De novo domestication of wild tomato using genome editing

Zsögön, Agustín; Čermák, Tomáš; Naves, Emmanuel Rezende; Notini, Marcela Morato; Edel, Kai H.; Weinl, Stefan; Freschi, Luciano; Voytas, Daniel F.; Kudla, Jörg; Peres, Lázaro Eustáquio Pereira

doi:10.1038/nbt.4272

Cited by 603 publications

(364 citation statements)

References 42 publications

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“…Further practical testing of the above approach would in addition reveal if there is merit in the ‘redomestication’ of major crops from their wild relatives and progenitors as a strategy for efficiently accessing wild gene pools for traits lost in the development of advanced cultivars but now considered beneficial for addressing agriculture's sustainability challenges (Langridge & Waugh, ). Recent research using CRISPR/Cas9 gene editing of target domestication‐related genes has shown promise for redomestications, with domesticated phenotypes that retain important wild attributes achievable starting from crop wild progenitors in the case of tomato (T. Li et al ., ; Zsögön et al ., ). It is known that wild relatives, progenitors and landraces of a number of major crops contain more variation in traits related to resource use efficiency and a plant's ability to interact positively with other crops and noncrop biotic components in complex production systems than do narrowly diverse advanced cultivars developed for monoculture (Kapulnik & Kushnir, ; Mutch & Young, ; Martín‐Robles et al ., ).…”

Section: Future Outlookmentioning

confidence: 97%

The role of genetics in mainstreaming the production of new and orphan crops to diversify food systems and support human nutrition

et al. 2019

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Summary Especially in low‐income nations, new and orphan crops provide important opportunities to improve diet quality and the sustainability of food production, being rich in nutrients, capable of fitting into multiple niches in production systems, and relatively adapted to low‐input conditions. The evolving space for these crops in production systems presents particular genetic improvement requirements that extensive gene pools are able to accommodate. Particular needs for genetic development identified in part with plant breeders relate to three areas of fundamental importance for addressing food production and human demographic trends and associated challenges, namely: facilitating integration into production systems; improving the processability of crop products; and reducing farm labour requirements. Here, we relate diverse involved target genes and crop development techniques. These techniques include transgressive methods that involve defining exemplar crop models for effective new and orphan crop improvement pathways. Research on new and orphan crops not only supports the genetic improvement of these crops, but they serve as important models for understanding crop evolutionary processes more broadly, guiding further major crop evolution. The bridging position of orphan crops between new and major crops provides unique opportunities for investigating genetic approaches for de novo domestications and major crop ‘rewildings’.

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Section: Future Outlookmentioning

confidence: 97%

The role of genetics in mainstreaming the production of new and orphan crops to diversify food systems and support human nutrition

et al. 2019

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“…The genome editing of CLV3 orthologues can produce multilocular siliques in several dry fruit crops, including Brassica rapa and B. napus (Fan et al , ; Yang et al , ). In addition, the genome editing of CLV1/2/3 also produced multiple locular fruits with increased size in fleshy fruit crops, such as tomato and groundcherry (Lemmon et al , ; Li et al , ; Rodrı´guez‐Leal et al , ; Xu et al , ; Zsögön et al , ).…”

Section: Receptor Kinase Signallingmentioning

confidence: 99%

“…Such information is essential if a comprehensive genome editing approach is to be applied. Some initial targets for fruit size have been targeted using editing approaches, with some success (Lemmon et al , ; Li et al , ; Rodríguez‐Leal et al , ; Zsögön et al , ), suggesting that, with a more comprehensive understanding of the genetic and signalling pathways underlying this trait, major gains could be achieved. In addition to improving fruit size in elite germplasm, genome editing can be used for improvement of orphan crops (Lemmon et al , ) or de novo domestication of crop wild relatives (Zsögön et al , ), which often harbour agronomically valuable disease resistance traits (Dangl et al , ).…”

