Applications and potential of genome editing in crop improvement

Sophisticated CRISPR/Cas tools for fine-tuning plant performance

Over the last years, the discovery of various natural and the development of a row of engineered CRISPR/Cas nucleases have made almost every site of plant genomes accessible for the induction of specific changes. Newly developed tools open up a wide range of possibilities for the induction of genetic variability, from changing a single bp to Mbps, and thus to fine-tune plant performance. Whereas early approaches focused on targeted mutagenesis, recently developed tools enable the induction of precise and predefined genomic modifications. The use of base editors allows the substitution of single nucleotides, whereas the use of prime editors and gene targeting methods enables the induction of larger sequence modifications from a few bases to several kbp. Recently, through CRISPR/Cas-mediated chromosome engineering, it became possible to induce heritable inversions and translocations in the Mbp range. Thus, a novel way of breaking and fixing genetic linkages has come into reach for breeders. In addition, sequence-specific recruitment of various factors involved in transcriptional and post-transcriptional regulation has been shown to provide an additional class of methods for the fine tuning of plant performance. In this review, we provide an overview of the most recent progress in the field of CRISPR/Cas-based tool development for plant genome engineering and try to evaluate the importance of these developments for breeding and biotechnological applications.

Control of Plant Growth and Defense by Photoreceptors: From Mechanisms to Opportunities in Agriculture

Plants detect and respond to the proximity of competitors using light signals perceived by photoreceptor proteins. A low ratio of red to far-red radiation (R:FR ratio) is a key signal of competition that is sensed by the photoreceptor phytochrome B (phyB). Low R:FR ratios increase the synthesis of growth-related hormones, including auxin and gibberellins, promoting stem elongation and other shade-avoidance responses. Other photoreceptors that help plants to optimize their developmental configuration and resource allocation patterns in the canopy include blue light photoreceptors, such as cryptochromes and phototropins, and UV receptors, such as UVR8. All photoreceptors act by directly or indirectly controlling the activity of two major regulatory nodes for growth and development: the COP1/SPA ubiquitin E3 ligase complex and the PIF transcription factors. phyB is also an important modulator of hormonal pathways that regulate plant defense against herbivores and pathogens, including the jasmonic acid signaling pathway. In this Perspective, we discuss recent advances on the studies of the mechanisms that link photoreceptors with growth and defense. Understanding these mechanisms is important to provide a functional platform for breeding programs aimed at improving plant productivity, stress tolerance, and crop health in species of agronomic interest, and to manipulate the light environments in protected agriculture.

Harnessing Knowledge from Maize and Rice Domestication for New Crop Breeding

Crop domestication has fundamentally altered the course of human history, causing a shift from hunter-gatherer to agricultural societies and stimulating the rise of modern civilization. A greater understanding of crop domestication would provide a theoretical basis for how we could improve current crops and develop new crops to deal with environmental challenges in a sustainable manner. Here, we provide a comprehensive summary of the similarities and differences in the domestication processes of maize and rice, two major staple food crops that feed the world. We propose that maize and rice might have evolved distinct genetic solutions toward domestication. Maize and rice domestication appears to be associated with distinct regulatory and evolutionary mechanisms. Rice domestication tended to select de novo, loss-of-function, coding variation, while maize domestication more frequently favored standing, gain-of-function, regulatory variation. At the gene network level, distinct genetic paths were used to acquire convergent phenotypes in maize and rice domestication, during which different central genes were utilized, orthologous genes played different evolutionary roles, and unique genes or regulatory modules were acquired for establishing new traits. Finally, we discuss how the knowledge gained from past domestication processes, together with emerging technologies, could be exploited to improve modern crop breeding and domesticate new crops to meet increasing human demands.

Multiallelic, Targeted Mutagenesis of Magnesium Chelatase With CRISPR/Cas9 Provides a Rapidly Scorable Phenotype in Highly Polyploid Sugarcane

Genome editing with sequence-specific nucleases, such as clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9), is revolutionizing crop improvement. Developing efficient genome-editing protocols for highly polyploid crops, including sugarcane (x = 10-13), remains challenging due to the high level of genetic redundancy in these plants. Here, we report the efficient multiallelic editing of magnesium chelatase subunit I (MgCh) in sugarcane. Magnesium chelatase is a key enzyme for chlorophyll biosynthesis. CRISPR/Cas9-mediated targeted co-mutagenesis of 49 copies/alleles of magnesium chelatase was confirmed via Sanger sequencing of cloned PCR amplicons. This resulted in severely reduced chlorophyll contents, which was scorable at the time of plant regeneration in the tissue culture. Heat treatment following the delivery of genome editing reagents elevated the editing frequency 2-fold and drastically promoted co-editing of multiple alleles, which proved necessary to create a phenotype that was visibly distinguishable from the wild type. Despite their yellow leaf color, the edited plants were established well in the soil and did not show noticeable growth retardation. This approach will facilitate the establishment of genome editing protocols for recalcitrant crops and support further optimization, including the evaluation of alternative RNA-guided nucleases to overcome the limitations of the protospacer adjacent motif (PAM) site or to develop novel delivery strategies for genome editing reagents.

