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Chen S, Han J, Wu S, Guo S, Tang Y, Zheng Y, Hu L, Zhang X, Zhang P, Zhang H, Ren G, Gao S. From non-coding RNAs to histone modification: The epigenetic mechanisms in tomato fruit ripening and quality regulation. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 215:109070. [PMID: 39191041 DOI: 10.1016/j.plaphy.2024.109070] [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: 05/22/2024] [Revised: 07/28/2024] [Accepted: 08/22/2024] [Indexed: 08/29/2024]
Abstract
Ripening is one of the most important stages of fruit development and determines the fruit quality. Various factors play a role in this process, with epigenetic mechanisms emerging as important players. Epigenetic regulation encompasses DNA methylation, histone modifications and variants, chromatin remodeling, RNA modifications, and non-coding RNAs. Over the past decade, studies using tomato as a model have made considerable progress in understanding the impact of epigenetic regulation on fleshy fruit ripening and quality. In this paper, we provide an overview of recent advancements in the epigenetic regulation of tomato fruit ripening and quality regulation, focusing on three main mechanisms: DNA/RNA modifications, non-coding RNAs, and histone modifications. Furthermore, we highlight the unresolved issues and challenges within this research field, offering perspectives for future investigations to drive agricultural innovation.
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Affiliation(s)
- Shengbo Chen
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Jiazhen Han
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Shu Wu
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Shangjing Guo
- Qingdao Agricultural University, Qingdao, 266109, China
| | - Yufei Tang
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Yujing Zheng
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Lei Hu
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Xingxing Zhang
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Peng Zhang
- Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | | | - Guodong Ren
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China.
| | - Shuai Gao
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China.
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Delen Y, Mural RV, Palali‐Delen S, Xu G, Schnable JC, Dweikat I, Yang J. Dissecting the genetic architecture of sunflower disc diameter using genome-wide association study. PLANT DIRECT 2024; 8:e70010. [PMID: 39385760 PMCID: PMC11464090 DOI: 10.1002/pld3.70010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 07/31/2024] [Accepted: 09/22/2024] [Indexed: 10/12/2024]
Abstract
Sunflower (Helianthus annuus L.) plays an essential role in meeting the demand for edible oil worldwide. The yield of sunflower seeds encompasses several component traits, including the disc diameter. Over three consecutive years, 2019, 2020, and 2022, we assessed phenotypic variation in disc diameter across a diverse set of sunflower accessions (N = 342) in replicated field trials. Upon aggregating the phenotypic data from multiple years, we estimated the broad sense heritability (H 2) of the disc diameter trait to be 0.88. A subset of N = 274 accessions was genotyped by using the tunable genotyping-by-sequencing (tGBS) method, resulting in 226,779 high-quality SNPs. Using these SNPs and the disc diameter phenotype, we conducted a genome-wide association study (GWAS) employing two statistical approaches: the mixed linear model (MLM) and the fixed and random model circulating probability unification (farmCPU). The MLM and farmCPU GWAS approaches identified 106 and 8 significant SNPs located close to 53 and 21 genes, respectively. The MLM analysis identified two significant peaks: a prominent signal on chromosome 10 and a relatively weaker signal on chromosome 16, both of which were also detected by farmCPU. The genetic loci associated with disc diameter, as well as the related candidate genes, present promising avenues for further functional validation and serve as a basis for sunflower oil yield improvement.
