Rapid improvement of domestication traits in an orphan crop by genome editing

Lemmon, Zachary H.; Reem, Nathan T.; Dalrymple, Justin; Soyk, Sebastian; Swartwood, Kerry; Rodríguez-Leal, Daniel; Eck, Joyce Van; Lippman, Zachary B.

doi:10.1038/s41477-018-0259-x

Cited by 386 publications

(283 citation statements)

References 18 publications

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“…Crop domestication has attracted much speculation over the years, and has recently attracted renewed attention because a range of experimental approaches now allow hypotheses to be directly addressed. These ranged from sophisticated analyses of archaeobotanical data, indicating that domestication is a dynamic process that occurred independently in various regions and involved many different crops (Fuller, 2007), to the de novo domestication of wild crop-relatives using genome editing (Lemmon et al, 2018;Li et al, 2018;Zs€ og€ on et al, 2018). These new developments mean that improved understanding of crop domestication could have direct implications for how we deal with human population pressure and climate change.…”

Section: Discussionmentioning

confidence: 99%

μCT trait analysis reveals morphometric differences between domesticated temperate small grain cereals and their wild relatives

et al. 2019

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Summary Wheat and barley are two of the founder crops domesticated in the Fertile Crescent, and currently represent crops of major economic importance in temperate regions. Due to impacts on yield, quality and end‐use, grain morphometric traits remain an important goal for modern breeding programmes and are believed to have been selected for by human populations. To directly and accurately assess the three‐dimensional (3D) characteristics of grains, we combine X‐ray microcomputed tomography (μ CT ) imaging techniques with bespoke image analysis tools and mathematical modelling to investigate how grain size and shape vary across wild and domesticated wheat and barley. We find that grain depth and, to a lesser extent, width are major drivers of shape change and that these traits are still relatively plastic in modern bread wheat varieties. Significant changes in grain depth are also observed to be associated with differences in ploidy. Finally, we present a model that can accurately predict the wild or domesticated status of a grain from a given taxa based on the relationship between three morphometric parameters (length, width and depth) and suggest its general applicability to both archaeological identification studies and breeding programmes.

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Section: Discussionmentioning

confidence: 99%

μCT trait analysis reveals morphometric differences between domesticated temperate small grain cereals and their wild relatives

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%

“…Interestingly, many of these genes have a conserved function in regulating fruit development in both dry and fleshy fruit types, suggesting broad applicability of common genome edits. For instance, CYP78A9 and CLV‐WUS pathway genes can regulate both silique size in Arabidopsis /rapeseed (Fan et al , ; Shi et al , ; Xiao et al , ; Xu et al , ; Yang et al , ) and fruit size in cherry/tomato (Lemmon et al , ; Li et al , ; Qi et al , ; Rodriguez‐Leal et al ., ; Xu et al , ). Besides, many of these genes have similar functions in regulating fruit size in Arabidopsis and other crops.…”

Section: Conclusion and Future Prospectsmentioning

confidence: 99%

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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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“…Importantly, however, even if in many cases crops' common phenotypes were reached via alterations in unrelated genes in past domestications, this does not preclude the targeting of orthologous sequences in the further domestication of orphan crops, as a transgressive approach from previous domestication pathways may still prove effective and could be more efficient (Lenser & Theißen, 2013). Indeed, the use of advanced molecular breeding methods such as gene editing to effect changes in domestication-related gene orthologues has been shown to be effective for orphan crops in some circumstances: for example, recent research on the solanaceous orphan crop groundcherry (Physalis pruinosa) using CRISPR/Cas9 to mutate orthologues of tomato domestication and improvement genes has shown promise (Lemmon et al, 2018).…”

Section: Across Various Crops (See Examples Inmentioning

confidence: 99%

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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Rapid improvement of domestication traits in an orphan crop by genome editing

Cited by 386 publications

References 18 publications

μCT trait analysis reveals morphometric differences between domesticated temperate small grain cereals and their wild relatives

μCT trait analysis reveals morphometric differences between domesticated temperate small grain cereals and their wild relatives

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

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

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