Fine-tuning sugar content in strawberry

Xing, Sinian; Chen, Kunling; Zhu, Haocheng; Zhang, Rui; Zhang, Huawei; Li, Bingbing; Gao, Caixia

doi:10.1186/s13059-020-02146-5

Cited by 119 publications

(82 citation statements)

References 61 publications

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“…Moreover, CBEs are also promising tools for editing cis elements to fine‐tune gene expression. For example, increased sugar content in strawberry fruits was recently created with this approach (Xing et al ., 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Improved plant cytosine base editors with high editing activity, purity, and specificity

Ren

Sretenovic

Liu

et al. 2021

Plant Biotechnology Journal

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Cytosine base editors (CBEs) are great additions to the expanding genome editing toolbox. To improve C-to-T base editing in plants, we first compared seven cytidine deaminases in the BE3like configuration in rice. We found A3A/Y130F-CBE_V01 resulted in the highest C-to-T base editing efficiency in both rice and Arabidopsis. Furthermore, we demonstrated this A3A/Y130F cytidine deaminase could be used to improve iSpyMacCas9-mediated C-to-T base editing at Arich PAMs. To showcase its applications, we first applied A3A/Y130F-CBE_V01 for multiplexed editing to generate microRNA-resistant mRNA transcripts as well as pre-mature stop codons in multiple seed trait genes. In addition, we harnessed A3A/Y130F-CBE_V01 for efficient artificial evolution of novel ALS and EPSPS alleles which conferred herbicide resistance in rice. To further improve C-to-T base editing, multiple CBE_V02, CBE_V03 and CBE_V04 systems were developed and tested in rice protoplasts. The CBE_V04 systems were found to have improved editing activity and purity with focal recruitment of more uracil DNA glycosylase inhibitors (UGIs) by the engineered single guide RNA 2.0 scaffold. Finally, we used whole-genome sequencing (WGS) to compare six CBE_V01 systems and four CBE_V04 systems for genome-wide off-target effects in rice. Different levels of cytidine deaminase-dependent and sgRNA-independent off-target effects were indeed revealed by WGS among edited lines by these CBE systems. We also investigated genome-wide sgRNA-dependent off-target effects by different CBEs in rice. This comprehensive study compared 21 different CBE systems, and benchmarked PmCDA1-CBE_V04 and A3A/ Y130F-CBE_V04 as next-generation plant CBEs with high editing efficiency, purity, and specificity.

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Section: Introductionmentioning

confidence: 99%

Improved plant cytosine base editors with high editing activity, purity, and specificity

Ren

Sretenovic

Liu

et al. 2021

Plant Biotechnology Journal

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“…Recently, CRISPR/Cas9-mediated deletion of the start codon site in a uORF of PHO1 improved inorganic orthophosphate tolerance in Arabidopsis (Reis et al, 2020). Another study reported that uORF editing of the FvebZIPs1.1 gene using a BE A3A-PBE system improved the sugar content in strawberries (Xing et al, 2020). Overall, many plant genes have been predicted to possess uORFs, and uORF editing is expected to become easier, owing to the availability of various CRISPR tools.…”

Section: Upstream Orf Editingmentioning

confidence: 99%

CRISPR-Mediated Engineering across the Central Dogma in Plant Biology for Basic Research and Crop Improvement

et al. 2021

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The central dogma (CD) of molecular biology is the transfer of genetic information from DNA to RNA to protein. Major CD processes governing genetic flow include the cell cycle, DNA replication, chromosome packaging, epigenetic changes, transcription, posttranscriptional alterations, translation, and posttranslational modifications. The CD processes are tightly regulated in plants to maintain genetic integrity throughout the life cycle and to pass genetic materials to next generation. Engineering of various CD processes involved in gene regulation will accelerate crop improvement to feed the growing world population. CRISPR technology enables programmable editing of CD processes to alter DNA, RNA, or protein, which would have been impossible in the past. Here, an overview of recent advancements in CRISPR tool development and CRISPR-based CD modulations that expedite basic and applied plant research is provided. Furthermore, CRISPR applications in major thriving areas of research, such as gene discovery (allele mining and cryptic gene activation), introgression (de novo domestication and haploid induction), and application of desired traits beneficial to farmers or consumers (biotic/abiotic stress-resilient crops, plant cell factories, and delayed senescence), are described. Finally, the global regulatory policies, challenges, and prospects for CRISPR-mediated crop improvement are discussed.

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Section: Enhancing Gene Expression In Crops By Editing Uorfs Usingmentioning

confidence: 99%

“…For example, editing of the uORF of LsGGP2, which encodes an enzyme involved in vitamin C biosynthesis, using the CRISPR-Cas9 system conferred enhanced oxidative stress tolerance and elevated ascorbate levels [84]. In addition, editing the conserved uORF of FvebZIP1.1, which fine-tunes carbon-nitrogen metabolism, resulted in enhanced sugar content in strawberries compared to wild-type [85] Generally, elevated expression of stress-related genes inhibits plant growth due to the tradeoff between growth and defense. For example, overexpression of AtJMT in rice led to drought tolerance but decreased growth and yield [86].…”

Section: Enhancing Gene Expression In Crops By Editing Uorfs Using Thmentioning

confidence: 99%

Application of Upstream Open Reading Frames (uORFs) Editing for the Development of Stress-Tolerant Crops

Park

Shim

et al. 2021

IJMS

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Global population growth and climate change are posing increasing challenges to the production of a stable crop supply using current agricultural practices. The generation of genetically modified (GM) crops has contributed to improving crop stress tolerance and productivity; however, many regulations are still in place that limit their commercialization. Recently, alternative biotechnology-based strategies, such as gene-edited (GE) crops, have been in the spotlight. Gene-editing technology, based on the clustered regularly interspaced short palindromic repeats (CRISPR) platform, has emerged as a revolutionary tool for targeted gene mutation, and has received attention as a game changer in the global biotechnology market. Here, we briefly introduce the concept of upstream open reading frames (uORFs) editing, which allows for control of the translation of downstream ORFs, and outline the potential for enhancing target gene expression by mutating uORFs. We discuss the current status of developing stress-tolerant crops, and discuss uORF targets associated with salt stress-responsive genes in rice that have already been verified by transgenic research. Finally, we overview the strategy for developing GE crops using uORF editing via the CRISPR-Cas9 system. A case is therefore made that the mutation of uORFs represents an efficient method for developing GE crops and an expansion of the scope of application of genome editing technology.

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Fine-tuning sugar content in strawberry

Cited by 119 publications

References 61 publications

Improved plant cytosine base editors with high editing activity, purity, and specificity

Improved plant cytosine base editors with high editing activity, purity, and specificity

CRISPR-Mediated Engineering across the Central Dogma in Plant Biology for Basic Research and Crop Improvement

Application of Upstream Open Reading Frames (uORFs) Editing for the Development of Stress-Tolerant Crops

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