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1.
From Green Super Rice to green agriculture: Reaping the promise of functional genomics research.
Yu, S, Ali, J, Zhou, S, Ren, G, Xie, H, Xu, J, Yu, X, Zhou, F, Peng, S, Ma, L, et al
Molecular plant. 2022;(1):9-26
Abstract
Producing sufficient food with finite resources to feed the growing global population while having a smaller impact on the environment has always been a great challenge. Here, we review the concept and practices of Green Super Rice (GSR) that have led to a paradigm shift in goals for crop genetic improvement and models of food production for promoting sustainable agriculture. The momentous achievements and global deliveries of GSR have been fueled by the integration of abundant genetic resources, functional gene discoveries, and innovative breeding techniques with precise gene and whole-genome selection and efficient agronomic management to promote resource-saving, environmentally friendly crop production systems. We also provide perspectives on new horizons in genomic breeding technologies geared toward delivering green and nutritious crop varieties to further enhance the development of green agriculture and better nourish the world population.
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2.
Attaining the promise of plant gene editing at scale.
Nasti, RA, Voytas, DF
Proceedings of the National Academy of Sciences of the United States of America. 2021;(22)
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Abstract
Crop improvement relies heavily on genetic variation that arises spontaneously through mutation. Modern breeding methods are very adept at combining this genetic variation in ways that achieve remarkable improvements in plant performance. Novel traits have also been created through mutation breeding and transgenesis. The advent of gene editing, however, marks a turning point: With gene editing, synthetic variation will increasingly supplement and, in some cases, supplant the genetic variation that occurs naturally. We are still in the very early stages of realizing the opportunity provided by plant gene editing. At present, typically only one or a few genes are targeted for mutation at a time, and most mutations result in loss of gene function. New technological developments, however, promise to make it possible to perform gene editing at scale. RNA virus vectors, for example, can deliver gene-editing reagents to the germ line through infection and create hundreds to thousands of diverse mutations in the progeny of infected plants. With developmental regulators, edited somatic cells can be induced to form meristems that yield seed-producing shoots, thereby increasing throughput and shrinking timescales for creating edited plants. As these approaches are refined and others developed, they will allow for accelerated breeding, the domestication of orphan crops and the reengineering of metabolism in a more directed manner than has ever previously been possible.
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Environmental risk assessment in agro-ecosystems: Revisiting the concept of receiving environment after the EFSA guidance document.
Arpaia, S
Ecotoxicology and environmental safety. 2021;:111676
Abstract
The environmental risk assessment (ERA) for genetically modified plants (GMPs) is a prerequisite for commercial approval of these new varieties according to regulatory systems worldwide. The first country to regulate GM crops was the USA and the issue of possible environmental impacts was based on the principles used in risk assessment of pesticides. Two main pillars of this approach are the use of surrogate species for testing effects on non-target organisms using a tiered assessment with clear thresholds to indicate the need to move between tiers. The latest EFSA guidance document on ERA of Genetically Modified Organisms considers specifically the receiving environment in preparation of ERA for commercial cultivation of GMPs. According to existing guidelines in the EU, the receiving environment is defined by three mutually interacting components: the characteristics of the environmental stressor (i.e. the GM plant), the bio-geographical regions where the commercial release of the crop is expected and the agricultural systems therein. Difference in agronomic and ecological conditions (e.g. use of different varieties, vegetation of adjacent areas, non-target species assemblages, sensitivity of local species to the stressors) suggests that explicit considerations of the receiving environments are necessary. Results from field experiments indicate that differences in cultivation practices, e.g. the herbicide regime used on herbicide-tolerant GM crops, may induce direct and indirect effects on wild plant distribution and abundance, with consequent repercussions on food webs based on these plants. Moreover, ecological literature indicates that the concept of surrogate species has clear limitations if applied broadly to any ERA. Starting from case studies regarding GMPs, this paper discusses some ecological and agronomic characteristics of agro-ecosystems, which have implications in the elaboration of both hazard and exposure analyses during ERA. The species selection approach indicated in the EFSA Guidance Document and the consideration of the area(s) of the expected release of the new variety may provide the basis to an ecologically sound ERA for a range of environmental stressors. The quality of the data that become available for risk managers with this approach may support a more transparent and dependable ERA and risk management for GMPs as well as for other potential environmental stressors in agro-ecosystems.
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Targeted DNA insertion in plants.
