TALEN-Based Mutagenesis of Lipoxygenase LOX3 Enhances the Storage Tolerance of Rice (Oryza sativa) Seeds

Lipoxygenases (LOXs): Will turning off this genetic switch help safeguard the flavor and nutritional quality of stored lipid-rich staple foods?

Beyond storage capacity, long-term grain storage faces significant challenges due to the activity of lipoxygenases (LOXs). These enzymes catalyze the production of volatiles from free fatty acids, leading to stale odors and off-flavors. These changes degrade the quality of stored grains, even under regulated conditions, affecting the profitability of stored products to the farmers and the assurance of high-quality food for consumers. While LOXs are essential for various biological functions, their impact on storage highlights the need for targeted research to mitigate their negative effects. Optimizing LOX activity could enhance grain storability, reduce spoilage, and improve nutrient retention. This review explores recent advancements in understanding the roles of LOXs, focusing on how they can be tailored to enhance nutritional quality and shelf life. By modulating LOX activity, it is possible to address quality deterioration, support more sustainable food systems, and contribute to better nutritional security for consumers.

Directed mutagenesis in fruit crops

Fruit crops are rich source of important vitamins, minerals, and dietary fibres. They are essential for global agriculture with respect to nutritional security. Globally, there is a rapid decline in the genetic base of fruit crops warranting breeding strategies to overcome the challenge. Applied mutagenesis has emerged as a viable approach for the focused enhancement of fruit crops utilizing precise genetic alterations to increase a variety of desirable characteristics. However, traditional mutagenesis using physical and chemical mutagens are majorly random in nature. Directed mutagenesis with advancements in genetic engineering and molecular technology allows precise manipulation of genes, which facilitates the efficient and precise knockout of target genes and the targeted insertion or modification of specific DNA sequences within the genome via homologous recombination (HR)-mediated gene replacement. This review presents an in-depth exploration of several directed mutagenesis techniques including CRISPR-Cas9, TILLING, TALEN, MutMap, and MutMap + emphasizing their transformative applications in fruit crops. It also discusses about space mutagenesis. These advanced techniques empower researchers to precisely introduce specific mutations into the genome, skilfully altering gene expression and reshaping protein function with remarkable precision. This review highlights successful examples of directed mutagenesis in a variety of fruit crops such as apples, grapes, citrus, and strawberries and elucidates the impact of directed mutagenesis on traits such as fruit size, colour, flavour, shelf-life, and resistance to diseases and environmental stresses.

OsLOX1 positively regulates seed vigor and drought tolerance in rice

The lipoxygenase (LOX) gene family is widely distributed in plants, and its activity is closely associated with seed viability and stress tolerance. In this study, we cloned the rice(Oryza sativa)lipoxygenase gene OsLOX1, a key participant in the 13-lipoxygenase metabolic pathway. Our primary focus was to investigate its role in mediating responses to drought stress and seed germination in rice. Histochemical staining and qPCR analysis indicated that the expression level of OsLOX1 was relatively high in leaves and early germinating seeds. Our findings revealed that mutant lines with CRISPR/Cas9-induced knockout of OsLOX1 exhibited reduced tolerance to drought stress compared with the wild-type. This was accompanied by elevated levels of H2O2 and malondialdehyde, and a decrease in the expression levels of genes associated with antioxidant enzymes. Furthermore, knockout of OsLOX1 reduced the longevity of rice seeds increased H2O2 and MDA levels, and decreased the activities of the antioxidant enzymes superoxide dismutase and catalase, compared with the wild-type. These findings demonstrated that OsLOX1 positively regulated rice seed vigor and drought stress.

Rice seed storability: From molecular mechanisms to agricultural practices

The storability of rice seeds is crucial for ensuring flexible planting options, agricultural seed security, and global food safety. With the intensification of global climate change and the constant fluctuations in agricultural production conditions, enhancing the storability of rice seeds has become particularly important. Seed storability is a complex quantitative trait regulated by both genetic and environmental factors. This article reviews the main regulatory mechanisms of rice seed storability, including the accumulation of seed storage proteins, late embryogenesis abundant (LEA) proteins, heat shock proteins, sugar signaling, hormonal regulation by gibberellins and abscisic acid, and the role of the ubiquitination pathway. Additionally, this article explores the improvement of storability using wild rice genes, molecular marker-assisted selection, and gene editing techniques such as CRISPR/Cas9 in rice breeding. By providing a comprehensive scientific foundation and practical guidance, this review aims to promote the development of rice varieties with enhanced storability to meet evolving agricultural demands.

Prolongation of seed viability and grain quality in rice by editing OsLOX1 using CRISPR/Cas9

Deterioration of rice (Oryza sativa L.) affects grain quality and seed viability during storage. Lipoxygenase (LOX), a key enzyme in lipid metabolism, directly affects the rate of ageing. Here, we found that knock-out of lipoxygenase gene OsLOX1 by CRISPR/Cas9 delayed loss of seed viability and quality. Transcriptome analysis showed that during storage, OsLOX1 affected transcription of multiple genes, including genes related to lipid metabolism and antioxidant pathways such as phosphatase and acetaldehyde dehydrogenase, which may regulate the seed storability. The genes significantly down- and up-regulated only in Ningjing 4 after NA for 13 months and 3 days of AA suggesting that OsLOX1 likely promoted seed viability in rice by balancing ageing and storage related genes, and regulated the seed storability through the amino acid synthesis and metabolic pathways. Moreover, knock-out of OsLOX1 without CRISPR/Cas9 not only improved the seed viability, but also had little impact on agronomic traits. More importantly, the OsLOX1 knock-out lines were approved in 2019 (Agricultural Foundation of China Report No. 770). Collectively, our study showed that knock-out of OsLOX1 is beneficial for prolongation of seed viability and can be directly applied to agricultural production.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-024-01506-4.

Advancing crop disease resistance through genome editing: a promising approach for enhancing agricultural production

Modern agriculture has encountered several challenges in achieving constant yield stability especially due to disease outbreaks and lack of long-term disease-resistant crop cultivars. In the past, disease outbreaks in economically important crops had a major impact on food security and the economy. On the other hand climate-driven emergence of new pathovars or changes in their host specificity further poses a serious threat to sustainable agriculture. At present, chemical-based control strategies are frequently used to control microbial pathogens and pests, but they have detrimental impact on the environment and also resulted in the development of resistant phyto-pathogens. As a replacement, cultivating engineered disease-resistant crops can help to minimize the negative impact of regular pesticides on agriculture and the environment. Although traditional breeding and genetic engineering have been instrumental in crop disease improvement but they have certain limitations such as labour intensity, time consumption, and low efficiency. In this regard, genome editing has emerged as one of the potential tools for improving disease resistance in crops by targeting multiple traits with more accuracy and efficiency. For instance, genome editing techniques, such as CRISPR/Cas9, CRISPR/Cas13, base editing, TALENs, ZFNs, and meganucleases, have proved successful in improving disease resistance in crops through targeted mutagenesis, gene knockouts, knockdowns, modifications, and activation of target genes. CRISPR/Cas9 is unique among these techniques because of its remarkable efficacy, low risk of off-target repercussions, and ease of use. Some primary targets for developing CRISPR-mediated disease-resistant crops are host-susceptibility genes (the S gene method), resistance genes (R genes) and pathogen genetic material that prevents their development, broad-spectrum disease resistance. The use of genome editing methods has the potential to notably ameliorate crop disease resistance and transform agricultural practices in the future. This review highlights the impact of phyto-pathogens on agricultural productivity. Next, we discussed the tools for improving disease resistance while focusing on genome editing. We provided an update on the accomplishments of genome editing, and its potential to improve crop disease resistance against bacterial, fungal and viral pathogens in different crop systems. Finally, we highlighted the future challenges of genome editing in different crop systems for enhancing disease resistance.

