CRISPRa-mediated transcriptional activation of the SlPR-1 gene in edited tomato plants

García-Murillo, Leonardo; Valencia-Lozano, Eliana; Priego-Ranero, Nicolás Alberto; Cabrera-Ponce, José Luis; Duarte-Aké, Fátima; Vizuet-de-Rueda, Juan Carlos; Rivera-Toro, Diana Marcela; Herrera-Ubaldo, Humberto; Folter, Stefan de; Álvarez-Venegas, Raúl

doi:10.1016/j.plantsci.2023.111617

Cited by 9 publications

(7 citation statements)

References 66 publications

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“…Randomly chosen masses from embryogenic lines, as well as secondary somatic embryos, were collected and fixed in 1 mL of FAE (3.7 % Formaldehyde, 10 % Acetic acid glacial, 50 % Ethanol) for two hours, at room temperature, followed by dehydration in a series of ethanol dilutions, as described by [ 14 ]. Fixed and dehydrated samples were embedded in Technovit 7100 (Heraeus Kulzer, cat.…”

Section: Methodsmentioning

confidence: 99%

“…#64709003) plus ethanol (1:1, v/v), and then embedded in the infiltration solution (Technovit 7100 plus hardener), according to the manufacturer´s instructions. Sections of 10-μm were prepared using a microtome as previously described [ 14 ]. Pictures were taken and analyzed on an upright Leica DM6000B microscope.…”

Section: Methodsmentioning

confidence: 99%

“…Total RNA from PEMs (cultured in MS-BK2iP medium) and individual embryos (15-days after being cultured in G9-2iP media), was isolated using Trizol (Invitrogen, Carlsbad, CA, USA). RT-qPCR was performed as previously described [ 14 ]. A Step-One® Real-time PCR system (Applied Biosystems, Foster City, CA, USA) was used for real-time PCR quantifications.…”

Section: Methodsmentioning

confidence: 99%

“…For instance, CRISPR activation (CRISPRa)-mediated histone acetylation has been used to enhance drought stress tolerance in Arabidopsis [ 13 ]. Recently, we generated epigenetically edited tomato plants via CRISPRa, by fusing dCas9 to the catalytic SET-domain of the tomato SlATX1 gene (ortholog to the histone H3 lysine 4 tri-methyltransferase ATX1 gene from Arabidopsis ) and showed that activation of defense genes protects tomato plants against pathogens [ 14 ]. Accordingly, up-regulation of target genes via synthetic epi-effectors is an attractive tool for targeted manipulation of the epigenome [ 7 ].…”

Section: Introductionmentioning

confidence: 99%

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Editing of SlWRKY29 by CRISPR-activation promotes somatic embryogenesis in Solanum lycopersicum cv. Micro-Tom

Valencia-Lozano,

Cabrera-Ponce,

Barraza

et al. 2024

PLoS ONE

Self Cite

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At present, the development of plants with improved traits like superior quality, high yield, or stress resistance, are highly desirable in agriculture. Accelerated crop improvement, however, must capitalize on revolutionary new plant breeding technologies, like genetically modified and gene-edited crops, to heighten food crop traits. Genome editing still faces ineffective methods for the transformation and regeneration of different plant species and must surpass the genotype dependency of the transformation process. Tomato is considered an alternative plant model system to rice and Arabidopsis, and a model organism for fleshy-fruited plants. Furthermore, tomato cultivars like Micro-Tom are excellent models for tomato research due to its short life cycle, small size, and capacity to grow at high density. Therefore, we developed an indirect somatic embryo protocol from cotyledonary tomato explants and used this to generate epigenetically edited tomato plants for the SlWRKY29 gene via CRISPR-activation (CRISPRa). We found that epigenetic reprogramming for SlWRKY29 establishes a transcriptionally permissive chromatin state, as determined by an enrichment of the H3K4me3 mark. A whole transcriptome analysis of CRISPRa-edited pro-embryogenic masses and mature somatic embryos allowed us to characterize the mechanism driving somatic embryo induction in the edited tomato cv. Micro-Tom. Furthermore, we show that enhanced embryo induction and maturation are influenced by the transcriptional effector employed during CRISPRa, as well as by the medium composition and in vitro environmental conditions such as osmotic components, plant growth regulators, and light intensity.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Editing of SlWRKY29 by CRISPR-activation promotes somatic embryogenesis in Solanum lycopersicum cv. Micro-Tom

Valencia-Lozano,

Cabrera-Ponce,

Barraza

et al. 2024

PLoS ONE

Self Cite

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“…Moreover, epigenome editing methods using advanced CRISPR/Cas9 or CRISPR off technologies directly increase the stress resilience of plants through epigenome engineering [132,133]. In recent years, quantitative epigenetics and epigenome engineering have been successfully applied in the epigenetic breeding of crop plants, including rice, tomato, potato, and soybean [134,135,136,137]. Compared to crops, the epigenetic mechanisms and variants in forest plants are relatively understudied.…”

Section: Epigenomicsmentioning

confidence: 99%

Multi-Omics Techniques for Forest Plant Breeding

Wang¹,

Li²,

Zhao³

2023

Preprint

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In recent years, the ecological and economic values of forest plants have been gradually recognized worldwide. However, the growing global demand for new forest plant varieties with higher wood production capacity and better stress tolerance cannot be satisfied by conventional phenotype-based breeding, marker-assisted selection, and genomic selection. In the recent past, diverse omics technologies, including genomics, transcriptomics, epigenomics, proteomics, and metabolomics, have been developed rapidly, providing powerful tools for the precision genetic breeding of forest plants. Genomics lays a solid foundation for understanding complex biological regulatory networks, while other omics technologies provide different perspectives at different levels. Multi-omics integration has combined the different omics technologies, becoming a powerful tool for genome-wide functional element identification in forest plant breeding. This review summarizes the recent progress of omics technologies and their applications in the genetic studies of forest plants. It will provide forest plant breeders with an elementary knowledge of multi-omics techniques for future breeding programs.

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Engineering Phytonutrient Content in Tomato by Genome Editing Technologies

Scarano,

Santino

2023

A Roadmap for Plant Genome Editing

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The application of precise genome editing represents an important step-forward in plant functional genomics research and crop improvement by generating tailored modifications within a target genome sequence. Among the genome editing technologies, the CRISPR/Cas9 system has been the most largely one applied in many crop species, thanks to its high customizable specificity. Tomato is one of the most cultivated and consumed horticultural crops worldwide and an ideal model plant for studying different physiological processes (e.g., plant development, response to biotic/abiotic stresses, fruit quality) by using different approaches, such as conventional breeding, classical transgenesis and genome editing technologies. In recent years, the number of studies on the genome editing application in tomato has increasingly grown, particularly for the improvement of fruit quality and nutritional value. In this chapter, we report about the main achievements provided by such technologies for engineering the content of nutritionally relevant compounds, such as polyphenols, carotenoids, vitamins, and other important phytonutrients in tomato fruit.

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CRISPRa-mediated transcriptional activation of the SlPR-1 gene in edited tomato plants

Cited by 9 publications

References 66 publications

Editing of SlWRKY29 by CRISPR-activation promotes somatic embryogenesis in Solanum lycopersicum cv. Micro-Tom

Editing of SlWRKY29 by CRISPR-activation promotes somatic embryogenesis in Solanum lycopersicum cv. Micro-Tom

Multi-Omics Techniques for Forest Plant Breeding

Engineering Phytonutrient Content in Tomato by Genome Editing Technologies

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