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Adamek K, Jones AMP, Torkamaneh D. Somatic Mutation Accumulations in Micropropagated Cannabis Are Proportional to the Number of Subcultures. PLANTS (BASEL, SWITZERLAND) 2024; 13:1910. [PMID: 39065436 PMCID: PMC11279941 DOI: 10.3390/plants13141910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 07/04/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024]
Abstract
Advancements in micropropagation techniques have made it easier to produce large numbers of cannabis clones, but these methods may also introduce genetic instability over successive generations. This instability often manifests as somaclonal variation, characterized by the progressive accumulation of genetic mutations or epigenetic alterations with each subculture. In this study, we examined how mutations accumulate in cannabis clones subjected to 6-11 subcultures. Using genotyping-by-sequencing, we identified 9405 polymorphic variants across 70 clones. The analysis revealed a correlation between the number of subcultures and the frequency of these mutations, revealing that genetic changes accumulate over successive subcultures despite clones sharing the same chronological age. Furthermore, we evaluated the functional impacts of accumulated mutations, with particular attention to implications on gene function and overall plant health. While rare, 14 high-impact variants were identified in genes that are important for plant development. Notably, six variants were also found in genes related to cannabinoid and terpene synthesis pathways, potentially affecting the plant's biochemical composition. These findings highlight the need for genetic assessments in micropropagation protocols, impacting plant breeding and conservation. Understanding genetic variations in clonally propagated plants optimizes practices for stability. Crucial for cannabis and horticultural plants, it emphasizes techniques to prevent genetic decay and ensure viability.
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Affiliation(s)
- Kristian Adamek
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada; (K.A.); (A.M.P.J.)
| | | | - Davoud Torkamaneh
- Département de Phytologie, Université Laval, Québec, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC G1V 0A6, Canada
- Centre de Recherche et d’Innovation sur les Végétaux (CRIV), Université Laval, Québec, QC G1V 0A6, Canada
- Institute Intelligence and Data (IID), Université Laval, Québec, QC G1V 0A6, Canada
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Goralogia GS, Andreatta IM, Conrad V, Xiong Q, Vining KJ, Strauss SH. Rare but diverse off-target and somatic mutations found in field and greenhouse grown trees expressing CRISPR/Cas9. Front Bioeng Biotechnol 2024; 12:1412927. [PMID: 38974658 PMCID: PMC11224489 DOI: 10.3389/fbioe.2024.1412927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 05/15/2024] [Indexed: 07/09/2024] Open
Abstract
Introduction: CRISPR gene editing, while highly efficient in creating desired mutations, also has the potential to cause off-target mutations. This risk is especially high in clonally propagated plants, where editing reagents may remain in the genome for long periods of time or in perpetuity. We studied a diverse population of Populus and Eucalyptus trees that had CRISPR/Cas9-containing transgenes that targeted one or two types of floral development genes, homologs of LEAFY and AGAMOUS. Methods: Using a targeted sequence approach, we studied approximately 20,000 genomic sites with degenerate sequence homology of up to five base pairs relative to guide RNA (gRNA) target sites. We analyzed those sites in 96 individual tree samples that represented 37 independent insertion events containing one or multiples of six unique gRNAs. Results: We found low rates of off-target mutations, with rates of 1.2 × 10-9 in poplar and 3.1 × 10-10 in eucalypts, respectively, comparable to that expected due to sexual reproduction. The rates of mutation were highly idiosyncratic among sites and not predicted by sequence similarity to the target sites; a subset of two gRNAs showed off-target editing of four unique genomic sites with up to five mismatches relative to the true target sites, reaching fixation in some gene insertion events and clonal ramets. The location of off-target mutations relative to the PAM site were essentially identical to that seen with on-target CRISPR mutations. Discussion: The low rates observed support many other studies in plants that suggest that the rates of off-target mutagenesis from CRISPR/Cas9 transgenes are negligible; our study extends this conclusion to trees and other long-lived plants where CRISPR/Cas9 transgenes were present in the genome for approximately four years.
