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

Insights into the synergistic effects of exogenous glycine betaine on the multiphase metabolism of oxyfluorfen in Oryza sativa for reducing environmental risks

Glycine betaine (GB), a secondary metabolite that regulates plant responses to biotic and abiotic stresses, may help reduce pesticide phytotoxicity, but this fact remains unestablished. This study investigated the physiological response of rice (Oryza sativa) to six dosages of oxyfluorfen (OFF) (0-0.25 mg/L) and two concentrations of GB (0 and 175 mg/L). GB treatment counteracted the considerable decrease in rice seedling growth caused by OFF treatment at doses higher than 0.15 mg/L. The biochemical processes and catalytic events associated with OFF-triggered degradation in rice were investigated using RNA-Seq-LC-Q-TOF-HRMS/MS after six rice root and shoot libraries were created and subjected to either OFF or OFF-GB. Rice treated with both GB and an ecologically relevant dose of OFF showed a marked upregulation of 1039 root genes and 111 shoot genes compared with those treated with OFF alone. Multiple OFF-degradative enzymes implicated in molecular metabolism and xenobiotic tolerance to environmental stress were identified by gene enrichment analysis. In comparison to treated with 0.25 mg/L OFF alone, exogenous GB administration decreased OFF accumulation, with the OFF concentration in roots being 44.47 % and in shoots being 51.03 %. The production of essential enzymes involved in the OFF decay process was attributed to certain genes with variable expression, including cytochrome P450, methyltransferase, glycosyltransferases, and acetyltransferases. Using LC-Q-TOF-HRMS/MS, 3 metabolites and 16 conjugates were identified in metabolic pathways including hydrolysis, acetylation, glycosylation, and interaction with amino acids in order to enhance OFF-degradative metabolism. All things considered, by reducing phytotoxicity and OFF buildup, external GB treatment can increase rice's resistance to oxidative stress caused by OFF. This study offers valuable insights into the function of GB in enhancing OFF degradation, which may have ramifications for designing genotypes that maximize OFF accumulation in rice crops and promote OFF degradation in paddy crops.

Accelerating crop improvement via integration of transcriptome-based network biology and genome editing

MAIN CONCLUSION

Big data and network biology infer functional coupling between genes. In combination with machine learning, network biology can dramatically accelerate the pace of gene discovery using modern transcriptomics approaches and be validated via genome editing technology for improving crops to stresses. Unlike other living things, plants are sessile and frequently face various environmental challenges due to climate change. The cumulative effects of combined stresses can significantly influence both plant growth and yields. In navigating the complexities of climate change, ensuring the nourishment of our growing population hinges on implementing precise agricultural systems. Conventional breeding methods have been commonly employed; however, their efficacy has been impeded by limitations in terms of time, cost, and infrastructure. Cutting-edge tools focussing on big data are being championed to usher in a new era in stress biology, aiming to cultivate crops that exhibit enhanced resilience to multifactorial stresses. Transcriptomics, combined with network biology and machine learning, is proving to be a powerful approach for identifying potential genes to target for gene editing, specifically to enhance stress tolerance. The integration of transcriptomic data with genome editing can yield significant benefits, such as gaining insights into gene function by modifying or manipulating of specific genes in the target plant. This review provides valuable insights into the use of transcriptomics platforms and the application of biological network analysis and machine learning in the discovery of novel genes, thereby enhancing the understanding of plant responses to combined or sequential stress. The transcriptomics as a forefront omics platform and how it is employed through biological networks and machine learning that lead to novel gene discoveries for producing multi-stress-tolerant crops, limitations, and future directions have also been discussed.