Section: Conclusion and Future Prospectsmentioning

confidence: 99%

Genetic and signalling pathways of dry fruit size: targets for genome editing‐based crop improvement

Hussain

Shi

Scheben

et al. 2020

Plant Biotechnology Journal

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Summary Fruit is seed‐bearing structures specific to angiosperm that form from the gynoecium after flowering. Fruit size is an important fitness character for plant evolution and an agronomical trait for crop domestication/improvement. Despite the functional and economic importance of fruit size, the underlying genes and mechanisms are poorly understood, especially for dry fruit types. Improving our understanding of the genomic basis for fruit size opens the potential to apply gene‐editing technology such as CRISPR/Cas to modulate fruit size in a range of species. This review examines the genes involved in the regulation of fruit size and identifies their genetic/signalling pathways, including the phytohormones, transcription and elongation factors, ubiquitin‐proteasome and microRNA pathways, G‐protein and receptor kinases signalling, arabinogalactan and RNA‐binding proteins. Interestingly, different plant taxa have conserved functions for various fruit size regulators, suggesting that common genome edits across species may have similar outcomes. Many fruit size regulators identified to date are pleiotropic and affect other organs such as seeds, flowers and leaves, indicating a coordinated regulation. The relationships between fruit size and fruit number/seed number per fruit/seed size, as well as future research questions, are also discussed.

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“…Very recently, Zsögön et al . () and Li et al . () engineered the S. pimpinellifolium wild ancestor of cultivated tomato by CRISPR multiplexing with six gRNAs, which resulted in the generation of gene‐edited plants with characteristics similar to those of cultivated tomato, i.e.…”

Section: From Trait Discovery To Trait Engineering: Gene Editingmentioning

confidence: 88%

“…Then, the ideal would be to reproduce directly in elite lines the allelic variation(s) responsible for improvement of the trait(s) of interest. Thanks to the recent advances in GE technologies, reaching this objective can be expected in the very near future, as very recently demonstrated by several studies (Rodríguez‐Leal et al ., ; Li et al ., ; Zsögön et al ., ).…”

Section: From Trait Discovery To Trait Engineering: Gene Editingmentioning

confidence: 97%

Trait discovery and editing in tomato

2018

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Summary Tomato (Solanum lycopersicum), which is used for both processing and fresh markets, is a major crop species that is the top ranked vegetable produced over the world. Tomato is also a model species for research in genetics, fruit development and disease resistance. Genetic resources available in public repositories comprise the 12 wild related species and thousands of landraces, modern cultivars and mutants. In addition, high quality genome sequences are available for cultivated tomato and for several wild relatives, hundreds of accessions have been sequenced, and databases gathering sequence data together with genetic and phenotypic data are accessible to the tomato community. Major breeding goals are productivity, resistance to biotic and abiotic stresses, and fruit sensorial and nutritional quality. New traits, including resistance to various biotic and abiotic stresses and root architecture, are increasingly being studied. Several major mutations and quantitative trait loci (QTLs) underlying traits of interest in tomato have been uncovered to date and, thanks to new populations and advances in sequencing technologies, the pace of trait discovery has considerably accelerated. In recent years, clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 gene editing (GE) already proved its remarkable efficiency in tomato for engineering favorable alleles and for creating new genetic diversity by gene disruption, gene replacement, and precise base editing. Here, we provide insight into the major tomato traits and underlying causal genetic variations discovered so far and review the existing genetic resources and most recent strategies for trait discovery in tomato. Furthermore, we explore the opportunities offered by CRISPR/Cas9 and their exploitation for trait editing in tomato.

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De novo domestication of wild tomato using genome editing

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Cited by 603 publications

References 42 publications

The role of genetics in mainstreaming the production of new and orphan crops to diversify food systems and support human nutrition

The role of genetics in mainstreaming the production of new and orphan crops to diversify food systems and support human nutrition

Genetic and signalling pathways of dry fruit size: targets for genome editing‐based crop improvement

Trait discovery and editing in tomato

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