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de Ronne M, Torkamaneh D. Discovery of major QTL and a massive haplotype associated with cannabinoid biosynthesis in drug-type Cannabis. THE PLANT GENOME 2025; 18:e70031. [PMID: 40415170 DOI: 10.1002/tpg2.70031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2024] [Revised: 03/21/2025] [Accepted: 03/21/2025] [Indexed: 05/27/2025]
Abstract
Cannabis (Cannabis sativa L.), once sidelined by decades of prohibition, has now gained recognition as a multifaceted and promising plant in both medical research and commercial applications following its recent legalization. This study leverages a genome-wide association study (GWAS) on 174 drug-type Cannabis accessions from the legal Canadian market, focusing on identifying quantitative trait loci (QTL) and candidate genes associated with eleven cannabinoid traits using 282K common single-nucleotide polymorphisms. This approach aims to transform our understanding of Cannabis genetics. We have pinpointed 33 significant markers that significantly influence cannabinoid production, promising to drive the development of Cannabis varieties with specific cannabinoid profiles. Among the notable findings is a massive haplotype of ∼60 Mb on chromosome 7 in Type I (i.e., tetrahydrocannabinol [THC]-dominant) accessions, highlighting a major genetic influence on cannabinoid profiles. These insights offer valuable guidance for Cannabis breeding programs, enabling the use of precise genetic markers to select and refine promising Cannabis varieties. This approach promises to speed up the breeding process, reduce costs significantly compared to traditional methods, and ensure that the resulting Cannabis varieties are optimized for specific medical and recreational needs. This study marks a significant stride toward fully integrating Cannabis into modern agricultural practices and genetic research, paving the way for future innovations.
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Affiliation(s)
- Maxime de Ronne
- Département de Phytologie, Université Laval, Québec City, Québec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, Québec, Canada
- Centre de recherche et d'innovation sur les végétaux (CRIV), Université Laval, Québec City, Québec, Canada
| | - Davoud Torkamaneh
- Département de Phytologie, Université Laval, Québec City, Québec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, Québec, Canada
- Centre de recherche et d'innovation sur les végétaux (CRIV), Université Laval, Québec City, Québec, Canada
- Institut intelligence et données (IID), Université Laval, Québec City, Québec, Canada
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Seifi S, Leckie KM, Giles I, O’Brien T, MacKenzie JO, Todesco M, Rieseberg LH, Baute GJ, Celedon JM. Mapping and characterization of a novel powdery mildew resistance locus (PM2) in Cannabis sativa L. FRONTIERS IN PLANT SCIENCE 2025; 16:1543229. [PMID: 40182551 PMCID: PMC11966446 DOI: 10.3389/fpls.2025.1543229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2024] [Accepted: 02/05/2025] [Indexed: 04/05/2025]
Abstract
Introduction Breeding genetic resistance to economically important crop diseases is the most sustainable strategy for disease management and enhancing agricultural and horticultural productivity, particularly where the application of synthetic pesticides is prohibited. Powdery mildew disease, caused by the biotrophic fungal pathogen Golovinomyces ambrosiae, is one of the most prevalent threats to the cannabis and hemp industry worldwide. Methods In this study, we used bulked-segregant analysis combined with high-throughput RNA sequencing (BSRSeq) to identify and map a novel single dominant resistance (R) locus (designated PM2), that strongly suppresses powdery mildew infection and sporulation in Cannabis sativa. Results and discussion BSA mapped PM2 to chromosome 9. Histochemical analysis revealed that PM2-induced resistance is mediated by a highly localized hypersensitive response mainly in the epidermal cells of the host. Importantly, genetic markers capable of tracking PM2 resistance in breeding populations were developed using associated SNPs identified in this study. The ability to track PM2 will allow for successful introgression of PM resistance into elite cannabis cultivars and help move towards a more sustainable cannabis industry.
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Affiliation(s)
- Soren Seifi
- Breeding and Genetics Department, Aurora Cannabis, Inc., Comox, BC, Canada
| | - Keegan M. Leckie
- Breeding and Genetics Department, Aurora Cannabis, Inc., Comox, BC, Canada
| | - Ingrid Giles
- Breeding and Genetics Department, Aurora Cannabis, Inc., Comox, BC, Canada
| | - Taylor O’Brien
- Breeding and Genetics Department, Aurora Cannabis, Inc., Comox, BC, Canada
| | - John O. MacKenzie
- Breeding and Genetics Department, Aurora Cannabis, Inc., Comox, BC, Canada
| | - Marco Todesco
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Loren H. Rieseberg
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Gregory J. Baute
- Breeding and Genetics Department, Aurora Cannabis, Inc., Comox, BC, Canada
| | - Jose M. Celedon
- Breeding and Genetics Department, Aurora Cannabis, Inc., Comox, BC, Canada
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Stack GM, Quade MA, Wilkerson DG, Monserrate LA, Bentz PC, Carey SB, Grimwood J, Toth JA, Crawford S, Harkess A, Smart LB. Comparison of Recombination Rate, Reference Bias, and Unique Pangenomic Haplotypes in Cannabis sativa Using Seven De Novo Genome Assemblies. Int J Mol Sci 2025; 26:1165. [PMID: 39940933 PMCID: PMC11818205 DOI: 10.3390/ijms26031165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2024] [Revised: 01/20/2025] [Accepted: 01/27/2025] [Indexed: 02/16/2025] Open
Abstract
Genomic characterization of Cannabis sativa has accelerated rapidly in the last decade as sequencing costs have decreased and public and private interest in the species has increased. Here, we present seven new chromosome-level haplotype-phased genomes of C. sativa. All of these genotypes were alive at the time of publication, and several have numerous years of associated phenotype data. We performed a k-mer-based pangenome analysis to contextualize these assemblies within over 200 existing assemblies. This allowed us to identify unique haplotypes and genomic diversity among Cannabis sativa genotypes. We leveraged linkage maps constructed from F2 progeny of two of the assembled genotypes to characterize the recombination rate across the genome showing strong periphery-biased recombination. Lastly, we re-aligned a bulk segregant analysis dataset for the major-effect flowering locus Early1 to several of the new assemblies to evaluate the impact of reference bias on the mapping results and narrow the locus to a smaller region of the chromosome. These new assemblies, combined with the continued propagation of the genotypes, will contribute to the growing body of genomic resources for C. sativa to accelerate future research efforts.
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Affiliation(s)
- George M. Stack
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA; (G.M.S.); (M.A.Q.); (D.G.W.); (L.A.M.); (J.A.T.)
| | - Michael A. Quade
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA; (G.M.S.); (M.A.Q.); (D.G.W.); (L.A.M.); (J.A.T.)
| | - Dustin G. Wilkerson
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA; (G.M.S.); (M.A.Q.); (D.G.W.); (L.A.M.); (J.A.T.)
| | - Luis A. Monserrate
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA; (G.M.S.); (M.A.Q.); (D.G.W.); (L.A.M.); (J.A.T.)
| | - Philip C. Bentz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA; (P.C.B.); (S.B.C.); (J.G.); (A.H.)
| | - Sarah B. Carey
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA; (P.C.B.); (S.B.C.); (J.G.); (A.H.)
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA; (P.C.B.); (S.B.C.); (J.G.); (A.H.)
| | - Jacob A. Toth
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA; (G.M.S.); (M.A.Q.); (D.G.W.); (L.A.M.); (J.A.T.)
| | | | - Alex Harkess
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA; (P.C.B.); (S.B.C.); (J.G.); (A.H.)
| | - Lawrence B. Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA; (G.M.S.); (M.A.Q.); (D.G.W.); (L.A.M.); (J.A.T.)
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Cull A, Joly DL. Development and validation of a minimal SNP genotyping panel for the differentiation of Cannabis sativa cultivars. BMC Genomics 2025; 26:83. [PMID: 39875833 PMCID: PMC11773717 DOI: 10.1186/s12864-025-11263-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2024] [Accepted: 01/20/2025] [Indexed: 01/30/2025] Open
Abstract
BACKGROUND Due to its previously illicit nature, Cannabis sativa had not fully reaped the benefits of recent innovations in genomics and plant sciences. However, Canada's legalization of C. sativa and products derived from its flower in 2018 triggered significant new demand for robust genotyping tools to assist breeders in meeting consumer demands. Early molecular marker-based research on C. sativa focused on screening for plant sex and chemotype, and more recent research has sought to use molecular markers to target traits of agronomic interest, to study populations and to differentiate between C. sativa cultivars. RESULTS In this study, we have conducted whole genome sequencing of 32 cultivars, mined the sequencing data for SNPs, developed a reduced SNP genotyping panel to discriminate between sequenced cultivars, then validated the 20-SNP panel using DNA from the sequenced cultivars and tested the assays on commercially available dried flower. The assay conversion rate was higher in DNA extracted from fresh plant material than in DNA extracted from dried flower samples. However, called genotypes were internally consistent, highlighting discrepancies between genotypes detected using sequencing data and observed using genotyping assays. The primary contributions of this work are to clearly document the process used to develop minimal SNP genotyping panels, the feasibility of using such panels to differentiate between C. sativa cultivars, and outline improvements and goals for future iterations of PCR-based, minimal SNP panels to enable efficient development genotyping tools to identify and screen C. sativa cultivars. CONCLUSIONS Our key recommendations are to increase sampling density to account for intra-cultivar variability; leverage higher read length paired-end short-read technology; conduct in-depth pre- and post-processing of reads, mapping, and variant calling data; integrate trait-associated loci to develop multi-purpose panels; and use iterative approaches for in vitro validation to ensure that only the most discriminant and performant SNPs are retained.
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Affiliation(s)
- Alex Cull
- Cannabis Innovation and Research Center, Université de Moncton, Moncton, New-Brunswick, Canada
| | - David L Joly
- Cannabis Innovation and Research Center, Université de Moncton, Moncton, New-Brunswick, Canada.
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Mostafaei Dehnavi M, Damerum A, Taheri S, Ebadi A, Panahi S, Hodgin G, Brandley B, Salami SA, Taylor G. Population genomics of a natural Cannabis sativa L. collection from Iran identifies novel genetic loci for flowering time, morphology, sex and chemotyping. BMC PLANT BIOLOGY 2025; 25:80. [PMID: 39838336 PMCID: PMC11748290 DOI: 10.1186/s12870-025-06045-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Accepted: 01/01/2025] [Indexed: 01/23/2025]
Abstract
BACKGROUND Future breeding and selection of Cannabis sativa L. for both drug production and industrial purposes require a source of germplasm with wide genetic variation, such as that found in wild relatives and progenitors of highly cultivated plants. Limited directional selection and breeding have occurred in this crop, especially informed by molecular markers. RESULTS This study investigated the population genomics of a natural cannabis collection comprising male and female individuals from various climatic zones in Iran. Using Genotyping-By-Sequencing (GBS), we sequenced 228 individuals from 35 populations. The data obtained enabled an association analysis, linking genotypes with key phenotypes such as inflorescence characteristics, flowering time, plant morphology, tetrahydrocannabinol (THC) and cannabidiol (CBD) content, and sex. We detected approximately 23,266 significant high-quality Single Nucleotide Polymorphisms (SNPs), establishing associations between markers and traits. The population structure analysis revealed that Iranian cannabis plants fall into five distinct groups. Additionally, a comparison with global data suggested that the Iranian populations is distinctive and generally closer to marijuana than to hemp, with some populations showing a closer affinity to hemp. The GWAS identified novel genetic loci associated with sex, yield, and chemotype traits in cannabis, which had not been previously reported. CONCLUSION The study's findings highlight the distinct genetic structure of Iranian Cannabis populations. The identification of novel genetic loci associated with important traits suggests potential targets for future breeding programs. This research underscores the value of the Iranian cannabis germplasm as a resource for breeding and selection efforts aimed at improving Cannabis for various uses.
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Affiliation(s)
- Mahboubeh Mostafaei Dehnavi
- Department of Plant Sciences, University of California, Davis, CA, USA
- Department of Horticultural Science, Faculty of Agriculture, University of Tehran, Karaj, Iran
| | - Annabelle Damerum
- Department of Plant Sciences, University of California, Davis, CA, USA
- Present address, Zymo Research Corp, Irvine, CA, USA
| | - Sadegh Taheri
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Ali Ebadi
- Department of Horticultural Science, Faculty of Agriculture, University of Tehran, Karaj, Iran
| | - Shadab Panahi
- Department of Horticultural Science, Faculty of Agriculture, University of Tehran, Karaj, Iran
| | - George Hodgin
- Biopharmaceutical Research Company, Castroville, CA, USA
| | - Brian Brandley
- Biopharmaceutical Research Company, Castroville, CA, USA
| | - Seyed Alireza Salami
- Department of Horticultural Science, Faculty of Agriculture, University of Tehran, Karaj, Iran.
- Industrial and Medical Cannabis Research Institute (IMCRI), Tehran, Iran.
| | - Gail Taylor
- Department of Plant Sciences, University of California, Davis, CA, USA.
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Frusciante L, Geminiani M, Shabab B, Olmastroni T, Roncucci N, Mastroeni P, Salvini L, Lamponi S, Trezza A, Santucci A. Enhancing Industrial Hemp ( Cannabis sativa) Leaf By-Products: Bioactive Compounds, Anti-Inflammatory Properties, and Potential Health Applications. Int J Mol Sci 2025; 26:548. [PMID: 39859264 PMCID: PMC11765263 DOI: 10.3390/ijms26020548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2024] [Revised: 12/21/2024] [Accepted: 01/08/2025] [Indexed: 01/27/2025] Open
Abstract
The sustainable utilization of biomass-derived bioactives addresses the growing demand for natural health products and supports sustainable development goals by reducing reliance on synthetic chemicals in healthcare. Cannabis sativa biomass, in particular, has emerged as a valuable resource within this context. This study focuses on the hydroethanolic extract of C. sativa leaves (CSE), which exhibited significant levels of phenolic compounds contributing to robust antioxidant activity. Evaluation using potassium ferricyanide, ABTS, and DPPH methods revealed potent radical scavenging activity comparable to the Trolox standard. UPLC-MS/MS profiling identified cannabinoids as the predominant secondary metabolites in CSE, with flavonoids also present in substantial quantities. This study investigated the anti-inflammatory potential of CSE on RAW 264.7 macrophages and IL-1β-stimulated C-20/A4 immortalized human chondrocytes, demonstrating protective effects without cytotoxic or mutagenic effects. Mechanistically, CSE reduced inflammation by inhibiting the MAPK and NF-κB signaling pathways. In silico approaches showed the ability of CSE's main metabolites to bind and influence MAPK and NF-κB activity, confirming in vitro evidence. Incorporating C. sativa leaf extract into a hyaluronic acid-based formulation showed biotechnological promise for treating joint inflammation. Future research should aim to elucidate the molecular mechanisms underlying these effects and explore the potential of CSE-derived compounds in mitigating osteoarthritis progression. This approach highlights the significance of utilizing annually increasing biomass waste for sustainable bioactivity and environmental impact reduction.
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Affiliation(s)
- Luisa Frusciante
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro, 53100 Siena, Italy; (L.F.); (B.S.); (T.O.); (P.M.); (S.L.); (A.T.); (A.S.)
| | - Michela Geminiani
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro, 53100 Siena, Italy; (L.F.); (B.S.); (T.O.); (P.M.); (S.L.); (A.T.); (A.S.)