Study on peanut protein oxidation and metabolomics/proteomics analysis of peanut response under hypoxic/re-aeration storage

To better understand the effect of oxygen levels in the storage environment on peanut protein oxidation and explore the mechanism, the functional properties and the oxidation degree of peanut proteins extracted from peanuts under conventional storage (CS), nitrogen modified atmosphere storage (NS, hypoxic) and re-aeration storage (RS) were investigated. Metabolomics and proteomics were employed to analyze peanut's response to hypoxic/re-aeration storage environment. The results showed that NS retarded the decline of the functional properties and the oxidation of peanut proteins, while the process were accelerated after re-aeration. That was the result of the metabolic changes of peanuts under different storage environments. The omics results presented the decreased (NS)/increased (RS) levels of the antioxidant-related proteins acetaldehyde dehydrogenase and glutathione S-transferase, and the inhibition (NS)/activation (RS) of metabolic pathways such as the TCA cycle and the pentose phosphate pathway. This study provided a reference for the re-aeration storage of other agricultural products.

Smart reprograming of plants against salinity stress using modern biotechnological tools

Climate change gives rise to numerous environmental stresses, including soil salinity. Salinity/salt stress is the second biggest abiotic factor affecting agricultural productivity worldwide by damaging numerous physiological, biochemical, and molecular processes. In particular, salinity affects plant growth, development, and productivity. Salinity responses include modulation of ion homeostasis, antioxidant defense system induction, and biosynthesis of numerous phytohormones and osmoprotectants to protect plants from osmotic stress by decreasing ion toxicity and augmented reactive oxygen species scavenging. As most crop plants are sensitive to salinity, improving salt tolerance is crucial in sustaining global agricultural productivity. In response to salinity, plants trigger stress-related genes, proteins, and the accumulation of metabolites to cope with the adverse consequence of salinity. Therefore, this review presents an overview of salinity stress in crop plants. We highlight advances in modern biotechnological tools, such as omics (genomics, transcriptomics, proteomics, and metabolomics) approaches and different genome editing tools (ZFN, TALEN, and CRISPR/Cas system) for improving salinity tolerance in plants and accomplish the goal of "zero hunger," a worldwide sustainable development goal proposed by the FAO.

Rice lipases: a conundrum in rice bran stabilization: a review on their impact and biotechnological interventions

Rice is a primary food and is one of the most important constituents of diets all around the world. Rice bran is a valuable component of rice, containing many oil-soluble vitamins, minerals, and oil. It is known for its ability to improve the economic value of rice. Further, it contains substantial quantities of minerals like potassium, calcium, magnesium, iron and antioxidants like tocopherols, tocotrienols, and γ-oryzanol, indicating that rice bran can be utilized effectively against several life-threatening disorders. It is difficult to fully utilize the necessary nutrients due to the presence of lipases in rice bran. These lipases break down lipids, specifically Triacylglycerol, into free fatty acids and glycerol. This review discusses physicochemical properties, mechanism of action, distribution, and activity of lipases in various components of rice seeds. The phylogenetic and gene expression analysis helped to understand the differential expression pattern of lipase genes at different growth phases of rice plant. Further, this review discusses various genetic and biotechnological approaches to decrease lipase activity in rice and other plants, which could potentially prevent the degradation of bran oil. The goal is to establish whether lipases are a major contributor to this issue and to develop rice varieties with improved bran stability. This information sets the stage for upcoming molecular research in this area.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01343-3.

Genome-wide identification and expression pattern analysis of lipoxygenase genes of chickpea (Cicer arietinum L.) in response to accelerated aging

Seed aging is a major problem which is caused by various factors such as unfavorable physiological, biochemical, and metabolic alterations in seed cells. Lipoxygenase (LOXs), an oxidoreductase enzyme that catalyzes the oxidation of polyunsaturated fatty acids, acts as a negative regulator in seed viability and vigour during storage. In this study, we identified ten putative LOX gene family members in the chickpea genome, designated as "CaLOX" which are mainly located in the cytoplasm and chloroplast. These genes share different physiochemical properties and similarities in their gene structures and conserved functional regions. The promoter region contained the cis-regulatory elements and transcription binding factors, which were mainly linked to biotic and abiotic stress, hormones, and light responsiveness. In this study, chickpea seeds were treated with accelerated aging treatment for 0, 2, and 4 days at 45°C and 85 % relative humidity. Increased level of reactive oxygen species, malondialdehyde, electrolyte leakage, proline, lipoxygenase (LOX) activity, and decreased catalase activity indicates cellular dysfunction and demonstrated seed deterioration. Quantitative real-time analysis reveals that 6 CaLOX genes were upregulated, and 4 CaLOX genes were downregulated during the seed aging process in chickpea. This comprehensive study will reveal the role of the CaLOX gene in response to aging treatment. The identified gene may be used to develop better-quality seeds in chickpea.

Tailoring crops with superior product quality through genome editing: an update

In this review, using genome editing, the quality trait alterations in important crops have been discussed, along with the challenges encountered to maintain the crop products' quality. The delivery of economic produce with superior quality is as important as high yield since it dictates consumer's acceptance and end use. Improving product quality of various agricultural and horticultural crops is one of the important targets of plant breeders across the globe. Significant achievements have been made in various crops using conventional plant breeding approaches, albeit, at a slower rate. To keep pace with ever-changing consumer tastes and preferences and industry demands, such efforts must be supplemented with biotechnological tools. Fortunately, many of the quality attributes are resultant of well-understood biochemical pathways with characterized genes encoding enzymes at each step. Targeted mutagenesis and transgene transfer have been instrumental in bringing out desired qualitative changes in crops but have suffered from various pitfalls. Genome editing, a technique for methodical and site-specific modification of genes, has revolutionized trait manipulation. With the evolution of versatile and cost effective CRISPR/Cas9 system, genome editing has gained significant traction and is being applied in several crops. The availability of whole genome sequences with the advent of next generation sequencing (NGS) technologies further enhanced the precision of these techniques. CRISPR/Cas9 system has also been utilized for desirable modifications in quality attributes of various crops such as rice, wheat, maize, barley, potato, tomato, etc. The present review summarizes salient findings and achievements of application of genome editing for improving product quality in various crops coupled with pointers for future research endeavors.

