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Arrones A, Antar O, Pereira-Dias L, Solana A, Ferrante P, Aprea G, Plazas M, Prohens J, Díez MJ, Giuliano G, Gramazio P, Vilanova S. A novel tomato interspecific ( Solanum lycopersicum var. cerasiforme and Solanum pimpinellifolium) MAGIC population facilitates trait association and candidate gene discovery in untapped exotic germplasm. HORTICULTURE RESEARCH 2024; 11:uhae154. [PMID: 39005998 PMCID: PMC11246243 DOI: 10.1093/hr/uhae154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 05/23/2024] [Indexed: 07/16/2024]
Abstract
We developed a novel eight-way tomato multiparental advanced generation intercross (MAGIC) population to improve the accessibility of tomato relatives genetic resources to geneticists and breeders. The interspecific tomato MAGIC population (ToMAGIC) was obtained by intercrossing four accessions each of Solanum lycopersicum var. cerasiforme and Solanum pimpinellifolium, which are the weedy relative and the ancestor of cultivated tomato, respectively. The eight exotic ToMAGIC founders were selected based on a representation of the genetic diversity and geographical distribution of the two taxa. The resulting MAGIC population comprises 354 lines, which were genotyped using a new 12k tomato single primer enrichment technology panel and yielded 6488 high-quality single-nucleotide polymorphism (SNPs). The genotyping data revealed a high degree of homozygosity, an absence of genetic structure, and a balanced representation of the founder genomes. To evaluate the potential of the ToMAGIC population, a proof of concept was conducted by phenotyping it for fruit size, plant pigmentation, leaf morphology, and earliness. Genome-wide association studies identified strong associations for the studied traits, pinpointing both previously identified and novel candidate genes near or within the linkage disequilibrium blocks. Domesticated alleles for fruit size were recessive and were found, at low frequencies, in wild/ancestral populations. Our findings demonstrate that the newly developed ToMAGIC population is a valuable resource for genetic research in tomato, offering significant potential for identifying new genes that govern key traits in tomato. ToMAGIC lines displaying a pyramiding of traits of interest could have direct applicability for integration into breeding pipelines providing untapped variation for tomato breeding.
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Affiliation(s)
- Andrea Arrones
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Oussama Antar
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Leandro Pereira-Dias
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Andrea Solana
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Paola Ferrante
- Agenzia Nazionale Per Le Nuove Tecnologie, L’energia e Lo Sviluppo Economico Sostenibile (ENEA), Casaccia Research Centre, Via Anguillarese 301, 00123 Rome, Italy
| | - Giuseppe Aprea
- Agenzia Nazionale Per Le Nuove Tecnologie, L’energia e Lo Sviluppo Economico Sostenibile (ENEA), Casaccia Research Centre, Via Anguillarese 301, 00123 Rome, Italy
| | - Mariola Plazas
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - María José Díez
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Giovanni Giuliano
- Agenzia Nazionale Per Le Nuove Tecnologie, L’energia e Lo Sviluppo Economico Sostenibile (ENEA), Casaccia Research Centre, Via Anguillarese 301, 00123 Rome, Italy
| | - Pietro Gramazio
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Santiago Vilanova
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
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Nguyen CC, Van Vu T, Shelake RM, Nguyen NT, Khanh TD, Kim WY, Kim JY. Generation of parthenocarpic tomato plants in multiple elite cultivars using the CRISPR/Cas9 system. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:13. [PMID: 38317771 PMCID: PMC10838257 DOI: 10.1007/s11032-024-01452-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 10/02/2023] [Indexed: 02/07/2024]
Abstract
Tomato (Solanum lycopersicum L.) is one of the most important crops in the world for its fruit production. Advances in cutting-edge techniques have enabled the development of numerous critical traits related to the quality and quantity of tomatoes. Genetic engineering techniques, such as gene transformation and gene editing, have emerged as powerful tools for generating new plant varieties with superior traits. In this study, we induced parthenocarpic traits in a population of elite tomato (ET) lines. At first, the adaptability of ET lines to genetic transformation was evaluated to identify the best-performing lines by transforming the SlANT1 gene overexpression cassette and then later used to produce the SlIAA9 knockout lines using the CRISPR/Cas9 system. ET5 and ET8 emerged as excellent materials for these techniques and showed higher efficiency. Typical phenotypes of knockout sliaa9 were clearly visible in G0 and G1 plants, in which simple leaves and parthenocarpic fruits were observed. The high efficiency of the CRISPR/Cas9 system in developing new tomato varieties with desired traits in a short period was demonstrated by generating T-DNA-free homozygous sliaa9 knockout plants in the G1 generation. Additionally, a simple artificial fertilization method was successfully applied to recover seed production from parthenocarpic plants, securing the use of these varieties as breeding materials. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-024-01452-1.