- SienabioACTIVE, University of Siena, Via Aldo Moro, 53100 Siena, Italy
| | - Behnaz Shabab
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro, 53100 Siena, Italy; (L.F.); (B.S.); (T.O.); (P.M.); (S.L.); (A.T.); (A.S.)
| | - Tommaso Olmastroni
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro, 53100 Siena, Italy; (L.F.); (B.S.); (T.O.); (P.M.); (S.L.); (A.T.); (A.S.)
| | - Neri Roncucci
- Tenuta di Mensanello, Località Mensanello, 34, 53034 Colle di Val d’Elsa, Italy;
| | - Pierfrancesco Mastroeni
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro, 53100 Siena, Italy; (L.F.); (B.S.); (T.O.); (P.M.); (S.L.); (A.T.); (A.S.)
| | - Laura Salvini
- Fondazione Toscana Life Sciences, Strada del Petriccio e Belriguardo, 53100 Siena, Italy;
| | - Stefania Lamponi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro, 53100 Siena, Italy; (L.F.); (B.S.); (T.O.); (P.M.); (S.L.); (A.T.); (A.S.)
- SienabioACTIVE, University of Siena, Via Aldo Moro, 53100 Siena, Italy
| | - Alfonso Trezza
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro, 53100 Siena, Italy; (L.F.); (B.S.); (T.O.); (P.M.); (S.L.); (A.T.); (A.S.)
| | - Annalisa Santucci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro, 53100 Siena, Italy; (L.F.); (B.S.); (T.O.); (P.M.); (S.L.); (A.T.); (A.S.)
- SienabioACTIVE, University of Siena, Via Aldo Moro, 53100 Siena, Italy
- ARTES 4.0, Viale Rinaldo Piaggio, 34, 56025 Pontedera, Italy
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de Ronne M, Boyle B, Torkamaneh D. AVITI as an alternative to Illumina for low-cost genome-wide genotyping. Genome 2025; 68:1-4. [PMID: 39970419 DOI: 10.1139/gen-2024-0068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2025]
Abstract
Advancements in sequencing technologies have dramatically transformed genomics research by enabling the analysis of genetic information with unprecedented scale and efficiency. Next-generation sequencing, renowned for its high-throughput capabilities, has significantly reduced costs and expanded the scope of sequencing applications. Among these, sequencing by synthesis on Illumina systems is predominant, favored for its accuracy and cost-effectiveness. However, emerging technologies like Element Biosciences' sequencing by Avidity (AVITI) are beginning to challenge this dominance. In this study, we sequenced and genotyped a library of 40 Cannabis samples using both the AVITI and Illumina NovaSeq systems. After filtering out low-quality variants, both technologies showed an 81.2% overlap with 98.9% concordance in genotype calls. AVITI stands out for its flexibility and reduced per-base costs, presenting a viable option particularly for mid-sized laboratories. As the scientific community continues to seek ways to lower genotyping expenses, the combination of the AVITI system with NanoGBS library preparation offers a cost-effective solution adaptable to a wide range of project sizes.
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Affiliation(s)
- Maxime de Ronne
- Département de Phytologie, Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Centre de recherche et d'innovation sur les végétaux (CRIV), Université Laval, Québec, QC, Canada
| | - Brian Boyle
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Davoud Torkamaneh
- Département de Phytologie, Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Centre de recherche et d'innovation sur les végétaux (CRIV), Université Laval, Québec, QC, Canada
- Institut intelligence et données (IID), Université Laval, Québec, QC, Canada
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Pancaldi F, Salentijn EMJ, Trindade LM. From fibers to flowering to metabolites: unlocking hemp (Cannabis sativa) potential with the guidance of novel discoveries and tools. JOURNAL OF EXPERIMENTAL BOTANY 2025; 76:109-123. [PMID: 39324630 DOI: 10.1093/jxb/erae405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 09/24/2024] [Indexed: 09/27/2024]
Abstract
Cannabis sativa L. is an ancient crop, but its agricultural adoption has been interrupted to prevent the use of marijuana as a psychoactive drug. Nevertheless, hemp-the C. sativa type with low concentrations of intoxicating Δ9-tetrahydrocannabinoid-is experiencing a resurgence in interest due to loosened cultivation restrictions and its potential as a multipurpose bio-based crop. Hemp has valuable applications, including production of medicines from its non-intoxicating cannabinoids, food, medical, and industrial uses of its seed oil rich in polyunsaturated fatty acids, and production of fibers for textiles and industry from its stems. Recently, several hemp genomic and genetic resources have been developed, allowing significant expansion of our knowledge of major hemp traits, such as synthesis of cannabinoids, oil, and fibers, and regulation of flowering and sex determination. Still, hemp is an underimproved crop, and its development will depend on the ability to expand and collectively use the novel resources arising from fast advancements in bioinformatics and plant phenotyping. This review discusses current genetic and genomic knowledge of the most important hemp traits, and provides a perspective on how to further expand such knowledge and tackle hemp improvement with the most up-to-date tools for plant and hemp research.
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Affiliation(s)
- Francesco Pancaldi
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Elma M J Salentijn
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Luisa M Trindade
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
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Jost R, Berkowitz O, Pegg A, Hurgobin B, Tamiru-Oli M, Welling MT, Deseo MA, Noorda H, Brugliera F, Lewsey MG, Doblin MS, Bacic A, Whelan J. Sink strength, nutrient allocation, cannabinoid yield, and associated transcript profiles vary in two drug-type Cannabis chemovars. JOURNAL OF EXPERIMENTAL BOTANY 2025; 76:152-174. [PMID: 39225376 PMCID: PMC11659186 DOI: 10.1093/jxb/erae367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 09/05/2024] [Indexed: 09/04/2024]
Abstract
Cannabis sativa L. is one of the oldest domesticated crops. Hemp-type cultivars, which predominantly produce non-intoxicating cannabidiol (CBD), have been selected for their fast growth, seed, and fibre production, while drug-type chemovars were bred for high accumulation of tetrahydrocannabinol (THC). We investigated how the generation of CBD-dominant chemovars by introgression of hemp- into drug-type Cannabis impacted plant performance. The THC-dominant chemovar showed superior sink strength, higher flower biomass, and demand-driven control of nutrient uptake. By contrast, the CBD-dominant chemovar hyperaccumulated phosphate in sink organs leading to reduced carbon and nitrogen assimilation in leaves, which limited flower biomass and cannabinoid yield. RNA-seq analyses determined organ- and chemovar-specific differences in expression of genes associated with nitrate and phosphate homeostasis as well as growth-regulating transcription factors that were correlated with measured traits. Among these were genes positively selected for during Cannabis domestication encoding an inhibitor of the phosphate starvation response, SPX DOMAIN GENE3, nitrate reductase, and two nitrate transporters. Altered nutrient sensing, acquisition, or distribution are likely a consequence of adaption to growth on marginal, low-nutrient-input lands in hemp. Our data provide evidence that such ancestral traits may become detrimental for female flower development and consequently overall CBD yield in protected cropping environments.
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Affiliation(s)
- Ricarda Jost
- Australian Research Council Research Hub for Medicinal Agriculture, Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC 3086, Australia
- La Trobe Institute for Sustainable Agriculture and Food, La Trobe University, Bundoora, VIC 3086, Australia
| | - Oliver Berkowitz
- Australian Research Council Research Hub for Medicinal Agriculture, Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC 3086, Australia
- La Trobe Institute for Sustainable Agriculture and Food, La Trobe University, Bundoora, VIC 3086, Australia
| | - Amelia Pegg
- Australian Research Council Research Hub for Medicinal Agriculture, Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC 3086, Australia
- La Trobe Institute for Sustainable Agriculture and Food, La Trobe University, Bundoora, VIC 3086, Australia
| | - Bhavna Hurgobin
- Australian Research Council Research Hub for Medicinal Agriculture, Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC 3086, Australia
- La Trobe Institute for Sustainable Agriculture and Food, La Trobe University, Bundoora, VIC 3086, Australia
| | - Muluneh Tamiru-Oli
- Australian Research Council Research Hub for Medicinal Agriculture, Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC 3086, Australia
- La Trobe Institute for Sustainable Agriculture and Food, La Trobe University, Bundoora, VIC 3086, Australia
| | - Matthew T Welling
- Australian Research Council Research Hub for Medicinal Agriculture, Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC 3086, Australia
- La Trobe Institute for Sustainable Agriculture and Food, La Trobe University, Bundoora, VIC 3086, Australia
| | - Myrna A Deseo
- Australian Research Council Research Hub for Medicinal Agriculture, Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC 3086, Australia
- La Trobe Institute for Sustainable Agriculture and Food, La Trobe University, Bundoora, VIC 3086, Australia
| | - Hannah Noorda
- Cann Group Limited, Port Melbourne, VIC 3207, Australia
| | | | - Mathew G Lewsey
- Australian Research Council Research Hub for Medicinal Agriculture, Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC 3086, Australia
- La Trobe Institute for Sustainable Agriculture and Food, La Trobe University, Bundoora, VIC 3086, Australia
- Australian Research Council Centre of Excellence in Plants for Space, La Trobe University, Bundoora, VIC, Australia
| | - Monika S Doblin
- Australian Research Council Research Hub for Medicinal Agriculture, Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC 3086, Australia
- La Trobe Institute for Sustainable Agriculture and Food, La Trobe University, Bundoora, VIC 3086, Australia
| | - Antony Bacic
- Australian Research Council Research Hub for Medicinal Agriculture, Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC 3086, Australia
- La Trobe Institute for Sustainable Agriculture and Food, La Trobe University, Bundoora, VIC 3086, Australia
| | - James Whelan
- Australian Research Council Research Hub for Medicinal Agriculture, Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC 3086, Australia
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10
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Wee Y B, Berkowitz O, Whelan J, Jost R. Same, yet different: towards understanding nutrient use in hemp- and drug-type Cannabis. JOURNAL OF EXPERIMENTAL BOTANY 2025; 76:94-108. [PMID: 39180219 PMCID: PMC11659179 DOI: 10.1093/jxb/erae362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 08/28/2024] [Indexed: 08/26/2024]
Abstract
Cannabis sativa L., one of the oldest cultivated crops, has a complex domestication history due to its diverse uses for fibre, seed, oil, and drugs, and its wide geographic distribution. This review explores how human selection has shaped the biology of hemp and drug-type Cannabis, focusing on acquisition and utilization of nitrogen and phosphorus, and how resulting changes in source-sink relations shape their contrasting phenology. Hemp has been optimized for rapid, slender growth and nutrient efficiency, whereas drug-type cultivars have been selected for compact growth with large phytocannabinoid-producing female inflorescences. Understanding these nutrient use and ontogenetic differences will enhance our general understanding of resource allocation in plants. Knowledge gained in comparison with other model species, such as tomato, rice, or Arabidopsis can help inform crop improvement and sustainability in the cannabis industry.
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Affiliation(s)
- Benjamin Wee Y
- ARC Research Hub for Medicinal Agriculture, Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora VIC 3086, Australia
- La Trobe Institute for Sustainable Agriculture & Food, La Trobe University, Bundoora VIC 3086, Australia
| | - Oliver Berkowitz
- ARC Research Hub for Medicinal Agriculture, Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora VIC 3086, Australia
- La Trobe Institute for Sustainable Agriculture & Food, La Trobe University, Bundoora VIC 3086, Australia
| | - James Whelan
- ARC Research Hub for Medicinal Agriculture, Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora VIC 3086, Australia
- La Trobe Institute for Sustainable Agriculture & Food, La Trobe University, Bundoora VIC 3086, Australia
- Present Address: College of Life Science, Zhejiang University, Hangzhou, Zhejiang, 310058, P.R. China
| | - Ricarda Jost
- ARC Research Hub for Medicinal Agriculture, Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora VIC 3086, Australia
- La Trobe Institute for Sustainable Agriculture & Food, La Trobe University, Bundoora VIC 3086, Australia
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11
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Fulvio F, Pieracci Y, Ascrizzi R, Bassolino L, Flamini G, Paris R. Insights into terpenes profiling and transcriptional analyses during flowering of different Cannabis sativa L. chemotypes. PHYTOCHEMISTRY 2025; 229:114294. [PMID: 39374748 DOI: 10.1016/j.phytochem.2024.114294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 09/18/2024] [Accepted: 09/30/2024] [Indexed: 10/09/2024]
Abstract
Terpenes, volatile compounds known for their aromatic and therapeutic properties, play a pivotal role in shaping the overall chemical profile of Cannabis sativa L. Their biosynthesis in planta occurs in trichomes and involves the 2-C-methyl-D-erythritol 4-phosphate (MEP) and the mevalonic acid (MVA) pathways, responsible for producing the substrates utilized by a family of enzymes, the terpene synthases (TPS), for terpene production. In this work, a comprehensive approach combining chemical analyses of the volatile compounds characterizing the aroma of the inflorescences three C. sativa genotypes collected at three stages of maturity and the transcriptional analyses of key genes involved in the terpene biosynthesis was adopted to study this pathway. The results revealed different terpene profiles among genotypes, which were characterized by peculiar compounds belonging to the sesqui- (CINBOL and Fibrante) or monoterpene (Ermo) categories. Both structural and putative regulatory genes were analysed by RT-qPCR, revealing distinct transcriptional profiles of Terpene Synthases, contributing to the diversity of mono and sesquiterpenes synthesized. Furthermore, the research delved into potential regulatory genes associated with trichome formation, a crucial factor influencing terpene accumulation. This integrated approach highlighted complex mechanisms governing terpene accumulation in cannabis, while also offering potential regulators putatively involved in this pathway.
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Affiliation(s)
- Flavia Fulvio
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops (CREA-CI), Via di Corticella 133, 40128, Bologna, Italy
| | - Ylenia Pieracci
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126, Pisa, Italy
| | - Roberta Ascrizzi
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126, Pisa, Italy; Interdepartmental Research Center "Nutraceuticals and Food for Health" (NUTRAFOOD), University of Pisa, Via Del Borghetto 80, 56124, Pisa, Italy
| | - Laura Bassolino
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops (CREA-CI), Via di Corticella 133, 40128, Bologna, Italy
| | - Guido Flamini
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126, Pisa, Italy; Interdepartmental Research Center "Nutraceuticals and Food for Health" (NUTRAFOOD), University of Pisa, Via Del Borghetto 80, 56124, Pisa, Italy
| | - Roberta Paris
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops (CREA-CI), Via di Corticella 133, 40128, Bologna, Italy.