Current status and prospects of plant genome editing in Australia

Plant genome editing, particularly CRISPR-Cas biotechnologies, has rapidly evolved and drawn enormous attention all around the world in the last decade. The cutting-edge technologies have had substantial impact on precise genome editing for manipulating gene expression, stacking gene mutations, and improving crop agronomic traits. Following the global trends, investigations on CRISPR-Cas have been thriving in Australia, especially in agriculture sciences. Importantly, CRISPR-edited plants, classified as SDN-1 organisms (SDN: site-directed nuclease), have been given a green light in Australia, with regulatory bodies indicating they will not be classified as a genetically modified organism (GMO) if no foreign DNA is present in an edited plant. As a result, genome-edited products would not attract the onerous regulation required for the introduction of a GMO, which could mean more rapid deployment of new varieties and products that could be traded freely in Australia, and potentially to export markets. In the present review, we discuss the current status and prospects of plant genome editing in Australia by highlighting several species of interest. Using these species as case studies, we discuss the priorities and potential of plant genome editing, as well as the remaining challenges.

Base editing with high efficiency in allotetraploid oilseed rape by A3A-PBE system

CRISPR/Cas-base editing is an emerging technology that could convert a nucleotide to another type at the target site. In this study, A3A-PBE system consisting of human A3A cytidine deaminase fused with a Cas9 nickase and uracil glycosylase inhibitor was established and developed in allotetraploid Brassica napus. We designed three sgRNAs to target ALS, RGA and IAA7 genes, respectively. Base-editing efficiency was demonstrated to be more than 20% for all the three target genes. Target sequencing results revealed that the editing window ranged from C1 to C10 of the PAM sequence. Base-edited plants of ALS conferred high herbicide resistance, while base-edited plants of RGA or IAA7 exhibited decreased plant height. All the base editing could be genetically inherited from T₀ to T₁ generation. Several Indel mutations were confirmed at the target sites for all the three sgRNAs. Furthermore, though no C to T substitution was detected at the most potential off-target sites, large-scale SNP variations were determined through whole-genome sequencing between some base-edited and wild-type plants. These results revealed that A3A-PBE base-editing system could effectively convert C to T substitution with high-editing efficiency and broadened editing window in oilseed rape. Mutants for ALS, IAA7 and RGA genes could be potentially applied to confer herbicide resistance for weed control or with better plant architecture suitable for mechanic harvesting.

Developments and Prospects in Imperative Underexploited Vegetable Legumes Breeding: A Review

Vegetable legumes are an essential source of carbohydrates, vitamins, and minerals, along with health-promoting bioactive chemicals. The demand for the use of either fresh or processed vegetable legumes is continually expanding on account of the growing consumer awareness about their well-balanced diet. Therefore, sustaining optimum yields of vegetable legumes is extremely important. Here we seek to present d etails of prospects of underexploited vegetable legumes for food availability, accessibility, and improved livelihood utilization. So far research attention was mainly focused on pulse legumes' performance as compared to vegetable legumes. Wild and cultivated vegetable legumes vary morphologically across diverse habitats. This could make them less known, underutilized, and underexploited, and make them a promising potential nutritional source in developing nations where malnutrition still exists. Research efforts are required to promote underexploited vegetable legumes, for improving their use to feed the ever-increasing population in the future. In view of all the above points, here we have discussed underexploited vegetable legumes with tremendous potential; namely, vegetable pigeon pea (Cajanus cajan), cluster bean (Cyamopsis tetragonoloba), winged bean (Psophocarpus tetragonolobus), dolichos bean (Lablab purpureus), and cowpea (Vigna unguiculata), thereby covering the progress related to various aspects such as pre-breeding, molecular markers, quantitative trait locus (QTLs), genomics, and genetic engineering. Overall, this review has summarized the information related to advancements in the breeding of vegetable legumes which will ultimately help in ensuring food and nutritional security in developing nations.

Plant Polyphenols-Biofortified Foods as a Novel Tool for the Prevention of Human Gut Diseases

Plant food biofortification is recently receiving remarkable attention, as it aims to increase the intake of minerals, vitamins, or antioxidants, crucial for their contribution to the general human health status and disease prevention. In this context, the study of the plant’s secondary metabolites, such as polyphenols, plays a pivotal role for the development of a new generation of plant crops, compensating, at least in part, the low nutritional quality of Western diets with a higher quality of dietary sources. Due to the prevalent immunomodulatory activity at the intestinal level, polyphenols represent a nutritionally relevant class of plant secondary metabolites. In this review, we focus on the antioxidant and anti-inflammatory properties of different classes of polyphenols with a specific attention to their potential in the prevention of intestinal pathological processes. We also discuss the latest biotechnology strategies and new advances of genomic techniques as a helpful tool for polyphenols biofortification and the development of novel, healthy dietary alternatives that can contribute to the prevention of inflammatory bowel diseases.

Anticipating and Identifying Collateral Damage in Genome Editing

Genome editing has powerful applications in research, healthcare, and agriculture. However, the range of possible molecular events resulting from genome editing has been underestimated and the technology remains unpredictable on, and away from, the target locus. This has considerable impact in providing a safe approach for therapeutic genome editing, agriculture, and other applications. This opinion article discusses how to anticipate and detect those editing events by a combination of assays to capture all possible genomic changes. It also discusses strategies for preventing unwanted effects, critical to appraise the benefit or risk associated with the use of the technology. Anticipating and verifying the result of genome editing are essential for the success for all applications.