Dong, OX, Ronald, PC
Proceedings of the National Academy of Sciences of the United States of America. 2021;(22)
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Abstract
Conventional methods of DNA sequence insertion into plants, using Agrobacterium-mediated transformation or microprojectile bombardment, result in the integration of the DNA at random sites in the genome. These plants may exhibit altered agronomic traits as a consequence of disruption or silencing of genes that serve a critical function. Also, genes of interest inserted at random sites are often not expressed at the desired level. For these reasons, targeted DNA insertion at suitable genomic sites in plants is a desirable alternative. In this paper we review approaches of targeted DNA insertion in plant genomes, discuss current technical challenges, and describe promising applications of targeted DNA insertion for crop genetic improvement.
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Application of Upstream Open Reading Frames (uORFs) Editing for the Development of Stress-Tolerant Crops.
Um, T, Park, T, Shim, JS, Kim, YS, Lee, GS, Choi, IY, Kim, JK, Seo, JS, Park, SC
International journal of molecular sciences. 2021;(7)
Abstract
Global population growth and climate change are posing increasing challenges to the production of a stable crop supply using current agricultural practices. The generation of genetically modified (GM) crops has contributed to improving crop stress tolerance and productivity; however, many regulations are still in place that limit their commercialization. Recently, alternative biotechnology-based strategies, such as gene-edited (GE) crops, have been in the spotlight. Gene-editing technology, based on the clustered regularly interspaced short palindromic repeats (CRISPR) platform, has emerged as a revolutionary tool for targeted gene mutation, and has received attention as a game changer in the global biotechnology market. Here, we briefly introduce the concept of upstream open reading frames (uORFs) editing, which allows for control of the translation of downstream ORFs, and outline the potential for enhancing target gene expression by mutating uORFs. We discuss the current status of developing stress-tolerant crops, and discuss uORF targets associated with salt stress-responsive genes in rice that have already been verified by transgenic research. Finally, we overview the strategy for developing GE crops using uORF editing via the CRISPR-Cas9 system. A case is therefore made that the mutation of uORFs represents an efficient method for developing GE crops and an expansion of the scope of application of genome editing technology.
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CRISPR-Cas-mediated chromosome engineering for crop improvement and synthetic biology.
Rönspies, M, Dorn, A, Schindele, P, Puchta, H
Nature plants. 2021;(5):566-573
Abstract
Plant breeding relies on the presence of genetic variation, as well as on the ability to break or stabilize genetic linkages between traits. The development of the genome-editing tool clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein (Cas) has allowed breeders to induce genetic variability in a controlled and site-specific manner, and to improve traits with high efficiency. However, the presence of genetic linkages is a major obstacle to the transfer of desirable traits from wild species to their cultivated relatives. One way to address this issue is to create mutants with deficiencies in the meiotic recombination machinery, thereby enhancing global crossover frequencies between homologous parental chromosomes. Although this seemed to be a promising approach at first, thus far, no crossover frequencies could be enhanced in recombination-cold regions of the genome. Additionally, this approach can lead to unintended genomic instabilities due to DNA repair defects. Therefore, efforts have been undertaken to obtain predefined crossovers between homologues by inducing site-specific double-strand breaks (DSBs) in meiotic, as well as in somatic plant cells using CRISPR-Cas tools. However, this strategy has not been able to produce a substantial number of heritable homologous recombination-based crossovers. Most recently, heritable chromosomal rearrangements, such as inversions and translocations, have been obtained in a controlled way using CRISPR-Cas in plants. This approach unlocks a completely new way of manipulating genetic linkages, one in which the DSBs are induced in somatic cells, enabling the formation of chromosomal rearrangements in the megabase range, by DSB repair via non-homologous end-joining. This technology might also enable the restructuring of genomes more globally, resulting in not only the obtainment of synthetic plant chromosome, but also of novel plant species.
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Genome editing of polyploid crops: prospects, achievements and bottlenecks.
