistant plants will be sent to the USDA PGRU greenhouses for genotyping and hybridizations.Fusarium head blight To assess accessions for resistance to Fusarium head blight, seed of each accession will be sown in 144-cell trays and grown for 3 to 4 weeks before transplanting into the field at the University of Kentucky North Farm Complex near Lexington, KY. Transplants will be planted into conventionally tilled soil using the production model typically practiced for burley tobacco production in rows spaced 1.07 m apart with 0.3 m between plants within the row. Drip irrigation will be provided as needed. Accessions will be planted in the field in a randomized complete block design with 10 plants per plot and 3 replications.Previous research at this location has shown that Fusarium head blight is endemic in this area so we will use natural inoculum to assess resistance.Fusarium disease will be assessed for incidence and severity using a quantitative rating scale (Gauthier, unpublished). Because accessions are expected to have varied and inconsistent maturity, ratings will take place every two weeks beginning at flowering. The area under the disease progress curve (AUPDC) will be calculated and means separated using Tukey's HSD. All statistics will be performed using R statistical packages.Powdery mildew To identify hemp accessions that are resistant to powdery mildew, each accession will be sown in 50 deep-well trays in a greenhouse and grown to 5 weeks of age as previously described by Stack et al (2021b). Plants will be transplanted into a research field at Cornell AgriTech in Geneva NY, with raised beds, black plastic mulch, and drip irrigation. Plants will be on 2 m center-row spacing with 1 m spacing between plants within a row. We will use a randomized complete block design with 5 plant plots and three replicates. Transplants will be allowed to grow for about 4 weeks prior to inoculation with the aggressive G. ambrosiae isolate, 19002. Plots will be rated by assessing the percent disease of each plot, and these ratings will be taken weekly following inoculation for a minimum of four weeks.Septoria leaf spotTo assess accessions for resistance to Septoria leaf spot, plants will be grown and transplanted into a research field at Cornell AgriTech as described for powdery mildew. A similar randomized complete block design will be used, as described for powdery mildew. Plants will be inoculated to runoff with a suspension of 104 conidia/mL of S. cannabis isolate 22384, which co-PD Smart has shown to be virulent on several different hemp cultivars (unpublished). Plants will be inoculated in the evening to have a longer period of leaf wetness and increase the chances of conidial germination and leaf infection. Plots will be rated and data analyzed as described for powdery mildew. Hemp leaf samples with Septoria leaf spot symptoms will be collected from the research field and PCR of the ITS region will be performed to ensure that the symptoms are caused by S. cannabis.Downy mildewTo assess accessions for resistance to P. cannabina, the causal agent of hemp downy mildew, plants will be grown as described above. Co-PD Smart has developed a high throughput screening method for hemp downy mildew using the Blackbird phenotyping system (Bierman et al. 2019). Using a cork borer, 1 cm leaf disks are cut from a minimum of three leaves from three different plants of each test cultivar. Inoculum will be prepared by rinsing sporangia from detached leaves as described by Giles et al (2022). Disks will be placed on a Blackbird tray containing water agar and inoculated by spraying a suspension of 1x104 sporangia/mL onto the disks. The blackbird imaging system takes eight images of each leaf disk once per day for seven days following inoculation. Each tray has space for 350 samples and a full tray takes about three hours to image. Once imaging is complete, each image will be processed through a pipeline that has been trained specifically to identify downy mildew on hemp leaves, and a percent disease for each leaf disk on each day is determined. The R statistical package is then used as described above to determine AUDPC and Tukey's mean separation.Obj. 2. Use molecular markers to genetically map resistance loci to these four diseases. As part of ongoing germplasm evaluations conducted in Geneva, NY, genome-wide association studies (GWAS) will be utilized to investigate population structure and the genetic control of each trait for at least 400 accessions that undergo two years of phenotyping in raised beds in Geneva, NY. Given that hemp is an outcrossing species, many