The Power of CRISPR-Cas9-Induced Genome Editing to Speed Up Plant Breeding

Cao, Hieu X.; Wang, Wenqin; Hien, Le Thi Thu; Vu, Giang T. H.

doi:10.1155/2016/5078796

Cited by 44 publications

(20 citation statements)

References 120 publications

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“…Therefore, to understand the function of genes and traits in duckweeds, developing tools that can stably and precisely manipulate the gene of interest is critical. To this end, the recently developed CRIPSR/Cas9 system, which was adapted from a naturally occurring genome editing system in bacteria and has been widely used in both animals and plants, is ideal (Cao et al ., ; Ma et al ., ; Yang, ). However, to our knowledge, no study has reported using CRISPR/Cas9 in duckweeds.…”

Section: Introductionmentioning

confidence: 98%

Efficient genetic transformation and CRISPR/Cas9‐mediated genome editing in Lemna aequinoctialis

Liu

Wang

et al. 2019

Plant Biotechnology Journal

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Summary The fast growth, ease of metabolic labelling and potential for feedstock and biofuels production make duckweeds not only an attractive model system for understanding plant biology, but also a potential future crop. However, current duckweed research is constrained by the lack of efficient genetic manipulation tools. Here, we report a case study on genome editing in a duckweed species, Lemna aequinoctialis, using a fast and efficient transformation and CRISPR/Cas9 tool. By optimizing currently available transformation protocols, we reduced the duration time of Agrobacterium‐mediated transformation to 5–6 weeks with a success rate of over 94%. Based on the optimized transformation protocol, we generated 15 (14.3% success rate) biallelic LaPDS mutants that showed albino phenotype using a CRISPR/Cas9 system. Investigations on CRISPR/Cas9‐mediated mutation spectrum among mutated L. aequinoctialis showed that most of mutations were short insertions and deletions. This study presents the first example of CRISPR/Cas9‐mediated genome editing in duckweeds, which will open new research avenues in using duckweeds for both basic and applied research.

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Section: Introductionmentioning

confidence: 98%

Efficient genetic transformation and CRISPR/Cas9‐mediated genome editing in Lemna aequinoctialis

Liu

Wang

et al. 2019

Plant Biotechnology Journal

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“…The RNA-guided Cas9 nuclease from the bacterial clustered regularly interspaced short palindromic repeats (CRISPR) adaptive immune system provides a powerful and versatile tool for genome engineering of eukaryotic organisms, including plants (Ran, 2013;Bortesi and Fischer, 2015;Cao et al, 2016;Pacher and Puchta, 2016;Puchta, 2017). By simply designing a 20-nt targeting sequence of the guide RNA (Jinek et al, 2012;Cong et al, 2013;Mali et al, 2013), the CRISPR/Cas9 can be targeted to create chromosomal double-stranded breaks (DSBs) at specific sites.…”

Section: Introductionmentioning

confidence: 99%

Endogenous sequence patterns predispose the repair modes of CRISPR/Cas9‐induced DNA double‐stranded breaks in Arabidopsis thaliana

Cao

Fauser

et al. 2017

The Plant Journal

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SUMMARYThe possibility to predict the outcome of targeted DNA double-stranded break (DSB) repair would be desirable for genome editing. Furthermore the consequences of mis-repair of potentially cell-lethal DSBs and the underlying pathways are not yet fully understood. Here we study the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-induced mutation spectra at three selected endogenous loci in Arabidopsis thaliana by deep sequencing of long amplicon libraries. Notably, we found sequence-dependent genomic features that affected the DNA repair outcome. Deletions of 1-bp to <1000-bp size and/or very short insertions, deletions >1 kbp (all due to NHEJ) and deletions combined with insertions between 5-bp to >100 bp [caused by a synthesis-dependent strand annealing (SDSA)-like mechanism] occurred most frequently at all three loci. The appearance of single-stranded annealing events depends on the presence and distance between repeats flanking the DSB. The frequency and size of insertions is increased if a sequence with high similarity to the target site was available in cis. Most deletions were linked to pre-existing microhomology. Deletion and/or insertion mutations were blunt-end ligated or via de novo generated microhomology. While most mutation types and, to some degree, their predictability are comparable with animal systems, the broad range of deletion mutations seems to be a peculiar feature of the plant A. thaliana.

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“…CRISPR/Cas9-mediated targeted gene modification was first introduced for plant genome editing and crop breeding purposes in 2013 1 . This revolutionary technology allows plant breeders to target very specific pieces of DNA without introduction of foreign DNA and to influence key traits accurately and quickly 2 . Although the CRISPR/Cas9 system is an excellent tool for genome editing, the next major challenge is to identify the resulting mutants due to the extent of off-target mutations and the differences in cleavage specificity among species 3 .…”

Section: Introductionmentioning

confidence: 99%

Discrimination of CRISPR/Cas9-induced mutants of rice seeds using near-infrared hyperspectral imaging

Feng

Peng

Chen

et al. 2017

Sci Rep

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Identifying individuals with target mutant phenotypes is a significant procedure in mutant exploitation for implementing genome editing technology in a crop breeding programme. In the present study, a rapid and non-invasive method was proposed to identify CRISPR/Cas9-induced rice mutants from their acceptor lines (huaidao-1 and nanjing46) using hyperspectral imaging in the near-infrared (NIR) range (874.41–1733.91 nm) combined with chemometric analysis. The hyperspectral imaging data were analysed using principal component analysis (PCA) for exploratory purposes, and a support vector machine (SVM) and an extreme learning machine (ELM) were applied to build discrimination models for classification. Meanwhile, PCA loadings and a successive projections algorithm (SPA) were used for extracting optimal spectral wavelengths. The SVM-SPA model achieved best performance, with classification accuracies of 93% and 92.75% being observed for calibration and prediction sets for huaidao-1 and 91.25% and 89.50% for nanjing46, respectively. Furthermore, the classification of mutant seeds was visualized on prediction maps by predicting the features of each pixel on individual hyperspectral images based on the SPA-SVM model. The above results indicated that NIR hyperspectral imaging together with chemometric data analysis could be a reliable tool for identifying CRISPR/Cas9-induced rice mutants, which would help to accelerate selection and crop breeding processes.

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The Power of CRISPR-Cas9-Induced Genome Editing to Speed Up Plant Breeding

Cited by 44 publications

References 120 publications

Efficient genetic transformation and CRISPR/Cas9‐mediated genome editing in Lemna aequinoctialis

Efficient genetic transformation and CRISPR/Cas9‐mediated genome editing in Lemna aequinoctialis

Endogenous sequence patterns predispose the repair modes of CRISPR/Cas9‐induced DNA double‐stranded breaks in Arabidopsis thaliana

Discrimination of CRISPR/Cas9-induced mutants of rice seeds using near-infrared hyperspectral imaging

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