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Balant M, Garnatje T, Vitales D, Hidalgo O, Chitwood DH. Intra-leaf modeling of Cannabis leaflet shape produces leaf models that predict genetic and developmental identities. THE NEW PHYTOLOGIST 2024; 243:781-796. [PMID: 38757746 DOI: 10.1111/nph.19817] [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: 04/28/2024] [Indexed: 05/18/2024]
Abstract
The iconic, palmately compound leaves of Cannabis have attracted significant attention in the past. However, investigations into the genetic basis of leaf shape or its connections to phytochemical composition have yielded inconclusive results. This is partly due to prominent changes in leaflet number within a single plant during development, which has so far prevented the proper use of common morphometric techniques. Here, we present a new method that overcomes the challenge of nonhomologous landmarks in palmate, pinnate, and lobed leaves, using Cannabis as an example. We model corresponding pseudo-landmarks for each leaflet as angle-radius coordinates and model them as a function of leaflet to create continuous polynomial models, bypassing the problems associated with variable number of leaflets between leaves. We analyze 341 leaves from 24 individuals from nine Cannabis accessions. Using 3591 pseudo-landmarks in modeled leaves, we accurately predict accession identity, leaflet number, and relative node number. Intra-leaf modeling offers a rapid, cost-effective means of identifying Cannabis accessions, making it a valuable tool for future taxonomic studies, cultivar recognition, and possibly chemical content analysis and sex identification, in addition to permitting the morphometric analysis of leaves in any species with variable numbers of leaflets or lobes.
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Affiliation(s)
- Manica Balant
- Institut Botànic de Barcelona, IBB (CSIC-CMCNB), Passeig del Migdia s.n., 08038, Barcelona, Spain
- Laboratori de Botànica, Unitat Associada al CSIC, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona (UB), Av. Joan XXIII 27-31, 08028, Barcelona, Spain
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Teresa Garnatje
- Institut Botànic de Barcelona, IBB (CSIC-CMCNB), Passeig del Migdia s.n., 08038, Barcelona, Spain
- Jardí Botànic Marimurtra - Fundació Carl Faust, pg. Carles Faust, 9, 17300, Blanes, Spain
| | - Daniel Vitales
- Institut Botànic de Barcelona, IBB (CSIC-CMCNB), Passeig del Migdia s.n., 08038, Barcelona, Spain
| | - Oriane Hidalgo
- Institut Botànic de Barcelona, IBB (CSIC-CMCNB), Passeig del Migdia s.n., 08038, Barcelona, Spain
- Royal Botanic Gardens, Kew, Richmond, TW9 3AE, UK
| | - Daniel H Chitwood
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Department of Computational Mathematics, Science & Engineering, Michigan State University, East Lansing, MI, 48824, USA
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Jung YJ, Kim MS, Cho YG. Trends and Prospects of Genetic and Molecular Research in Plants. PLANTS (BASEL, SWITZERLAND) 2024; 13:1545. [PMID: 38891353 PMCID: PMC11174468 DOI: 10.3390/plants13111545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024]
Abstract
With the exponential advancements in biotechnology research, various studies are being conducted to overcome productivity limitations in crop breeding [...].
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Affiliation(s)
- Yu Jin Jung
- Division of Horticultural Biotechnology, School of Biotechnology, Hankyong National University, Anseong 17579, Republic of Korea
- Institute of Genetic Engineering, Hankyong National University, Anseong 17579, Republic of Korea
| | - Me-Sun Kim
- College of Agriculture and Life & Environment Sciences, Chungbuk National University, Cheongju 28644, Republic of Korea; (M.-S.K.); (Y.-G.C.)
| | - Yong-Gu Cho
- College of Agriculture and Life & Environment Sciences, Chungbuk National University, Cheongju 28644, Republic of Korea; (M.-S.K.); (Y.-G.C.)