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Affiliation(s)
- Cam Chau Nguyen
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Korea
- Faculty of Biotechnology, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Tien Van Vu
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Korea
| | - Rahul Mahadev Shelake
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Korea
| | - Nhan Thi Nguyen
- Institute of Environmental Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | | | - Woe-Yeon Kim
- Division of Applied Life Science (BK21+) and Research Institute of Life Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Korea
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Baranov D, Dolgov S, Timerbaev V. New Advances in the Study of Regulation of Tomato Flowering-Related Genes Using Biotechnological Approaches. PLANTS (BASEL, SWITZERLAND) 2024; 13:359. [PMID: 38337892 PMCID: PMC10856997 DOI: 10.3390/plants13030359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/21/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024]
Abstract
The tomato is a convenient object for studying reproductive processes, which has become a classic. Such complex processes as flowering and fruit setting require an understanding of the fundamental principles of molecular interaction, the structures of genes and proteins, the construction of signaling pathways for transcription regulation, including the synchronous actions of cis-regulatory elements (promoter and enhancer), trans-regulatory elements (transcription factors and regulatory RNAs), and transposable elements and epigenetic regulators (DNA methylation and acetylation, chromatin structure). Here, we discuss the current state of research on tomatoes (2017-2023) devoted to studying the function of genes that regulate flowering and signal regulation systems using genome-editing technologies, RNA interference gene silencing, and gene overexpression, including heterologous expression. Although the central candidate genes for these regulatory components have been identified, a complete picture of their relationship has yet to be formed. Therefore, this review summarizes the latest achievements related to studying the processes of flowering and fruit set. This work attempts to display the gene interaction scheme to better understand the events under consideration.
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Affiliation(s)
- Denis Baranov
- Laboratory of Expression Systems and Plant Genome Modification, Branch of Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290 Pushchino, Russia; (D.B.); (S.D.)
- Laboratory of Plant Genetic Engineering, All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia
| | - Sergey Dolgov
- Laboratory of Expression Systems and Plant Genome Modification, Branch of Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290 Pushchino, Russia; (D.B.); (S.D.)
- Laboratory of Plant Genetic Engineering, All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia
| | - Vadim Timerbaev
- Laboratory of Expression Systems and Plant Genome Modification, Branch of Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290 Pushchino, Russia; (D.B.); (S.D.)