Unlocking male sterility in horticultural crops through gene editing technology for precision breeding applications: presentation of a case study in tomato

Plant male sterility (MS) refers to the failure of the production of functional anthers, viable pollen grains and/or fertile sperm cells. This feature has great potential in horticultural crops for the exploitation of heterosis through the development of F1 hybrid varieties. MS in plants can occur spontaneously or can be induced artificially by exploiting biotechnological tools, such as the editing of genes involved in spore formation or pollen development. The success of such an approach strongly depends both on preliminary knowledge of the involved genes and on effective procedures for in vitro transfection/regeneration of whole plants. Furthermore, according to previous studies based on CRISPR/Cas9 technology, the efficacy of targeting and the resulting mutation profile are critically influenced by intrinsic factors, such as the CRISPR target primary sequence sites and chromatin signatures, which are often associated with varying levels of chromatin accessibility across different genomic regions. This relationship underscores the complexity of CRISPR-based genome editing and highlights the need to identify a precise suitable target. Our paper reports the results obtained for site-specific in vivo mutagenesis via a CRISPR/Cas9-mediated strategy applied to the MYB80 gene, which is a promising target for implementing male sterility in horticultural crops. We highlight the main steps that play a key role in the whole experimental pipeline, which aims at the generation of CRISPR/Cas-edited DNA-free tomato plants. This goal was achieved via protoplast-based technology and by directly delivering a ribonucleoprotein complex consisting of the Cas9 protein and in vitro synthesized single guide RNAs that can target different positions of the gene under investigation. Overall findings and insights are presented and critically discussed.

A Gemini Virus-Derived Autonomously Replicating System for HDR-Mediated Genome Editing of the EPSP Synthase Gene in Indica Rice

CRISPR/Cas9-mediated homology-directed repair (HDR) is a powerful tool for precise genome editing in plants, but its efficiency remains low, particularly for targeted amino acid substitutions or gene knock-ins. Successful HDR requires the simultaneous presence of Cas9, guide RNA, and a repair template (RT) in the same cell nucleus. Among these, the timely availability of the RT at the double-strand break (DSB) site is a critical bottleneck. To address this, we developed a sequential transformation strategy incorporating a deconstructed wheat dwarf virus (dWDV)-based autonomously replicating delivery system, effectively simplifying the process into a two-component system. Using this approach, we successfully achieved the targeted editing of the OsEPSPS gene in rice with a 10 percent HDR efficiency, generating three lines (TIPS1, TIPS2, and TIPS3) with amino acid substitutions (T172I and P177S) in the native EPSPS protein. The modifications were confirmed through Sanger sequencing and restriction digestion assays, and the edited lines showed no yield penalties compared to wild-type plants. This study demonstrates the utility of viral replicons in delivering gene-editing tools for precise genome modification, offering a promising approach for efficient HDR in crop improvement programs.

The Role of Genetic Resistance in Rice Disease Management

Rice (Oryza sativa) is a crucial staple crop for global food security, particularly in Asia. However, rice production faces significant challenges from various diseases that can cause substantial yield losses. This review explores the role of genetic resistance in rice disease management, focusing on the molecular mechanisms underlying plant-pathogen interactions and strategies for developing resistant varieties. The paper discusses qualitative and quantitative resistance, emphasizing the importance of resistance (R) genes, defense-regulator genes, and quantitative trait loci (QTLs) in conferring broad-spectrum disease resistance. Gene-for-gene relationships in rice-pathogen interactions are examined, particularly for Xanthomonas oryzae pv. oryzae and Magnaporthe oryzae. The review also covers recent advancements in breeding techniques, including marker-assisted selection, genetic engineering, and genome editing technologies like CRISPR-Cas. These approaches offer promising avenues for enhancing disease resistance in rice while maintaining yield potential. Understanding and exploiting genetic resistance mechanisms is crucial for developing durable and broad-spectrum disease-resistant rice varieties, essential for ensuring sustainable rice production and global food security in the face of evolving pathogen threats and changing environmental conditions.