Biotechnological interventions for improving the seed longevity in cereal crops: progress and prospects

Seed longevity is a measure of the viability of seeds during long-term storage and is crucial for germplasm conservation and crop improvement programs. Also, longevity is an important trait for ensuring food and nutritional security. Thus, a better understanding of various factors regulating seed longevity is requisite to improve this trait and to minimize the genetic drift during the regeneration of germplasm. In particular, seed deterioration of cereal crops during storage adversely affects agricultural productivity and food security. The irreversible process of seed deterioration involves a complex interplay between different genes and regulatory pathways leading to: loss of DNA integrity, membrane damage, inactivation of storage enzymes and mitochondrial dysfunction. Identifying the genetic determinants of seed longevity and manipulating them using biotechnological tools hold the key to ensuring prolonged seed storage. Genetics and genomics approaches had identified several genomic regions regulating the longevity trait in major cereals such as: rice, wheat, maize and barley. However, very few studies are available in other Poaceae members, including millets. Deploying omics tools, including genomics, proteomics, metabolomics, and phenomics, and integrating the datasets will pinpoint the precise molecular determinants affecting the survivability of seeds. Given this, the present review enumerates the genetic factors regulating longevity and demonstrates the importance of integrated omics strategies to dissect the molecular machinery underlying seed deterioration. Further, the review provides a roadmap for deploying biotechnological approaches to manipulate the genes and genomic regions to develop improved cultivars with prolonged storage potential.

Understanding of the various aspects of gene regulatory networks related to crop improvement

The hierarchical relationship between transcription factors, associated proteins, and their target genes is defined by a gene regulatory network (GRN). GRNs allow us to understand how the genotype and environment of a plant are incorporated to control the downstream physiological responses. During plant growth or environmental acclimatization, GRNs are diverse and can be differently regulated across tissue types and organs. An overview of recent advances in the development of GRN that speed up basic and applied plant research is given here. Furthermore, the overview of genome and transcriptome involving GRN research along with the exciting advancement and application are discussed. In addition, different approaches to GRN predictions were elucidated. In this review, we also describe the role of GRN in crop improvement, crop plant manipulation, stress responses, speed breeding and identifying genetic variations/locus. Finally, the challenges and prospects of GRN in plant biology are discussed.

Application of CRISPR-Mediated Gene Editing for Crop Improvement

Plant gene editing has become an important molecular tool to revolutionize modern breeding of crops. Over the past years, remarkable advancement has been made in developing robust and efficient editing methods for plants. Despite a variety of available genome editing methods, the discovery of most recent system of clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins (CRISPR-Cas) has been one of the biggest advancement in this path, with being the most efficient approach for genome manipulation. Until recently, genetic manipulations were confined to methods, like Agrobacterium-mediated transformations, zinc-finger nucleases, and TAL effector nucleases. However this technology supersedes all other methods for genetic modification. This RNA-guided CRISPR-Cas system is being rapidly developed with enhanced functionalities for better use and greater possibilities in biological research. In this review, we discuss and sum up the application of this simple yet powerful tool of CRISPR-Cas system for crop improvement with recent advancement in this technology.

Reverse genetic approaches for breeding nutrient-rich and climate-resilient cereal and food legume crops

In the last decade, advancements in genomics tools and techniques have led to the discovery of many genes. Most of these genes still need to be characterized for their associated function and therefore, such genes remain underutilized for breeding the next generation of improved crop varieties. The recent developments in different reverse genetic approaches have made it possible to identify the function of genes controlling nutritional, biochemical, and metabolic traits imparting drought, heat, cold, salinity tolerance as well as diseases and insect-pests. This article focuses on reviewing the current status and prospects of using reverse genetic approaches to breed nutrient-rich and climate resilient cereal and food legume crops.

Potential of Genome Editing to Capture Diversity From Australian Wild Rice Relatives

Rice, a staple food worldwide and a model crop, could benefit from the introduction of novel genetics from wild relatives. Wild rice in the AA genome group closely related to domesticated rice is found across the tropical world. Due to their locality outside the range of domesticated rice, Australian wild rice populations are a potential source of unique traits for rice breeding. These rice species provide a diverse gene pool for improvement that could be utilized for desirable traits such as stress resistance, disease tolerance, and nutritional qualities. However, they remain poorly characterized. The CRISPR/Cas system has revolutionized gene editing and has improved our understanding of gene functions. Coupled with the increasing availability of genomic information on the species, genes in Australian wild rice could be modified through genome editing technologies to produce new domesticates. Alternatively, beneficial alleles from these rice species could be incorporated into cultivated rice to improve critical traits. Here, we summarize the beneficial traits in Australian wild rice, the available genomic information and the potential of gene editing to discover and understand the functions of novel alleles. Moreover, we discuss the potential domestication of these wild rice species for health and economic benefits to rice production globally.

Identification, Analysis, and Confirmation of Seed Storability-Related Loci in Dongxiang Wild Rice (Oryza rufipogon Griff.)

Dongxiang wild rice (Oryza rufipogon Griff.) (DXWR) has strong seed storability and identifying its elite gene resources may facilitate genetic improvements in rice seed storability. In this study, we developed two backcross inbred lines (BILs) populations, with DXWR as a common donor parent and two rice varieties (F6 and R974) as recipient parents. Bulked segregant analysis via whole genome sequencing (BSA-seq) was used to identify seed storability-related loci in the DXWR and F6 population. Two main genomic regions containing 18,550,000–20,870,000 bp on chromosome 4 and 7,860,000–9,780,000 bp on chromosome 9 were identified as candidate loci of DXWR seed storability; these overlapped partially with seed storability-related quantitative trait loci (QTLs) discovered in previous studies, suggesting that these loci may provide important regions for isolating the responsible genes. In total, 448 annotated genes were predicted within the identified regions, of which 274 and 82 had nonsynonymous and frameshift mutations, respectively. We detected extensive metabolic activities and cellular processes during seed storability and confirmed the effects of the seed storability-related candidate loci using four BILs from DXWR and R974. These results may facilitate the cloning of DXWR seed storability-related genes, thereby elucidating rice seed storability and its improvement potential.