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12
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Cheng YC, Houston R. The development of two fast genotyping assays for the differentiation of hemp from marijuana. J Forensic Sci 2025; 70:49-60. [PMID: 39551963 DOI: 10.1111/1556-4029.15663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2024] [Revised: 10/20/2024] [Accepted: 10/29/2024] [Indexed: 11/19/2024]
Abstract
The legalization of hemp cultivation in the United States has raised the need for reliable methods to distinguish between legal hemp and illegal marijuana. Genetic analysis has emerged as a powerful tool, surpassing traditional chemical methods in specific aspects, such as analyzing trace amounts, aged samples, and different parts of the sample. Genetic differences in cannabinoid synthase genes offer promise for precise crop type determination, particularly focusing on genes like tetrahydrocannabinolic acid synthase (THCAS), cannabidiolic acid synthase (CBDAS), and cannabichromenic acid synthase (CBCAS). However, previous research faced several challenges in developing discriminatory genetic markers, including limited sample sizes, high similarity between the synthase genes, and the presence of pseudo synthase genes. A comprehensive study using Next-Generation Sequencing (NGS) introduced a differentiation flowchart based on THCAS, CBDAS, and THCAS pseudogenes. To bridge the gap between NGS and the practical requirements of crime laboratories, two rapid genotyping assays were developed: a CE-based SNaPshot™ assay and a TaqMan™ real-time PCR assay. While the SNaPshot™ assay effectively differentiated various hemp and marijuana types, differentiation was limited with marijuana samples containing THC% close to the 0.3% legal threshold (0.3%-1%). The TaqMan™ qPCR SNP genotyping assay provided quicker results, making it an efficient choice for crime laboratories. However, this method had the same limitations as the SNaPshot™ assay with addtional challenges in differentiating edible hemp seed samples, and it did not provide additional CBD information. The study also highlighted the influence of two variants of one THCAS pseudogene on chemotype determination, emphasizing the necessity for precise genetic analysis for accurate categorization of cannabis varieties.
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Affiliation(s)
- Ya-Chih Cheng
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, Huntsville, Texas, USA
| | - Rachel Houston
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, Huntsville, Texas, USA
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13
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Enríquez DJ, Alonso JC, Hille L, Brand S, Holzgrabe U, Vergara D, Montoya G, Ramírez YA. Unveiling Colombia's medicinal Cannabis sativa treasure trove: Phenotypic and Chemotypic diversity in legal cultivation. PHYTOCHEMICAL ANALYSIS : PCA 2025; 36:246-260. [PMID: 39169651 DOI: 10.1002/pca.3436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 06/21/2024] [Accepted: 06/22/2024] [Indexed: 08/23/2024]
Abstract
INTRODUCTION Cannabis sativa is a highly versatile plant with a long history of cultivation and domestication. It produces multiple compounds that exert distinct and valuable therapeutic effects by modulating diverse biological systems, including the endocannabinoid system (ECS). Access to standardized, metabolically diverse, and reproducible C. sativa chemotypes and chemovars is essential for physicians to optimize individualized patient treatment and for industries to conduct drug-discovery campaigns. OBJECTIVE This study aimed to characterize and assess the phytochemical diversity of C. sativa chemotypes in diverse ecological regions of Colombia, South America. METHODOLOGY Ten cannabinoids and 23 terpenes were measured using liquid and gas chromatography, in addition to other phenotypic traits, in 156 C. sativa plants that were grown in diverse ecological regions in Colombia, a hotspot for global biodiversity. RESULTS Our results reveal significant phytochemical diversity in Colombian-grown C. sativa plants, with four distinct chemotypes based on cannabinoid profile. The significant amount of usually uncommon terpenes suggests that Colombia's environments may have unique capabilities that allow the plant to express these compounds. Colombia's diverse climates offer enormous cultivation potential, making it a key player in both domestic and international medicinal and recreational C. sativa trade. CONCLUSION These findings underscore Colombia's capacity to pioneer global C. sativa production diversification, particularly in South America with new emerging markets.
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Affiliation(s)
- Diego J Enríquez
- Facultad de Ingeniería, Diseño y Ciencias Aplicadas, Universidad Icesi, Cali, Valle del Cauca, Colombia
| | - Julio C Alonso
- Facultad de Ciencias Administrativas y Económicas, Universidad Icesi, Cali, Valle del Cauca, Colombia
| | - Lucas Hille
- Institute for Chemistry and Biochemistry, Free University of Berlin, Berlin, Germany
| | - Stefan Brand
- Symrise AG, Mühlenfeldstrasse1, Holzminden, Germany
| | - Ulrike Holzgrabe
- Institute for Pharmacy and Food Chemistry, University of Würzburg. Am Hubland 97074, Würzburg, Germany
| | - Daniela Vergara
- Harvest New York, Cornell Cooperative Extension, Geneva, New York, USA
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado, USA
| | - Guillermo Montoya
- Facultad de Ingeniería, Diseño y Ciencias Aplicadas, Universidad Icesi, Cali, Valle del Cauca, Colombia
| | - Yesid A Ramírez
- Facultad de Ingeniería, Diseño y Ciencias Aplicadas, Universidad Icesi, Cali, Valle del Cauca, Colombia
- Institute for Pharmacy and Food Chemistry, University of Würzburg. Am Hubland 97074, Würzburg, Germany
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14
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Shi J, Toscani M, Dowling CA, Schilling S, Melzer R. Identification of genes associated with sex expression and sex determination in hemp (Cannabis sativa L.). JOURNAL OF EXPERIMENTAL BOTANY 2025; 76:175-190. [PMID: 39468733 DOI: 10.1093/jxb/erae429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 10/26/2024] [Indexed: 10/30/2024]
Abstract
Dioecy in flowering plants has evolved independently many times, and thus the genetic mechanisms underlying sex determination are diverse. In hemp (Cannabis sativa), sex is controlled by a pair of sex chromosomes (XX for females and XY for males). In an attempt to understand the molecular mechanism responsible for sex expression in hemp plants, we carried out RNA sequencing of male and female plants at different developmental stages. Using a pipeline involving differential gene expression analysis and weighted gene co-expression network analysis, we identified genes important for male and female flower development. We also demonstrate that sex-biased expression is already established at very early vegetative stages, before the onset of reproductive development, and identify several genes encoding transcription factors of the REM, bZIP, and MADS families as candidate sex-determination genes in hemp. Our findings demonstrate that the gene regulatory networks governing male and female development in hemp diverge at a very early stage, leading to profound morphological differences between male and female hemp plants.
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Affiliation(s)
- Jiaqi Shi
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
| | - Matteo Toscani
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
| | - Caroline A Dowling
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
| | - Susanne Schilling
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
| | - Rainer Melzer
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
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15
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Ryu BR, Gim GJ, Shin YR, Kang MJ, Kim MJ, Kwon TH, Lim YS, Park SH, Lim JD. Chromosome-level Haploid Assembly of Cannabis sativa L. cv. Pink Pepper. Sci Data 2024; 11:1442. [PMID: 39732708 PMCID: PMC11682139 DOI: 10.1038/s41597-024-04288-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Accepted: 12/16/2024] [Indexed: 12/30/2024] Open
Abstract
As molecular research on hemp (Cannabis sativa L.) continues to advance, there is a growing need for the accumulation of more diverse genome data and more accurate genome assemblies. In this study, we report the three-way assembly data of a cannabidiol (CBD)-rich cannabis variety, 'Pink Pepper' cultivar using sequencing technology: PacBio Single Molecule Real-Time (SMRT) technology, Illumina sequencing technology, and Oxford Nanopore Technology (ONT). This assembly anchors scaffolds to the ten chromosomes of hemp, and to avoid confusion with previous cannabis genetic research, the chromosomes have been labeled based on an earlier reference genome. The total assembled genome length is 770 Gbp, with a GC content of 34.09% and a repeat region accounting for 77.13% of the genome. This assembly, which incorporates the unique strengths of the three sequencing technologies, demonstrated the highest complete BUSCO scores (97.8%-99.6%) among the reported cannabis genomes, as evaluated using three different BUSCO databases. With annotations for 30,459 protein-coding genes, this dataset can serve as a valuable resource for advancing genetic research on hemp.
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Affiliation(s)
- Byeong-Ryeol Ryu
- Department of Bio-Health Convergence, Kangwon National University, Chuncheon, 24341, Republic of Korea
- Institute of Cannabis Research, Colorado State University-Pueblo, 2200 Bonforte Blvd, Pueblo, CO, 81001-4901, USA
| | - Gyeong-Ju Gim
- National Agrobiodiversity Center, National Academy of Agricultural Science, Rural Development Administration, Jeonju, 54874, Republic of Korea
| | - Ye-Rim Shin
- Department of Bio-Health Convergence, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Min-Ji Kang
- Department of Bio-Health Convergence, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Min-Jun Kim
- Department of Bio-Health Convergence, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Tae-Hyung Kwon
- Institute of Biological Resources, Chuncheon Bioindustry Foundation, Chuncheon, 24232, Republic of Korea
| | - Young-Seok Lim
- Department of Bio-Health Convergence, Kangwon National University, Chuncheon, 24341, Republic of Korea
- Department of Bio-Health Technology, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Sang-Hyuck Park
- Institute of Cannabis Research, Colorado State University-Pueblo, 2200 Bonforte Blvd, Pueblo, CO, 81001-4901, USA.
| | - Jung-Dae Lim
- Department of Bio-Health Convergence, Kangwon National University, Chuncheon, 24341, Republic of Korea.
- Department of Bio-Functional Material, Kangwon National University, Samcheok, 25949, Republic of Korea.
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16
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Conneely LJ, Hurgobin B, Ng S, Tamiru-Oli M, Lewsey MG. Characterization of the Cannabis sativa glandular trichome epigenome. BMC PLANT BIOLOGY 2024; 24:1075. [PMID: 39538149 PMCID: PMC11562870 DOI: 10.1186/s12870-024-05787-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Accepted: 11/05/2024] [Indexed: 11/16/2024]
Abstract
BACKGROUND The relationship between epigenomics and plant specialised metabolism remains largely unexplored despite the fundamental importance of epigenomics in gene regulation and, potentially, yield of products of plant specialised metabolic pathways. The glandular trichomes of Cannabis sativa are an emerging model system that produce large quantities of cannabinoid and terpenoid specialised metabolites with known medicinal and commercial value. To address this lack of epigenomic data, we mapped H3K4 trimethylation, H3K56 acetylation, H3K27 trimethylation post-translational modifications and the histone variant H2A.Z, using chromatin immunoprecipitation, in C. sativa glandular trichomes, leaf, and stem tissues. Corresponding transcriptomic (RNA-seq) datasets were integrated, and tissue-specific analyses conducted to relate chromatin states to glandular trichome specific gene expression. RESULTS The promoters of cannabinoid and terpenoid biosynthetic genes, specialised metabolite transporter genes, defence related genes, and starch and sucrose metabolism were enriched specifically in trichomes for histone marks H3K4me3 and H3K56ac, consistent with active transcription. We identified putative trichome-specific enhancer elements by identifying intergenic regions of H3K56ac enrichment, a histone mark that maintains enhancer accessibility, then associated these to putative target genes using the tissue specific gene transcriptomic data. Bi-valent chromatin loci specific to glandular trichomes, marked with H3K4 trimethylation and H3K27 trimethylation, were associated with genes of MAPK signalling pathways and plant specialised metabolism pathways, supporting recent hypotheses that implicate bi-valent chromatin in plant defence. The histone variant H2A.Z was largely found in intergenic regions and enriched in chromatin that contained genes involved in DNA homeostasis. CONCLUSION We report the first genome-wide histone post-translational modification maps for C. sativa glandular trichomes, and more broadly for glandular trichomes in plants. Our findings have implications in plant adaptation and stress responses and provide a basis for enhancer-mediated, targeted, gene transformation studies in plant glandular trichomes.
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Affiliation(s)
- Lee J Conneely
- La Trobe Institute for Sustainable Agriculture and Food, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia
- Australian Research Council Centre of Excellence in Plants for Space, La Trobe University, Bundoora, VIC, Australia
| | - Bhavna Hurgobin
- La Trobe Institute for Sustainable Agriculture and Food, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia
| | - Sophia Ng
- La Trobe Institute for Sustainable Agriculture and Food, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia
| | - Muluneh Tamiru-Oli
- La Trobe Institute for Sustainable Agriculture and Food, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia
| | - Mathew G Lewsey
- La Trobe Institute for Sustainable Agriculture and Food, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia.
- Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia.
- Australian Research Council Centre of Excellence in Plants for Space, La Trobe University, Bundoora, VIC, Australia.
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17
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Cho JY, Ryu DH, Hamayun M, Lee SH, Jung JH, Kim HY. Scent Knows Better: Utilizing Volatile Organic Compounds as a Robust Tool for Identifying Higher Cannabidiol- and Tetrahydrocannabinol-Containing Cannabis Cultivars in Field Conditions. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:24711-24723. [PMID: 39468951 DOI: 10.1021/acs.jafc.4c06652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/30/2024]
Abstract
The primary cannabinoids cannabidiol (CBD) and tetrahydrocannabinol (THC), found in cannabis, are known to originate from genetic diversity, resulting in distinct characteristics. This study aimed to identify VOC markers to distinguish between higher CBD and THC cannabis cultivars under field conditions. Among the 58 VOCs, β-caryophyllene and α-humulene were primary VOCs across all cannabis cultivars. Intriguingly, certain terpene VOCs exhibited contrasting trends between higher CBD and higher THC cannabis cultivars. Eudesma-3,7(11)-diene and α-guaiol consistently appeared as highlighted compounds, suggesting their potential to distinguish between higher CBD and THC cannabis cultivars. ROC curve analysis revealed approximately 94% predictive accuracy for these putative markers. Given the current focus on VOCs as sensor markers for plant health, growth, and quality, the identified VOC markers─applicable across varieties and growth stages─could enable nondestructive, rapid, and accurate identification of CBD- and THC-rich cannabis species in field conditions.
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Affiliation(s)
- Jwa Yeong Cho
- Smart Farm Research Center, Korea Institute of Science and Technology (KIST), Gangneung, Gangwon 25451, Republic of Korea
| | - Da Hye Ryu
- Smart Farm Research Center, Korea Institute of Science and Technology (KIST), Gangneung, Gangwon 25451, Republic of Korea
| | - Muhammad Hamayun
- Smart Farm Research Center, Korea Institute of Science and Technology (KIST), Gangneung, Gangwon 25451, Republic of Korea
- Department of Botany, Garden Campus, Abdul Wali Khan University Mardan, Nowshera Mardan Rd, Mardan 23200, Pakistan
| | - Su Hyeon Lee
- Department of southern area crop science, National institute of crop science, Rural development administration, Miryang, Gyeongnam 50424, Republic of Korea
| | - Je Hyeong Jung
- Division of Biotechnology, College of Life Sciences & Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Ho-Youn Kim
- Smart Farm Research Center, Korea Institute of Science and Technology (KIST), Gangneung, Gangwon 25451, Republic of Korea
- Natural Product Applied Science, KIST school, University of Science and Technology (UST), Gangneung, Gangwon 25451, Republic of Korea
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18
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Gagalova KK, Yan Y, Wang S, Matzat T, Castellarin SD, Birol I, Edwards D, Schuetz M. Leaf pigmentation in Cannabis sativa: Characterization of anthocyanin biosynthesis in colorful Cannabis varieties. PLANT DIRECT 2024; 8:e70016. [PMID: 39600728 PMCID: PMC11588432 DOI: 10.1002/pld3.70016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 08/19/2024] [Accepted: 10/01/2024] [Indexed: 11/29/2024]
Abstract
Cannabis plants produce a spectrum of secondary metabolites, encompassing cannabinoids and more than 300 non-cannabinoid compounds. Among these, anthocyanins have important functions in plants and also have well documented health benefits. Anthocyanins are largely responsible for the red/purple color phenotypes in plants. Although some well-known Cannabis varieties display a wide range of red/purple pigmentation, the genetic underpinnings of anthocyanin biosynthesis have not been well characterized in Cannabis. This study unveils the genetic diversity of anthocyanin biosynthesis genes found in Cannabis, and we characterize the diversity of anthocyanins and related phenolics found in four differently pigmented Cannabis varieties. Our investigation revealed that the genes 4CL, CHS, F3H, F3'H, FLS, DFR, ANS, and OMT exhibited the strongest correlation with anthocyanin accumulation in Cannabis leaves. The results of this study enhance our understanding of the anthocyanin biosynthetic pathway and shed light on the molecular mechanisms governing Cannabis leaf pigmentation.
