CRISPR/Cas9: a promising way to exploit genetic variation in plants

Rani, Reema; Yadav, Prashant; Barbadikar, Kalyani M.; Baliyan, Nikita; Malhotra, Era Vaidya; Singh, B. K.; Kumar, Arun; Singh, Dhiraj

doi:10.1007/s10529-016-2195-z

Cited by 49 publications

(26 citation statements)

References 78 publications

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“…Similarly to zinc finger nucleases (ZFN) and TALENs, CRISPR-Cas is able to make a double-strand break (DSB) at a precisely specified location in the genome, but it is much more versatile and easy to use, because the specificity of the target sequence is achieved by a separate guide RNA (gRNA) that can be easily designed and readily synthesised rather than by the protein structure itself (ZFN, TALEN). The use in plants has recently been reviewed by Luo et al (2016), Paul and Qi (2016), Hilscher et al (2016), and Rani et al (2016). …”

Section: Introductionmentioning

confidence: 99%

New traits in crops produced by genome editing techniques based on deletions

Wiel

Schaart

Lotz

et al. 2017

Plant Biotechnol Rep

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One of the most promising New Plant Breeding Techniques is genome editing (also called gene editing) with the help of a programmable site-directed nuclease (SDN). In this review, we focus on SDN-1, which is the generation of small deletions or insertions (indels) at a precisely defined location in the genome with zinc finger nucleases (ZFN), TALENs, or CRISPR-Cas9. The programmable nuclease is used to induce a double-strand break in the DNA, while the repair is left to the plant cell itself, and mistakes are introduced, while the cell is repairing the double-strand break using the relatively error-prone NHEJ pathway. From a biological point of view, it could be considered as a form of targeted mutagenesis. We first discuss improvements and new technical variants for SDN-1, in particular employing CRISPR-Cas, and subsequently explore the effectiveness of targeted deletions that eliminate the function of a gene, as an approach to generate novel traits useful for improving agricultural sustainability, including disease resistances. We compare them with examples of deletions that resulted in novel functionality as known from crop domestication and classical mutation breeding (both using radiation and chemical mutagens). Finally, we touch upon regulatory and access and benefit sharing issues regarding the plants produced.

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Section: Introductionmentioning

confidence: 99%

New traits in crops produced by genome editing techniques based on deletions

Wiel

Schaart

Lotz

et al. 2017

Plant Biotechnol Rep

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“…The applicability of GETs in the field of plant biology was already demonstrated in the model species Arabidopsis thaliana (Christian et al, 2010; Osakabe et al, 2010; Cermak et al, 2011; Li et al, 2013) and Nicotiana benthamiana (Nekrasov et al, 2013; Gao et al, 2015) as well as in other crops including rice, sorghum, wheat, corn, soybean, tobacco, potato, petunia, sweet orange, liver worth, and poplar (Shan et al, 2014; Luo et al, 2016; Rani et al, 2016). Stable inheritance of homozygous mutations induced by GETs and segregation of the mutation in the off springs was reported in several species (Maeder et al, 2008; Christian et al, 2010; Zhang et al, 2010; Qi et al, 2013; Brooks et al, 2014; Fauser et al, 2014; Feng et al, 2014; Jia et al, 2014; Schiml et al, 2014; Zhang et al, 2014; Zhou et al, 2014; Forner et al, 2015).…”

Section: Targeted Genome Engineering Techniquesmentioning

confidence: 99%

“…There is no general strategy for obtaining successful modifications. In silico approaches can help to predict candidates for resistance (Sanseverino and Ercolano, 2012) and to select target site, minimizing the occurrence of off-targets (Peng et al, 2016; Rani et al, 2016). Identification of amino acid residues under selective pressure can also provide valuable support (Iovieno et al, 2015).…”

Section: Targeted Genome Engineering Techniquesmentioning

confidence: 99%

Genome-Editing Technologies for Enhancing Plant Disease Resistance

et al. 2016

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One of the greatest challenges for agricultural science in the 21st century is to improve yield stability through the progressive development of superior cultivars. The increasing numbers of infectious plant diseases that are caused by plant-pathogens make it ever more necessary to develop new strategies for plant disease resistance breeding. Targeted genome engineering allows the introduction of precise modifications directly into a commercial variety, offering a viable alternative to traditional breeding methods. Genome editing is a powerful tool for modifying crucial players in the plant immunity system. In this work, we propose and discuss genome-editing strategies and targets for improving resistance to phytopathogens. First of all, we present the opportunities to rewrite the effector-target sequence for avoiding effector-target molecular interaction and also to modify effector-target promoters for increasing the expression of target genes involved in the resistance process. In addition, we describe potential approaches for obtaining synthetic R-genes through genome-editing technologies (GETs). Finally, we illustrate a genome editing flowchart to modify the pathogen recognition sites and engineer an R-gene that mounts resistance to some phylogenetically divergent pathogens. GETs potentially mark the beginning of a new era, in which synthetic biology affords a basis for obtaining a reinforced plant defense system. Nowadays it is conceivable that by modulating the function of the major plant immunity players, we will be able to improve crop performance for a sustainable agriculture.

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“…Only two studies in perennial species have applied the CRISPR/Cas9 technology, one in sweet orange (Jia and Wang, 2014), and other in Populus tomentosa (Fan et al, 2015); however, to date there are no studies linking NGS and CRISPR/Cas9 or showing if genetic changes induced by Cas9/sgRNA are inherited to subsequent generations in those species. Thus, the main applications of this technique are targeting food quality traits, susceptibility to pathogens or metabolomics engineering in diverting important regulatory pathways from valuable end-products (Rani et al, 2016). …”

Section: Crispr/cas9 Technologymentioning

confidence: 99%

Application of Genomic Technologies to the Breeding of Trees

et al. 2016

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The recent introduction of next generation sequencing (NGS) technologies represents a major revolution in providing new tools for identifying the genes and/or genomic intervals controlling important traits for selection in breeding programs. In perennial fruit trees with long generation times and large sizes of adult plants, the impact of these techniques is even more important. High-throughput DNA sequencing technologies have provided complete annotated sequences in many important tree species. Most of the high-throughput genotyping platforms described are being used for studies of genetic diversity and population structure. Dissection of complex traits became possible through the availability of genome sequences along with phenotypic variation data, which allow to elucidate the causative genetic differences that give rise to observed phenotypic variation. Association mapping facilitates the association between genetic markers and phenotype in unstructured and complex populations, identifying molecular markers for assisted selection and breeding. Also, genomic data provide in silico identification and characterization of genes and gene families related to important traits, enabling new tools for molecular marker assisted selection in tree breeding. Deep sequencing of transcriptomes is also a powerful tool for the analysis of precise expression levels of each gene in a sample. It consists in quantifying short cDNA reads, obtained by NGS technologies, in order to compare the entire transcriptomes between genotypes and environmental conditions. The miRNAs are non-coding short RNAs involved in the regulation of different physiological processes, which can be identified by high-throughput sequencing of RNA libraries obtained by reverse transcription of purified short RNAs, and by in silico comparison with known miRNAs from other species. All together, NGS techniques and their applications have increased the resources for plant breeding in tree species, closing the former gap of genetic tools between trees and annual species.

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CRISPR/Cas9: a promising way to exploit genetic variation in plants

Cited by 49 publications

References 78 publications

New traits in crops produced by genome editing techniques based on deletions

New traits in crops produced by genome editing techniques based on deletions

Genome-Editing Technologies for Enhancing Plant Disease Resistance

Application of Genomic Technologies to the Breeding of Trees

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