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Affiliation(s)
- Yavuz Delen
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
| | - Ravi V. Mural
- Department of Agronomy, Horticulture and Plant ScienceSouth Dakota State UniversityBrookingsSDUSA
| | - Semra Palali‐Delen
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
- Center for Plant Science InnovationUniversity of Nebraska‐LincolnLincolnNEUSA
| | - Gen Xu
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
- Center for Plant Science InnovationUniversity of Nebraska‐LincolnLincolnNEUSA
| | - James C. Schnable
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
- Center for Plant Science InnovationUniversity of Nebraska‐LincolnLincolnNEUSA
| | - Ismail Dweikat
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
| | - Jinliang Yang
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
- Center for Plant Science InnovationUniversity of Nebraska‐LincolnLincolnNEUSA
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Guan H, Yang X, Lin Y, Xie B, Zhang X, Ma C, Xia R, Chen R, Hao Y. The hormone regulatory mechanism underlying parthenocarpic fruit formation in tomato. FRONTIERS IN PLANT SCIENCE 2024; 15:1404980. [PMID: 39119498 PMCID: PMC11306060 DOI: 10.3389/fpls.2024.1404980] [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: 03/22/2024] [Accepted: 07/05/2024] [Indexed: 08/10/2024]
Abstract
Parthenocarpic fruits, known for their superior taste and reliable yields in adverse conditions, develop without the need for fertilization or pollination. Exploring the physiological and molecular mechanisms behind parthenocarpic fruit development holds both theoretical and practical significance, making it a crucial area of study. This review examines how plant hormones and MADS-box transcription factors control parthenocarpic fruit formation. It delves into various aspects of plant hormones-including auxin, gibberellic acid, cytokinins, ethylene, and abscisic acid-ranging from external application to biosynthesis, metabolism, signaling pathways, and their interplay in influencing parthenocarpic fruit development. The review also explores the involvement of MADS family gene functions in these processes. Lastly, we highlight existing knowledge gaps and propose directions for future research on parthenocarpy.
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Affiliation(s)
- Hongling Guan
- College of Horticulture, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, School of Biology and Agriculture, Shaoguan University, Shaoguan, China
| | - Xiaolong Yang
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Yuxiang Lin
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Baoxing Xie
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xinyue Zhang
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Chongjian Ma
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, School of Biology and Agriculture, Shaoguan University, Shaoguan, China
| | - Rui Xia
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Riyuan Chen
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Yanwei Hao
- College of Horticulture, South China Agricultural University, Guangzhou, China
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Maupilé L, Chaib J, Boualem A, Bendahmane A. Parthenocarpy, a pollination-independent fruit set mechanism to ensure yield stability. TRENDS IN PLANT SCIENCE 2024:S1360-1385(24)00151-1. [PMID: 39034223 DOI: 10.1016/j.tplants.2024.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 06/11/2024] [Accepted: 06/17/2024] [Indexed: 07/23/2024]
Abstract
Fruit development is essential for flowering plants' reproduction and a significant food source. Climate change threatens fruit yields due to its impact on pollination and fertilization processes, especially vulnerable to extreme temperatures, insufficient light, and pollinator decline. Parthenocarpy, the development of fruit without fertilization, offers a solution, ensuring yield stability in adverse conditions and enhancing fruit quality. Parthenocarpic fruits not only secure agricultural production but also exhibit improved texture, appearance, and shelf life, making them desirable for food processing and other applications. Recent research unveils the molecular mechanisms behind parthenocarpy, implicating transcription factors (TFs), noncoding RNAs, and phytohormones such as auxin, gibberellin (GA), and cytokinin (CK). Here we review recent findings, construct regulatory models, and identify areas for further research.
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Affiliation(s)
- Lea Maupilé
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France; Vilmorin & Cie, Route d'Ennezat, 63720 Chappes, France
| | - Jamila Chaib
- Vilmorin & Cie, Paraje La Reserva, 04725 La Mojonera, Spain
| | - Adnane Boualem
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France; Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France.
| | - Abdelhafid Bendahmane
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France; Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France.
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5
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Tian S, Zhang Z, Qin G, Xu Y. Parthenocarpy in Cucurbitaceae: Advances for Economic and Environmental Sustainability. PLANTS (BASEL, SWITZERLAND) 2023; 12:3462. [PMID: 37836203 PMCID: PMC10574560 DOI: 10.3390/plants12193462] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023]
Abstract
Parthenocarpy is an important agricultural trait that not only produces seedless fruits, but also increases the rate of the fruit set under adverse environmental conditions. The study of parthenocarpy in Cucurbitaceae crops has considerable implications for cultivar improvement. This article provides a comprehensive review of relevant studies on the parthenocarpic traits of several major Cucurbitaceae crops and offers a perspective on future developments and research directions.