Quantitative Trait Locus Mapping of Seed Vigor in Soybean under -20 °C Storage and Accelerated Aging Conditions via RAD Sequencing

Due to its fast deterioration, soybean (Glycine max L.) has an inherently poor seed vigor. Vigor loss occurring during storage is one of the main obstacles to soybean production in the tropics. To analyze the genetic background of seed vigor, soybean seeds of a recombinant inbred line (RIL) population derived from the cross between Zhonghuang24 (ZH24, low vigor cultivar) and Huaxia3hao (HX3, vigorous cultivar) were utilized to identify the quantitative trait loci (QTLs) underlying the seed vigor under -20 °C conservation and accelerated aging conditions. According to the linkage analysis, multiple seed vigor-related QTLs were identified under both -20 °C and accelerated aging storage. Two major QTLs and eight QTL hotspots localized on chromosomes 3, 6, 9, 11, 15, 16, 17, and 19 were detected that were associated with seed vigor across two storage conditions. The indicators of seed vigor did not correlate well between the two aging treatments, and no common QTLs were detected in RIL populations stored in two conditions. These results indicated that deterioration under accelerated aging conditions was not reflective of natural aging at -20 °C. Additionally, we suggest 15 promising candidate genes that could possibly determine the seed vigor in soybeans, which would help explore the mechanisms responsible for maintaining high seed vigor.

Targeted genome modifications in cereal crops

The recent advent of customizable endonucleases has led to remarkable advances in genetic engineering, as these molecular scissors allow for the targeted introduction of mutations or even precisely predefined genetic modifications into virtually any genomic target site of choice. Thanks to its unprecedented precision, efficiency, and functional versatility, this technology, commonly referred to as genome editing, has become an effective force not only in basic research devoted to the elucidation of gene function, but also for knowledge-based improvement of crop traits. Among the different platforms currently available for site-directed genome modifications, RNA-guided clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) endonucleases have proven to be the most powerful. This review provides an application-oriented overview of the development of customizable endonucleases, current approaches to cereal crop breeding, and future opportunities in this field.

High Drying Temperature Accelerates Sunflower Seed Deterioration by Regulating the Fatty Acid Metabolism, Glycometabolism, and Abscisic Acid/Gibberellin Balance

Sunflower seed storage is accompanied by the loss of seed vigor. Seed drying is a key link between seed harvest and seed storage; however, to date, the effect of seed drying on sunflower seed deterioration during storage remains unclear. The present study performed hot air drying for sunflower seeds with an initial moisture content of 30% to examine the manner in which drying temperature (35, 40, 45, 50, and 55°C) affects the drying performance and seed vigor following storage process (6 and 12 months). A drying temperature of 40°C was evidently safe for sunflower seeds, whereas the high drying temperatures (HTD, 45, 50, and 55°C) significantly lowered sunflower seed vigor by regulating the fatty acid metabolism, glycometabolism, and abscisic acid (ABA)/gibberellin (GA) balance. HDT significantly increased the seed damage rate and accelerated sunflower seed deterioration during natural and artificial aging process. Further biochemical analysis indicated that HDT significantly increased lipoxygenase and dioxygenase activities, leading to malonaldehyde and reactive oxygen species over-accumulation during storage. During early seed germination, HDT significantly inhibited fatty acid hydrolysis and glycometabolism by decreasing triacylglycerol lipase, CoA-SH oxidase, and invertase activities. Moreover, HDT remarkably increased ABA levels but reduced GA levels by regulating gene expressions and metabolic enzyme activities during early imbibitions. Cumulatively, the seed drying effect on sunflower seed vigor deterioration during the storage process may be strongly related to fatty acid oxidation and hydrolysis metabolism, toxic substance accumulation, and ABA/GA balance.

Mobilization of storage lipid reserve and expression analysis of lipase and lipoxygenase genes in rice (Oryza sativa var. Pusa Basmati 1) bran during germination

Storage lipid mobilization by lipases and lipoxygenases (LOXs) in response to developmental cues take place during seed germination. After rice grain milling, the endogenous lipases and LOXs present in the bran fraction come in contact with the storage lipid reserve or triacylglycerol (TAG). Lipases catalyze the hydrolysis of TAGs to non-esterified fatty acids (NEFAs) and glycerol. The NEFAs, especially linoleic acid (18:2) produced, are further subjected to oxidative rancidity via peroxidation reaction catalyzed by LOXs. This results in the production of conjugated hydroperoxides of 18:2 that influence the off-flavors in rice bran lipids. The aim of this study is to understand how lipid mobilization and expression of lipase and LOX genes occur in the bran of germinating rice grains (Oryza sativavar. Pusa Basmati 1). Our results show that the primary source of storage lipids in bran is TAG, and its mobilization starts at 4 days after imbibition (4 DAI). Using publically available RNA-seq data and phylogeny analyses, we selected a total of 18 lipase and 16 LOX genes in rice for their expression profiles during onset of lipid mobilization. Gene expression analyses revealed OsLip1, OsLip9, and OsLip13; and OsLOX3 and OsLOX14 as the predominantly expressed genes in bran of germinating rice grains. This study explores two important events in the germinating rice grains, namely, mobilization of storage lipids and expression pattern of lipase and LOX genes. The information generated in this study can be used to efficiently manipulate the genes to enhance the shelf-stability of bran lipid reserve.

A CEP Peptide Receptor-Like Kinase Regulates Auxin Biosynthesis and Ethylene Signaling to Coordinate Root Growth and Symbiotic Nodulation in Medicago truncatula

Because of the large amount of energy consumed during symbiotic nitrogen fixation, legumes must balance growth and symbiotic nodulation. Both lateral roots and nodules form on the root system, and the developmental coordination of these organs under conditions of reduced nitrogen (N) availability remains elusive. We show that the Medicago truncatula COMPACT ROOT ARCHITECTURE2 (MtCRA2) receptor-like kinase is essential to promote the initiation of early symbiotic nodulation and to inhibit root growth in response to low N. C-TERMINALLY ENCODED PEPTIDE (MtCEP1) peptides can activate MtCRA2 under N-starvation conditions, leading to a repression of YUCCA2 (MtYUC2) auxin biosynthesis gene expression, and therefore of auxin root responses. Accordingly, the compact root architecture phenotype of cra2 can be mimicked by an auxin treatment or by overexpressing MtYUC2, and conversely, a treatment with YUC inhibitors or an MtYUC2 knockout rescues the cra2 root phenotype. The MtCEP1-activated CRA2 can additionally interact with and phosphorylate the MtEIN2 ethylene signaling component at Ser643 and Ser924, preventing its cleavage and thereby repressing ethylene responses, thus locally promoting the root susceptibility to rhizobia. In agreement with this interaction, the cra2 low nodulation phenotype is rescued by an ein2 mutation. Overall, by reducing auxin biosynthesis and inhibiting ethylene signaling, the MtCEP1/MtCRA2 pathway balances root and nodule development under low-N conditions.

Plastid Transformation: How Does it Work? Can it Be Applied to Crops? What Can it Offer?