Overexpression of improved EPSPS gene results in field level glyphosate tolerance and higher grain yield in rice

Glyphosate is a popular, systemic, broad-spectrum herbicide used in modern agriculture. Being a structural analog of phosphoenolpyruvate (PEP), it inhibits 5-enolpyruvylshikimate 3-phosphate synthase (EPSPS) which is responsible for the biosynthesis of aromatic amino acids and various aromatic secondary metabolites. Taking a lead from glyphosate-resistant weeds, two mutant variants of the rice EPSPS gene were developed by amino acid substitution (T173I + P177S; TIPS-OsEPSPS and G172A + T173I + P177S; GATIPS-OsEPSPS). These mutated EPSPS genes were overexpressed in rice under the control of either native EPSPS or constitutive promoters (maize ubiquitin [ZmUbi] promoter). The overexpression of TIPS-OsEPSPS under the control of the ZmUbi promoter resulted in higher tolerance to glyphosate (up to threefold of the recommended dose) without affecting the fitness and related agronomic traits of plants in both controlled and field conditions. Furthermore, such rice lines produced 17%-19% more grains compared to the wild type (WT) in the absence of glyphosate application and the phenylalanine and tryptophan contents in the transgenic seeds were found to be significantly higher in comparison with WT seeds. Our results also revealed that the native promoter guided expression of modified EPSPS genes did not significantly improve the glyphosate tolerance. The present study describing the introduction of a crop-specific TIPS mutation in class I aroA gene of rice and its overexpression have potential to substantially improve the yield and field level glyphosate tolerance in rice. This is the first report to observe that the EPSPS has role to play in improving grain yield of rice.

Genomic interventions for sustainable agriculture

Agricultural production faces a Herculean challenge to feed the increasing global population. Food production systems need to deliver more with finite land and water resources while exerting the least negative influence on the ecosystem. The unpredictability of climate change and consequent changes in pests/pathogens dynamics aggravate the enormity of the challenge. Crop improvement has made significant contributions towards food security, and breeding climate-smart cultivars are considered the most sustainable way to accelerate food production. However, a fundamental change is needed in the conventional breeding framework in order to respond adequately to the growing food demands. Progress in genomics has provided new concepts and tools that hold promise to make plant breeding procedures more precise and efficient. For instance, reference genome assemblies in combination with germplasm sequencing delineate breeding targets that could contribute to securing future food supply. In this review, we highlight key breakthroughs in plant genome sequencing and explain how the presence of these genome resources in combination with gene editing techniques has revolutionized the procedures of trait discovery and manipulation. Adoption of new approaches such as speed breeding, genomic selection and haplotype-based breeding could overcome several limitations of conventional breeding. We advocate that strengthening varietal release and seed distribution systems will play a more determining role in delivering genetic gains at farmer's field. A holistic approach outlined here would be crucial to deliver steady stream of climate-smart crop cultivars for sustainable agriculture.

The importance of genomic variation for biodiversity, ecosystems and people

The 2019 United Nations Global assessment report on biodiversity and ecosystem services estimated that approximately 1 million species are at risk of extinction. This primarily human-driven loss of biodiversity has unprecedented negative consequences for ecosystems and people. Classic and emerging approaches in genetics and genomics have the potential to dramatically improve these outcomes. In particular, the study of interactions among genetic loci within and between species will play a critical role in understanding the adaptive potential of species and communities, and hence their direct and indirect effects on biodiversity, ecosystems and people. We explore these population and community genomic contexts in the hope of finding solutions for maintaining and improving ecosystem services and nature's contributions to people.

Structural Aspects of DNA Repair and Recombination in Crop Improvement

The adverse effects of global climate change combined with an exponentially increasing human population have put substantial constraints on agriculture, accelerating efforts towards ensuring food security for a sustainable future. Conventional plant breeding and modern technologies have led to the creation of plants with better traits and higher productivity. Most crop improvement approaches (conventional breeding, genome modification, and gene editing) primarily rely on DNA repair and recombination (DRR). Studying plant DRR can provide insights into designing new strategies or improvising the present techniques for crop improvement. Even though plants have evolved specialized DRR mechanisms compared to other eukaryotes, most of our insights about plant-DRRs remain rooted in studies conducted in animals. DRR mechanisms in plants include direct repair, nucleotide excision repair (NER), base excision repair (BER), mismatch repair (MMR), non-homologous end joining (NHEJ) and homologous recombination (HR). Although each DRR pathway acts on specific DNA damage, there is crosstalk between these. Considering the importance of DRR pathways as a tool in crop improvement, this review focuses on a general description of each DRR pathway, emphasizing on the structural aspects of key DRR proteins. The review highlights the gaps in our understanding and the importance of studying plant DRR in the context of crop improvement.

Fine-tuning sugar content in strawberry

Fine-tuning quantitative traits for continuous subtle phenotypes is highly advantageous. We engineer the highly conserved upstream open reading frame (uORF) of FvebZIPs1.1 in strawberry (Fragaria vesca), using base editor A3A-PBE. Seven novel alleles are generated. Sugar content of the homozygous T1 mutant lines is 33.9-83.6% higher than that of the wild-type. We also recover a series of transgene-free mutants with 35 novel genotypes containing a continuum of sugar content. All the novel genotypes could be immediately fixed in subsequent generations by asexual reproduction. Genome editing coupled with asexual reproduction offers tremendous opportunities for quantitative trait improvement.

Engineering drought tolerance in plants through CRISPR/Cas genome editing

Drought stress is primarily responsible for heavy yield losses and productivity in major crops and possesses the greatest threat to the global food security. While conventional and molecular breeding approaches along with genetic engineering techniques have been instrumental in developing drought-tolerant crop varieties, these methods are cumbersome, time consuming and the genetically modified varieties are not widely accepted due to regulatory concerns. Plant breeders are now increasingly centring towards the recently available genome-editing tools for improvement of agriculturally important traits. The advent of multiple sequence-specific nucleases has facilitated precise gene modification towards development of novel climate ready crop variants. Amongst the available genome-editing platforms, the clustered regularly interspaced short palindromic repeat-Cas (CRISPR/Cas) system has emerged as a revolutionary tool for its simplicity, adaptability, flexibility and wide applicability. In this review, we focus on understanding the molecular mechanism of drought response in plants and the application of CRISPR/Cas genome-editing system towards improved tolerance to drought stress.