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Affiliation(s)
- Shouwei Tian
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Zeliang Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Genji Qin
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yong Xu
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
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Kashojiya S, Lu Y, Takayama M, Komatsu H, Minh LHT, Nishida K, Shirasawa K, Miura K, Nonaka S, Masuda JI, Kondo A, Ezura H, Ariizumi T. Modification of tomato breeding traits and plant hormone signaling by target-AID, the genome-editing system inducing efficient nucleotide substitution. HORTICULTURE RESEARCH 2022; 9:uhab004. [PMID: 35043178 PMCID: PMC8795821 DOI: 10.1093/hr/uhab004] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 01/19/2022] [Accepted: 10/21/2021] [Indexed: 06/14/2023]
Abstract
Target activation-induced cytidine deaminase (Target-AID), a novel CRISPR/Cas9-based genome-editing tool, confers the base-editing capability on the Cas9 genome-editing system. It involves the fusion of cytidine deaminase (CDA), which catalyzes cytidine (C) to uridine (U) substitutions, to the mutated nickase-type nCas9 or deactivated-type dCas9. To confirm and extend the applicability of the Target-AID genome-editing system in tomatoes (Solanum lycopersicum L.), we transformed the model tomato cultivar "Micro-Tom" and commercial tomato cultivars using this system by targeting SlDELLA, which encodes a negative regulator of the plant phytohormone gibberellic acid (GA) signaling pathway. We confirmed that the nucleotide substitutions were induced by the Target-AID system, and we isolated mutants showing high GA sensitivity in both "Micro-Tom" and the commercial cultivars. Moreover, by successfully applying this system to ETHYLENE RECEPTOR 1 (SlETR1) with single sgRNA targeting, double sgRNA targeting, as well as dual-targeting of both SlETR1 and SlETR2 with a single sgRNA, we demonstrated that the Target-AID genome-editing system is a promising tool for molecular breeding in tomato crops. This study highlights an important aspect of the scientific and agricultural potential of the combinatorial use of the Target-AID and other base-editing systems.
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Affiliation(s)
- Sachiko Kashojiya
- Faculty of Life and Environmental Sciences, University of Tsukuba, Gene Research Center, Tsukuba, Ibaraki 305-8572, Japan
- Japan Society for Promotion of Science, 5-3-1, Kojimachi, Tokyo 102-0083, Japan
| | - Yu Lu
- Faculty of Life and Environmental Sciences, University of Tsukuba, Gene Research Center, Tsukuba, Ibaraki 305-8572, Japan
- Japan Society for Promotion of Science, 5-3-1, Kojimachi, Tokyo 102-0083, Japan
| | - Mariko Takayama
- Faculty of Life and Environmental Sciences, University of Tsukuba, Gene Research Center, Tsukuba, Ibaraki 305-8572, Japan
| | - Hiroki Komatsu
- Faculty of Life and Environmental Sciences, University of Tsukuba, Gene Research Center, Tsukuba, Ibaraki 305-8572, Japan
| | - Luyen Hieu Thi Minh
- Faculty of Life and Environmental Sciences, University of Tsukuba, Gene Research Center, Tsukuba, Ibaraki 305-8572, Japan
| | - Keiji Nishida
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo 657-8501, Japan
- Engineering Biology Research Center, Kobe University, 7-1-49, Minatojima Minami Machi, Chuo-ku, Kobe 650-0047, Japan
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Kenji Miura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Gene Research Center, Tsukuba, Ibaraki 305-8572, Japan
| | - Satoko Nonaka
- Faculty of Life and Environmental Sciences, University of Tsukuba, Gene Research Center, Tsukuba, Ibaraki 305-8572, Japan
| | - Jun-ichiro Masuda
- Faculty of Life and Environmental Sciences, University of Tsukuba, Gene Research Center, Tsukuba, Ibaraki 305-8572, Japan
- Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki, Miyazaki 889-2192, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo 657-8501, Japan