In recent years, plant genetic engineering has advanced agriculture in terms of crop improvement, stress and disease resistance, and pharmaceutical biosynthesis. Cells from land plants and algae contain three organelles that harbor DNA: the nucleus, plastid, and mitochondria. Although the most common approach for many plant species is the introduction of foreign DNA into the nucleus (nuclear transformation) via Agrobacterium- or biolistics-mediated delivery of transgenes, plastid transformation offers an alternative means for plant transformation. Since there are many copies of the chloroplast genome in each cell, higher levels of protein accumulation can often be achieved from transgenes inserted in the chloroplast genome compared to the nuclear genome. Chloroplasts are therefore becoming attractive hosts for the introduction of new agronomic traits, as well as for the biosynthesis of high-value pharmaceuticals, biomaterials and industrial enzymes. This review provides a comprehensive historical and biological perspective on plastid transformation, with a focus on current and emerging approaches such as the use of single-walled carbon nanotubes (SWNTs) as DNA delivery vehicles, overexpressing morphogenic regulators to enhance regeneration ability, applying genome editing techniques to accelerate double-stranded break formation, and reconsidering protoplasts as a viable material for plastid genome engineering, even in transformation-recalcitrant species.

Genome Editing Technologies for Rice Improvement: Progress, Prospects, and Safety Concerns

Rice (Oryza sativa) is an important staple food crop worldwide; to meet the growing nutritional requirements of the increasing population in the face of climate change, qualitative and quantitative traits of rice need to be improved. Stress-tolerant crop varieties must be developed with stable or higher yields under stress conditions. Genome editing and speed breeding have improved the accuracy and pace of rice breeding. New breeding technologies including genome editing have been established in rice, expanding the potential for crop improvement. Recently, other genome editing techniques such as CRISPR-directed evolution, CRISPR-Cas12a, and base editors have also been used for efficient genome editing in rice. Since rice is an excellent model system for functional studies due to its small genome and close syntenic relationships with other cereal crops, new genome-editing technologies continue to be developed for use in rice. In this review, we focus on genome-editing tools for rice improvement to address current challenges and provide examples of genome editing in rice. We also shed light on expanding the scope of genome editing and systems for delivering homology-directed repair templates. Finally, we discuss safety concerns and methods for obtaining transgene-free crops.

Genetically modified crops: current status and future prospects

While transgenic technology has heralded a new era in crop improvement, several concerns have precluded their widespread acceptance. Alternative technologies, such as cisgenesis and genome-editing may address many of such issues and facilitate the development of genetically engineered crop varieties with multiple favourable traits. Genetic engineering and plant transformation have played a pivotal role in crop improvement via introducing beneficial foreign gene(s) or silencing the expression of endogenous gene(s) in crop plants. Genetically modified crops possess one or more useful traits, such as, herbicide tolerance, insect resistance, abiotic stress tolerance, disease resistance, and nutritional improvement. To date, nearly 525 different transgenic events in 32 crops have been approved for cultivation in different parts of the world. The adoption of transgenic technology has been shown to increase crop yields, reduce pesticide and insecticide use, reduce CO₂ emissions, and decrease the cost of crop production. However, widespread adoption of transgenic crops carrying foreign genes faces roadblocks due to concerns of potential toxicity and allergenicity to human beings, potential environmental risks, such as chances of gene flow, adverse effects on non-target organisms, evolution of resistance in weeds and insects etc. These concerns have prompted the adoption of alternative technologies like cisgenesis, intragenesis, and most recently, genome editing. Some of these alternative technologies can be utilized to develop crop plants that are free from any foreign gene hence, it is expected that such crops might achieve higher consumer acceptance as compared to the transgenic crops and would get faster regulatory approvals. In this review, we present a comprehensive update on the current status of the genetically modified (GM) crops under cultivation. We also discuss the issues affecting widespread adoption of transgenic GM crops and comment upon the recent tools and techniques developed to address some of these concerns.

Genetic and genomic approaches to address rapid rancidity of rice bran

Rice bran is an invaluable by-product of paddy processing industry. It is rich in minerals, protein, lipids, and crude fiber. In addition, it also possesses compounds with anti-oxidant, anti-allergic, anti-diabetic, and anti-cancer properties. It forms a basis for the extraction of rice bran oil and preparation of various functional foods with health benefits and potential to prevent chronic health issues. Nevertheless, the rapid deterioration of bran upon storage acts as a major limitation in exploiting the full potential of rice bran. In this review, we have discussed three strategies to address rapid rancidity of rice bran and enhance its shelf life and storability vis-a-vis emphasizing the importance of rice bran in terms of its nutritional composition. One strategy is through exploitation of the null mutations in the genes governing lipases and lipoxygenases leading to nonfunctional enzymes (enzyme deficient approach), another strategy is through reducing the PUFA content that is more prone to oxidation (substrate deficient approach) and a third strategy is through enhancing the antioxidant content that effectively terminate the lipid peroxidation by donating the hydrogen atom.

Development and characterization of marker-free and transgene insertion site-defined transgenic wheat with improved grain storability and fatty acid content

Development of marker-free and transgene insertion site-defined (MFTID) transgenic plants is essential for safe application of transgenic crops. However, MFTID plants have not been reported for wheat (Triticum aestivum). Here, we prepared a RNAi cassette for suppressing lipoxygenase (LOX) gene expression in wheat grains using a double right border T-DNA vector. The resultant construct was introduced into wheat genome via Agrobacterium-mediated transformation, with four homozygous marker-free transgenic lines (namely GLRW-1, -3, -5 and -8) developed. Aided by the newly published wheat genome sequence, the T-DNA insertion sites in GLRW-3 and GLRW-8 were elucidated at base-pair resolution. While the T-DNA in GLRW-3 inserted in an intergenic region, that of GLRW-8 inactivated an endogenous gene, which was thus excluded from further analysis. Compared to wild -type (WT) control, GLRW-1, -3 and -5 showed decreased LOX gene expression, lower LOX activity and less lipid peroxidation in the grains; they also exhibited significantly higher germination rates and better seedling growth after artificial ageing treatment. Interestingly, the three GLRW lines also had substantially increased contents of several fatty acids (e.g., linoleic acid and linolenic acid) in their grain and flour samples than WT control. Collectively, our data suggest that suppression of grain LOX activity can be employed to improve the storability and fatty acid content of wheat seeds and that the MFTID line GLRW-3 is likely of commercial value. Our approach may also be useful for developing the MFTID transgenic lines of other crops with enhanced grain storability and fatty acid content.

Transcription Factor bHLH2 Represses CYSTEINE PROTEASE77 to Negatively Regulate Nodule Senescence

Legume-rhizobia symbiosis is a time-limited process due to the onset of senescence, which results in the degradation of host plant cells and symbiosomes. A number of transcription factors, proteases, and functional genes have been associated with nodule senescence; however, whether other proteases or transcription factors are involved in nodule senescence remains poorly understood. In this study, we identified an early nodule senescence mutant in Medicago truncatula, denoted basic helix-loop-helix transcription factor2 (bhlh2), that exhibits decreased nitrogenase activity, acceleration of plant programmed cell death (PCD), and accumulation of reactive oxygen species (ROS). The results suggest that MtbHLH2 plays a negative role in nodule senescence. Nodules of wild-type and bhlh2-TALEN mutant plants at 28 d postinoculation were used for transcriptome sequencing. The transcriptome data analysis identified a papain-like Cys protease gene, denoted MtCP77, that could serve as a potential target of MtbHLH2. Electrophoretic mobility shift assays and chromatin immunoprecipitation analysis demonstrated that MtbHLH2 directly binds to the promoter of MtCP77 to inhibit its expression. MtCP77 positively regulates nodule senescence by accelerating plant PCD and ROS accumulation. In addition, the expression of MtbHLH2 in the nodules gradually decreased from the meristematic zone to the nitrogen fixation zone, whereas the expression of MtCP77 showed enhancement. These results indicate that MtbHLH2 and MtCP77 have opposite functions in the regulation of nodule senescence. These results reveal significant roles for MtbHLH2 and MtCP77 in plant PCD, ROS accumulation, and nodule senescence, and improve our understanding of the regulation of the nodule senescence process.

