Source: OREGON STATE UNIVERSITY submitted to
THE ESSENCE OF CANNABACEAE: COMPARATIVE GENOMICS AND METABOLOMICS TO UNRAVEL THE COMPLEXITIES OF AROMA AND FLAVOR
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
NEW
Funding Source
Reporting Frequency
Annual
Accession No.
1028026
Grant No.
2022-67013-36393
Project No.
ORE01015
Proposal No.
2021-07849
Multistate No.
(N/A)
Program Code
A1103
Project Start Date
Jan 15, 2022
Project End Date
Jan 14, 2025
Grant Year
2022
Project Director
Hendrix, D. A.
Recipient Organization
OREGON STATE UNIVERSITY
(N/A)
CORVALLIS,OR 97331
Performing Department
Biochemistry & Biophysics
Non Technical Summary
The Cannabaceae family, which includes Cannabis sativa (hemp) and Humulus lupulus (hop), constitutes a multi-billion-dollar industry in the US, with over one billion dollars in sales for Oregon alone. Hemp and hop are high-value ingredients, prized for their production of specialized metabolites and pharmacologically relevant effects. The flowers of both plants are valuable for flavor and aroma, there is a need for research on alleles that control the biosynthesis of terpenes and other volatile organic compounds (VOCs). There is a need for comparative approaches for studying hop and hemp to reveal how they evolved, diverged, and what genotypes may regulate production of flavor and aroma compounds.Objective 1: Build a web-accessible infrastructure to study the comparative genomics and metabolomics of the Cannabaceae. We will create a web-accessible framework for comparative genomics in hop and hemp, and for organizing available data on VOC abundance. We will identify orthologous gene groups, and build a comparative genomics infrastructure for hop and hemp.Objective 2: Characterize the conservation and variability of VOC pathways in hop and hemp. We will quantify VOC levels using GC-MS, and gene expression using RNA-seq. We will compare co-expression networks between hop and hemp, and characterize the conservation of VOC pathways.Objective 3: Characterize the functional properties of metabolites and variants. We will build co-expression networks for both transcript and metabolite expression. We will identify genomic variants associated with metabolite expression. We will validate the role of these alleles in the activity of enzymes in an in vitro context.
Animal Health Component
0%
Research Effort Categories
Basic
100%
Applied
(N/A)
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2012230100050%
2011730100050%
Goals / Objectives
The goal of our proposal is to enhance flavor and aroma in hop and hemp by identifying alleles that are responsible for the production of specific volatile organic compounds (VOCs). Hop and hemp are part of the Cannabaceae family, and they share common metabolic pathways. More work is needed to bridge the gap in knowledge about commonalities between these two closely-related species, thereby informing and improving research efforts for both species. First, we will create a web-accessible infrastructure and resource for Cannabaceae genomics, transcriptomics, and we will organize what is known about the biosynthesis of compounds that enhance flavor and aroma. Second, we will use genomics, metabolomics, and data science approaches to elucidate the allelic architecture that enhances the biosynthesis of VOCs, including terpenes, by using populations of hop and hemp, and third, we will validate these experimentally by heterologous expression.