- Engineering Biology Research Center, Kobe University, 7-1-49, Minatojima Minami Machi, Chuo-ku, Kobe 650-0047, Japan
| | - Hiroshi Ezura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Gene Research Center, Tsukuba, Ibaraki 305-8572, Japan
- Tsukuba Plant Innovation Research Center, University of Tsukuba, Ibaraki 305-8572, Japan
| | - Tohru Ariizumi
- Faculty of Life and Environmental Sciences, University of Tsukuba, Gene Research Center, Tsukuba, Ibaraki 305-8572, Japan
- Tsukuba Plant Innovation Research Center, University of Tsukuba, Ibaraki 305-8572, Japan
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Nagata T, Lombardo F, Ezura H. Complementation of the tomato HWS gene with its Arabidopsis counterpart demonstrates conservation of the gene function between both species. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2021; 38:387-390. [PMID: 34782827 PMCID: PMC8562581 DOI: 10.5511/plantbiotechnology.21.0729a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 07/29/2021] [Indexed: 06/13/2023]
Abstract
The HAWAIIAN SKIRT (HWS) gene was originally described in Arabidopsis for the characteristic fusion of sepals in the mutant. A tomato line mutated in the putative ortholog gene was isolated in a previous study. The tomato hws-1 mutant showed facultative parthenocarpy and produced fruits with elevated Brix, revealing the gene as a hopeful resource for crop improvement. To confirm the orthology relationship between the Arabidopsis and tomato HWS genes, the hws-1 mutant was complemented with either the tomato wild-type genomic fragment or the Arabidopsis sequence of the gene. In both complementation experiments, defective phenotypes of hws-1 are rescued, albeit to different extents. Recovery of these phenotypes, which include parthenocarpic fruit production, increased Brix, loss of leaflet serration, alteration of bud and petal shape, firmly establishes SlHWS as an ortholog of the originally described HWS in Arabidopsis. This work indicates that the function of HWS is likely to be conserved in a wide range of plant species.
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Affiliation(s)
- Toshifumi Nagata
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Fabien Lombardo
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Hiroshi Ezura
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
- Tsukuba Plant Innovation Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
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Lombardo F, Gramazio P, Ezura H. Increase in Phloem Area in the Tomato hawaiian skirt Mutant Is Associated with Enhanced Sugar Transport. Genes (Basel) 2021; 12:genes12060932. [PMID: 34207298 PMCID: PMC8234570 DOI: 10.3390/genes12060932] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 06/13/2021] [Accepted: 06/15/2021] [Indexed: 11/29/2022] Open
Abstract
The HAWAIIAN SKIRT (HWS) gene has been described in Arabidopsis, rice, tomato and poplar where it seems to perform distinct functions with relatively little overlap. In tomato, alteration of the gene function confers facultative parthenocarpy, thought to be a consequence of changes in the microRNA metabolism. In the rice mutant, improvement in panicle architecture is associated with an increase in grain yield. Knowing that hws tomato fruits show a higher Brix level, it was suspected that vascular bundles might also be altered in this species, in a similar fashion to the rice phenotype. The pedicel structure of the hws-1 line was therefore examined under the microscope and sugar concentrations from phloem exudate were determined in an enzymatic assay. A distinct increase in the phloem area was observed as well as a higher sugar content in mutant phloem exudates, which is hypothesized to contribute to the high Brix level in the mutant fruits. Furthermore, the described phenotype in this study bridges the gap between Arabidopsis and rice phenotypes, suggesting that the modulation of the microRNA metabolism by HWS influences traits of agricultural interest across several species.