Mutagenesis in Rice: The Basis for Breeding a New Super Plant

The high selection pressure applied in rice breeding since its domestication thousands of years ago has caused a narrowing in its genetic variability. Obtaining new rice cultivars therefore becomes a major challenge for breeders and developing strategies to increase the genetic variability has demanded the attention of several research groups. Understanding mutations and their applications have paved the way for advances in the elucidation of a genetic, physiological, and biochemical basis of rice traits. Creating variability through mutations has therefore grown to be among the most important tools to improve rice. The small genome size of rice has enabled a faster release of higher quality sequence drafts as compared to other crops. The move from structural to functional genomics is possible due to an array of mutant databases, highlighting mutagenesis as an important player in this progress. Furthermore, due to the synteny among the Poaceae, other grasses can also benefit from these findings. Successful gene modifications have been obtained by random and targeted mutations. Furthermore, following mutation induction pathways, techniques have been applied to identify mutations and the molecular control of DNA damage repair mechanisms in the rice genome. This review highlights findings in generating rice genome resources showing strategies applied for variability increasing, detection and genetic mechanisms of DNA damage repair.

An EU Perspective on Biosafety Considerations for Plants Developed by Genome Editing and Other New Genetic Modification Techniques (nGMs)

The question whether new genetic modification techniques (nGM) in plant development might result in non-negligible negative effects for the environment and/or health is significant for the discussion concerning their regulation. However, current knowledge to address this issue is limited for most nGMs, particularly for recently developed nGMs, like genome editing, and their newly emerging variations, e.g., base editing. This leads to uncertainties regarding the risk/safety-status of plants which are developed with a broad range of different nGMs, especially genome editing, and other nGMs such as cisgenesis, transgrafting, haploid induction or reverse breeding. A literature survey was conducted to identify plants developed by nGMs which are relevant for future agricultural use. Such nGM plants were analyzed for hazards associated either (i) with their developed traits and their use or (ii) with unintended changes resulting from the nGMs or other methods applied during breeding. Several traits are likely to become particularly relevant in the future for nGM plants, namely herbicide resistance (HR), resistance to different plant pathogens as well as modified composition, morphology, fitness (e.g., increased resistance to cold/frost, drought, or salinity) or modified reproductive characteristics. Some traits such as resistance to certain herbicides are already known from existing GM crops and their previous assessments identified issues of concern and/or risks, such as the development of herbicide resistant weeds. Other traits in nGM plants are novel; meaning they are not present in agricultural plants currently cultivated with a history of safe use, and their underlying physiological mechanisms are not yet sufficiently elucidated. Characteristics of some genome editing applications, e.g., the small extent of genomic sequence change and their higher targeting efficiency, i.e., precision, cannot be considered an indication of safety per se, especially in relation to novel traits created by such modifications. All nGMs considered here can result in unintended changes of different types and frequencies. However, the rapid development of nGM plants can compromise the detection and elimination of unintended effects. Thus, a case-specific premarket risk assessment should be conducted for nGM plants, including an appropriate molecular characterization to identify unintended changes and/or confirm the absence of unwanted transgenic sequences.

Genome editing of oncogenes with ZFNs and TALENs: caveats in nuclease design

Background

Gene knockout technologies involving programmable nucleases have been used to create knockouts in several applications. Gene editing using Zinc-finger nucleases (ZFNs), Transcription activator like effectors (TALEs) and CRISPR/Cas systems has been used to create changes in the genome in order to make it non-functional. In the present study, we have looked into the possibility of using six fingered CompoZr ZFN pair to target the E6 gene of HPV 16 genome.

Methods

HPV 16^+ve cell lines; SiHa and CaSki were used for experiments. CompoZr ZFNs targeting E6 gene were designed and constructed by Sigma-Aldrich. TALENs targeting E6 and E7 genes were made using TALEN assembly kit. Gene editing was monitored by T7E1 mismatch nuclease and Nuclease resistance assays. Levels of E6 and E7 were further analyzed by RT-PCR, western blot as well as immunoflourescence analyses. To check if there is any interference due to methylation, cell lines were treated with sodium butyrate, and Nocodazole.

Results

Although ZFN editing activity in yeast based MEL-I assay was high, it yielded very low activity in tumor cell lines; only 6% editing in CaSki and negligible activity in SiHa cell lines. Though editing efficiency was better in CaSki, no significant reduction in E6 protein levels was observed in immunocytochemical analysis. Further, in silico analysis of DNA binding prediction revealed that some of the ZFN modules bound to sequence that did not match the target sequence. Hence, alternate ZFN pairs for E6 and E7 were not synthesized since no further active sites could be identified by in silico analyses. Then we designed TALENs to target E6 and E7 gene. TALENs designed to target E7 gene led to reduction of E7 levels in CaSki and SiHa cervical cancer cell lines. However, TALEN designed to target E6 gene did not yield any editing activity.

Conclusions

Our study highlights that designed nucleases intended to obtain bulk effect should have a reasonable editing activity which reflects phenotypically as well. Nucleases with low editing efficiency, intended for generation of knockout cell lines nucleases could be obtained by single cell cloning. This could serve as a criterion for designing ZFNs and TALENs.

Electronic supplementary material

The online version of this article (10.1186/s12935-018-0666-0) contains supplementary material, which is available to authorized users.

Cas9/sgRNA-based genome editing and other reverse genetic approaches for functional genomic studies in rice

One of the important and direct ways of investigating the function of a gene is to characterize the phenotypic consequences associated with loss or gain-of-function of the corresponding gene. These mutagenesis strategies have been successfully deployed in Arabidopsis, and subsequently extended to crop species including rice. Researchers have made vast advancements in the area of rice genomics and functional genomics, as it is a diploid plant with a relatively smaller genome size unlike other cereals. The advent of rice genome research and the annotation of high-quality genome sequencing along with the developments in databases and computer searches have enabled the functional characterization of unknown genes in rice. Further, with the improvements in the efficiency of regeneration and transformation protocols, it has now become feasible to produce sizable mutant populations in indica rice varieties also. In this review, various mutagenesis methods, the current status of the mutant resources, limitations and strengths of insertional mutagenesis approaches and also results obtained with suitable screens for stress tolerance in rice are discussed. In addition, targeted genome editing using clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) or Cas9/single-guide RNA system and its potential applications in generating transgene-free rice plants through genome engineering as an efficient alternative to classical transgenic technology are also discussed.