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Affiliation(s)
- Kristina K. Gagalova
- Centre for Crop and Disease Management, School of Molecular and Life SciencesCurtin UniversityPerthWAAustralia
- Canada's Michael Smith Genome Sciences CentreBC CancerVancouverBCCanada
| | - Yifan Yan
- Wine Research CentreUniversity of British ColumbiaVancouverBCCanada
| | - Shumin Wang
- Department of BotanyUniversity of British ColumbiaVancouverBCCanada
| | - Till Matzat
- Wine Research CentreUniversity of British ColumbiaVancouverBCCanada
| | | | - Inanc Birol
- Canada's Michael Smith Genome Sciences CentreBC CancerVancouverBCCanada
- Department of Medical GeneticsUniversity of British ColumbiaVancouverBCCanada
| | - David Edwards
- School of Biological Sciences and Institute of AgricultureUniversity of Western AustraliaCrawleyWestern AustraliaAustralia
| | - Mathias Schuetz
- Department of BotanyUniversity of British ColumbiaVancouverBCCanada
- Department of BiologyKwantlen Polytechnic UniversitySurreyBCCanada
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19
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Mansueto L, Kretzschmar T, Mauleon R, King GJ. Building a community-driven bioinformatics platform to facilitate Cannabis sativa multi-omics research. GIGABYTE 2024; 2024:gigabyte137. [PMID: 39469541 PMCID: PMC11515022 DOI: 10.46471/gigabyte.137] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Accepted: 10/06/2024] [Indexed: 10/30/2024] Open
Abstract
Global changes in cannabis legislation after decades of stringent regulation and heightened demand for its industrial and medicinal applications have spurred recent genetic and genomics research. An international research community emerged and identified the need for a web portal to host cannabis-specific datasets that seamlessly integrates multiple data sources and serves omics-type analyses, fostering information sharing. The Tripal platform was used to host public genome assemblies, gene annotations, quantitative trait loci and genetic maps, gene and protein expression data, metabolic profiles and their sample attributes. Single nucleotide polymorphisms were called using public resequencing datasets on three genomes. Additional applications, such as SNP-Seek and MapManJS, were embedded into Tripal. A multi-omics data integration web-service Application Programming Interface (API), developed on top of existing Tripal modules, returns generic tables of samples, properties and values. Use cases demonstrate the API's utility for various omics analyses, enabling researchers to perform multi-omics analyses efficiently. Availability and implementation The web portal can be accessed at www.icgrc.info.
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Affiliation(s)
- Locedie Mansueto
- Southern Cross University, Military Road, Lismore New South Wales, 2480, Australia
| | - Tobias Kretzschmar
- Southern Cross University, Military Road, Lismore New South Wales, 2480, Australia
| | - Ramil Mauleon
- Southern Cross University, Military Road, Lismore New South Wales, 2480, Australia
- International Rice Research Institute, Pili Drive, Los Baños Laguna, 4031, Philippines
| | - Graham J. King
- Southern Cross University, Military Road, Lismore New South Wales, 2480, Australia
- Recombics, Alstonville, New South Wales, 2480, Australia
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20
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Mansueto L, McNally KL, Kretzschmar T, Mauleon R. CannSeek? Yes we Can! An open-source single nucleotide polymorphism database and analysis portal for Cannabis sativa. GIGABYTE 2024; 2024:gigabyte135. [PMID: 39416656 PMCID: PMC11480739 DOI: 10.46471/gigabyte.135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Accepted: 09/13/2024] [Indexed: 10/19/2024] Open
Abstract
A growing interest in Cannabis sativa uses for food, fiber, and medicine, and recent changes in regulations have spurred numerous genomic studies of this once-prohibited plant. Cannabis research uses Next Generation Sequencing technologies for genomics and transcriptomics. While other crops have genome portals enabling access and analysis of numerous genotyping data from diverse accessions, leading to the discovery of alleles for important traits, this is absent for cannabis. The CannSeek web portal aims to address this gap. Single nucleotide polymorphism datasets were generated by identifying genome variants from public resequencing data and genome assemblies. Results and accompanying trait data are hosted in the CannSeek web application, built using the Rice SNP-Seek infrastructure with improvements to allow multiple reference genomes and provide a web-service Application Programming Interface. The tools built into the portal allow phylogenetic analyses, varietal grouping and identifications, and favorable haplotype discovery for cannabis accessions using public sequencing data. Availability and implementation The CannSeek portal is available at https://icgrc.info/cannseek, https://icgrc.info/genotype_viewer.
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Affiliation(s)
- Locedie Mansueto
- Southern Cross University, Military Road, Lismore New South Wales 2480, Australia
| | - Kenneth L. McNally
- International Rice Research Institute, Pili Drive, Los Baños Laguna 4031, Philippines
| | - Tobias Kretzschmar
- Southern Cross University, Military Road, Lismore New South Wales 2480, Australia
| | - Ramil Mauleon
- Southern Cross University, Military Road, Lismore New South Wales 2480, Australia
- International Rice Research Institute, Pili Drive, Los Baños Laguna 4031, Philippines
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21
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Ndlangamandla VV, Salawu-Rotimi A, Bushula-Njah VS, Hlongwane NL, Sibandze GF, Gebashe FC, Mchunu NP. Finally Freed- Cannabis in South Africa: A Review Contextualised within Global History, Diversity, and Chemical Profiles. PLANTS (BASEL, SWITZERLAND) 2024; 13:2695. [PMID: 39409565 PMCID: PMC11478489 DOI: 10.3390/plants13192695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Revised: 09/18/2024] [Accepted: 09/19/2024] [Indexed: 10/20/2024]
Abstract
Cannabis sativa L. is a monotypic genus belonging to the family Cannabaceae. It is one of the oldest species cultivated by humans, believed to have originated in Central Asia. In pivotal judgements in 2016 and 2018, the South African Constitutional Court legalised the use of Cannabis within the country for medicinal and recreational purposes, respectively. These decrees opened opportunities for in-depth research where previously there had been varying sentiments for research to be conducted on the plant. This review seeks to examine the history, genetic diversity, and chemical profile of Cannabis. The cultivation of Cannabis by indigenous people of southern Africa dates back to the eighteenth century. Indigenous rural communities have been supporting their livelihoods through Cannabis farming even before its legalisation. However, there are limited studies on the plant's diversity, both morphologically and genetically, and its chemical composition. Also, there is a lack of proper documentation of Cannabis varieties in southern Africa. Currently, the National Centre for Biotechnology Information (NCBI) has 15 genome assemblies of Cannabis obtained from hemp and drug cultivars; however, none of these are representatives of African samples. More studies are needed to explore the species' knowledge gaps on genetic diversity and chemical profiles to develop the Cannabis sector in southern Africa.
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Affiliation(s)
- Valencia V. Ndlangamandla
- School of Life Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal, Westville Campus, Private Bag X 54001, Durban 4000, South Africa; (V.V.N.); (N.P.M.)
- Agricultural Research Council-Biotechnology Platform Onderstepoort Veterinary Research, Private Bag X 5, Onderstepoort 0110, South Africa; (A.S.-R.); (V.S.B.-N.); (N.L.H.)
| | - Adeola Salawu-Rotimi
- Agricultural Research Council-Biotechnology Platform Onderstepoort Veterinary Research, Private Bag X 5, Onderstepoort 0110, South Africa; (A.S.-R.); (V.S.B.-N.); (N.L.H.)
| | - Vuyiswa S. Bushula-Njah
- Agricultural Research Council-Biotechnology Platform Onderstepoort Veterinary Research, Private Bag X 5, Onderstepoort 0110, South Africa; (A.S.-R.); (V.S.B.-N.); (N.L.H.)
| | - Nompilo L. Hlongwane
- Agricultural Research Council-Biotechnology Platform Onderstepoort Veterinary Research, Private Bag X 5, Onderstepoort 0110, South Africa; (A.S.-R.); (V.S.B.-N.); (N.L.H.)
| | - Gugu F. Sibandze
- Eswatini Institute for Research in Traditional Medicine, Medicinal and Indigenous Food Plants, University of Eswatini, Private Bag 4, Kwaluseni M201, Eswatini;
| | - Fikisiwe C. Gebashe
- School of Life Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal, Westville Campus, Private Bag X 54001, Durban 4000, South Africa; (V.V.N.); (N.P.M.)
| | - Nokuthula P. Mchunu
- School of Life Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal, Westville Campus, Private Bag X 54001, Durban 4000, South Africa; (V.V.N.); (N.P.M.)
- National Research Foundation, Meiring Naude, Pretoria 0001, South Africa
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22
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Sng BJR, Jeong YJ, Leong SH, Jeong JC, Lee J, Rajani S, Kim CY, Jang IC. Genome-wide identification of cannabinoid biosynthesis genes in non-drug type Cannabis (Cannabis sativa L.) cultivar. J Cannabis Res 2024; 6:35. [PMID: 39244597 PMCID: PMC11380790 DOI: 10.1186/s42238-024-00246-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/28/2024] [Indexed: 09/09/2024] Open
Abstract
BACKGROUND Cannabis sativa cultivars can be classified as marijuana or hemp, depending on its amount of the psychoactive cannabinoid Δ9-tetrahydrocannabinolic acid (THCA). Hemp Cheungsam is a non-drug type Cannabis sativa that is characterized by low THCA content. However, the transcripts and expression profile of cannabinoid biosynthesis pathway genes of hemp Cheungsam have not been investigated. METHODS RNA-sequencing (RNA-seq) was performed on three different tissue types (flower, leaf, and stem) of hemp Cheungsam to understand their transcriptomes. The expression of cannabinoid biosynthesis pathway genes was further analyzed in each tissue type. Multiple sequence alignment and conserved domain analyses were used to investigate the homologs of cannbinoid biosynthesis genes. RESULTS We found that the cannabinoid biosynthesis pathway was mainly expressed in the flowers of hemp Cheungsam, similar to other Cannabis cultivars. However, expression of cannabidiolic acid (CBDA) synthase was much higher than THCA synthase and cannabichromenic acid (CBCA) synthase, suggesting that the transcription profile favors CBDA biosynthesis. Sequence analysis of cannabinoid biosynthesis pathway genes suggested the identity of orthologs in hemp Cheungsam. CONCLUSIONS Cannabinoid biosynthesis in hemp Cheungsam mostly occurs in the flowers, compared to other plant organs. While CBDA synthase expression is high, THCA and CBCA synthase expression is considerably low, indicating lesser THCA biosynthesis and thus low THCA content. Sequence analysis of key genes (CBDA, THCA, and CBCA synthases) of the cannabinoid biosynthetic pathway indicates that orthologs are present in hemp Cheungsam.
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Affiliation(s)
- Benny Jian Rong Sng
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Yu Jeong Jeong
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Korea
| | - Sing Hui Leong
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Jae Cheol Jeong
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Korea
| | - Jiyoung Lee
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Korea
| | - Sarojam Rajani
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Cha Young Kim
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Korea.
| | - In-Cheol Jang
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore.
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23
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Monthony AS, de Ronne M, Torkamaneh D. Exploring ethylene-related genes in Cannabis sativa: implications for sexual plasticity. PLANT REPRODUCTION 2024; 37:321-339. [PMID: 38218931 DOI: 10.1007/s00497-023-00492-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 12/11/2023] [Indexed: 01/15/2024]
Abstract
KEY MESSAGE Presented here are model Yang cycle, ethylene biosynthesis and signaling pathways in Cannabis sativa. C. sativa floral transcriptomes were used to predict putative ethylene-related genes involved in sexual plasticity in the species. Sexual plasticity is a phenomenon, wherein organisms possess the ability to alter their phenotypic sex in response to environmental and physiological stimuli, without modifying their sex chromosomes. Cannabis sativa L., a medically valuable plant species, exhibits sexual plasticity when subjected to specific chemicals that influence ethylene biosynthesis and signaling. Nevertheless, the precise contribution of ethylene-related genes (ERGs) to sexual plasticity in cannabis remains unexplored. The current study employed Arabidopsis thaliana L. as a model organism to conduct gene orthology analysis and reconstruct the Yang Cycle, ethylene biosynthesis, and ethylene signaling pathways in C. sativa. Additionally, two transcriptomic datasets comprising male, female, and chemically induced male flowers were examined to identify expression patterns in ERGs associated with sexual determination and sexual plasticity. These ERGs involved in sexual plasticity were categorized into two distinct expression patterns: floral organ concordant (FOC) and unique (uERG). Furthermore, a third expression pattern, termed karyotype concordant (KC) expression, was proposed, which plays a role in sex determination. The study revealed that CsERGs associated with sexual plasticity are dispersed throughout the genome and are not limited to the sex chromosomes, indicating a widespread regulation of sexual plasticity in C. sativa.
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Affiliation(s)
- Adrian S Monthony
- Département de Phytologie, Université Laval, Québec City, Québec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, Québec, Canada
- Centre de Recherche et d'innovation sur les végétaux (CRIV), Université Laval, Québec City, Québec, Canada
- Institut intelligence et données (IID), Université Laval, Québec City, Québec, Canada
| | - Maxime de Ronne
- Département de Phytologie, Université Laval, Québec City, Québec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, Québec, Canada
- Centre de Recherche et d'innovation sur les végétaux (CRIV), Université Laval, Québec City, Québec, Canada
- Institut intelligence et données (IID), Université Laval, Québec City, Québec, Canada
| | - Davoud Torkamaneh
- Département de Phytologie, Université Laval, Québec City, Québec, Canada.
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, Québec, Canada.
- Centre de Recherche et d'innovation sur les végétaux (CRIV), Université Laval, Québec City, Québec, Canada.
- Institut intelligence et données (IID), Université Laval, Québec City, Québec, Canada.