Detection of 30 bp DNA fragments with a sensitive modified Southern blot analysis

To evaluate crops generated by new breeding techniques, it is important to confirm the removal of recombinant DNAs (rDNAs) derived from foreign genes including unintentionally introduced short rDNA(s). We attempted to develop a sensitive detection method for such short rDNAs using Southern blot analysis and performed a model study targeting single-copy endogenous genes in plants. To increase the detection sensitivity, the general protocol for Southern blot analysis was modified. In the model study, we used endogenous-gene-targeting probes in which complementary sequences were serially replaced by dummy sequences, and detected complementary sequences as well as 30 bp. We further evaluated the sensitivity using short rDNAs derived from GM sequences as pseudoinsertions, and the results demonstrated that rDNA-insertions as small as 30 bp could be detected. The results suggested that unintentionally introduced rDNA-insertions were 30 bp or more in length could be detected by the Southern blot analysis.

Gene Pyramiding for Sustainable Crop Improvement against Biotic and Abiotic Stresses

Sustainable agricultural production is endangered by several ecological factors, such as drought, extreme temperatures, excessive salts, parasitic ailments, and insect pest infestation. These challenging environmental factors may have adverse effects on future agriculture production in many countries. In modern agriculture, conventional crop-breeding techniques alone are inadequate for achieving the increasing population’s food demand on a sustainable basis. The advancement of molecular genetics and related technologies are promising tools for the selection of new crop species. Gene pyramiding through marker-assisted selection (MAS) and other techniques have accelerated the development of durable resistant/tolerant lines with high accuracy in the shortest period of time for agricultural sustainability. Gene stacking has not been fully utilized for biotic stress resistance development and quality improvement in most of the major cultivated crops. This review emphasizes on gene pyramiding techniques that are being successfully deployed in modern agriculture for improving crop tolerance to biotic and abiotic stresses for sustainable crop improvement.

Genome-Edited Triple-Recessive Mutation Alters Seed Dormancy in Wheat

Common wheat has three sets of sub-genomes, making mutations difficult to observe, especially for traits controlled by recessive genes. Here, we produced hexaploid wheat lines with loss of function of homeoalleles of Qsd1, which controls seed dormancy in barley, by Agrobacterium-mediated CRISPR/Cas9. Of the eight transformed wheat events produced, three independent events carrying multiple mutations in wheat Qsd1 homeoalleles were obtained. Notably, one line had mutations in every homeoallele. We crossed this plant with wild-type cultivar Fielder to generate a transgene-free triple-recessive mutant, as revealed by Mendelian segregation. The mutant showed a significantly longer seed dormancy period than wild-type, which may result in reduced pre-harvest sprouting of grains on spikes. PCR, southern blotting, and whole-genome shotgun sequencing revealed that this segregant lacked transgenes in its genomic sequence. This technique serves as a model for trait improvement in wheat, particularly for genetically recessive traits, based on locus information from diploid barley.

Plant Genome Editing and the Relevance of Off-Target Changes

Site-directed nucleases (SDNs) used for targeted genome editing are powerful new tools to introduce precise genetic changes into plants. Like traditional approaches, such as conventional crossing and induced mutagenesis, genome editing aims to improve crop yield and nutrition. Next-generation sequencing studies demonstrate that across their genomes, populations of crop species typically carry millions of single nucleotide polymorphisms and many copy number and structural variants. Spontaneous mutations occur at rates of ∼10-8 to 10-9 per site per generation, while variation induced by chemical treatment or ionizing radiation results in higher mutation rates. In the context of SDNs, an off-target change or edit is an unintended, nonspecific mutation occurring at a site with sequence similarity to the targeted edit region. SDN-mediated off-target changes can contribute to a small number of additional genetic variants compared to those that occur naturally in breeding populations or are introduced by induced-mutagenesis methods. Recent studies show that using computational algorithms to design genome editing reagents can mitigate off-target edits in plants. Finally, crops are subject to strong selection to eliminate off-type plants through well-established multigenerational breeding, selection, and commercial variety development practices. Within this context, off-target edits in crops present no new safety concerns compared to other breeding practices. The current generation of genome editing technologies is already proving useful to develop new plant varieties with consumer and farmer benefits. Genome editing will likely undergo improved editing specificity along with new developments in SDN delivery and increasing genomic characterization, further improving reagent design and application.

Biotechnological Exploration of Transformed Root Culture for Value-Added Products

Medicinal plants produce valuable secondary metabolites with anticancer, analgesic, anticholinergic or other activities, but low metabolite levels and limited available tissue restrict metabolite yields. Transformed root cultures, also called hairy roots, provide a feasible approach for producing valuable secondary metabolites. Various strategies have been used to enhance secondary metabolite production in hairy roots, including increasing substrate availability, regulating key biosynthetic genes, multigene engineering, combining genetic engineering and elicitation, using transcription factors (TFs), and introducing new genes. In this review, we focus on recent developments in hairy roots from medicinal plants, techniques to boost production of desired secondary metabolites, and the development of new technologies to study these metabolites. We also discuss recent trends, emerging applications, and future perspectives.