Multiplexed CRISPR/Cas9-mediated metabolic engineering of γ-aminobutyric acid levels in Solanum lycopersicum

In recent years, the type II CRISPR system has become a widely used and robust technique to implement site-directed mutagenesis in a variety of species including model and crop plants. However, few studies manipulated metabolic pathways in plants using the CRISPR system. Here, we introduced the pYLCRISPR/Cas9 system with one or two single-site guide RNAs to target the tomato phytoene desaturase gene. An obvious albino phenotype was observed in T0 regenerated plants, and more than 61% of the desired target sites were edited. Furthermore, we manipulated the γ-aminobutyric acid (GABA) shunt in tomatoes using a multiplex pYLCRISPR/Cas9 system that targeted five key genes. Fifty-three genome-edited plants were obtained following single plant transformation, and these samples represented single to quadruple mutants. The GABA accumulation in both the leaves and fruits of genomically edited lines was significantly enhanced, and the GABA content in the leaves of quadruple mutants was 19-fold higher than that in wild-type plants. Our data demonstrate that the multiplex CRISPR/Cas9 system can be exploited to precisely edit tomato genomic sequences and effectively create multisite knockout mutations, which could shed new light on plant metabolic engineering regulations.

MtCAS31 Aids Symbiotic Nitrogen Fixation by Protecting the Leghemoglobin MtLb120-1 Under Drought Stress in Medicago truncatula

Symbiotic nitrogen fixation (SNF) in legume root nodules injects millions of tons of nitrogen into agricultural lands and provides ammonia to non-legume crops under N-deficient conditions. During plant growth and development, environmental stresses, such as drought, salt, cold, and heat stress are unavoidable. This raises an interesting question as to how the legumes cope with the environmental stress along with SNF. Under drought stress, dehydrin proteins are accumulated, which function as protein protector and osmotic substances. In this study, we found that the dehydrin MtCAS31 (cold-acclimation-specific 31) functions in SNF in Medicago truncatula during drought stress. We found that MtCAS31 is expressed in nodules and interacts with leghemoglobin MtLb120-1. The interaction between the two proteins protects MtLb120-1 from denaturation under thermal stress in vivo. Compared to wild type, cas31 mutants display a lower nitrogenase activity, a lower ATP/ADP ratio, higher expression of nodule senescence genes and higher accumulation of amyloplasts under dehydration conditions. The results suggested that MtCAS31 protects MtLb120-1 from the damage of drought stress. We identified a new function for dehydrins in SNF under drought stress, which enriches the understanding of the molecular mechanism of dehydrins.

Genome Editing in Rice: Recent Advances, Challenges, and Future Implications

Rice (Oryza sativa L.) is the major food source for more than three billion people of the world. In the last few decades, the classical, mutational, and molecular breeding approaches have brought about tremendous increase in rice productivity with the development of novel rice varieties. However, stagnation in rice yield has been reported in recent decade owing to several factors including the emergence of pests and phyto pathogens, climate change, and other environmental issues posing great threat to global food security. There is an urgent need to produce more rice and associated cereals to satisfy the mammoth task of feeding a still growing population expected to reach 9.7 billion by 2050. Advances in genomics and emergence of multiple genome-editing technologies through use of engineered site-specific nucleases (SSNs) have revolutionized the field of plant science and agriculture. Among them, the CRISPR/Cas9 system is the most advanced and widely accepted because of its simplicity, robustness, and high efficiency. The availability of huge genomic resources together with a small genome size makes rice more suitable and feasible for genetic manipulation. As such, rice has been increasingly used to test the efficiency of different types of genome editing technologies to study the functions of various genes and demonstrate their potential in genetic improvement. Recently developed approaches including CRISPR/Cpf1 system and base editors have evolved as more efficient and accurate genome editing tools which might accelerate the pace of crop improvement. In the present review, we focus on the genome editing strategies for rice improvement, thereby highlighting the applications and advancements of CRISPR/Cas9 system. This review also sheds light on the role of CRISPR/Cpf1 and base editors in the field of genome editing highlighting major challenges and future implications of these tools in rice improvement.

Genome Editing in Rice: Recent Advances, Challenges, and Future Implications

Rice (Oryza sativa L.) is the major food source for more than three billion people of the world. In the last few decades, the classical, mutational, and molecular breeding approaches have brought about tremendous increase in rice productivity with the development of novel rice varieties. However, stagnation in rice yield has been reported in recent decade owing to several factors including the emergence of pests and phyto pathogens, climate change, and other environmental issues posing great threat to global food security. There is an urgent need to produce more rice and associated cereals to satisfy the mammoth task of feeding a still growing population expected to reach 9.7 billion by 2050. Advances in genomics and emergence of multiple genome-editing technologies through use of engineered site-specific nucleases (SSNs) have revolutionized the field of plant science and agriculture. Among them, the CRISPR/Cas9 system is the most advanced and widely accepted because of its simplicity, robustness, and high efficiency. The availability of huge genomic resources together with a small genome size makes rice more suitable and feasible for genetic manipulation. As such, rice has been increasingly used to test the efficiency of different types of genome editing technologies to study the functions of various genes and demonstrate their potential in genetic improvement. Recently developed approaches including CRISPR/Cpf1 system and base editors have evolved as more efficient and accurate genome editing tools which might accelerate the pace of crop improvement. In the present review, we focus on the genome editing strategies for rice improvement, thereby highlighting the applications and advancements of CRISPR/Cas9 system. This review also sheds light on the role of CRISPR/Cpf1 and base editors in the field of genome editing highlighting major challenges and future implications of these tools in rice improvement.

Gene Editing With TALEN and CRISPR/Cas in Rice

Engineered, site-specific nucleases induce genomic double-strand DNA breaks and break repair processes enable genome editing in a plethora of eukaryotic genomes. TALENs (transcription activator-like effector nucleases) and CRISPR/Cas (clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins) are potent biotechnological tools used for genome editing. In rice, species-tailored editing tools have proven to be efficient and easy to use. Both tools are capable of generating DNA double-strand breaks (DSBs) in vivo and such breaks can be repaired either by error-prone NHEJ (nonhomologous end joining) that leads to nucleotide insertions or deletions or by HDR (homology-directed repair) if an appropriate exogenous DNA template is provided. NHEJ repair often results in gene knockout, while HDR results in precise nucleotide sequence or gene replacement. In this review, we revisit the molecular mechanisms underlying DSB repair in eukaryotes and review the TALEN and CRISPR technologies (CRISPR/Cas9, CRISPR/Cpf1, and Base Editor) developed and utilized for genome editing by scientists in rice community.