An enhanced classification system of various rice plant diseases based on multi-level handcrafted feature extraction technique

The rice plant is one of the most significant crops in the world, and it suffers from various diseases. The traditional methods for rice disease detection are complex and time-consuming, mainly depending on the expert's experience. The explosive growth in image processing, computer vision, and deep learning techniques provides effective and innovative agriculture solutions for automatically detecting and classifying these diseases. Moreover, more information can be extracted from the input images due to different feature extraction techniques. This paper proposes a new system for detecting and classifying rice plant leaf diseases by fusing different features, including color texture with Local Binary Pattern (LBP) and color features with Color Correlogram (CC). The proposed system consists of five stages. First, input images acquire RGB images of rice plants. Second, image preprocessing applies data augmentation to solve imbalanced problems, and logarithmic transformation enhancement to handle illumination problems has been applied. Third, the features extraction stage is responsible for extracting color features using CC and color texture features using multi-level multi-channel local binary pattern (MCLBP). Fourth, the feature fusion stage provides complementary and discriminative information by concatenating the two types of features. Finally, the rice image classification stage has been applied using a one-against-all support vector machine (SVM). The proposed system has been evaluated on three benchmark datasets with six classes: Blast (BL), Bacterial Leaf Blight (BLB), Brown Spot (BS), Tungro (TU), Sheath Blight (SB), and Leaf Smut (LS) have been used. Rice Leaf Diseases First Dataset, Second Dataset, and Third Dataset achieved maximum accuracy of 99.53%, 99.4%, and 99.14%, respectively, with processing time from [Formula: see text]. Hence, the proposed system has achieved promising results compared to other state-of-the-art approaches.

Genomic insights into cytokinin oxidase/dehydrogenase (CKX) gene family, identification, phylogeny and synteny analysis for its possible role in regulating seed number in Pigeonpea (Cajanus cajan (L.) Millsp.)

Cytokinin oxidase/dehydrogenase (CKX) regulates cytokinin levels in plants which are vital for plant growth and development. However, there is a paucity of evidence regarding their role in controlling embryo/seed development in pigeonpea. This comprehensive study provides information on the identification and characterization of CKX genes in pigeonpea. A genome-wide analysis identified 18 CKX genes, each with distinct structure, expression patterns, and possible diverse functions. Domain analysis revealed the presence of the sequences including FAD and CK-Binding domain, and subcellular localization analysis showed that almost 50 % of them reside within the nucleus. They were observed to be located unevenly on chromosome numbers 2, 4, 6, 7, and 11 with a majority of them present on the scaffolds. The 8 homologous pairs and various orthologous gene pairs provided further insights into their evolution pattern. Further, SNP/Indels variation in CKX genes and haplotype groups among contrasting genotypes for SNPP (seed number per pod) were analyzed. Spatiotemporal expression analysis revealed the significant expression pattern of CcCKX15, CcCKX17, and CcCKX2 in genotypes carrying low SNPP reiterating their possible role as negative regulators. These genes can be potential targets to undertake seed and biomass improvement in pigeonpea.

Comprehensive analyses show the enhancement effect of exogenous melatonin on fluroxypyr-meptyl multiple phase metabolisms in Oryza sativa for reducing environmental risks

The role of melatonin (MT), an essential phytohormone controlling the physiological and biochemical reactions of plants to biotic and abiotic stress, in alleviating pesticide phytotoxicity remains unclear. This study explores the effects of MT (0 and 200 mg/L) and six doses of fluroxypyr-meptyl (FLUME) (0-0.14 mg/L) on the physiological response of rice (Oryza sativa). FLUME exposure inhibited the growth of rice seedlings, with MT treatment ameliorating this effect. To determine the biochemical processes and catalytic events involved in FLUME breakdown in rice, six rice root and shoot libraries exposed to either FLUME or FLUME-MT were generated and then subjected to RNA-Seq-LC-Q-TOF-HRMS/MS analyses. The results showed that 1510 root genes and 139 shoot genes exhibited higher upregulation in plants treated with an ecologically realistic FLUME concentration and MT than in those treated with FLUME alone. Gene enrichment analysis revealed numerous FLUME-degradative enzymes operating in xenobiotic tolerance to environmental stress and molecular metabolism. Regarding the FLUME degradation process, certain differentially expressed genes were responsible for producing important enzymes, such as cytochrome P450, glycosyltransferases, and acetyltransferases. Four metabolites and ten conjugates in the pathways involving hydrolysis, malonylation, reduction, glycosylation, or acetylation were characterized using LC-Q-TOF-HRMS/MS to support FLUME-degradative metabolism. Overall, external application of MT can increase rice tolerance to FLUME-induced oxidative stress by reducing phytotoxicity and FLUME accumulation. This study provides insights into MT's role in facilitating FLUME degradation, with potential implications for engineering genotypes supporting FLUME degradation in paddy crops.