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24
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Mansueto L, Tandayu E, Mieog J, Garcia-de Heer L, Das R, Burn A, Mauleon R, Kretzschmar T. HASCH - A high-throughput amplicon-based SNP-platform for medicinal cannabis and industrial hemp genotyping applications. BMC Genomics 2024; 25:818. [PMID: 39210290 PMCID: PMC11363669 DOI: 10.1186/s12864-024-10734-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 08/22/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND Cannabis sativa is seeing a global resurgence as a food, fiber and medicinal crop for industrial hemp and medicinal Cannabis industries respectively. However, a widespread moratorium on the use and research of C. sativa throughout most of the 20th century has seen the development of improved cultivars for specific end uses lag behind that of conventional crops. While C. sativa research and development has seen significant investments in the recent past, resulting in a suite of publicly available genomic resources and tools, a versatile and cost-effective mid-density genotyping platform for applied purposes in breeding and pre-breeding is lacking. Here we report on a first mid-density fixed-target SNP platform for C. sativa. RESULTS The High-throughput Amplicon-based SNP-platform for medicinal Cannabis and industrial Hemp (HASCH) was designed using a combination of filtering and Integer Linear Programming on publicly available whole-genome sequencing and RNA sequencing data, supplemented with in-house generated genotyping-by-sequencing (GBS) data. HASCH contains 1,504 genome-wide targets of high call rate (97% mean) and even distribution across the genome, designed to be highly informative (> 0.3 minor allele frequency) across both medicinal cannabis and industrial hemp gene pools. Average numbers of mismatch SNP between any two accessions were 251 for medicinal cannabis (N = 116) and 272 for industrial hemp (N = 87). Comparing HASCH data with corresponding GBS data on a collection of diverse C. sativa accessions demonstrated high concordance and resulted in comparable phylogenies and genetic distance matrices. Using HASCH on a segregating F2 population derived from a cross between a tetrahydrocannabinol (THC)-dominant and a cannabidiol (CBD)-dominant accession resulted in a genetic map consisting of 310 markers, comprising 10 linkage groups and a total size of 582.7 cM. Quantitative Trait Locus (QTL) mapping identified a major QTL for CBD content on chromosome 7, consistent with previous findings. CONCLUSION HASCH constitutes a versatile, easy to use and cost-effective genotyping solution for the rapidly growing Cannabis research community. It provides consistent genetic fingerprints of 1504 SNPs with wide applicability genetic resource management, quantitative genetics and breeding.
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Affiliation(s)
- Locedie Mansueto
- Southern Cross Plant Science, Faculty of Science and Engineering, Southern Cross University, 1 Military Road, East Lismore, NSW, 2480, Australia
| | - Erwin Tandayu
- Southern Cross Plant Science, Faculty of Science and Engineering, Southern Cross University, 1 Military Road, East Lismore, NSW, 2480, Australia
| | - Jos Mieog
- Southern Cross Plant Science, Faculty of Science and Engineering, Southern Cross University, 1 Military Road, East Lismore, NSW, 2480, Australia
| | - Lennard Garcia-de Heer
- Southern Cross Plant Science, Faculty of Science and Engineering, Southern Cross University, 1 Military Road, East Lismore, NSW, 2480, Australia
| | - Rekhamani Das
- Southern Cross Plant Science, Faculty of Science and Engineering, Southern Cross University, 1 Military Road, East Lismore, NSW, 2480, Australia
| | - Adam Burn
- Southern Cross Plant Science, Faculty of Science and Engineering, Southern Cross University, 1 Military Road, East Lismore, NSW, 2480, Australia
| | - Ramil Mauleon
- Southern Cross Plant Science, Faculty of Science and Engineering, Southern Cross University, 1 Military Road, East Lismore, NSW, 2480, Australia
- International Rice Research Institute, Pili Drive, Los Banos, Laguna, Philippines
| | - Tobias Kretzschmar
- Southern Cross Plant Science, Faculty of Science and Engineering, Southern Cross University, 1 Military Road, East Lismore, NSW, 2480, Australia.
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25
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Chen BZ, Yang ZJ, Wang WB, Hao TT, Yu PB, Dong Y, Yu WB. Chromosome-level genome assembly and annotation of Flueggea virosa (Phyllanthaceae). Sci Data 2024; 11:875. [PMID: 39138223 PMCID: PMC11322648 DOI: 10.1038/s41597-024-03681-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Accepted: 07/25/2024] [Indexed: 08/15/2024] Open
Abstract
Flueggea virosa (Roxb. ex Willd.) Royle, an evergreen shrub and small tree in the Phyllanthaceae family, holds significant potential in garden landscaping and pharmacological applications. However, the lack of genomic data has hindered further scientific understanding of its horticultural and medicinal values. In this study, we have assembled a haplotype-resolved genome of F. virosa for the first time. The two haploid genomes, named haplotype A genome and haplotype B genome, are 487.33 Mb and 477.53 Mb in size, respectively, with contig N50 lengths of 31.45 Mb and 32.81 Mb. More than 99% of the assembled sequences were anchored to 13 pairs of pseudo-chromosomes. Furthermore, 21,587 and 21,533 protein-coding genes were predicted in haplotype A and haplotype B genomes, respectively. The availability of this chromosome-level genome fills the gap in genomic data for F. virosa and provides valuable resources for molecular studies of this species, supporting future research on speciation, functional genomics, and comparative genomics within the Phyllanthaceae family.
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Affiliation(s)
- Bao-Zheng Chen
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Zi-Jiang Yang
- Bioinformatics group, Wageningen University and Research, Wageningen, Netherlands
| | - Wei-Bin Wang
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Ting-Ting Hao
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Peng-Ban Yu
- Center for Integrative Conservation and Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
| | - Yang Dong
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, 650201, China.
| | - Wen-Bin Yu
- Center for Integrative Conservation and Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China.
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China.
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26
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Hancock J, Livingston SJ, Samuels L. Building a biofactory: Constructing glandular trichomes in Cannabis sativa. CURRENT OPINION IN PLANT BIOLOGY 2024; 80:102549. [PMID: 38761520 DOI: 10.1016/j.pbi.2024.102549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/12/2024] [Accepted: 04/18/2024] [Indexed: 05/20/2024]
Abstract
Flowers of Cannabis sativa L. are densely covered with glandular trichomes containing cannabis resin that is used for medicinal and recreational purposes. The highly productive glandular trichomes have been described as 'biofactories.' In this review, we use this analogy to highlight recent advances in cannabis cell biology, metabolomics, and transcriptomics. The biofactory is built by epidermal outgrowths that differentiate into peltate-like glandular trichome heads, consisting of a disc of interconnected secretory cells with unique cellular structures. Cannabinoid and terpenoid products are warehoused in the extracellular storage cavity. Finally, multicellular stalks raise the glandular heads above the epidermis, giving cannabis flower their frosty appearance.
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Affiliation(s)
- Jessica Hancock
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| | - Samuel J Livingston
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| | - Lacey Samuels
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada.
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27
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Dowling CA, Shi J, Toth JA, Quade MA, Smart LB, McCabe PF, Schilling S, Melzer R. A FLOWERING LOCUS T ortholog is associated with photoperiod-insensitive flowering in hemp (Cannabis sativa L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:383-403. [PMID: 38625758 DOI: 10.1111/tpj.16769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/15/2024] [Accepted: 04/02/2024] [Indexed: 04/18/2024]
Abstract
Hemp (Cannabis sativa L.) is an extraordinarily versatile crop, with applications ranging from medicinal compounds to seed oil and fibre products. Cannabis sativa is a short-day plant, and its flowering is highly controlled by photoperiod. However, substantial genetic variation exists for photoperiod sensitivity in C. sativa, and photoperiod-insensitive ("autoflower") cultivars are available. Using a bi-parental mapping population and bulked segregant analysis, we identified Autoflower2, a 0.5 Mbp locus significantly associated with photoperiod-insensitive flowering in hemp. Autoflower2 contains an ortholog of the central flowering time regulator FLOWERING LOCUS T (FT) from Arabidopsis thaliana which we termed CsFT1. We identified extensive sequence divergence between alleles of CsFT1 from photoperiod-sensitive and insensitive cultivars of C. sativa, including a duplication of CsFT1 and sequence differences, especially in introns. Furthermore, we observed higher expression of one of the CsFT1 copies found in the photoperiod-insensitive cultivar. Genotyping of several mapping populations and a diversity panel confirmed a correlation between CsFT1 alleles and photoperiod response, affirming that at least two independent loci involved in the photoperiodic control of flowering, Autoflower1 and Autoflower2, exist in the C. sativa gene pool. This study reveals the multiple independent origins of photoperiod insensitivity in C. sativa, supporting the likelihood of a complex domestication history in this species. By integrating the genetic relaxation of photoperiod sensitivity into novel C. sativa cultivars, expansion to higher latitudes will be permitted, thus allowing the full potential of this versatile crop to be reached.
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Affiliation(s)
- Caroline A Dowling
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- UCD Earth Institute, University College Dublin, Dublin, Ireland
| | - Jiaqi Shi
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- UCD Earth Institute, University College Dublin, Dublin, Ireland
| | - Jacob A Toth
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, New York, USA
| | - Michael A Quade
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, New York, USA
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, New York, USA
| | - Paul F McCabe
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- UCD Earth Institute, University College Dublin, Dublin, Ireland
| | - Susanne Schilling
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- UCD Earth Institute, University College Dublin, Dublin, Ireland
| | - Rainer Melzer
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- UCD Earth Institute, University College Dublin, Dublin, Ireland
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28
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Leckie KM, Sawler J, Kapos P, MacKenzie JO, Giles I, Baynes K, Lo J, Baute GJ, Celedon JM. Loss of daylength sensitivity by splice site mutation in Cannabis pseudo-response regulator. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:2020-2036. [PMID: 38525679 DOI: 10.1111/tpj.16726] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/08/2024] [Accepted: 03/10/2024] [Indexed: 03/26/2024]
Abstract
Photoperiod insensitivity (auto-flowering) in drug-type Cannabis sativa circumvents the need for short day (SD) flowering requirements making outdoor cultivation in high latitudes possible. However, the benefits of photoperiod insensitivity are counterbalanced by low cannabinoid content and poor flower quality in auto-flowering genotypes. Despite recent studies in cannabis flowering, a mechanistic understanding of photoperiod insensitivity is still lacking. We used a combination of genome-wide association study and genetic fine-mapping to identify the genetic cause of auto-flowering in cannabis. We then used gene expression analyses and transient transformation assays to characterize flowering time control. Herein, we identify a splice site mutation within circadian clock gene PSEUDO-RESPONSE REGULATOR 37 (CsPRR37) in auto-flowering cannabis. We show that CsPRR37 represses FT expression and its circadian oscillations transition to a less repressive state during SD as compared to long days (LD). We identify several key circadian clock genes whose expression is altered in auto-flowering cannabis, particularly under non-inductive LD. Research into the pervasiveness of this mutation and others affecting flowering time will help elucidate cannabis domestication history and advance cannabis breeding toward a more sustainable outdoor cultivation system.
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Affiliation(s)
- Keegan M Leckie
- Breeding and Genetics Department, Aurora Cannabis, Inc., 1590 Galbraith Rd, Comox, British Columbia, V9M 4A1, Canada
| | - Jason Sawler
- Breeding and Genetics Department, Aurora Cannabis, Inc., 1590 Galbraith Rd, Comox, British Columbia, V9M 4A1, Canada
| | - Paul Kapos
- Breeding and Genetics Department, Aurora Cannabis, Inc., 1590 Galbraith Rd, Comox, British Columbia, V9M 4A1, Canada
| | - John O MacKenzie
- Breeding and Genetics Department, Aurora Cannabis, Inc., 1590 Galbraith Rd, Comox, British Columbia, V9M 4A1, Canada
| | - Ingrid Giles
- Breeding and Genetics Department, Aurora Cannabis, Inc., 1590 Galbraith Rd, Comox, British Columbia, V9M 4A1, Canada
| | - Katherine Baynes
- Breeding and Genetics Department, Aurora Cannabis, Inc., 1590 Galbraith Rd, Comox, British Columbia, V9M 4A1, Canada
| | - Jessica Lo
- Breeding and Genetics Department, Aurora Cannabis, Inc., 1590 Galbraith Rd, Comox, British Columbia, V9M 4A1, Canada
| | - Gregory J Baute
- Breeding and Genetics Department, Aurora Cannabis, Inc., 1590 Galbraith Rd, Comox, British Columbia, V9M 4A1, Canada
| | - Jose M Celedon
- Breeding and Genetics Department, Aurora Cannabis, Inc., 1590 Galbraith Rd, Comox, British Columbia, V9M 4A1, Canada
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29
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Boissinot J, Adamek K, Jones AMP, Normandeau E, Boyle B, Torkamaneh D. Comparative restriction enzyme analysis of methylation (CREAM) reveals methylome variability within a clonal in vitro cannabis population. FRONTIERS IN PLANT SCIENCE 2024; 15:1381154. [PMID: 38872884 PMCID: PMC11169872 DOI: 10.3389/fpls.2024.1381154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 05/14/2024] [Indexed: 06/15/2024]
Abstract
The primary focus of medicinal cannabis research is to ensure the stability of cannabis lines for consistent administration of chemically uniform products to patients. In recent years, tissue culture has emerged as a valuable technique for genetic preservation and rapid multiplication of cannabis clones. However, there is concern that the physical and chemical conditions of the growing media can induce somaclonal variation, potentially impacting the viability and uniformity of clones. To address this concern, we developed Comparative Restriction Enzyme Analysis of Methylation (CREAM), a novel method to assess DNA methylation patterns and used it to study a population of 78 cannabis clones maintained in tissue culture. Through bioinformatics analysis of the methylome, we successfully detected 2,272 polymorphic methylated regions among the clones. Remarkably, our results demonstrated that DNA methylation patterns were preserved across subcultures within the clonal population, allowing us to distinguish between two subsets of clonal lines used in this study. These findings significantly contribute to our understanding of the epigenetic variability within clonal lines in medicinal cannabis produced through tissue culture techniques. This knowledge is crucial for understanding the effects of tissue culture on DNA methylation and ensuring the consistency and reliability of medicinal cannabis products with therapeutic properties. Additionally, the CREAM method is a fast and affordable technology to get a first glimpse at methylation in a biological system. It offers a valuable tool for studying epigenetic variation in other plant species, thereby facilitating broader applications in plant biotechnology and crop improvement.
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Affiliation(s)
- Justin Boissinot
- Département de phytologie, Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Centre de recherche et d’innovation sur les végétaux (CRIV), Université Laval, Québec, QC, Canada
- Institut intelligence et données (IID), Université Laval, Québec, QC, Canada
| | - Kristian Adamek
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | | | - Eric Normandeau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Brian Boyle
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Davoud Torkamaneh
- Département de phytologie, Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Centre de recherche et d’innovation sur les végétaux (CRIV), Université Laval, Québec, QC, Canada
- Institut intelligence et données (IID), Université Laval, Québec, QC, Canada
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30
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Kaminski KP, Hoeng J, Goffman F, Schlage WK, Latino D. Opportunities, Challenges, and Scientific Progress in Hemp Crops. Molecules 2024; 29:2397. [PMID: 38792258 PMCID: PMC11124073 DOI: 10.3390/molecules29102397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/16/2024] [Accepted: 05/18/2024] [Indexed: 05/26/2024] Open
Abstract
The resurgence of cannabis (Cannabis sativa L.) has been propelled by changes in the legal framework governing its cultivation and use, increased demand for hemp-derived products, and studies recognizing the industrial and health benefits of hemp. This has led to the creation of novel high-cannabidiol, low-Δ9-tetrahydrocannabinol varieties, enabling hemp crop expansion worldwide. This review elucidates the recent implications for hemp cultivation in Europe, with a focus on the legislative impacts on the cultivation practices, prospective breeding efforts, and dynamic scientific landscape surrounding this crop. We also review the current cultivars' cannabinoid composition of the European hemp market and its major differences with that of the United States.