Project Methods
For objective 1, we propose build a web-accessible meta-database of all available gas chromatography-mass spectrometry (GC-MS) data for hop and hemp, and create a unifying resource to serve as the basis of future studies.Available data from literature for a given cultivar will be mined for relationships between enzymes and associated compounds.We will to use JBrowse 2, including the built-in synteny browser for visualizing conserved genomic loci. We will also identify orthologous genes in the Cannabaceae family, which will allow us to study the evolution and conservation of genes relevant for the biosynthesis of terpenes and other volatile compounds. We will align reference proteomes for the species under investigation, including hemp and hop and other members of the Cannabaceae family.We will identify orthologous gene groups (OGGs) from the above set of species using OrthoFinder.We will investigate OGGs with genes only from members of the Cannabaceae, as well as OGGs with all species present, to assess sequence evolution among more highly-conserved groups, well as a comparison to genes from our pathways of interest.Objective 2 will begin by selecting 25 hop and 25 hemp cultivars for GC-MS. These cultivars will be selected based on consultation with our stakeholders (John I. Haas and OregonCBD) and based on diverse flavor and aroma characteristics. After performing GC-MS and measuring their metabolic profiles, we will identify a diverse subset of 8 hop and 8 hemp cultivars for RNA-sequencing. The RNA-sequencing will identify both gene expression and allelic variation in the different cultivars for the genes of interest, as well as other genes that could be relevant.As part of this objective, we will perform an untargeted metabolomics approach using GC-MS to identify and quantify the metabolite composition across different cultivars within hemp and hop. Additionally, we will investigate the levels of monoterpenes and sesquiterpenes following a GC-MS approach described previously.Briefly, the plant material will be harvested and immediately frozen in liquid nitrogen. The plant material will be ground to a fine powder in a liquid nitrogen cooled mortar and pestle, and the powder divided into two equal portions. The first portion will be placed in RNAlater for RNA isolation and sequencing, while the remaining material will be weighed and extracted with hexane (10 mL per 1 g of tissue) containing 0.03% (vol:vol) of toluene as an internal standard in a sealed glass vial. The tissue will be extracted for a total of two hours at room temperature, and then the plant material pelleted via centrifugation. The cleared extract will be transferred to a new glass vial and stored at -20 °C until GC-MS analysis. Volatile compounds separation will be achieved using a Shimadzu GC-MS equipped with 60-m DB-5MS column and a quadrupole mass spectrometry detector with electron ionization source. Known metabolite quantification will be accomplished by comparison to standard curves of commercially available or synthetic compounds. While we are specifically interested in terpenes and other volatile compounds for our proposed work, the strength of the untargeted GC-MS approach will allow us to characterize a broad range of metabolites beyond terpenes. The data collected will be a starting point for future projects related to other volatile compounds, with the goal of mapping compounds that contribute most to flavor. However, for this study our focus will be on metabolites that are common between hop and hemp, where insight into flavoring will be gained from a comparative approach. Industry consultants have recommended a list of compounds as critical targets for this study.We propose to select 8 hop and 8 hemp cultivars for RNA-sequencing (RNA-seq). These cultivars will be selected based on the outcomes of our GC-MS experiments for the most diverse terpene composition. We will sequence three biological replicates per cultivar, for a total of 48 samples (25 each from hop and hemp). To measure the expression level of genes involved in VOC biosynthesis, fresh flowers will be selected at the developmental stage preceding standard harvest times for the flowers and flash-frozen in liquid nitrogen upon collection.we will identify genes that show differential expression (DE) across cultivars (intra-species), as well as orthologous pairs of genes in hop and hemp that show significant differences in expression across species (inter-species). Our DE analysis will be guided by alignment to the reference genome assemblies for each species

Progress 01/15/22 to 01/14/23

Outputs
Target Audience:The target audience for this project includes research scientists in the field of hop and hemp research, as well as members of the hop and hemp industry. Because this is a three-year project that has effectively two-years of funds, and because of some challenges with growing plants in the first year, we have moved the bulk of the work to years 2 and 3 of the project. This will also make it more feasible to maintain salaries of trainees employed by this project without a "gap year". For this reason, there is nothing to report regarding our audience. That said, we have initiated work on a public database of existing data on terpene levels for different cultivars of hop and hemp found in the literature. We have collected 13 articles with at least 13 associated data tables, one from each paper. The challenge with this is that the publications typically embed these tables in the publication PDF file, and they aren't always easily collected and require some manual typing of values into a unified format for collection and for presenting in our database. We have also collected paired samples from hemp plants, and are growing hop samples currently in greenhouses. This tissue collection is the basis of the proposed experiements that we will conduct this year. More detail on the collected samples will be provided in the other textboxes of this report. Changes/Problems:As stated previously, we sought to keep things uniform for hop and hemp, we wanted to grow them both under the same conditions. However, we could not get approval to grow hemp outdoors, leading us to grow both hop and hemp in greenhouses. This proved to be more challenging than anticipated for hop cone (flower) collection and these plants are still growing. That said, we expect that we will be on track with hop samples collected and analyzed by the next report date. However, these challenges only minimally affect our progress. The project is a three-year project, but with 2 years of funding to carry out the work. Therefore, it is beneficial for us to move the work to years 2 and 3 for the project, which will avoid any "gap years" for personnel or trainees. We are in the fourth month of year 2, and therefore are making good progress. What opportunities for training and professional development has the project provided?The work has several opportunities for professional development. This includes, plant husbandry, growing plants in the greenhouse, sample collection, data analysis, and data curation. Because this is a three-year project with two years of funding, we have put the work of the project in years 2 and 3, to avoid a "gap year" for paying salaries etc. At the moment, we are beginning the work of the proposed project, and therefore have little to report, but expect this to change in next year's progress report. How have the results been disseminated to communities of interest? Nothing Reported What do you plan to do during the next reporting period to accomplish the goals?We expect to have a manuscript submitted, or at least in preparation for the next reporting period. The sample and data collection will happen over this summer and fall, and we expect to have data collected by Fall term. We will then work towards publications and disseminating our results.