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Affiliation(s)
- Fabien Lombardo
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan;
- Correspondence:
| | - Pietro Gramazio
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan;
| | - Hiroshi Ezura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan;
- Tsukuba Plant Innovation Research Center, University of Tsukuba, Tsukuba 305-8572, Japan;
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Yuan S, Kawasaki S, Abdellatif IMY, Nishida K, Kondo A, Ariizumi T, Ezura H, Miura K. Efficient base editing in tomato using a highly expressed transient system. PLANT CELL REPORTS 2021; 40:667-676. [PMID: 33550455 DOI: 10.1007/s00299-021-02662-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 01/06/2021] [Indexed: 06/12/2023]
Abstract
KEY MESSAGE Base editing in tomatoes was achieved by transient expression. The Solanaceae plants, particularly the tomato (Solanum lycopersicum), is of huge economic value worldwide. The tomato is a unique model plant for studying the functions of genes related to fruit ripening. Deeper understanding of tomatoes is of great importance for both plant research and the economy. Genome editing technology, such as CRISPR/Cas9, has been used for functional genetic research. However, some challenges, such as low transformation efficiency, remain with this technology. Moreover, the foreign Cas9 and gRNA expression cassettes must be removed to obtain null-segregants In this study, we used a high-level transient expression system to improve the base editing technology. A high-level transient expression system has been established previously using geminiviral replication and a double terminator. The pBYR2HS vector was used for this transient expression system. nCas9-CDA and sgRNA-SlHWS were introduced into this vector, and the protein and RNA were then transiently expressed in tomato tissues by agroinfiltration. The homozygous mutant produced by base editing was obtained in the next generation with an efficiency of about 18%. nCas9-free next-generation plants were 71%. All the homozygous base-edited plants in next generation are nCas9-free. These findings show that the high-level transient expression system is useful for base editing in tomatoes.
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Affiliation(s)
- Shaoze Yuan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Shunsuke Kawasaki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Islam M Y Abdellatif
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Keiji Nishida
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, 657-8501, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, 657-8501, Japan
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, 657-8501, Japan
| | - Tohru Ariizumi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
- Tsukuba-Plant Innovation Research Center, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Hiroshi Ezura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
- Tsukuba-Plant Innovation Research Center, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Kenji Miura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan.
- Tsukuba-Plant Innovation Research Center, University of Tsukuba, Tsukuba, 305-8572, Japan.
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He M, Song S, Zhu X, Lin Y, Pan Z, Chen L, Chen D, Hu G, Huang B, Chen M, Wu C, Chen R, Bouzayen M, Zouine M, Hao Y. SlTPL1 Silencing Induces Facultative Parthenocarpy in Tomato. FRONTIERS IN PLANT SCIENCE 2021; 12:672232. [PMID: 34093628 PMCID: PMC8174789 DOI: 10.3389/fpls.2021.672232] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/19/2021] [Indexed: 05/07/2023]
Abstract
Facultative parthenocarpy is of great practical value. However, the molecular mechanism underlying facultative parthenocarpy remains elusive. Transcriptional co-repressors (TPL) act as a central regulatory hub controlling all nine phytohormone pathways. Previously, we proved that SlTPLs participate in the auxin signaling pathway by interacting with auxin/indole acetic acid (Aux/IAAs) in tomato; however, their function in fruit development has not been studied. In addition to their high expression levels during flower development, the interaction between SlTPL1 and SlIAA9 stimulated the investigation of its functional significance via RNA interference (RNAi) technology, whereby the translation of a protein is prevented by selective degradation of its encoded mRNA. Down-regulation of SlTPL1 resulted in facultative parthenocarpy. Plants of SlTPL1-RNAi transgenic lines produced similar fruits which did not show any pleiotropic effects under normal conditions. However, they produced seedless fruits upon emasculation and under heat stress conditions. Furthermore, SlTPL1-RNAi flower buds contained higher levels of cytokinins and lower levels of abscisic acid. To reveal how SlTPL1 regulates facultative parthenocarpy, RNA-seq was performed to identify genes regulated by SlTPL1 in ovaries before and after fruit set. The results showed that down-regulation of SlTPL1 resulted in reduced expression levels of cytokinin metabolism-related genes, and all transcription factors such as MYB, CDF, and ERFs. Conversely, down-regulation of SlTPL1 induced the expression of genes related to cell wall and cytoskeleton organization. These data provide novel insights into the molecular mechanism of facultative tomato parthenocarpy and identify SlTPL1 as a key factor regulating these processes.