Schaart, JG, van de Wiel, CCM, Smulders, MJM
Transgenic research. 2021;(4):337-351
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Abstract
Plant breeding aims to develop improved crop varieties. Many crops have a polyploid and often highly heterozygous genome, which may make breeding of polyploid crops a real challenge. The efficiency of traditional breeding based on crossing and selection has been improved by using marker-assisted selection (MAS), and MAS is also being applied in polyploid crops, which helps e.g. for introgression breeding. However, methods such as random mutation breeding are difficult to apply in polyploid crops because there are multiple homoeologous copies (alleles) of each gene. Genome editing technology has revolutionized mutagenesis as it enables precisely selecting targets. The genome editing tool CRISPR/Cas is especially valuable for targeted mutagenesis in polyploids, as all alleles and/or copies of a gene can be targeted at once. Even multiple genes, each with multiple alleles, may be targeted simultaneously. In addition to targeted mutagenesis, targeted replacement of undesirable alleles by desired ones may become a promising application of genome editing for the improvement of polyploid crops, in the near future. Several examples of the application of genome editing for targeted mutagenesis are described here for a range of polyploid crops, and achievements and bottlenecks are highlighted.
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Current progress and challenges in crop genetic transformation.
Anjanappa, RB, Gruissem, W
Journal of plant physiology. 2021;:153411
Abstract
Plant transformation remains the most sought-after technology for functional genomics and crop genetic improvement, especially for introducing specific new traits and to modify or recombine already existing traits. Along with many other agricultural technologies, the global production of genetically engineered crops has steadily grown since they were first introduced 25 years ago. Since the first transfer of DNA into plant cells using Agrobacterium tumefaciens, different transformation methods have enabled rapid advances in molecular breeding approaches to bring crop varieties with novel traits to the market that would be difficult or not possible to achieve with conventional breeding methods. Today, transformation to produce genetically engineered crops is the fastest and most widely adopted technology in agriculture. The rapidly increasing number of sequenced plant genomes and information from functional genomics data to understand gene function, together with novel gene cloning and tissue culture methods, is further accelerating crop improvement and trait development. These advances are welcome and needed to make crops more resilient to climate change and to secure their yield for feeding the increasing human population. Despite the success, transformation remains a bottleneck because many plant species and crop genotypes are recalcitrant to established tissue culture and regeneration conditions, or they show poor transformability. Improvements are possible using morphogenetic transcriptional regulators, but their broader applicability remains to be tested. Advances in genome editing techniques and direct, non-tissue culture-based transformation methods offer alternative approaches to enhance varietal development in other recalcitrant crops. Here, we review recent developments in plant transformation and regeneration, and discuss opportunities for new breeding technologies in agriculture.
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New plant breeding techniques and their regulatory implications: An opportunity to advance metabolomics approaches.
Enfissi, EMA, Drapal, M, Perez-Fons, L, Nogueira, M, Berry, HM, Almeida, J, Fraser, PD
Journal of plant physiology. 2021;:153378
Abstract
Over the previous decades, biotechnological innovations have led to improved agricultural productivity, more nutritious foods and lower chemical usage. Both in western societies and Low Medium Income Countries (LMICs). However, the projected increases in the global population, means the production of nutritious food stuffs must increase dramatically. Building on existing genetic modification technologies a series of New Plant Breeding Technologies (NPBT) has recently emerged. These approaches include, Agro-infiltration, grafting, cis and intragenesis and gene editing technologies. How these new techniques should be regulated has fostered considerable debate. Concerns have also been raised, to ensure over-regulation does not arise, creating administrative and economic burden. In this article the existing landscape of genetically modified crops is reviewed and the potential of several New Plant Breeding Techniques (NPBT) described. Metabolomics is an omic technology that has developed in a concurrent manner with biotechnological advances in plant breeding. There is potentially further opportunities to advance our metabolomic technologies to characterise the outputs of New Plant Breeding Technologies, in a manner that is beneficial both from an academic, biosafety and industrial perspective.
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10.
CRISPR/Cas systems: opportunities and challenges for crop breeding.
Biswas, S, Zhang, D, Shi, J
Plant cell reports. 2021;(6):979-998
Abstract
Increasing crop production to meet the demands of a growing population depends largely on crop improvement through new plant-breeding techniques (NPBT) such as genome editing. CRISPR/Cas systems are NPBTs that enable efficient target-specific gene editing in crops, which is supposed to accelerate crop breeding in a way that is different from genetically modified (GM) technology. Herein, we review the applications of CRISPR/Cas systems in crop breeding focusing on crop domestication, heterosis, haploid induction, and synthetic biology, and summarize the screening methods of CRISPR/Cas-induced mutations in crops. We highlight the importance of molecular characterization of CRISPR/Cas-edited crops, and pay special attentions to emerging highly specific genome-editing tools such as base editors and prime editors. We also discuss future improvements of CRISPR/Cas systems for crop improvement.