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Affiliation(s)
| | - Julia Hoeng
- Vectura Fertin Pharma, 4058 Basel, Switzerland
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31
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Cheng YC, Houston R. The development of a next-generation sequencing panel targeting cannabinoid synthase genes to distinguish between marijuana and hemp. Electrophoresis 2024; 45:948-957. [PMID: 38326083 DOI: 10.1002/elps.202300233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 01/12/2024] [Accepted: 01/27/2024] [Indexed: 02/09/2024]
Abstract
Hemp and marijuana, both derived from Cannabis sativa L. (C. sativa), are subject to divergent legal regulations due to their different Δ9-tetrahydrocannabinol (Δ9-THC) contents. Cannabinoid synthase genes are considered the key enzymes that determine the chemical composition or chemotype of a particular cultivar. However, existing methods for crop type differentiation based on previous synthase gene theories have limitations in terms of precision and specificity, and a wider range of cannabis varieties must be considered when examining cannabis-based genetic markers. A custom next-generation sequencing (NGS) panel was developed targeting all synthase genes, including Δ9-THC acid synthase, cannabidiolic acid synthase, and cannabichromenic acid synthase, as well as the pseudogenes across diverse C. sativa samples, spanning reference hemp and marijuana, commercial hemp derivatives, and seized marijuana extracts. Interpretation of NGS data revealed a relationship between genotypes and underlying chemotypes, with the principal component analysis indicating a clear distinction between hemp and marijuana clusters. This differentiation was attributed to variations in both synthase genes and pseudogene variants. Finally, this study proposes a genetic cannabis classification method using a differentiation flow chart with novel synthase markers. The flow chart successfully differentiated hemp from marijuana with a 1.3% error rate (n = 147).
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Affiliation(s)
- Ya-Chih Cheng
- Department of Forensic Science, Sam Houston State University, Huntsville, Texas, USA
| | - Rachel Houston
- Department of Forensic Science, Sam Houston State University, Huntsville, Texas, USA
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32
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de Ronne M, Lapierre É, Torkamaneh D. Genetic insights into agronomic and morphological traits of drug-type cannabis revealed by genome-wide association studies. Sci Rep 2024; 14:9162. [PMID: 38644388 PMCID: PMC11033274 DOI: 10.1038/s41598-024-58931-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 04/04/2024] [Indexed: 04/23/2024] Open
Abstract
Cannabis sativa L., previously concealed by prohibition, is now a versatile and promising plant, thanks to recent legalization, opening doors for medical research and industry growth. However, years of prohibition have left the Cannabis research community lagging behind in understanding Cannabis genetics and trait inheritance compared to other major crops. To address this gap, we conducted a comprehensive genome-wide association study (GWAS) of nine key agronomic and morphological traits, using a panel of 176 drug-type Cannabis accessions from the Canadian legal market. Utilizing high-density genotyping-by-sequencing (HD-GBS), we successfully generated dense genotyping data in Cannabis, resulting in a catalog of 800 K genetic variants, of which 282 K common variants were retained for GWAS analysis. Through GWAS analysis, we identified 18 markers significantly associated with agronomic and morphological traits. Several identified markers exert a substantial phenotypic impact, guided us to putative candidate genes that reside in high linkage-disequilibrium (LD) with the markers. These findings lay a solid foundation for an innovative cannabis research, leveraging genetic markers to inform breeding programs aimed at meeting diverse needs in the industry.
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Affiliation(s)
- Maxime de Ronne
- Département de Phytologie, Université Laval, Quebec City, Québec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Québec, Canada
- Centre de Recherche et d'innovation sur les Végétaux (CRIV), Université Laval, Quebec City, Québec, Canada
- Institut Intelligence et Données (IID), Université Laval, Quebec City, Québec, Canada
| | - Éliana Lapierre
- Département de Phytologie, Université Laval, Quebec City, Québec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Québec, Canada
- Centre de Recherche et d'innovation sur les Végétaux (CRIV), Université Laval, Quebec City, Québec, Canada
- Institut Intelligence et Données (IID), Université Laval, Quebec City, Québec, Canada
| | - Davoud Torkamaneh
- Département de Phytologie, Université Laval, Quebec City, Québec, Canada.
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Québec, Canada.
- Centre de Recherche et d'innovation sur les Végétaux (CRIV), Université Laval, Quebec City, Québec, Canada.
- Institut Intelligence et Données (IID), Université Laval, Quebec City, Québec, Canada.
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33
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Zhang C, Jiang M, Liu J, Wu B, Liu C. Genome-wide view and characterization of natural antisense transcripts in Cannabis Sativa L. PLANT MOLECULAR BIOLOGY 2024; 114:47. [PMID: 38632206 DOI: 10.1007/s11103-024-01434-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 02/25/2024] [Indexed: 04/19/2024]
Abstract
Natural Antisense Transcripts (NATs) are a kind of complex regulatory RNAs that play crucial roles in gene expression and regulation. However, the NATs in Cannabis Sativa L., a widely economic and medicinal plant rich in cannabinoids remain unknown. In this study, we comprehensively predicted C. sativa NATs genome-wide using strand-specific RNA sequencing (ssRNA-Seq) data, and validated the expression profiles by strand-specific quantitative reverse transcription PCR (ssRT-qPCR). Consequently, a total of 307 NATs were predicted in C. sativa, including 104 cis- and 203 trans- NATs. Functional enrichment analysis demonstrated the potential involvement of the C. sativa NATs in DNA polymerase activity, RNA-DNA hybrid ribonuclease activity, and nucleic acid binding. Finally, 18 cis- and 376 trans- NAT-ST pairs were predicted to produce 621 cis- and 5,679 trans- small interfering RNA (nat-siRNAs), respectively. These nat-siRNAs were potentially involved in the biosynthesis of cannabinoids and cellulose. All these results will shed light on the regulation of NATs and nat-siRNAs in C. sativa.
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Affiliation(s)
- Chang Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, 100193, Beijing, China
| | - Mei Jiang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, 100193, Beijing, China
- School of Pharmaceutical Sciences, Qilu University of Technology, Shandong Academy of Sciences, Jinan, China
| | - Jingting Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, 100193, Beijing, China
| | - Bin Wu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, 100193, Beijing, China.
| | - Chang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, 100193, Beijing, China.
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34
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Wei H, Yang Z, Niyitanga S, Tao A, Xu J, Fang P, Lin L, Zhang L, Qi J, Ming R, Zhang L. The reference genome of seed hemp (Cannabis sativa) provides new insights into fatty acid and vitamin E synthesis. PLANT COMMUNICATIONS 2024; 5:100718. [PMID: 37717143 PMCID: PMC10811365 DOI: 10.1016/j.xplc.2023.100718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 09/06/2023] [Accepted: 09/13/2023] [Indexed: 09/18/2023]
Affiliation(s)
- Huawei Wei
- Key Laboratory of Ministry of Education for Genetic Breeding and Multiple Utilization of Crops/Key Laboratory of Ministry of Agriculture and Rural Affairs for Biological Breeding of Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Fujian Public Platform for Germplasm Resources of Bast Fiber Crops/Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zuqing Yang
- Key Laboratory of Ministry of Education for Genetic Breeding and Multiple Utilization of Crops/Key Laboratory of Ministry of Agriculture and Rural Affairs for Biological Breeding of Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Fujian Public Platform for Germplasm Resources of Bast Fiber Crops/Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Sylvain Niyitanga
- Key Laboratory of Ministry of Education for Genetic Breeding and Multiple Utilization of Crops/Key Laboratory of Ministry of Agriculture and Rural Affairs for Biological Breeding of Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Fujian Public Platform for Germplasm Resources of Bast Fiber Crops/Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Aifen Tao
- Key Laboratory of Ministry of Education for Genetic Breeding and Multiple Utilization of Crops/Key Laboratory of Ministry of Agriculture and Rural Affairs for Biological Breeding of Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Fujian Public Platform for Germplasm Resources of Bast Fiber Crops/Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiantang Xu
- Key Laboratory of Ministry of Education for Genetic Breeding and Multiple Utilization of Crops/Key Laboratory of Ministry of Agriculture and Rural Affairs for Biological Breeding of Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Fujian Public Platform for Germplasm Resources of Bast Fiber Crops/Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Pingping Fang
- Key Laboratory of Ministry of Education for Genetic Breeding and Multiple Utilization of Crops/Key Laboratory of Ministry of Agriculture and Rural Affairs for Biological Breeding of Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Fujian Public Platform for Germplasm Resources of Bast Fiber Crops/Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lihui Lin
- Key Laboratory of Ministry of Education for Genetic Breeding and Multiple Utilization of Crops/Key Laboratory of Ministry of Agriculture and Rural Affairs for Biological Breeding of Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Fujian Public Platform for Germplasm Resources of Bast Fiber Crops/Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Liemei Zhang
- Key Laboratory of Ministry of Education for Genetic Breeding and Multiple Utilization of Crops/Key Laboratory of Ministry of Agriculture and Rural Affairs for Biological Breeding of Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jianmin Qi
- Key Laboratory of Ministry of Education for Genetic Breeding and Multiple Utilization of Crops/Key Laboratory of Ministry of Agriculture and Rural Affairs for Biological Breeding of Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Fujian Public Platform for Germplasm Resources of Bast Fiber Crops/Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ray Ming
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Liwu Zhang
- Key Laboratory of Ministry of Education for Genetic Breeding and Multiple Utilization of Crops/Key Laboratory of Ministry of Agriculture and Rural Affairs for Biological Breeding of Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Fujian Public Platform for Germplasm Resources of Bast Fiber Crops/Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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35
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Stack GM, Cala AR, Quade MA, Toth JA, Monserrate LA, Wilkerson DG, Carlson CH, Mamerto A, Michael TP, Crawford S, Smart CD, Smart LB. Genetic Mapping, Identification, and Characterization of a Candidate Susceptibility Gene for Powdery Mildew in Cannabis sativa. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:51-61. [PMID: 37750850 DOI: 10.1094/mpmi-04-23-0043-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Powdery mildew (PM) in Cannabis sativa is most frequently caused by the biotrophic fungus Golovinomyces ambrosiae. Based on previously characterized variation in susceptibility to PM, biparental populations were developed by crossing the most resistant cultivar evaluated, 'FL 58', with a susceptible cultivar, 'TJ's CBD'. F1 progeny were evaluated and displayed a range of susceptibility, and two were self-pollinated to generate two F2 populations. In 2021, the F2 populations (n = 706) were inoculated with PM and surveyed for disease severity. In both F2 populations, 25% of the progeny were resistant, while the remaining 75% showed a range of susceptibility. The F2 populations, as well as selected F1 progeny and the parents, were genotyped with a single-nucleotide polymorphism array, and a consensus genetic map was produced. A major effect quantitative trait locus on C. sativa chromosome 1 (Chr01) and other smaller-effect quantitative trait loci (QTL) on four other chromosomes were identified. The most associated marker on Chr01 was located near CsMLO1, a candidate susceptibility gene. Genomic DNA and cDNA sequencing of CsMLO1 revealed a 6.8-kb insertion in FL 58, relative to TJ's CBD, of which 846 bp are typically spliced into the mRNA transcript encoding a premature stop codon. Molecular marker assays were developed using CsMLO1 sequences to distinguish PM-resistant and PM-susceptible genotypes. These data support the hypothesis that a mutated MLO susceptibility gene confers resistance to PM in C. sativa and provides new genetic resources to develop resistant cultivars. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- George M Stack
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY 14456, U.S.A
| | - Ali R Cala
- Plant Pathology and Plant Microbe Biology Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY 14456, U.S.A
| | - Michael A Quade
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY 14456, U.S.A
| | - Jacob A Toth
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY 14456, U.S.A
| | - Luis A Monserrate
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY 14456, U.S.A
| | - Dustin G Wilkerson
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY 14456, U.S.A
| | - Craig H Carlson
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY 14456, U.S.A
| | - Allen Mamerto
- Plant Molecular and Cellular Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, U.S.A
| | - Todd P Michael
- Plant Molecular and Cellular Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, U.S.A
| | | | - Christine D Smart
- Plant Pathology and Plant Microbe Biology Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY 14456, U.S.A
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY 14456, U.S.A
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36
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Sirangelo TM. NLR- and mlo-Based Resistance Mechanisms against Powdery Mildew in Cannabis sativa. PLANTS (BASEL, SWITZERLAND) 2023; 13:105. [PMID: 38202413 PMCID: PMC10780410 DOI: 10.3390/plants13010105] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/26/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024]
Abstract
Powdery mildew (PM) is one of the most common Cannabis sativa diseases. In spite of this, very few documented studies have characterized the resistance genes involved in PM defense mechanisms, or sources of natural genetic resistance in cannabis. The focus of the present work is on the two primary mechanisms for qualitative resistance against PM. The first is based on resistance (R) genes characterized by conserved nucleotide-binding site and/or leucine-rich repeat domains (NLRs). The second one involves susceptibility (S) genes, and particularly mildew resistance locus o (MLO) genes, whose loss-of-function mutations seem to be a reliable way to protect plants from PM infection. Cannabis defenses against PM are thus discussed, mainly detailing the strategies based on these two mechanisms. Emerging studies about this research topic are also reported and, based on the most significant results, a potential PM resistance model in cannabis plant-pathogen interactions is proposed. Finally, innovative approaches, based on the pyramiding of multiple R genes, as well as on genetic engineering and genome editing methods knocking out S genes, are discussed, to obtain durable PM-resistant cannabis cultivars with a broad-spectrum resistance range.
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Affiliation(s)
- Tiziana M Sirangelo
- ENEA-Italian National Agency for New Technologies, Energy and Sustainable Economic Development-Division Biotechnologies and Agroindustry, 00123 Rome, Italy
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37
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Tang Q, Xu Y, Gao F, Xu Y, Cheng C, Deng C, Chen J, Yuan X, Zhang X, Su J. Transcriptomic and metabolomic analyses reveal the differential accumulation of phenylpropanoids and terpenoids in hemp autotetraploid and its diploid progenitor. BMC PLANT BIOLOGY 2023; 23:616. [PMID: 38049730 PMCID: PMC10696708 DOI: 10.1186/s12870-023-04630-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 11/23/2023] [Indexed: 12/06/2023]
Abstract
BACKGROUND Cannabis sativa, a dioecious plant that has been cultivated worldwide for thousands of years, is known for its secondary metabolites, especially cannabinoids, which possess several medicinal effects. In this study, we investigated the autopolyploidization effects on the biosynthesis and accumulation of these metabolites, transcriptomic and metabolomic analyses were performed to explore the gene expression and metabolic variations in industrial hemp autotetraploids and their diploid progenitors. RESULTS Through these analyses, we obtained 1,663 differentially expressed metabolites and 1,103 differentially expressed genes. Integrative analysis revealed that phenylpropanoid and terpenoid biosynthesis were regulated by polyploidization. No substantial differences were found in the cannabidiol or tetrahydrocannabinol content between tetraploids and diploids. Following polyploidization, some transcription factors, including nine bHLH and eight MYB transcription factors, affected the metabolic biosynthesis as regulators. Additionally, several pivotal catalytic genes, such as flavonol synthase/flavanone 3-hydroxylase, related to the phenylpropanoid metabolic pathway, were identified as being modulated by polyploidization. CONCLUSIONS This study enhances the overall understanding of the impact of autopolyploidization in C. sativa and the findings may encourage the application of polyploid breeding for increasing the content of important secondary metabolites in industrial hemp.
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Affiliation(s)
- Qing Tang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, Hunan, China
- Center for Industrial Hemp Science and Technology Innovation, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, Hunan, China
| | - Ying Xu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, Hunan, China
| | - Feng Gao
- Yunnan Academy of Industrial Hemp, Kunming, 650214, Yunnan, China
| | - Ying Xu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, Hunan, China
| | - Chaohua Cheng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, Hunan, China
- Center for Industrial Hemp Science and Technology Innovation, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, Hunan, China
| | - Canhui Deng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, Hunan, China
| | - Jiquan Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, Hunan, China
| | - Xiaoge Yuan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, Hunan, China
| | - Xiaoyu Zhang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, Hunan, China
| | - Jianguang Su
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, Hunan, China.