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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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Guenzi-Tiberi P, Istace B, Alsos IG, Coissac E, Lavergne S, Aury JM, Denoeud F. LocoGSE, a sequence-based genome size estimator for plants. FRONTIERS IN PLANT SCIENCE 2024; 15:1328966. [PMID: 38550287 PMCID: PMC10972871 DOI: 10.3389/fpls.2024.1328966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 02/22/2024] [Indexed: 06/21/2024]
Abstract
Extensive research has focused on exploring the range of genome sizes in eukaryotes, with a particular emphasis on land plants, where significant variability has been observed. Accurate estimation of genome size is essential for various research purposes, but existing sequence-based methods have limitations, particularly for low-coverage datasets. In this study, we introduce LocoGSE, a novel genome size estimator designed specifically for low-coverage datasets generated by genome skimming approaches. LocoGSE relies on mapping the reads on single copy consensus proteins without the need for a reference genome assembly. We calibrated LocoGSE using 430 low-coverage Angiosperm genome skimming datasets and compared its performance against other estimators. Our results demonstrate that LocoGSE accurately predicts monoploid genome size even at very low depth of coverage (<1X) and on highly heterozygous samples. Additionally, LocoGSE provides stable estimates across individuals with varying ploidy levels. LocoGSE fills a gap in sequence-based plant genome size estimation by offering a user-friendly and reliable tool that does not rely on high coverage or reference assemblies. We anticipate that LocoGSE will facilitate plant genome size analysis and contribute to evolutionary and ecological studies in the field. Furthermore, at the cost of an initial calibration, LocoGSE can be used in other lineages.
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Affiliation(s)
- Pierre Guenzi-Tiberi
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Benjamin Istace
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Inger Greve Alsos
- The Arctic University Museum of Norway, UiT The Arctic University of Norway, Tromsø, Norway
| | - Eric Coissac
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA (Laboratoire d’Ecologie Alpine), Grenoble, France
| | - Sébastien Lavergne
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA (Laboratoire d’Ecologie Alpine), Grenoble, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - France Denoeud
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
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Govindarajan RK, Mishra AK, Cho KH, Kim KH, Yoon KM, Baek KH. Biosynthesis of Phytocannabinoids and Structural Insights: A Review. Metabolites 2023; 13:metabo13030442. [PMID: 36984882 PMCID: PMC10051821 DOI: 10.3390/metabo13030442] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/09/2023] [Accepted: 03/14/2023] [Indexed: 03/30/2023] Open
Abstract
Cannabis belongs to the family Cannabaceae, and phytocannabinoids are produced by the Cannabis sativa L. plant. A long-standing debate regarding the plant is whether it contains one or more species. Phytocannabinoids are bioactive natural products found in flowers, seeds, and fruits. They can be beneficial for treating human diseases (such as multiple sclerosis, neurodegenerative diseases, epilepsy, and pain), the cellular metabolic process, and regulating biological function systems. In addition, several phytocannabinoids are used in various therapeutic and pharmaceutical applications. This study provides an overview of the different sources of phytocannabinoids; further, the biosynthesis of bioactive compounds involving various pathways is elucidated. The structural classification of phytocannabinoids is based on their decorated resorcinol core and the bioactivities of naturally occurring cannabinoids. Furthermore, phytocannabinoids have been studied in terms of their role in animal models and antimicrobial activity against bacteria and fungi; further, they show potential for therapeutic applications and are used in treating various human diseases. Overall, this review can help deepen the current understanding of the role of biotechnological approaches and the importance of phytocannabinoids in different industrial applications.
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Affiliation(s)
| | - Awdhesh Kumar Mishra
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Gyeongbuk, Republic of Korea
| | - Kiu-Hyung Cho
- Gyeongbuk Institute for Bioindustry, Andong 36618, Gyeongbuk, Republic of Korea
| | - Ki-Hyun Kim
- Gyeongbuk Institute for Bioindustry, Andong 36618, Gyeongbuk, Republic of Korea
| | - Kyoung Mi Yoon
- Gyeongbuk Institute for Bioindustry, Andong 36618, Gyeongbuk, Republic of Korea
| | - Kwang-Hyun Baek
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Gyeongbuk, Republic of Korea
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