Impacts
What was accomplished under these goals? Overview of Sample Collection We have collected flower samples from hemp, but are still working towards collecting flower samples from hops. Because we sought to keep things uniform for hop and hemp, we wanted to grow them both under the same conditions. However, we could not get approval to grow hemp outdoors, leading us to grow both hop and hemp in greenhouses. This proved to be more challenging than anticipated for hop cone (flower) collection and these plants are still growing. That said, we expect that we will be on track with hop samples collected and analyzed by the next report date. Hemp Collection We are collecting paired female flower samples from diverse hemp accessions for parallel analysis of cannabinoid/terpene profiles and gene expression. The first collection was done March 30, 2023, from fourteen hemp accessions. They were immediately flash frozen on dry ice, then stored at -80C. Table 1: hemp accessions that have been collected. Accession Arab-32 Berry Blossom Carmagnola x Arcadia Carmagnola x Santiam Carmagnola x Umpqua CBDV CBCW-8 HD Cherry Laos Mango Biche Nurse Lilly Solodiol CBD Special Sauce Temperanillo Hop Sample Collection Rhizomes from 25 genetically diverse hop cultivars (Table 2 below) were dug and transplanted into 3.8-liter pots during February 2023. Three replications of each cultivar were potted up and then placed in a greenhouse with 16-h light, 8-h dark period with a constant temperature of 24 Celsius. All plants were subsequently re-potted into 18.9-liter pots during April, 2023. Plants were trained up string inside of the GH and allowed to grow to a height of 3-m. Excess growth was re-trained onto the same string. Plants were watered daily and fertilized bi-weekly with "Miracle Grow" (https://miraclegro.com/en-us/shop/plant-food/miracle-gro-water-soluble-all-purpose-plant-food/miracle-gro-water-soluble-all-purpose-plant-food.html). At no point in time were the plants allowed to be stressed for water or temperature. Finally, all plant diseases and insect pests were controlled as needed using chemicals labeled for use in hops. Of the 25 cultivars grown for this study, only six (6) have formed cones. Of the six that have formed cones only one cultivar is near ready for harvesting cones. These cones will be harvested on May 15th. The other five (5) lines with cones present will be harvested during the week of May 22-26, 2023. The remaining 19 cultivars could potentially form cones. However, the current state of these genotypes is that they have not formed axillary branches that would have flowering nodes on them. There is one other issue noted from this study using greenhouse grown hop plants. We have noticed in all cases where cones have formed that lupulin gland production is significantly reduced in greenhouse grown plants versus plants grown out in field conditions. Whether or not this has an impact upon this study is not known at this time. All attempts will be made to collect cones from hop plants present in the greenhouse. The contingency for this study is to harvest these cultivars from outdoor plots. The original design for this experiment was to grow plants in an outdoor hop garden to maximize cone production and have lupulin production optimized. These cultivars are already planted in a hop garden and will be harvested during the Fall, 2023 at their optimum maturity date (historically recorded and estimated precisely by dry matter content). Table 2. List of cultivars and status of cone formation May 10, 2023. Cultivar Flower Status Cone Status Northern Brewer Short, no flowers Triumph No flowers Tea maker No flowers Aurora No flowers Cascade Flowers Cones Mt Rainier Flowers Cones Galena No flowers Giggle N No flowers Whitsbred Golding No flowers Hallertauer Tradition No flowers Hallertauer Mittelfrue Short, no flowers Horizon Some flowers Some cones Kitamidori Flowers Cones Centennial No flowers Pride of Kent Short, no flowers Saazer No flowers Sorachi Ace Flowers Cones Comet No flowers Target No flowers Brewers Gold Short, no flowers Chinook Flowers Cones Perle No flowers Eye Viking Short, no flowers Nugget No flowers Backa No flowers

Publications