- Laboratory of Plant Genetic Engineering, All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia
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Baranov D, Timerbaev V. Recent Advances in Studying the Regulation of Fruit Ripening in Tomato Using Genetic Engineering Approaches. Int J Mol Sci 2024; 25:760. [PMID: 38255834 PMCID: PMC10815249 DOI: 10.3390/ijms25020760] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 12/28/2023] [Accepted: 01/02/2024] [Indexed: 01/24/2024] Open
Abstract
Tomato (Solanum lycopersicum L.) is one of the most commercially essential vegetable crops cultivated worldwide. In addition to the nutritional value, tomato is an excellent model for studying climacteric fruits' ripening processes. Despite this, the available natural pool of genes that allows expanding phenotypic diversity is limited, and the difficulties of crossing using classical selection methods when stacking traits increase proportionally with each additional feature. Modern methods of the genetic engineering of tomatoes have extensive potential applications, such as enhancing the expression of existing gene(s), integrating artificial and heterologous gene(s), pointing changes in target gene sequences while keeping allelic combinations characteristic of successful commercial varieties, and many others. However, it is necessary to understand the fundamental principles of the gene molecular regulation involved in tomato fruit ripening for its successful use in creating new varieties. Although the candidate genes mediate ripening have been identified, a complete picture of their relationship has yet to be formed. This review summarizes the latest (2017-2023) achievements related to studying the ripening processes of tomato fruits. This work attempts to systematize the results of various research articles and display the interaction pattern of genes regulating the process of tomato fruit ripening.
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Affiliation(s)
- Denis Baranov
- Laboratory of Expression Systems and Plant Genome Modification, Branch of Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, 142290 Pushchino, Russia;
- Laboratory of Plant Genetic Engineering, All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia
| | - Vadim Timerbaev
- Laboratory of Expression Systems and Plant Genome Modification, Branch of Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, 142290 Pushchino, Russia;
- Laboratory of Plant Genetic Engineering, All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia
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Bogomolov A, Zolotareva K, Filonov S, Chadaeva I, Rasskazov D, Sharypova E, Podkolodnyy N, Ponomarenko P, Savinkova L, Tverdokhleb N, Khandaev B, Kondratyuk E, Podkolodnaya O, Zemlyanskaya E, Kolchanov NA, Ponomarenko M. AtSNP_TATAdb: Candidate Molecular Markers of Plant Advantages Related to Single Nucleotide Polymorphisms within Proximal Promoters of Arabidopsis thaliana L. Int J Mol Sci 2024; 25:607. [PMID: 38203780 PMCID: PMC10779315 DOI: 10.3390/ijms25010607] [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: 10/31/2023] [Revised: 12/18/2023] [Accepted: 12/30/2023] [Indexed: 01/12/2024] Open
Abstract
The mainstream of the post-genome target-assisted breeding in crop plant species includes biofortification such as high-throughput phenotyping along with genome-based selection. Therefore, in this work, we used the Web-service Plant_SNP_TATA_Z-tester, which we have previously developed, to run a uniform in silico analysis of the transcriptional alterations of 54,013 protein-coding transcripts from 32,833 Arabidopsis thaliana L. genes caused by 871,707 SNPs located in the proximal promoter region. The analysis identified 54,993 SNPs as significantly decreasing or increasing gene expression through changes in TATA-binding protein affinity to the promoters. The existence of these SNPs in highly conserved proximal promoters may be explained as intraspecific diversity kept by the stabilizing natural selection. To support this, we hand-annotated papers on some of the Arabidopsis genes possessing these SNPs or on their orthologs in other plant species and demonstrated the effects of changes in these gene expressions on plant vital traits. We integrated in silico estimates of the TBP-promoter affinity in the AtSNP_TATAdb knowledge base and showed their significant correlations with independent in vivo experimental data. These correlations appeared to be robust to variations in statistical criteria, genomic environment of TATA box regions, plants species and growing conditions.