In planta particle bombardment (iPB): A new method for plant transformation and genome editing

Transformation is a key step in modern breeding technology that involves genome editing. The requirement for in vitro tissue culture and regeneration hampers application of this technology to commercially important varieties of many crop species. To overcome this problem, we developed a simple and reproducible in planta transformation method in wheat (Tritticum aestivum L.). Our in planta particle bombardment (iPB) method utilizes the shoot apical meristem (SAM) as a target tissue. The SAM contains a subepidermal cell layer termed L2, from which germ cells later develop during floral organogenesis. The iPB method can also be used for genome editing through transient CRISPR/Cas9 expression or direct delivery of the CRISPR/Cas9 ribonucleoprotein. In this review, we describe the iPB technology and provide an overview of its current and future applications in plant transformation and genome editing.

Advances in studies on ion transporters involved in salt tolerance and breeding crop cultivars with high salt tolerance

Soil salinity is a global major abiotic stress threatening crop productivity. In salty conditions, plants may suffer from osmotic, ionic, and oxidative stresses, resulting in inhibition of growth and development. To deal with these stresses, plants have developed a series of tolerance mechanisms, including osmotic adjustment through accumulating compatible solutes in the cytoplasm, reactive oxygen species (ROS) scavenging through enhancing the activity of anti-oxidative enzymes, and Na+/K+ homeostasis regulation through controlling Na+ uptake and transportation. In this review, recent advances in studies of the mechanisms of salt tolerance in plants are described in relation to the ionome, transcriptome, proteome, and metabolome, and the main factor accounting for differences in salt tolerance among plant species or genotypes within a species is presented. We also discuss the application and roles of different breeding methodologies in developing salt-tolerant crop cultivars. In particular, we describe the advantages and perspectives of genome or gene editing in improving the salt tolerance of crops.

CRISPR-Cas9-mediated induction of heritable chromosomal translocations in Arabidopsis

Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein (Cas) technology has been applied in plant breeding mainly on genes for improving single or multiple traits^1-4. Here we show that this technology can also be used to restructure plant chromosomes. Using the Cas9 nuclease from Staphylococcus aureus⁵, we were able to induce reciprocal translocations in the Mbp range between heterologous chromosomes in Arabidopsis thaliana. Of note, translocation frequency was about five times more efficient in the absence of the classical non-homologous end-joining pathway. Using egg-cell-specific expression of the Cas9 nuclease and consecutive bulk screening, we were able to isolate heritable events and establish lines homozygous for the translocation, reaching frequencies up to 2.5% for individual lines. Using molecular and cytological analysis, we confirmed that the chromosome-arm exchanges we obtained between chromosomes 1 and 2 and between chromosomes 1 and 5 of Arabidopsis were conservative and reciprocal. The induction of chromosomal translocations enables mimicking of genome evolution or modification of chromosomes in a directed manner, fixing or breaking genetic linkages between traits on different chromosomes. Controlled restructuring of plant genomes has the potential to transform plant breeding.

Investigation of CRISPR/Cas9-induced SD1 rice mutants highlights the importance of molecular characterization in plant molecular breeding

Although Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated 9 (Cas9) system has been widely used for basic research in model plants, its application for applied breeding in crops has faced strong regulatory obstacles, due mainly to a poor understanding of the authentic output of this system, particularly in higher generations. In this study, different from any previous studies, we investigated in detail the molecular characteristics and production performance of CRISPR/Cas9-generated SD1 (semi-dwarf 1) mutants from T₂ to T₄ generations, of which the selection of T₁ and T₂ was done only by visual phenotyping for semidwarf plants. Our data revealed not only on- and off-target mutations with small or lager indels but also exogenous elements in T₂ plants. All indel mutants passed stably to T₃ or T₄ without additional modifications independent on the presence of Cas9, while some lines displayed unexpected hereditary patterns of Cas9 or some exogenous elements. In addition, effects of various SD1 alleles on rice height and yield differed depending on genetic backgrounds. Taken together, our data showed that the CRISPR/Cas9 system is effective in producing homozygous mutants for functional analysis, but it may be not as precise as expected in rice, and that early and accurate molecular characterization and screening must be carried out for generations before transitioning of the CRISPR/Cas9 system from laboratory to field.

Genome optimization for improvement of maize breeding

We propose a new model to improve maize breeding that incorporates doubled haploid production, genomic selection, and genome optimization. Breeding 4.0 has been considered the next era of plant breeding. It is clear that the Breeding 4.0 era for maize will feature the integration of multi-disciplinary technologies including genomics and phenomics, gene editing and synthetic biology, and Big Data and artificial intelligence. The breeding approach of passively selecting ideal genotypes from designated genetic pools must soon evolve to virtual design of optimized genomes by pyramiding superior alleles using computational simulation. An optimized genome expressing optimal phenotypes, which may never actually be created, can function as a blueprint for breeding programs to use minimal materials and hybridizations to achieve maximum genetic gain. We propose a new breeding pipeline, "genomic design breeding," that incorporates doubled haploid production, genomic selection, and genome optimization and is facilitated by different scales of trait predictions and decision-making models. Successful implementation of the proposed model will facilitate the evolution of maize breeding from "art" to "science" and eventually to "intelligence," in the Breeding 4.0 era.