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Affiliation(s)
- Greg S. Goralogia
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, United States
| | - Isabella M. Andreatta
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, United States
| | - Victoria Conrad
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, United States
| | - Qin Xiong
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Science, Nanjing Forestry University, Nanjing, China
| | - Kelly J. Vining
- Department of Horticulture, Oregon State University, Corvallis, OR, United States
| | - Steven H. Strauss
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, United States
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Liu H, Fang H, Zhang G, Li J, Zhang X, Li Y. De novo transcriptome profiling reveals the patterns of gene expression in plum fruits with bud mutations. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:909-919. [PMID: 38974351 PMCID: PMC11222343 DOI: 10.1007/s12298-024-01472-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 06/05/2024] [Accepted: 06/10/2024] [Indexed: 07/09/2024]
Abstract
Bud mutation is a common technique for plant breeding and can provide a large number of breeding materials. Through traditional breeding methods, we obtained a plum plant with bud mutations (named "By") from an original plum variety (named "B"). The ripening period of "By" fruit was longer than that of "B" fruit, and its taste was better. In order to understand the characteristics of these plum varieties, we used transcriptome analysis and compared the gene expression patterns in fruits from the two cultivars. Subsequently, we identified the biological processes regulated by the differentially expressed genes (DEGs). Gene ontology (GO) analysis revealed that these DEGs were highly enriched for "single-organism cellular process" and "transferase activity". KEGG analysis demonstrated that the main pathways affected by the bud mutations were plant hormone signal transduction, starch and sucrose metabolism. The IAA, CKX, ARF, and SnRK2 genes were identified as the key regulators of plant hormone signal transduction. Meanwhile, TPP, the beta-glucosidase (EC3.2.1.21) gene, and UGT72E were identified as candidate DEGs affecting secondary metabolite synthesis. The transcriptome sequencing (RNA-seq) data were also validated using RT-qPCR experiments. The transcriptome analysis demonstrated that plant hormones play a significant role in extending the maturity period of plum fruit, with IAA, CKX, ARF, and SnRK2 serving as the key regulators of this process. Further, TPP, beta-glucosidase (EC3.2.1.21), and UGT72E appeared to mediate the synthesis of various soluble secondary metabolites, contributing to the aroma of plum fruits. The expression of BAG6 was upregulated in "B" as the fruit matured, but it was downregulated in "By". This indicated that "B" may have stronger resistance, especially fungal resistance. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-024-01472-3.
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Affiliation(s)
- Huiyan Liu
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, School of Food Science and Engineering, Ningxia University, Yinchuan, 750021 Ningxia China
| | - Haitian Fang
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, School of Food Science and Engineering, Ningxia University, Yinchuan, 750021 Ningxia China
| | - Guangdi Zhang
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, School of Food Science and Engineering, Ningxia University, Yinchuan, 750021 Ningxia China
- Ningxia Facility Horticulture Engineering Technology Center, Yinchuan, 750021 Ningxia China
- Technological Innovation Center of Horticulture, Ningxia University), Ningxia Hui Autonomous Region, Yinchuan, 750021 Ningxia China
| | - Jianshe Li
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, School of Food Science and Engineering, Ningxia University, Yinchuan, 750021 Ningxia China
- Ningxia Facility Horticulture Engineering Technology Center, Yinchuan, 750021 Ningxia China
- Technological Innovation Center of Horticulture, Ningxia University), Ningxia Hui Autonomous Region, Yinchuan, 750021 Ningxia China
| | - Xiangjun Zhang
- School of Life Science, Ningxia University, Yinchuan, 750021 Ningxia China
| | - Yu Li
- Technological Innovation Center of Horticulture, Ningxia University), Ningxia Hui Autonomous Region, Yinchuan, 750021 Ningxia China
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Wang T, Zheng Z, Deng L, Li W, Yuan Y, Zhang M, Sun G, He S, Wang J, Wang Z, Xiong B. Effect of Natural Variation and Rootstock on Fruit Quality and Volatile Organic Compounds of ' Kiyomi tangor' ( Citrus reticulata Blanco) Citrus. Int J Mol Sci 2023; 24:16810. [PMID: 38069133 PMCID: PMC10706780 DOI: 10.3390/ijms242316810] [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: 10/19/2023] [Revised: 11/16/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
In this study, we compared the fruit quality and color of 'Kiyomi' (WT) and its mutant (MT) grafted on Ziyang xiangcheng (Cj) (WT/Cj, MT/Cj), and the MT grafted on Trifoliate orange (Pt) (MT/Pt). The differences in sugar, organic acid, flavonoids, phenols, and volatile substances of the three materials were also analyzed by high performance liquid chromatography (HPLC) and headspace solid-phase microextraction-gas chromatography-mass spectrometry (HS-SPME-GC-MS). The results showed significant differences in the appearance of WT/Cj, MT/Cj, and MT/Pt. MT/Pt, compared to WT/Cj, MT/Cj, had lower sugar, acid, phenol and flavonoid contents in the pulp. However, MT/Pt pulp was higher in vitamin C (VC), and the peel had significantly higher total phenol and flavonoid contents. In terms of pulp, WT/Cj had the greatest diversity of volatile organic compounds (VOCs). 4-methyl-1-pentanol was significantly higher in MT/Cj pulp, while MT/Pt pulp had a unique octanoic acid, methyl ester. VOCs were more diverse in the peels of the three materials. β-Myrcene and valencen were significantly higher in MT/Cj peels. In contrast, 16 unique VOCs were detected in MT/Pt, and D-limonene content was significantly higher than in WT/Cj and MT/Cj. The results suggest Trifoliate orange is a suitable rootstock for MT.
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Affiliation(s)
- Tie Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhendong Zheng
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Lijun Deng
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Weijia Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Ya Yuan
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Mingfei Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Guochao Sun
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Siya He
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Jun Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhihui Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Bo Xiong
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
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