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Affiliation(s)
- Anton Bogomolov
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
| | - Karina Zolotareva
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
| | - Sergey Filonov
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
- Natural Science Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Irina Chadaeva
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
| | - Dmitry Rasskazov
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
| | - Ekaterina Sharypova
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
| | - Nikolay Podkolodnyy
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
- Institute of Computational Mathematics and Mathematical Geophysics, Novosibirsk 630090, Russia
| | - Petr Ponomarenko
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
| | - Ludmila Savinkova
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
| | - Natalya Tverdokhleb
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
| | - Bato Khandaev
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
- Natural Science Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Ekaterina Kondratyuk
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
- Siberian Federal Scientific Centre of Agro-BioTechnologies of the Russian Academy of Sciences, Krasnoobsk 630501, Novosibirsk Region, Russia
| | - Olga Podkolodnaya
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
| | - Elena Zemlyanskaya
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
- Natural Science Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Nikolay A. Kolchanov
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
- Natural Science Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Mikhail Ponomarenko
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; (A.B.); (K.Z.); (S.F.); (I.C.); (D.R.); (E.S.); (N.P.); (P.P.); (L.S.); (N.T.); (B.K.); (E.K.); (O.P.); (E.Z.); (N.A.K.)
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Vats S, Kumar V, Mandlik R, Patil G, Sonah H, Roy J, Sharma TR, Deshmukh R. Reference Guided De Novo Genome Assembly of Transformation Pliable Solanum lycopersicum cv. Pusa Ruby. Genes (Basel) 2023; 14:570. [PMID: 36980842 PMCID: PMC10047940 DOI: 10.3390/genes14030570] [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: 12/20/2022] [Revised: 02/17/2023] [Accepted: 02/22/2023] [Indexed: 03/02/2023] Open
Abstract
Solanum lycopersicum cv. Pusa Ruby (PR) is a superior tomato cultivar routinely used as a model tomato variety. Here, we report a reference-guided genome assembly for PR, covering 97.6% of the total single-copy genes in the solanales order. The PR genome contains 34,075 genes and 423,288 variants, out of which 127,131 are intragenic and 1232 are of high impact. The assembly was packaged according to PanSol guidelines (N50 = 60,396,827) with the largest scaffold measuring 85 megabases. The similarity of the PR genome assembly to Heinz1706, M82, and Fla.8924 was measured and the results suggest PR has the lowest affinity towards the hybrid Fla.8924. We then analyzed the regeneration efficiency of PR in comparison to another variety, Pusa Early Dwarf (PED). PR was found to have a high regeneration rate (45.51%) and therefore, we performed allele mining for genes associated with regeneration and found that only AGAMOUS-LIKE15 has a null mutation. Further, allele mining for fruit quality-related genes was also executed. The PR genome has an Ovate mutation leading to round fruit shape, causing economically undesirable fruit cracking. This genomic data can be potentially used for large scale crop improvement programs as well as functional annotation studies.
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Affiliation(s)
- Sanskriti Vats
- National Agri-Food Biotechnology Institute (NABI), Mohali 140306, Punjab, India
- Regional Centre for Biotechnology, Faridabad 121001, Haryana, India
| | - Virender Kumar
- National Agri-Food Biotechnology Institute (NABI), Mohali 140306, Punjab, India
- Regional Centre for Biotechnology, Faridabad 121001, Haryana, India
| | - Rushil Mandlik
- National Agri-Food Biotechnology Institute (NABI), Mohali 140306, Punjab, India
- Department of Biotechnology, Panjab University, Chandigarh 160014, Punjab, India
| | - Gunvant Patil
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79410, USA
| | - Humira Sonah
- National Agri-Food Biotechnology Institute (NABI), Mohali 140306, Punjab, India
| | - Joy Roy
- National Agri-Food Biotechnology Institute (NABI), Mohali 140306, Punjab, India
| | - Tilak Raj Sharma
- Department of Crop Science, Indian Council of Agriculture Research (ICAR), Krishi Bhavan, New Delhi 110001, Delhi, India
| | - Rupesh Deshmukh
- Department of Biotechnology, Central University of Haryana, Mahendragarh 123031, Haryana, India
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Wada N, Osakabe K, Osakabe Y. Type I-D CRISPR System-Mediated Genome Editing in Plants. Methods Mol Biol 2023; 2653:21-38. [PMID: 36995617 DOI: 10.1007/978-1-0716-3131-7_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Genome editing has revolutionized plant research and plant breeding by enabling precise genome manipulation. In particular, the application of type II CRISPR-Cas9 systems to genome editing has proved an important milestone, accelerating genetic engineering and the analysis of gene function. On the other hand, the potential of other types of CRISPR-Cas systems, especially many of the most abundant type I CRISPR-Cas systems, remains unexplored. We recently developed a novel genome editing tool, TiD, based on the type I-D CRISPR-Cas system. In this chapter, we describe a protocol for genome editing of plant cells using TiD. This protocol allows the application of TiD to induce short insertion and deletions (indels) or long-range deletions at target sites with high specificity in tomato cells.