- Center for Industrial Hemp Science and Technology Innovation, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, Hunan, China.
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38
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Wang Q, Zhao X, Jiang Y, Jin B, Wang L. Functions of Representative Terpenoids and Their Biosynthesis Mechanisms in Medicinal Plants. Biomolecules 2023; 13:1725. [PMID: 38136596 PMCID: PMC10741589 DOI: 10.3390/biom13121725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/25/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
Terpenoids are the broadest and richest group of chemicals obtained from plants. These plant-derived terpenoids have been extensively utilized in various industries, including food and pharmaceuticals. Several specific terpenoids have been identified and isolated from medicinal plants, emphasizing the diversity of biosynthesis and specific functionality of terpenoids. With advances in the technology of sequencing, the genomes of certain important medicinal plants have been assembled. This has improved our knowledge of the biosynthesis and regulatory molecular functions of terpenoids with medicinal functions. In this review, we introduce several notable medicinal plants that produce distinct terpenoids (e.g., Cannabis sativa, Artemisia annua, Salvia miltiorrhiza, Ginkgo biloba, and Taxus media). We summarize the specialized roles of these terpenoids in plant-environment interactions as well as their significance in the pharmaceutical and food industries. Additionally, we highlight recent findings in the fields of molecular regulation mechanisms involved in these distinct terpenoids biosynthesis, and propose future opportunities in terpenoid research, including biology seeding, and genetic engineering in medicinal plants.
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Affiliation(s)
| | | | | | | | - Li Wang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (Q.W.); (X.Z.); (Y.J.); (B.J.)
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39
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Stack GM, Snyder SI, Toth JA, Quade MA, Crawford JL, McKay JK, Jackowetz JN, Wang P, Philippe G, Hansen JL, Moore VM, Rose JKC, Smart LB. Cannabinoids function in defense against chewing herbivores in Cannabis sativa L. HORTICULTURE RESEARCH 2023; 10:uhad207. [PMID: 38023471 PMCID: PMC10681003 DOI: 10.1093/hr/uhad207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 10/07/2023] [Indexed: 12/01/2023]
Abstract
In the decades since the first cannabinoids were identified by scientists, research has focused almost exclusively on the function and capacity of cannabinoids as medicines and intoxicants for humans and other vertebrates. Very little is known about the adaptive value of cannabinoid production, though several hypotheses have been proposed including protection from ultraviolet radiation, pathogens, and herbivores. To test the prediction that genotypes with greater concentrations of cannabinoids will have reduced herbivory, a segregating F2 population of Cannabis sativa was leveraged to conduct lab- and field-based bioassays investigating the function of cannabinoids in mediating interactions with chewing herbivores. In the field, foliar cannabinoid concentration was inversely correlated with chewing herbivore damage. On detached leaves, Trichoplusia ni larvae consumed less leaf area and grew less when feeding on leaves with greater concentrations of cannabinoids. Scanning electron and light microscopy were used to characterize variation in glandular trichome morphology. Cannabinoid-free genotypes had trichomes that appeared collapsed. To isolate cannabinoids from confounding factors, artificial insect diet was amended with cannabinoids in a range of physiologically relevant concentrations. Larvae grew less and had lower rates of survival as cannabinoid concentration increased. These results support the hypothesis that cannabinoids function in defense against chewing herbivores.
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Affiliation(s)
- George M Stack
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY 14456, United States
| | - Stephen I Snyder
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, United States
| | - Jacob A Toth
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY 14456, United States
| | - Michael A Quade
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY 14456, United States
| | - Jamie L Crawford
- Plant Breeding Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, United States
| | - John K McKay
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, United States
| | | | - Ping Wang
- Department of Entomology, Cornell University, Cornell AgriTech, Geneva, NY 14456, United States
| | - Glenn Philippe
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, United States
| | - Julie L Hansen
- Plant Breeding Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, United States
| | - Virginia M Moore
- Plant Breeding Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, United States
| | - Jocelyn K C Rose
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, United States
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY 14456, United States
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Matros A, Menz P, Gill AR, Santoscoy A, Dawson T, Seiffert U, Burton RA. Non-invasive assessment of cultivar and sex of Cannabis sativa L. by means of hyperspectral measurement. PLANT-ENVIRONMENT INTERACTIONS (HOBOKEN, N.J.) 2023; 4:258-274. [PMID: 37822731 PMCID: PMC10564378 DOI: 10.1002/pei3.10116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 05/24/2023] [Accepted: 05/30/2023] [Indexed: 10/13/2023]
Abstract
Cannabis sativa L. is a versatile crop attracting increasing attention for food, fiber, and medical uses. As a dioecious species, males and females are visually indistinguishable during early growth. For seed or cannabinoid production, a higher number of female plants is economically advantageous. Currently, sex determination is labor-intensive and costly. Instead, we used rapid and non-destructive hyperspectral measurement, an emerging means of assessing plant physiological status, to reliably differentiate males and females. One industrial hemp (low tetrahydrocannabinol [THC]) cultivar was pre-grown in trays before transfer to the field in control soil. Reflectance spectra were acquired from leaves during flowering and machine learning algorithms applied allowed sex classification, which was best using a radial basis function (RBF) network. Eight industrial hemp (low THC) cultivars were field grown on fertilized and control soil. Reflectance spectra were acquired from leaves at early development when the plants of all cultivars had developed between four and six leaf pairs and in three cases only flower buds were visible (start of flowering). Machine learning algorithms were applied, allowing sex classification, differentiation of cultivars and fertilizer regime, again with best results for RBF networks. Differentiating nutrient status and varietal identity is feasible with high prediction accuracy. Sex classification was error-free at flowering but less accurate (between 60% and 87%) when using spectra from leaves at early growth stages. This was influenced by both cultivar and soil conditions, reflecting developmental differences between cultivars related to nutritional status. Hyperspectral measurement combined with machine learning algorithms is valuable for non-invasive assessment of C. sativa cultivar and sex. This approach can potentially improve regulatory security and productivity of cannabis farming.
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Affiliation(s)
- Andrea Matros
- ARC Centre of Excellence in Plant Energy Biology, School of Agriculture, Food and WineUniversity of AdelaideAdelaideSouth AustraliaAustralia
- Present address:
Compolytics GmbHBarlebenSaxony‐AnhaltGermany
| | - Patrick Menz
- Biosystems EngineeringFraunhofer IFFMagdeburgGermany
| | - Alison R. Gill
- ARC Centre of Excellence in Plant Energy Biology, School of Agriculture, Food and WineUniversity of AdelaideAdelaideSouth AustraliaAustralia
| | | | - Tim Dawson
- Australian Hemp Seed CompanyGawlerSouth AustraliaAustralia
| | - Udo Seiffert
- Biosystems EngineeringFraunhofer IFFMagdeburgGermany
- Australian Plant Phenomics Facility, School of Agriculture, Food and Wine & Waite Research InstituteUniversity of AdelaideUrrbraeSouth AustraliaAustralia
- Present address:
Compolytics GmbHBarlebenSaxony‐AnhaltGermany
| | - Rachel A. Burton
- ARC Centre of Excellence in Plant Energy Biology, School of Agriculture, Food and WineUniversity of AdelaideAdelaideSouth AustraliaAustralia
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Shelake RM, Jadhav AM, Bhosale PB, Kim JY. Unlocking secrets of nature's chemists: Potential of CRISPR/Cas-based tools in plant metabolic engineering for customized nutraceutical and medicinal profiles. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108070. [PMID: 37816270 DOI: 10.1016/j.plaphy.2023.108070] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/12/2023]
Abstract
Plant species have evolved diverse metabolic pathways to effectively respond to internal and external signals throughout their life cycle, allowing adaptation to their sessile and phototropic nature. These pathways selectively activate specific metabolic processes, producing plant secondary metabolites (PSMs) governed by genetic and environmental factors. Humans have utilized PSM-enriched plant sources for millennia in medicine and nutraceuticals. Recent technological advances have significantly contributed to discovering metabolic pathways and related genes involved in the biosynthesis of specific PSM in different food crops and medicinal plants. Consequently, there is a growing demand for plant materials rich in nutrients and bioactive compounds, marketed as "superfoods". To meet the industrial demand for superfoods and therapeutic PSMs, modern methods such as system biology, omics, synthetic biology, and genome editing (GE) play a crucial role in identifying the molecular players, limiting steps, and regulatory circuitry involved in PSM production. Among these methods, clustered regularly interspaced short palindromic repeats-CRISPR associated protein (CRISPR/Cas) is the most widely used system for plant GE due to its simple design, flexibility, precision, and multiplexing capabilities. Utilizing the CRISPR-based toolbox for metabolic engineering (ME) offers an ideal solution for developing plants with tailored preventive (nutraceuticals) and curative (therapeutic) metabolic profiles in an ecofriendly way. This review discusses recent advances in understanding the multifactorial regulation of metabolic pathways, the application of CRISPR-based tools for plant ME, and the potential research areas for enhancing plant metabolic profiles.
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Affiliation(s)
- Rahul Mahadev Shelake
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Republic of Korea.
| | - Amol Maruti Jadhav
- Research Institute of Green Energy Convergence Technology (RIGET), Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Pritam Bhagwan Bhosale
- Department of Veterinary Medicine, Research Institute of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Republic of Korea; Division of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea; Nulla Bio Inc, 501 Jinju-daero, Jinju, 52828, Republic of Korea.
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Xie Z, Mi Y, Kong L, Gao M, Chen S, Chen W, Meng X, Sun W, Chen S, Xu Z. Cannabis sativa: origin and history, glandular trichome development, and cannabinoid biosynthesis. HORTICULTURE RESEARCH 2023; 10:uhad150. [PMID: 37691962 PMCID: PMC10485653 DOI: 10.1093/hr/uhad150] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 07/18/2023] [Indexed: 09/12/2023]
Abstract
Is Cannabis a boon or bane? Cannabis sativa has long been a versatile crop for fiber extraction (industrial hemp), traditional Chinese medicine (hemp seeds), and recreational drugs (marijuana). Cannabis faced global prohibition in the twentieth century because of the psychoactive properties of ∆9-tetrahydrocannabinol; however, recently, the perspective has changed with the recognition of additional therapeutic values, particularly the pharmacological potential of cannabidiol. A comprehensive understanding of the underlying mechanism of cannabinoid biosynthesis is necessary to cultivate and promote globally the medicinal application of Cannabis resources. Here, we comprehensively review the historical usage of Cannabis, biosynthesis of trichome-specific cannabinoids, regulatory network of trichome development, and synthetic biology of cannabinoids. This review provides valuable insights into the efficient biosynthesis and green production of cannabinoids, and the development and utilization of novel Cannabis varieties.
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Affiliation(s)
- Ziyan Xie
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin 150040, China
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Yaolei Mi
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin 150040, China
- College of Life Science, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Lingzhe Kong
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin 150040, China
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Maolun Gao
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin 150040, China
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Shanshan Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Weiqiang Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Xiangxiao Meng
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Wei Sun
- College of Life Science, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Shilin Chen
- College of Life Science, Northeast Forestry University, Harbin 150040, China
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Zhichao Xu
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin 150040, China
- College of Life Science, Northeast Forestry University, Harbin 150040, China
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Camargo FDG, Santamaria-Torres M, Cala MP, Guevara-Suarez M, Restrepo SR, Sánchez-Camargo A, Fernández-Niño M, Corujo M, Gallo Molina AC, Cifuentes J, Serna JA, Cruz JC, Muñoz-Camargo C, Gonzalez Barrios AF. Genome-Scale Metabolic Reconstruction, Non-Targeted LC-QTOF-MS Based Metabolomics Data, and Evaluation of Anticancer Activity of Cannabis sativa Leaf Extracts. Metabolites 2023; 13:788. [PMID: 37512495 PMCID: PMC10385671 DOI: 10.3390/metabo13070788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/18/2023] [Accepted: 06/19/2023] [Indexed: 07/30/2023] Open
Abstract
Over the past decades, Colombia has suffered complex social problems related to illicit crops, including forced displacement, violence, and environmental damage, among other consequences for vulnerable populations. Considerable effort has been made in the regulation of illicit crops, predominantly Cannabis sativa, leading to advances such as the legalization of medical cannabis and its derivatives, the improvement of crops, and leaving an open window to the development of scientific knowledge to explore alternative uses. It is estimated that C. sativa can produce approximately 750 specialized secondary metabolites. Some of the most relevant due to their anticancer properties, besides cannabinoids, are monoterpenes, sesquiterpenoids, triterpenoids, essential oils, flavonoids, and phenolic compounds. However, despite the increase in scientific research on the subject, it is necessary to study the primary and secondary metabolism of the plant and to identify key pathways that explore its great metabolic potential. For this purpose, a genome-scale metabolic reconstruction of C. sativa is described and contextualized using LC-QTOF-MS metabolic data obtained from the leaf extract from plants grown in the region of Pesca-Boyaca, Colombia under greenhouse conditions at the Clever Leaves facility. A compartmentalized model with 2101 reactions and 1314 metabolites highlights pathways associated with fatty acid biosynthesis, steroids, and amino acids, along with the metabolism of purine, pyrimidine, glucose, starch, and sucrose. Key metabolites were identified through metabolomic data, such as neurine, cannabisativine, cannflavin A, palmitoleic acid, cannabinoids, geranylhydroquinone, and steroids. They were analyzed and integrated into the reconstruction, and their potential applications are discussed. Cytotoxicity assays revealed high anticancer activity against gastric adenocarcinoma (AGS), melanoma cells (A375), and lung carcinoma cells (A549), combined with negligible impact against healthy human skin cells.