CCT domain-containing genes in cereal crops: flowering time and beyond

The review summarizes the functions of the plant special transcription factors CCT family genes in multiple traits and discusses the molecular breeding strategies with CCT family genes in the future. Plants integrate circadian clock and external signals such as temperature and photoperiod to synchronize flowering with seasonal environmental changes. This process makes cereal crops including short-day crops, such as rice and maize, and long-day crops, such as wheat and barley, better adapt to varied growth zones from temperate to tropical regions. CCT family genes involve circadian clock and photoperiodic flowering pathways and help plants set a suitable flowering time to produce offspring. Beyond the flowering time, CCT family genes in cereal crops are associated with biomass and grain yield. Moreover, recent studies showed that they also associate with photosynthesis, nutrition use efficiency and stress tolerance. Here, we systematically review the progress in functional characterization of CCT family genes in flowering, geographical adaptation and grain yield formation, raise the core questions related to their molecular mechanisms and discuss how to practice them in genetic improvement in cereal crops by combining gene diagnosis and top-level design.

Base Editing: The Ever Expanding Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) Tool Kit for Precise Genome Editing in Plants

Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9), a newly developed genome-editing tool, has revolutionized animal and plant genetics by facilitating modification of target genes. This simple, convenient base-editing technology was developed to improve the precision of genome editing. Base editors generate precise point mutations by permanent base conversion at a specific point, with very low levels of insertions and deletions. Different plant base editors have been established by fusing various nucleobase deaminases with Cas9, Cas13, or Cas12a (Cpf1), proteins. Adenine base editors can efficiently convert adenine (A) to guanine (G), whereas cytosine base editors can convert cytosine (C) to thymine (T) in the target region. RNA base editors can induce a base substitution of A to inosine (I) or C to uracil (U). In this review, we describe the precision of base editing systems and their revolutionary applications in plant science; we also discuss the limitations and future perspectives of this approach.

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

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.

Simplified adenine base editors improve adenine base editing efficiency in rice

Adenine base editors (ABEs) have been exploited to introduce targeted adenine (A) to guanine (G) base conversions in various plant genomes, including rice, wheat and Arabidopsis. However, the ABEs reported thus far are all quite inefficient at many target sites in rice, which hampers their applications in plant genome engineering and crop breeding. Here, we show that unlike in the mammalian system, a simplified base editor ABE-P1S (Adenine Base Editor-Plant version 1 Simplified) containing the ecTadA*7.10-nSpCas9 (D10A) fusion has much higher editing efficiency in rice compared to the widely used ABE-P1 consisting of the ecTadA-ecTadA*7.10-nSpCas9 (D10A) fusion. We found that the protein expression level of ABE-P1S is higher than that of ABE-P1 in rice calli and protoplasts, which may explain the higher editing efficiency of ABE-P1S in different rice varieties. Moreover, we demonstrate that the ecTadA*7.10-nCas9 fusion can be used to improve the editing efficiency of other ABEs containing SaCas9 or the engineered SaKKH-Cas9 variant. These more efficient ABEs will help advance trait improvements in rice and other crops.

Efficient induction of haploid plants in wheat by editing of TaMTL using an optimized Agrobacterium-mediated CRISPR system

The use of CRISPR/LbCpf1 and CRISPR/xCas9 systems in wheat have not yet been reported. In this study, we compared the efficiencies of three CRISPR editing systems (SpCas9, LbCpf1, and xCas9), and three different promoters (OsU6a, TaU3, and TaU6) that drive single-guide (sg)RNA, which were introduced into wheat via Agrobacterium-mediated transformation. The results indicated that TaU3 was a better choice than OsU6a or TaU6. The editing efficiency was higher using two sgRNAs than one sgRNA, and mutants with a large fragment deletion between the two sgRNAs were produced. The LbCpf1 and xCas9 systems could both be used successfully. Two endogenous genes, TaWaxy and TaMTL, were edited with high efficiency by the optimized SpCas9 system, with the highest efficiency (80.5%) being achieved when using TaU3 and two sgRNAs to target TaWaxy. Rates of seed set in the TaMTL-edited T0 transgenic plants were much lower than that of the wild-type. A haploid induction rate of 18.9% was found in the TaMTL-edited T1 plants using the CRISPR/SpCas9 system. Mutants with reverse insertion of the deleted sequences of TaMTL and TaWaxy between the two sgRNAs were identified in the edited T0 plants. In addition, wheat grains lacking embryos or endosperms were observed in the TaMTL-edited T1 generation.

Principles, Applications, and Biosafety of Plant Genome Editing Using CRISPR-Cas9

The terms genome engineering, genome editing, and gene editing, refer to modifications (insertions, deletions, substitutions) in the genome of a living organism. The most widely used approach to genome editing nowadays is based on Clustered Regularly Interspaced Short Palindromic Repeats and associated protein 9 (CRISPR-Cas9). In prokaryotes, CRISPR-Cas9 is an adaptive immune system that naturally protects cells from DNA virus infections. CRISPR-Cas9 has been modified to create a versatile genome editing technology that has a wide diversity of applications in medicine, agriculture, and basic studies of gene functions. CRISPR-Cas9 has been used in a growing number of monocot and dicot plant species to enhance yield, quality, and nutritional value, to introduce or enhance tolerance to biotic and abiotic stresses, among other applications. Although biosafety concerns remain, genome editing is a promising technology with potential to contribute to food production for the benefit of the growing human population. Here, we review the principles, current advances and applications of CRISPR-Cas9-based gene editing in crop improvement. We also address biosafety concerns and show that humans have been exposed to Cas9 protein homologues long before the use of CRISPR-Cas9 in genome editing.