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Affiliation(s)
- Naoki Wada
- Graduate School of Technology, Industrial and Social Sciences, Tokushima University, Tokushima, Japan
| | - Keishi Osakabe
- Graduate School of Technology, Industrial and Social Sciences, Tokushima University, Tokushima, Japan
| | - Yuriko Osakabe
- School of Life Science and Technology, Tokyo Institute of Technology, Kanagawa, Japan.
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Tang Y, Li H, Liu C, He Y, Wang H, Zhao T, Xu X, Li J, Yang H, Jiang J. CRISPR-Cas9-mediated mutagenesis of the SlSRM1-like gene leads to abnormal leaf development in tomatoes. BMC PLANT BIOLOGY 2022; 22:13. [PMID: 34979927 PMCID: PMC8722279 DOI: 10.1186/s12870-021-03397-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 12/13/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Leaves, which are the most important organs of plants, can not only fix carbon sources through photosynthesis, but also absorb nutrients through transpiration. Leaf development directly determines the growth, flowering and fruiting of plants. There are many factors that affect leaf development, such as the growth environment, gene expression, and hormone synthesis. In this study, tomatoes were used to study the role of the transcription factor Solanum lycopersicum salt-related MYB1-like (SlSRM1-like) in the development of tomato leaves. RESULTS Loss-of-function of the SlSRM1-like gene mediated by clustered, regularly interspaced, short palindromic repeat (CRISPR)/CRISPR-associated 9 (Cas9) resulted in abnormal tomato leaf morphology, including thinner leaves, wrinkled edges, raised veins, disordered edge veins, and left and right asymmetry. An analysis of the transcription levels of genes related to leaf development revealed that the expression of these genes was significantly altered in the SlSRM1-like mutants (SlSRM1-like-Ms). Moreover, the SlSRM1-like gene was expressed at higher transcription levels in young tissues than in old tissues, and its expression was also induced in response to auxin. In addition, the transcription levels of genes related to the auxin pathway, which regulates tomato growth and development, were severely affected in the SlSRM1-like-Ms. Therefore, it is hypothesized that the SlSRM1-like gene functions in the regulation of tomato leaf development through the auxin-related pathway. CONCLUSIONS In this study, we successfully knocked out the SlSRM1-like gene in the tomato variety Ailsa Craig using CRISPR technology and found that knockout of the SlSRM1-like gene resulted in abnormal development of tomato leaves. Further research indicated that SlSRM1-like regulated tomato leaf development through auxin-related pathways. The results provide an important reference for the functional study of other SRM1-like genes in plants and provide new insights into the regulation of leaf development in tomato and other plants.
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Affiliation(s)
- Yao Tang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030 Heilongjiang Province China
| | - Huijia Li
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030 Heilongjiang Province China
| | - Chunxin Liu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030 Heilongjiang Province China
| | - Yuqing He
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030 Heilongjiang Province China
| | - Hexuan Wang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030 Heilongjiang Province China
| | - Tingting Zhao
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030 Heilongjiang Province China
| | - Xiangyang Xu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030 Heilongjiang Province China
| | - Jingfu Li
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030 Heilongjiang Province China
| | - Huanhuan Yang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030 Heilongjiang Province China
| | - Jingbin Jiang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030 Heilongjiang Province China
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