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Affiliation(s)
- Fidias D González Camargo
- Group of Product and Process Design, Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá 111711, Colombia
- Applied Genomics Research Group Vice-Presidency for Research and Creation, Universidad de los Andes, Bogotá 111711, Colombia
| | - Mary Santamaria-Torres
- Metabolomics Core Facility-MetCore Vice-Presidency for Research and Creation, Universidad de los Andes, Bogotá 111711, Colombia
| | - Mónica P Cala
- Metabolomics Core Facility-MetCore Vice-Presidency for Research and Creation, Universidad de los Andes, Bogotá 111711, Colombia
| | - Marcela Guevara-Suarez
- Applied Genomics Research Group Vice-Presidency for Research and Creation, Universidad de los Andes, Bogotá 111711, Colombia
| | - Silvia Restrepo Restrepo
- Laboratory of Mycology and Phytopathology (LAMFU), Department of Biological Sciences and Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá 111711, Colombia
| | - Andrea Sánchez-Camargo
- Group of Product and Process Design, Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá 111711, Colombia
| | - Miguel Fernández-Niño
- Leibniz-Institute of Plant Biochemistry, Department of Bioorganic Chemistry, Weinberg 3, 06110 Halle, Germany
| | - María Corujo
- Ecomedics S.A.S., Commercially Known as Clever Leaves, Calle 95 # 11A-94, Bogota 110221, Colombia
| | - Ada Carolina Gallo Molina
- Chemical and Biochemical Processes Group, Department of Chemical and Environmental Engineering, National University of Colombia, Bogotá 11001, Colombia
| | - Javier Cifuentes
- Research Group on Nanobiomaterials, Cell Engineering and Bioprinting (GINIB), Department of Biomedical Engineering, Universidad de los Andes, Bogotá 111711, Colombia
| | - Julian A Serna
- Research Group on Nanobiomaterials, Cell Engineering and Bioprinting (GINIB), Department of Biomedical Engineering, Universidad de los Andes, Bogotá 111711, Colombia
| | - Juan C Cruz
- Research Group on Nanobiomaterials, Cell Engineering and Bioprinting (GINIB), Department of Biomedical Engineering, Universidad de los Andes, Bogotá 111711, Colombia
| | - Carolina Muñoz-Camargo
- Research Group on Nanobiomaterials, Cell Engineering and Bioprinting (GINIB), Department of Biomedical Engineering, Universidad de los Andes, Bogotá 111711, Colombia
| | - Andrés F Gonzalez Barrios
- Group of Product and Process Design, Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá 111711, Colombia
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Stats AK, Sweat KG, Masson RN, Conrow KD, Frazier AE, Leung MCK. The Desert Whale: the boom and bust of hemp in Arizona. J Cannabis Res 2023; 5:19. [PMID: 37291630 DOI: 10.1186/s42238-023-00187-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 05/04/2023] [Indexed: 06/10/2023] Open
Abstract
BACKGROUND This paper examines the factors that led to the collapse of hemp grown for cannabidiol (CBD) in Arizona, the United States of America (USA), and particularly in Yuma County, which is a well-established agricultural area in the state. METHODS This research uses a combination of mapping analysis along with a survey of hemp farmers to assess the reasons why the hemp industry collapsed as well as to foster solutions to these problems. RESULTS In 2019, 5430 acres were sown with hemp seed in Arizona with 3890 acres inspected by the state to determine if they could be harvested. By 2021, there were only 156 acres planted, and only 128 of those acres were inspected by the state for compliance. (Crop mortality accounts for the difference between acres sown and acres inspected.) CONCLUSIONS: A lack of knowledge about the hemp life cycle greatly contributed to the failure of high CBD hemp crops in Arizona. Other problems included noncompliance with tetrahydrocannabinol limits, poor sources for seeds and inconsistent genetics of the hemp varieties sold to farmers, and diseases that hemp plants were susceptible to such as Pythium crown and root rot and beet curly top virus. Addressing these factors will go far in making hemp a profitable and widespread crop in Arizona. Additionally, hemp grown for other traditional uses (e.g., fiber or seed oil) as well as new applications (e.g., microgreens, hempcrete, and phytoremediation) offers other pathways for successful hemp agriculture in this state.
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Affiliation(s)
| | - Ken G Sweat
- School of Mathematical and Natural Sciences, New College of Interdisciplinary Arts and Sciences, Arizona State University, 4701 W Thunderbird Rd, Glendale, AZ, 85306, USA.
| | - Robert N Masson
- Cooperative Extension, the University of Arizona, Tucson, USA
| | - Kendra D Conrow
- School of Mathematical and Natural Sciences, New College of Interdisciplinary Arts and Sciences, Arizona State University, 4701 W Thunderbird Rd, Glendale, AZ, 85306, USA
| | - Amy E Frazier
- School of Geographical Sciences & Urban Planning, Tempe, USA
| | - Maxwell C K Leung
- School of Mathematical and Natural Sciences, New College of Interdisciplinary Arts and Sciences, Arizona State University, 4701 W Thunderbird Rd, Glendale, AZ, 85306, USA.
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Ingvardsen CR, Brinch-Pedersen H. Challenges and potentials of new breeding techniques in Cannabis sativa. FRONTIERS IN PLANT SCIENCE 2023; 14:1154332. [PMID: 37360738 PMCID: PMC10285108 DOI: 10.3389/fpls.2023.1154332] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/24/2023] [Indexed: 06/28/2023]
Abstract
Cannabis sativa L. is an ancient crop used for fiber and seed production and not least for its content of cannabinoids used for medicine and as an intoxicant drug. Due to the psychedelic effect of one of the compounds, tetrahydrocannabinol (THC), many countries had regulations or bands on Cannabis growing, also as fiber or seed crop. Recently, as many of these regulations are getting less tight, the interest for the many uses of this crop is increasing. Cannabis is dioecious and highly heterogenic, making traditional breeding costly and time consuming. Further, it might be difficult to introduce new traits without changing the cannabinoid profile. Genome editing using new breeding techniques might solve these problems. The successful use of genome editing requires sequence information on suitable target genes, a genome editing tool to be introduced into plant tissue and the ability to regenerate plants from transformed cells. This review summarizes the current status of Cannabis breeding, uncovers potentials and challenges of Cannabis in an era of new breeding techniques and finally suggests future focus areas that may help to improve our overall understanding of Cannabis and realize the potentials of the plant.
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The B1080/B1192 molecular marker identifies hemp plants with functional THCA synthase and total THC content above legal limit. Gene 2023; 858:147198. [PMID: 36641078 DOI: 10.1016/j.gene.2023.147198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 01/09/2023] [Indexed: 01/13/2023]
Abstract
In Cannabis sativa L. the presence of delta 9-tetrahydrocannabinolic acid (THCA) above legal limit is a challenging issue that still restricts the industrial exploitation of this promising crop. In recent years, the interest of entrepreneurs and growers who see hemp as a dynamic and profitable crop was joined by the growing knowledge on C. sativa genetics and genomics, accelerated by the application of high throughput tools. Despite the renewed interest in the species, much remains to be clarified, especially about the long-standing problem of THCA in hemp inflorescences, which could even result in the seizure of the whole harvest. Although several hypotheses have been formulated on the accumulation of this metabolite in industrial varieties, none is conclusive yet. In this work, individuals of a population of the hemp cultivar 'FINOLA' obtained from commercial seeds were investigated for total THC level and examined at molecular level. A marker linked to THCA synthase was found at a high incidence in both male and female plants, suggesting a considerable genetic variability within the seed batch. Full-length sequences encoding for putatively functional THCA synthases were isolated for the first time from the genome of both female and male plants of an industrial hemp variety and, using transcriptional analysis, the THCA synthase expression was quantified in mature inflorescences of individuals identified by the marker. Biochemical analyses finally demonstrated for these plants a 100% association between the predicted and actual chemotype.
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Welling MT, Deseo MA, O’Brien M, Clifton J, Bacic A, Doblin MS. Metabolomic analysis of methyl jasmonate treatment on phytocannabinoid production in Cannabis sativa. FRONTIERS IN PLANT SCIENCE 2023; 14:1110144. [PMID: 37025140 PMCID: PMC10070988 DOI: 10.3389/fpls.2023.1110144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 03/07/2023] [Indexed: 06/19/2023]
Abstract
Cannabis sativa is a multi-use and chemically complex plant which is utilized for food, fiber, and medicine. Plants produce a class of psychoactive and medicinally important specialized metabolites referred to as phytocannabinoids (PCs). The phytohormone methyl jasmonate (MeJA) is a naturally occurring methyl ester of jasmonic acid and a product of oxylipin biosynthesis which initiates and regulates the biosynthesis of a broad range of specialized metabolites across a number of diverse plant lineages. While the effects of exogenous MeJA application on PC production has been reported, treatments have been constrained to a narrow molar range and to the targeted analysis of a small number of compounds. Using high-resolution mass spectrometry with data-dependent acquisition, we examined the global metabolomic effects of MeJA in C. sativa to explore oxylipin-mediated regulation of PC biosynthesis and accumulation. A dose-response relationship was observed, with an almost two-fold increase in PC content found in inflorescences of female clones treated with 15 mM MeJA compared to the control group. Comparison of the inflorescence metabolome across MeJA treatments coupled with targeted transcript analysis was used to elucidate key regulatory components contributing to PC production and metabolism more broadly. Revealing these biological signatures improves our understanding of the role of the oxylipin pathway in C. sativa and provides putative molecular targets for the metabolic engineering and optimization of chemical phenotype for medicinal and industrial end-uses.
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Liu J, Zhang C, Jiang M, Ni Y, Xu Y, Wu W, Huang L, Newmaster SG, Kole C, Wu B, Liu C. Identification of circular RNAs of Cannabis sativa L. potentially involved in the biosynthesis of cannabinoids. PLANTA 2023; 257:72. [PMID: 36862222 DOI: 10.1007/s00425-023-04104-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
We identified circRNAs in the Cannabis sativa L. genome and examined their association with 28 cannabinoids in three tissues of C. sativa. Nine circRNAs are potentially involved in the biosynthesis of six cannabinoids. Cannabis sativa L. has been widely used in the production of medicine, textiles, and food for over 2500 years. The main bioactive compounds in C. sativa are cannabinoids, which have multiple important pharmacological actions. Circular RNAs (circRNAs) play essential roles in growth and development, stress resistance, and the biosynthesis of secondary metabolites. However, the circRNAs in C. sativa remain unknown. In this study, to explore the role of circRNAs in cannabinoid biosynthesis, we performed RNA-Seq and metabolomics analysis on the leaves, roots, and stems of C. sativa. We identified 741 overlapping circRNAs by three tools, of which 717, 16, and 8 circRNAs were derived from exonic, intronic, and intergenic, respectively. Functional enrichment analysis indicated that the parental genes (PGs) of circRNAs were enriched in many processes related to biological stress responses. We found that most of the circRNAs showed tissue-specific expression and 65 circRNAs were significantly correlated with their PGs (P < 0.05, |r|≥ 0.5). We also determined 28 cannabinoids by High-performance liquid chromatography-ESI-triple quadrupole-linear ion trap mass spectrometry. Ten circRNAs, including ciR0159, ciR0212, ciR0153, ciR0149, ciR0016, ciR0044, ciR0022, ciR0381, ciR0006, and ciR0025 were found to be associated with six cannabinoids by weighted gene co-expression network analysis. Twenty-nine of 53 candidate circRNAs, including 9 cannabinoids related were validated successfully using PCR amplification and Sanger sequencing. Taken together, all these results would help to enhance our acknowledge of the regulation of circRNAs, and lay the foundation for breeding new C. sativa cultivars with high cannabinoids through manipulating circRNAs.
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Affiliation(s)
- Jingting Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, People's Republic of China
| | - Chang Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, People's Republic of China
| | - Mei Jiang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, People's Republic of China
| | - Yang Ni
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, People's Republic of China
| | - Yicen Xu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, People's Republic of China
| | - Wuwei Wu
- Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, People's Republic of China
| | - Linfang Huang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, People's Republic of China
| | - Steven G Newmaster
- Natural Health Product Research Alliance, College of Biological Sciences, University of Guelph, Guelph, ON, N1G2W1, Canada
| | - Chittaranjan Kole
- International Climate Resilient Crop Genomics Consortium and International Phytomedomics and Nutriomics Consortium, Kolkata, 700094, India
| | - Bin Wu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, People's Republic of China.
| | - Chang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, People's Republic of China.
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Liu J, Ni Y, Liu C. Polymeric structure of the Cannabis sativa L. mitochondrial genome identified with an assembly graph model. Gene 2023; 853:147081. [PMID: 36470482 DOI: 10.1016/j.gene.2022.147081] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 11/14/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022]
Abstract
Cannabis sativa L. belongs to the family Cannabaceae in Rosales. It has been widely used as medicines, building materials, and textiles. Elucidating its genome is critical for molecular breeding and synthetic biology study. Many studies have shown that the mitochondrial genomes (mitogenomes) and even chloroplast genomes (plastomes) had complex polymeric structures. Using the Nanopore sequencing platform, we sequenced, assembled, and analyzed its mitogenome and plastome. The resulting unitig graph suggested that the mitogenome had a complex polymeric structure. However, a gap-free, circular sequence was further assembled from the unitig graph. In contrast, a circular sequence representing the plastome was obtained. The mitogenome major conformation was 415,837 bp long, and the plastome was 153,927 bp long. To test if the repeat sequences promote recombination, which corresponds to the branch points in the structure, we tested the sequences around repeats by long-read mapping. Among 208 pairs of predicted repeats, the mapping results supported the presence of cross-over around 25 pairs of repeats. Subsequent PCR amplification confirmed the presence of cross-over around 15 of the 25 repeats. By comparing the mitogenome and plastome sequences, we identified 19 mitochondria plastid DNAs, including seven complete genes (trnW-CCA, trnP-UGG, psbJ, trnN-GUU, trnD-GUC, trnH-GUG, trnM-CAU) and nine gene fragments. Furthermore, the selective pressure analysis results showed that five genes (atp1, ccmB, ccmC, cox1, nad7) had 19 positively selected sites. Lastly, we predicted 28 RNA editing sites. A total of 8 RNA editing sites located in the coding regions were successfully validated by PCR amplification and Sanger sequencing, of which four were synonymous, and four were nonsynonymous. In particular, the RNA editing events appeared to be tissue-specific in C. sativa mitogenome. In summary, we have confirmed the major confirmation of C. sativa mitogenome and characterized its structural features in detail. These results provide critical information for future variety breeding and resource development for C. sativa.
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Affiliation(s)
- Jingting Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, PR China
| | - Yang Ni
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, PR China
| | - Chang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, PR China.
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Padgitt-Cobb LK, Pitra NJ, Matthews PD, Henning JA, Hendrix DA. An improved assembly of the "Cascade" hop ( Humulus lupulus) genome uncovers signatures of molecular evolution and refines time of divergence estimates for the Cannabaceae family. HORTICULTURE RESEARCH 2023; 10:uhac281. [PMID: 36818366 PMCID: PMC9930403 DOI: 10.1093/hr/uhac281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 12/22/2022] [Indexed: 06/16/2023]
Abstract
We present a chromosome-level assembly of the Cascade hop (Humulus lupulus L. var. lupulus) genome. The hop genome is large (2.8 Gb) and complex, and early attempts at assembly were fragmented. Recent advances have made assembly of the hop genome more tractable, transforming the extent of investigation that can occur. The chromosome-level assembly of Cascade was developed by scaffolding the previously reported Cascade assembly generated with PacBio long-read sequencing and polishing with Illumina short-read DNA sequencing. We developed gene models and repeat annotations and used a controlled bi-parental mapping population to identify significant sex-associated markers. We assessed molecular evolution in gene sequences, gene family expansion and contraction, and time of divergence from Cannabis sativa and other closely related plant species using Bayesian inference. We identified the putative sex chromosome in the female genome based on significant sex-associated markers from the bi-parental mapping population. While the estimate of repeat content (~64%) is similar to the estimate for the hemp genome, syntenic blocks in hop contain a greater percentage of LTRs. Hop is enriched for disease resistance-associated genes in syntenic gene blocks and expanded gene families. The Cascade chromosome-level assembly will inform cultivation strategies and serve to deepen our understanding of the hop genomic landscape, benefiting hop researchers and the Cannabaceae genomics community.
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Affiliation(s)
- Lillian K Padgitt-Cobb
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA
| | - Nicholi J Pitra
- Department of Research and Development, Hopsteiner, S.S. Steiner, Inc., 1 West Washington Avenue, Yakima, Washington 98903, USA
| | - Paul D Matthews
- Department of Research and Development, Hopsteiner, S.S. Steiner, Inc., 1 West Washington Avenue, Yakima, Washington 98903, USA
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