The coding loci of evolution and domestication: current knowledge and implications for bio-inspired genome editing

One promising application of CRISPR/Cas9 is to create targeted mutations to introduce traits of interest into domesticated organisms. However, a major current limitation for crop and livestock improvement is to identify the precise genes and genetic changes that must be engineered to obtain traits of interest. Here, we discuss the advantages of bio-inspired genome editing, i.e. the engineered introduction of natural mutations that have already been associated with traits of interest in other lineages (breeds, populations or species). To obtain a landscape view of potential targets for genome editing, we used Gephebase (www.gephebase.org), a manually curated database compiling published data about the genes responsible for evolutionary and domesticated changes across eukaryotes, and examined the >1200 mutations that have been identified in the coding regions of more than 700 genes in animals, plants and yeasts. We observe that our genetic knowledge is relatively important for certain traits, such as xenobiotic resistance, and poor for others. We also note that protein-null alleles, often owing to nonsense and frameshift mutations, represent a large fraction of the known loci of domestication (42% of identified coding mutations), compared with intraspecific (27%) and interspecific evolution (11%). Although this trend may be subject to detection, publication and curation biases, it is consistent with the idea that breeders have selected large-effect mutations underlying adaptive traits in specific settings, but that these mutations and associated phenotypes would not survive the vagaries of changing external and internal environments. Our compilation of the loci of evolution and domestication uncovers interesting options for bio-inspired and transgene-free genome editing.

From gene editing to genome engineering: restructuring plant chromosomes via CRISPR/Cas

In the last years, tremendous progress has been achieved in the field of gene editing in plants. By the induction of single site-specific double-strand breaks (DSBs), the knockout of genes by non-homologous end joining has become routine in many plant species. Recently, the efficiency of inducing pre-planned mutations by homologous recombination has also been improved considerably. However, very little effort has been undertaken until now to achieve more complex changes in plant genomes by the simultaneous induction of several DSBs. Several reports have been published on the efficient induction of deletions. However, the induction of intrachromosomal inversions and interchromosomal recombination by the use of CRISPR/Cas has only recently been reported. In this review, we want to sum up these results and put them into context with regards to what is known about natural chromosome rearrangements in plants. Moreover, we review the recent progress in CRISPR/Cas-based mammalian chromosomal rearrangements, which might be inspiring for plant biologists. In the long run, the controlled restructuring of plant genomes should enable us to link or break linkage of traits at will, thus defining a new area of plant breeding.

Establishment of nDart1-tagged lines of Koshihikari, an elite variety of rice in Japan

To utilize a transposon-tagged mutant as a breeding material in rice, an endogenous DNA transposon, nDart1-0, was introduced into Koshihikari by successive backcrossing together with aDart1-27, an active autonomous element. The founder line for nDart1-tagged lines of Koshihikari carried nDart1-0 on chromosome 9 and transposed nDart1-12s on chromosomes 1 and 8 and nDart1-3 on chromosome 11. In nDart1-tagged lines, there were the most abnormal phenotypic mutants and many aberrant chlorophyll mutants at seedling stage. At mature stage, many semi-sterile mutants were observed. Dwarf, reduced culm number and lesion mimic mutants were also found. In total, 43.2% of the lines segregated some phenotypic mutants. Thus, the nDart1-tagged lines of Koshihikari are expected to be potentially useful for screening stress-tolerant mutants under abiotic or biotic stress conditions.

Directed Evolution of Plant Processes: Towards a Green (r)Evolution?

Directed evolution (DE) is a powerful approach for generating proteins with new chemical and physical properties. It mimics the principles of Darwinian evolution by imposing selective pressure on a large population of molecules harboring random genetic variation in DNA, such that sequences with specific desirable properties are generated and selected. We propose that combining DE and genome-editing (DE-GE) technologies represents a powerful tool to discover and integrate new traits into plants for agronomic and biotechnological gain. DE-GE has the potential to deliver a new green (r)evolution research platform that can provide novel solutions to major trait delivery aspirations for sustainable agriculture, climate-resilient crops, and improved food security and nutritional quality.

CRISPR/Cas brings plant biology and breeding into the fast lane

CRISPR/Cas is in the process of inducing the biggest transformation of plant breeding since the green revolution. Whereas initial efforts focused mainly on changing single traits by error prone non-homologous end joining, the last two years saw a tremendous technical progress achieving more complex genetic, epigenetic and transcriptional changes. The efficiencies of inducing directed changes by homologous recombination have been improved significantly and strategies to break genetic linkages by inducing chromosomal rearrangements have been developed. Cas13 systems have been applied to degrade viral and mRNA in plants. Most importantly, a historical breakthrough was accomplished: By introducing multiple genomic changes simultaneously, domestication of wild species in a single generation has been demonstrated, speeding up breeding dramatically.

Genetic dissection of drought and heat-responsive agronomic traits in wheat

High yield and wide adaptation are principal targets of wheat breeding but are hindered by limited knowledge on genetic basis of agronomic traits and abiotic stress tolerances. In this study, 277 wheat accessions were phenotyped across 30 environments with non-stress, drought-stressed, heat-stressed, and drought-heat-stressed treatments and were subjected to genome-wide association study using 395 681 single nucleotide polymorphisms. We detected 295 associated loci including consistent loci for agronomic traits across different treatments and eurytopic loci for multiple abiotic stress tolerances. A total of 22 loci overlapped with quantitative trait loci identified by biparental quantitative trait loci mapping. Six loci were simultaneously associated with agronomic traits and abiotic stress tolerance, four of which fell within selective sweep regions. Selection in Chinese wheat has increased the frequency of superior marker alleles controlling yield-related traits in the four loci during past decades, which conversely diminished favourable genetic variation controlling abiotic stress tolerance in the same loci; two promising candidate paralogous genes colocalized with such loci, thereby providing potential targets for studying the molecular mechanism of stress tolerance-productivity trade-off. These results uncovering promising alleles controlling agronomic traits and/or multiple abiotic stress tolerances, providing insights into heritable covariation between yield and abiotic stress tolerance, will accelerate future efforts for wheat improvement.

