Applications and potential of genome editing in crop improvement

Zhang, Yi; Massel, Karen; Godwin, Ian D.; Gao, Caixia

doi:10.1186/s13059-018-1586-y

Cited by 329 publications

(209 citation statements)

References 117 publications

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“…The CRISPR/Cas genome editing system offers great potential for gene editing in plants and animals (Doudna and Charpentier ; Zhang et al ). The target sequences of the most widely used Cas, SpCas9, are restricted to genomic sites containing an NGG protospacer adjacent motif (PAM), thus limiting the availability of suitable target sites and reducing the utility of SpCas9.…”

Section: Introductionmentioning

confidence: 99%

Expanding the scope of CRISPR/Cas9‐mediated genome editing in plants using an xCas9 and Cas9‐NG hybrid

Niu

Li³

et al. 2020

JIPB

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Summary The widely used Streptococcus pyogenes Cas9 (SpCas9) requires NGG as a protospacer adjacent motif (PAM) for genome editing. Although SpCas9 is a powerful genome‐editing tool, its use has been limited on the targetable genomic locus lacking NGG PAM. The SpCas9 variants xCas9 and Cas9‐NG have been developed to recognize NG, GAA, and GAT PAMs in human cells. Here, we show that xCas9 cannot recognize NG PAMs in tomato, and Cas9‐NG can recognize some of our tested NG PAMs in the tomato and Arabidopsis genomes. In addition, we engineered SpCas9 (XNG‐Cas9) based on mutations from both xCas9 and Cas9‐NG, and found that XNG‐Cas9 can efficiently mutagenize endogenous target sites with NG, GAG, GAA, and GAT PAMs in the tomato or Arabidopsis genomes. The PAM compatibility of XNG‐Cas9 is the broadest reported to date among Cas9s (SpCas9 and Cas9‐NG) active in plant.

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Section: Introductionmentioning

confidence: 99%

Expanding the scope of CRISPR/Cas9‐mediated genome editing in plants using an xCas9 and Cas9‐NG hybrid

Niu

Li³

et al. 2020

JIPB

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“…Genome editing has now been used to generate useful traits in many crops-such as rice, maize, wheat, sugarcane, soybean, potato, sorghum, orange, cucumber, tomato, flax and cassava-targeting herbicide resistance, drought-stress tolerance, thermosensitive genic male sterility, disease resistance and altered product quality, with some in the process of release for commercial cultivation 9 . The stewardship of gene-edited lines in combination with an appropriate deployment strategy is essential to meet environmental health and safety standards.…”

Section: Fig 1 | Overview Of the Development Of Genome-edited Linesmentioning

confidence: 99%

A SWEET solution to rice blight

et al. 2019

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“…Genome editing tools in V. umbellata assembly: Editing tools have the potential to precisely change the architecture of a genome with the desired precision. These tools can modify the genomic architecture precisely to achieve the required accuracy (Zhang et al, 2018). These tools have been efficiently used for trait discovery and for the generation of crops with high crop yields .…”

Section: Transcription Factorsmentioning

confidence: 99%

Rice Bean (Vigna umbellata) draft genome sequence: unravelling the late flowering and unpalatability related genomic resources for efficient domestication of this underutilized crop

Kaul

Eswaran

Thangaraj

et al. 2019

Preprint

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Rice bean is a less well known and underutilized legume crop that has proved to be highly favourable due to its rich nutritional value in comparison with other members of the Vigna family. As an initiative to compose rice bean (Vigna umbellata) genomic resource, the size of 414 mega-base pairs with an estimate of 31276 highly confidential genes from 15521 scaffolds and functional coverage of 96.08% was sequenced from 30X coverage data from Illumina and PacBio platform. Rice bean genome assembly was found to be exquisitely close to V. angularis (experimental control/outgroup), V. radiata and V. unguiculata, however, V. angularis being the closest. Heuristically, the assembled genome was further aligned with 31 leguminous plants (13 complete genomes and 18 partial genomes), by collinearity block mapping. Further, we predicted similar discriminant results by complete CDS alignment. In contrast, 17 medically influential genomes from NIGMS-NIH, when compared with rice bean assembly for LCB clusters led to identification of more than 18000 genes from the entire selected medicinal genomes. Empirical construction of all genome comparisons revealed symplesiomorphic character in turn uncovering the lineage of genetic and functional features of rice beans. Signifiacantly, we found deserving late-flowering genes, palatablyindexed uncommon genes that regulate various metabolite pathways, related to abiotic and biotic stress pathways and those that are specific to photoperiod and disease resistance and so on. Further, we developed a repository for underutilised crop genome facility using D3.js at www.nicg.in. Therefore, the findings from this report addresses the genomic value of rice bean to be escalated via breeding by allied and applied approaches.Research), IBPR (International Board for Plant Genetic Resources) and ICUC (International Centre for Underutilized Crops) organisations, form a network called FOSRIN (Food Security through Ricebean Research in India and Nepal), wherein Rice bean has been labeled as one of the future crops foreseen for domestication by farmers in marginal lands (Venkatesha 2012).Despite the nutritional excellence of rice bean, the prevailing lack of awareness of its complete nutritional benefits means that rice bean can be categorized as an underutilized crop. Rice bean can become established and grow in various soil types. It is pest resistant and presents tremendous potential as a nutritious fodder and high-quality grain. The major drawbacks of this pulse crop of the kharif season include late flowering, indeterminate nature and tastelessness. Furthermore, there are meagre possibilities for the improvement of rice bean due to its predominant landraces, nominal modern plant breeding and limited seed supply. Consequently, the high diversity retained within its limited geographical distribution and the existence of few marketing channels mean that there is a great scope for the genetic improvement of rice bean. Despite the importance of rice bean as a multipurpose legume utilized for culinary purpos...

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Applications and potential of genome editing in crop improvement

Cited by 329 publications

References 117 publications

Expanding the scope of CRISPR/Cas9‐mediated genome editing in plants using an xCas9 and Cas9‐NG hybrid

Expanding the scope of CRISPR/Cas9‐mediated genome editing in plants using an xCas9 and Cas9‐NG hybrid

A SWEET solution to rice blight

Rice Bean (Vigna umbellata) draft genome sequence: unravelling the late flowering and unpalatability related genomic resources for efficient domestication of this underutilized crop

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