Enzymatic and Non-Enzymatic Mechanisms Contribute to Lipid Oxidation During Seed Aging

Storage of seeds is accompanied by loss of germination and oxidation of storage and membrane lipids. A lipidomic analysis revealed that during natural and artificial aging of Arabidopsis seeds, levels of several diacylglycerols and free fatty acids, such as linoleic acid and linolenic acid as well as free oxidized fatty acids and oxygenated triacylglycerols, increased. Lipids can be oxidized by enzymatic or non-enzymatic processes. In the enzymatic pathway, lipoxygenases (LOXs) catalyze the first oxygenation step of polyunsaturated fatty acids. Analysis of lipid levels in mutants with defects in the two 9-LOX genes revealed that the strong increase in free 9-hydroxy- and 9-keto-fatty acids is dependent on LOX1 but not LOX5. Fatty acid oxidation correlated with an aging-induced decrease of germination, raising the question of whether these oxylipins negatively regulate germination. However, seeds of the lox1 mutant were only slightly more tolerant to aging, indicating that 9-LOX products contribute to but are not the major cause of loss of germination during aging. In contrast to free oxidized fatty acids, accumulation of oxygenated triacylglycerols upon accelerated aging was mainly based on non-enzymatic oxidation of seed storage lipids.

Plant genome editing with TALEN and CRISPR

Genome editing promises giant leaps forward in advancing biotechnology, agriculture, and basic research. The process relies on the use of sequence specific nucleases (SSNs) to make DNA double stranded breaks at user defined genomic loci, which are subsequently repaired by two main DNA repair pathways: non-homologous end joining (NHEJ) and homology directed repair (HDR). NHEJ can result in frameshift mutations that often create genetic knockouts. These knockout lines are useful for functional and reverse genetic studies but also have applications in agriculture. HDR has a variety of applications as it can be used for gene replacement, gene stacking, and for creating various fusion proteins. In recent years, transcription activator-like effector nucleases and clustered regularly interspaced palindromic repeats (CRISPR) and CRISPR associated protein 9 or CRISPR from Prevotella and Francisella 1 have emerged as the preferred SSNs for research purposes. Here, we review their applications in plant research, discuss current limitations, and predict future research directions in plant genome editing.

Synthetic strategies for plant signalling studies: molecular toolbox and orthogonal platforms

Plants deploy a wide array of signalling networks integrating environmental cues with growth, defence and developmental responses. The high level of complexity, redundancy and connection between several pathways hampers a comprehensive understanding of involved functional and regulatory mechanisms. The implementation of synthetic biology approaches is revolutionizing experimental biology in prokaryotes, yeasts and animal systems and can likewise contribute to a new era in plant biology. This review gives an overview on synthetic biology approaches for the development and implementation of synthetic molecular tools and techniques to interrogate, understand and control signalling events in plants, ranging from strategies for the targeted manipulation of plant genomes up to the spatiotemporally resolved control of gene expression using optogenetic approaches. We also describe strategies based on the partial reconstruction of signalling pathways in orthogonal platforms, like yeast, animal and in vitro systems. This allows a targeted analysis of individual signalling hubs devoid of interconnectivity with endogenous interacting components. Implementation of the interdisciplinary synthetic biology tools and strategies is not exempt of challenges and hardships but simultaneously most rewarding in terms of the advances in basic and applied research. As witnessed in other areas, these original theoretical-experimental avenues will lead to a breakthrough in the ability to study and comprehend plant signalling networks.

Progress of targeted genome modification approaches in higher plants

Transgene integration in plants is based on illegitimate recombination between non-homologous sequences. The low control of integration site and number of (trans/cis)gene copies might have negative consequences on the expression of transferred genes and their insertion within endogenous coding sequences. The first experiments conducted to use precise homologous recombination for gene integration commenced soon after the first demonstration that transgenic plants could be produced. Modern transgene targeting categories used in plant biology are: (a) homologous recombination-dependent gene targeting; (b) recombinase-mediated site-specific gene integration; (c) oligonucleotide-directed mutagenesis; (d) nuclease-mediated site-specific genome modifications. New tools enable precise gene replacement or stacking with exogenous sequences and targeted mutagenesis of endogeneous sequences. The possibility to engineer chimeric designer nucleases, which are able to target virtually any genomic site, and use them for inducing double-strand breaks in host DNA create new opportunities for both applied plant breeding and functional genomics. CRISPR is the most recent technology available for precise genome editing. Its rapid adoption in biological research is based on its inherent simplicity and efficacy. Its utilization, however, depends on available sequence information, especially for genome-wide analysis. We will review the approaches used for genome modification, specifically those for affecting gene integration and modification in higher plants. For each approach, the advantages and limitations will be noted. We also will speculate on how their actual commercial development and implementation in plant breeding will be affected by governmental regulations.

Consumer acceptance of food crops developed by genome editing

One of the major problems regarding consumer acceptance of genetically modified organisms (GMOs) is the possibility that their transgenes could have adverse effects on the environment and/or human health. Genome editing, represented by the CRISPR/Cas9 system, can efficiently achieve transgene-free gene modifications and is anticipated to generate a wide spectrum of plants. However, the public attitude against GMOs suggests that people will initially be unlikely to accept these plants. We herein explored the bottlenecks of consumer acceptance of transgene-free food crops developed by genome editing and made some recommendations. People should not pursue a zero-risk bias regarding such crops. Developers are encouraged to produce cultivars with a trait that would satisfy consumer needs. Moreover, they should carefully investigate off-target mutations in resultant plants and initially refrain from agricultural use of multiplex genome editing for better risk-benefit communication. The government must consider their regulatory status and establish appropriate regulations if necessary. The government also should foster communication between the public and developers. If people are informed of the benefits of genome editing-mediated plant breeding and trust in the relevant regulations, and if careful risk-benefit communication and sincere considerations for the right to know approach are guaranteed, then such transgene-free crops could gradually be integrated into society.

Programmable Site-Specific Nucleases for Targeted Genome Engineering in Higher Eukaryotes

Recent advances in the targeted genome engineering enable molecular biologists to generate sequence specific modifications with greater efficiency and higher specificity in complex eukaryotic genomes. Programmable site-specific DNA cleavage reagents and cellular DNA repair mechanisms have made this possible. These reagents have become powerful tools for delivering a site-specific genomic double-strand break (DSB) at the desired chromosomal locus, which produces sequence alterations through error-prone non-homologous end joining (NHEJ) resulting in gene inactivations/knockouts. Alternatively, the DSB can be repaired through homology-directed repair (HDR) using a donor DNA template, which leads to the introduction of desired sequence modifications at the predetermined site. Here, we summarize the role of three classes of nucleases; zinc finger nucleases (ZFNs), transcription activator like effector nucleases (TALENs), and clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9) system in achieving targeted genome modifications. Further, we discuss the progress towards the applications of programmable site-specific nucleases (SSNs) in treating human diseases and other biological applications in economically important higher eukaryotic organisms such as plants and livestock. J. Cell. Physiol. 231: 2380-2392, 2016. © 2016 Wiley Periodicals, Inc.