Perspectives on the Application of Genome-Editing Technologies in Crop Breeding

Most conventional and modern crop-improvement methods exploit natural or artificially induced genetic variations and require laborious characterization of the progenies of multiple generations derived from time-consuming genetic crosses. Genome-editing systems, in contrast, provide the means to rapidly modify genomes in a precise and predictable way, making it possible to introduce improvements directly into elite varieties. Here, we describe the range of applications available to agricultural researchers using existing genome-editing tools. In addition to providing examples of genome-editing applications in crop breeding, we discuss the technical and social challenges faced by breeders using genome-editing tools for crop improvement.

The emerging and uncultivated potential of CRISPR technology in plant science

The application of clustered regularly interspaced short palindromic repeats (CRISPR) for genetic manipulation has revolutionized life science over the past few years. CRISPR was first discovered as an adaptive immune system in bacteria and archaea, and then engineered to generate targeted DNA breaks in living cells and organisms. During the cellular DNA repair process, various DNA changes can be introduced. The diverse and expanding CRISPR toolbox allows programmable genome editing, epigenome editing and transcriptome regulation in plants. However, challenges in plant genome editing need to be fully appreciated and solutions explored. This Review intends to provide an informative summary of the latest developments and breakthroughs of CRISPR technology, with a focus on achievements and potential utility in plant biology. Ultimately, CRISPR will not only facilitate basic research, but also accelerate plant breeding and germplasm development. The application of CRISPR to improve germplasm is particularly important in the context of global climate change as well as in the face of current agricultural, environmental and ecological challenges.

Source-Sink Regulation in Crops under Water Deficit

To meet the food demands of an increasing world population, it is necessary to improve crop production; a task that is made more challenging by the changing climate. Several recent reports show that increasing the capacity of plants to assimilate carbon (source strength), or to tap into the internal carbon reservoir (sink strength), has the potential to improve plant productivity in the field under water-deficit conditions. Here, we review the effects of water deficit on the source-sink communication, as well as the respective regulatory mechanisms underpinning plant productivity. We also highlight stress-tolerant traits that can contribute to harness source and sink strengths towards producing high-yielding and drought-tolerant crops, depending on the drought scenario.

De Novo Domestication: An Alternative Route toward New Crops for the Future

Current global agricultural production must feed over 7 billion people. However, productivity varies greatly across the globe and is under threat from both increased competitions for land and climate change and associated environmental deterioration. Moreover, the increase in human population size and dietary changes are putting an ever greater burden on agriculture. The majority of this burden is met by the cultivation of a very small number of species, largely in locations that differ from their origin of domestication. Recent technological advances have raised the possibility of de novo domestication of wild plants as a viable solution for designing ideal crops while maintaining food security and a more sustainable low-input agriculture. Here we discuss how the discovery of multiple key domestication genes alongside the development of technologies for accurate manipulation of several target genes simultaneously renders de novo domestication a route toward crops for the future.

Plant breeding at the speed of light: the power of CRISPR/Cas to generate directed genetic diversity at multiple sites

Classical plant breeding was extremely successful in generating high yielding crop varieties. Yet, in modern crops, the long domestication process has impoverished the genetic diversity available for breeding. This is limiting further improvements of elite germplasm by classical approaches. The CRISPR/Cas system now enables promising new opportunities to create genetic diversity for breeding in an unprecedented way. Due to its multiplexing ability, multiple targets can be modified simultaneously in an efficient way, enabling immediate pyramiding of multiple beneficial traits into an elite background within one generation. By targeting regulatory elements, a selectable range of transcriptional alleles can be generated, enabling precise fine-tuning of desirable traits. In addition, by targeting homologues of so-called domestication genes within one generation, it is now possible to catapult neglected, semi-domesticated and wild plants quickly into the focus of mainstream agriculture. This further enables the use of the enormous genetic diversity present in wild species or uncultured varieties of crops as a source of allele-mining, widely expanding the crop germplasm pool.

Proposed U.S. regulation of gene-edited food animals is not fit for purpose

Dietary DNA is generally regarded as safe to consume, and is a routine ingredient of food obtained from any living organism. Millions of naturally-occurring DNA variations are observed when comparing the genomic sequence of any two healthy individuals of a given species. Breeders routinely select desired traits resulting from this DNA variation to develop new cultivars and varieties of food plants and animals. Regulatory agencies do not evaluate these new varieties prior to commercial release. Gene editing tools now allow plant and animal breeders to precisely introduce useful genetic variation into agricultural breeding programs. The U.S. Department of Agriculture (USDA) announced that it has no plans to place additional regulations on gene-edited plants that could otherwise have been developed through traditional breeding prior to commercialization. However, the U.S. Food and Drug Administration (FDA) has proposed mandatory premarket new animal drug regulatory evaluation for all food animals whose genomes have been intentionally altered using modern molecular technologies including gene editing technologies. This runs counter to U.S. biotechnology policy that regulatory oversight should be triggered by unreasonable risk, and not by the fact that an organism has been modified by a particular process or technique. Breeder intention is not associated with product risk. Harmonizing the regulations associated with gene editing in food species is imperative to allow both plant and animal breeders access to gene editing tools to introduce useful sustainability traits like disease resistance, climate adaptability, and food quality attributes into U.S. agricultural breeding programs.