of the accessions may be heterogeneous; therefore at least two plants within each of the 400 accessions will be genotyped, ideally with probe-based SNP assays with markers placed at least every 500 kb along the genome. Genotypes will be used in conjunction with collected phenotypes to identify genomic regions and genetic markers associated with resistance to the four hemp diseases described previously.Cuttings from individual plants with unique resistance to any of the tested diseases in this project will be collected from the field and we will attempt to root these cuttings in Geneva, NY. Any unique individual that is rooted and produces a vigorous plant that could be used for subsequent evaluations will be genotyped with the same genotyping platform that is utilized for the other accessions in the collection. In this way, a common set of genotypes will be obtained for each accession and from individual plants with unique disease resistance profiles.SNP markers that are found to be closely associated with disease resistance can be converted into PACE assays and tested on a Bio-Rad Opus real-time PCR instrument. Validated markers can be utilized for marker assisted selection by the USDA ARS PGRU hemp breeding project or other hemp breeding programs.Obj. 3. Develop resistant pre-breeding lines that are publicly available. The project will aim to introgress resistance into essential oil, fiber, and grain market hemp germplasm. Rooted cuttings taken from resistant hemp plants in the field evaluation trials will be used to make crosses with plants derived from high-yielding accessions. F2 populations will be generated by self-pollinating a single F1 plant from the hybridizations with the aim of producing at least 200 F2 seeds for each population. F2 populations can be tested for agronomic trait performance in addition to disease resistance. Populations can be requested by collaborators, and seeds of superior-performing resistant selections will be made publicly available on GRIN-Global.Outreach and extension effortsOne of the primary deliverables of this project will be accession-specific disease evaluation data added to the GRIN-Global database. Currently, the database includes information on chemical composition and morphological descriptors of hemp accessions. This project will provide disease resistance data that will prove vital for public and private breeders. Beginning in Year 3, PI and Co-PIs will execute a series of publicity pieces such as articles in industry journals (such as Hemp Industries Association, Hemp Industry Daily, and US Hemp Roundtable) and communications through government listservs.

Progress 09/01/23 to 08/31/24

Outputs
Target Audience:The target audience has been hemp breeders and growers in the hemp community that are interested in hemp disease resistance. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Three graduate students have been actively engaged with this project. Students have been learning how to manage plants and pathogen cultures.They have worked with single conidial isolates, inoculated plants, rated plants for disease severity, analyzed disease data, and presented their results at professional conferences. How have the results been disseminated to communities of interest?Scientific proceedings were presented at two professional conferences and three field days. Managing Septoria Leaf Spot of Hemp, Caused by the Fungus Septoria cannabis (2024) Schwartz, JA. Gordon T., Stansell Z., and Smart CD. American Phytopathological Society Northeastern Division Meeting. Ithaca, NY 27 March 6-8, 2024. Biology, Management, and Breeding for Septoria Leaf Spot-Resistant Hemp. Schwartz, JA. Gordon T., Stansell Z., and Smart CD. American Phytopathological Society Annual Meeting. Memphis, TN July 27-30, 2024. Screening for new sources of resistance to hemp powdery mildew in diverse Cannabis sativa germplasm (2024) Vignale L. Herrmann, T, Gordon T., Stansell Z., Smart CD, Smart LB. American Phytopathological Society Annual Meeting. Memphis, TN July 27-30, 2024. USDA ARS PGRU Hemp Germplasm Laboratory Stakeholder meeting, Geneva, NY, 11 September 2024, 9:00 am to 4:30 pm Cornell University Cannabinoid Field Day, Geneva, NY, 13 September 2024, 9:00 am to 4:00 pm. What do you plan to do during the next reporting period to accomplish the goals?An additional 100 accessions will be selected for disease resistance screening of these 4 diseases during the 2025 field season. Resistant accessions selected this year will be selected for inbreeding and early generations will be tested for resistance in the 2025 field trials.