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Affiliation(s)
- Mi He
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Shiwei Song
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Xiaoyang Zhu
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Yuxiang Lin
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Zanlin Pan
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Lin Chen
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Da Chen
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Guojian Hu
- Laboratory Genomics and Biotechnology of Fruits, INRA, Toulouse INP, University of Toulouse, Toulouse, France
| | - Baowen Huang
- Laboratory Genomics and Biotechnology of Fruits, INRA, Toulouse INP, University of Toulouse, Toulouse, France
| | - Mengyi Chen
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, China
- Institute of Bioengineering, Guangdong Academy of Sciences, Guangzhou, China
| | - Caiyu Wu
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Riyuan Chen
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Mondher Bouzayen
- Laboratory Genomics and Biotechnology of Fruits, INRA, Toulouse INP, University of Toulouse, Toulouse, France
| | - Mohammed Zouine
- Laboratory Genomics and Biotechnology of Fruits, INRA, Toulouse INP, University of Toulouse, Toulouse, France
- *Correspondence: Mohammed Zouine,
| | - Yanwei Hao
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, China
- Yanwei Hao,
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Komatsu H, Abdellatif IMY, Yuan S, Ono M, Nonaka S, Ezura H, Ariizumi T, Miura K. Genome editing in PDS genes of tomatoes by non-selection method and of Nicotiana benthamiana by one single guide RNA to edit two orthologs. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2020; 37:213-221. [PMID: 32821229 PMCID: PMC7434671 DOI: 10.5511/plantbiotechnology.20.0527b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The CRISPR/Cas9 system is widely used for targeted mutagenesis in many organisms including plants. For application of this system, tissue culture methods need to be established. In this study, detailed methods for introduction of mutations in tomato and Nicotiana benthamiana plants using the CRISPR/Cas9 system are described. The methods include tissue culture protocols for tomato and N. benthamiana. We also demonstrate the methodology to generate Cas9-free genome edited tomato plants and use of one single guide RNA (sgRNA) to edit two orthologs in N. benthamiana. The examples of editing the PHYTOENE DESATURASE (PDS) genes in these plants are also provided. The Cas9-free tomato line was obtained when tomato plants were cultured on a non-selective medium after transformation with the CRISPR/Cas9 system. Two orthologs of PDS in N. benthamiana were mutated using a sgRNA, because these orthologs contain the same nucleotide sequences with PAM motif. These mutations were inherited to the next generation. The mutations in the PDS genes resulted in an albino phenotype in tomato and N. benthamiana plants. These results demonstrate that the non-selective method is one of the ways to obtain Cas9-free genome editing in tomato plants and that the two orthologs can be edited by one sgRNA in N. benthamiana.
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Affiliation(s)
- Hiroki Komatsu
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki 305-8572, Japan
| | - Islam M. Y. Abdellatif
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki 305-8572, Japan
| | - Shaoze Yuan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki 305-8572, Japan
| | - Misaki Ono
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki 305-8572, Japan
| | - Satoko Nonaka
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki 305-8572, Japan
- Tsukuba-Plant Innovation Research Center, University of Tsukuba, Ibaraki 305-8572, Japan
| | - Hiroshi Ezura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki 305-8572, Japan
- Tsukuba-Plant Innovation Research Center, University of Tsukuba, Ibaraki 305-8572, Japan
| | - Tohru Ariizumi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki 305-8572, Japan
- Tsukuba-Plant Innovation Research Center, University of Tsukuba, Ibaraki 305-8572, Japan
- E-mail: Tel & Fax: +81-29-853-4710
| | - Kenji Miura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki 305-8572, Japan
- Tsukuba-Plant Innovation Research Center, University of Tsukuba, Ibaraki 305-8572, Japan
- E-mail: Tel & Fax: +81-29-853-6401
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