Impacts
What was accomplished under these goals? Septoria leaf spot: One-hundred-five accessions were evaluated for Septoria leaf spot resistance in Geneva, NY. Seeds were planted in flats in a greenhouse on 15 May, where they were regularly maintained and watered. The transplants were set in the field by hand into 4 ft wide raised beds covered with plastic mulch on 30 May. Each plot consisted of 5 plants with 3 ft spacing in between plants, 3 ft spacing in between plots, and 7.5 ft spacing in between rows. The field was established in a randomized complete block design with 3 repetitions of 105 accessions. Plots were irrigated and fertigated as needed via a drip line with 24-8-16 Miracle Gro all-purpose, water-soluble fertilizer. Plastic weed cloth was applied in between rows and was supplemented with hand-weeding as needed. Inoculum was created with a single conidial isolate of Septoria cannabis collected from Geneva, NY. 100 μl/L of Silwet was added to the inoculum and a final concentration of 6.4 *10^5 conidial suspension was applied using a battery-powered backpack sprayer on 3 July. Approximately 30 mL of inoculum was applied to each plant. Symptoms were first observed 7 days post inoculation. Disease severity ratings were visually estimated on a scale of 0 to 100%. The first disease severity rating was on 10 July, and disease severity continued to be visually estimated each week until 14 August for a total of 6 ratings. Disease severity values for each accession as recorded on the last day of rating, 14 August, were uploaded to GRIN-Global, 2024_SEPTORIA_MCCARTHY01. Fourteen accessions are reported with less than 1% disease severity, and 36 accessions are reported with greater than 10% septoria severity. Four accessions report septoria severity of over 30% severity at the final evaluation point, and two accessions G 33382 and G 33635 had over 70% severity in the field trial. Powdery mildew: One-hundred-five accessions were evaluated for hemp powdery mildew resistance in Geneva, NY. Transplants were established in the field in the same way described above for Septoria leaf spot. Disease severity ratings were visually estimated on a scale of 0 to 100%. Plots were inoculated with a single conidial isolate of Golovinomyces ambrosiae, the fungus that causes hemp powdery mildew. The first disease severity rating was on 1 August 2024 and plants were assessed for disease severity every week until the last rating on 28 August 2024. More than 15 accessions were considered highly resistant with final severities below 5% and one accession G 33827 was routinely observed to have disease severity over 75%. In another field-planted sequencing trial, 418 accessions were evaluated and reported for powdery in GRIN-Global 2024-HA24-PGRU-SEQUENCING-Z1. Twenty-seven accessions are reported as less than 1% severity and 13 accessions are reported as over 90% severity on the final rating date, 25 September 2024. Downy mildew: One-hundred-five accessions were evaluated for hemp downy mildew resistance in Geneva, NY. Seeds were sown and grown to approximately 6-weeks of age. Leaf punches were taken from the plants and evaluated with a Blackbird high-throughput automated phenotyping system and rated with a neural network and though manual observation. Additionally, detached leaflets were evaluated on petri plates. All leaf tissue was inoculated with a liquid suspension of zoospores at 105 spores per ml. Rating took place every day from 5 days to 9 days post inoculation. For each accession, there were three replicates situated in a randomized complete block design for each phenotyping method. Evaluation method development is ongoing, but initial results for these controlled environment inoculations are promising. There were 15 accessions that were observed to have highly resistant phenotypes with disease severity below 5% across the rating methods. These included accessions with origins from European, Chinese, and U.S. feral lines. There were also 17 accessions that had high disease severity including G 33312 and G 33338. Fusarium head blight: One-hundred-five accessions were transplanted in Lexington, KY on 11 July 2024, in a randomized complete block design with 10 plants per plot and 3 replications for a total of 2730 plants evaluated. Transplants were planted into conventionally tilled soil using the production model typically practiced for burley tobacco production (no raised beds and no plastic) in rows spaced 1.07 m apart with 0.3 m between plants within the row. Previous research at this location has shown that Fusarium head blight (FHB) is endemic in this area, so natural inoculum was relied upon to establish disease. Fusarium disease was assessed for incidence and severity using a quantitative rating scale (Gauthier, unpublished). Ratings took place every week from 11 July to 25 September 2024, for a total of 11 ratings. Disease assessments and plant development stage were recorded. Disease ratings were generated for 88 accessions and 79 of those accessions had severity ratings of 0%. Only 9 accessions had FHB severity above 0%. G 33591, G 33296, G 33350, and G 33202 had severities above 6% while G 33342, G 33337, G 33299, and G 33200 had FHB severity above 3%. The FHB trial data has been summarized and uploaded onto GRIN-Global, 2024_FUSARIUM_HB_UKY. FHB disease severity may have been exceptionally low in 2024 due to hot temperatures and drought in Lexington this summer. A hurricane that came through on September 27th, and low FHB levels in neighboring small grains plots also complicated disease progression and rating.

Publications