Rapid improvement of grain appearance in three-line hybrid rice via CRISPR/Cas9 editing of grain size genes

KEY MESSAGE

Genetic editing of grain size genes quickly improves three-line hybrid rice parents to increase the appearance quality and yield of hybrid rice. Grain size affects rice yield and quality. In this study, we used CRISPR/Cas9 to edit the grain size gene GW8 in the maintainer line WaitaiB (WTB) and restorer line Guanghui998 (GH998). The new slender sterile line WTEA (gw8) was obtained in the BC2F1 generation by transferring the grain mutation of the maintainer plant to the corresponding sterile line WantaiA (WTA, GW8) in the T1 generation. Two slender restorer lines, GH998E1 (gw8(II)) and GH998E2 (gw8(I)), were obtained in T1 generation. In the early stage, new sterile and restorer lines in grain mutations were created by targeted editing of GS3, TGW3, and GW8 genes. These parental lines were mated to detect the impact of grain-type mutations on hybrid rice yield and quality. Mutations in gs3, gw8, and tgw3 had a minimal impact on agronomic traits except the grain size and thousand-grain weight. The decrease in grain width in the combination mainly came from gw8/gw8, gs3/gs3 increased the grain length, gs3/gs3-gw8/gw8 had a more significant effect on the grain length, and gs3/gs3-gw8/gw8(I) contributed more to grain length than gs3/gs3-gw8/gw8(II). The heterozygous TGW3/tgw3 may not significantly increase grain length. Electron microscopy revealed that the low-chalky slender-grain variety had a cylindrical grain shape, a uniform distribution of endosperm cells, and tightly arranged starch grains. Quantitative fluorescence analysis of endospermdevelopment-related genes showed that the combination of slender grain hybrid rice caused by gs3 and gw8 mutations promoted endosperm development and improved appearance quality. An appropriate grain size mutation resulted in hybrid rice varieties with high yield and quality.

The potential of genome editing to create novel alleles of resistance genes in rice

Rice, a staple food for a significant portion of the global population, faces persistent threats from various pathogens and pests, necessitating the development of resilient crop varieties. Deployment of resistance genes in rice is the best practice to manage diseases and reduce environmental damage by reducing the application of agro-chemicals. Genome editing technologies, such as CRISPR-Cas, have revolutionized the field of molecular biology, offering precise and efficient tools for targeted modifications within the rice genome. This study delves into the application of these tools to engineer novel alleles of resistance genes in rice, aiming to enhance the plant's innate ability to combat evolving threats. By harnessing the power of genome editing, researchers can introduce tailored genetic modifications that bolster the plant's defense mechanisms without compromising its essential characteristics. In this study, we synthesize recent advancements in genome editing methodologies applicable to rice and discuss the ethical considerations and regulatory frameworks surrounding the creation of genetically modified crops. Additionally, it explores potential challenges and future prospects for deploying edited rice varieties in agricultural landscapes. In summary, this study highlights the promise of genome editing in reshaping the genetic landscape of rice to confront emerging challenges, contributing to global food security and sustainable agriculture practices.

Low mutation rate of spontaneous mutants enables detection of causative genes by comparing whole genome sequences

In the early 1900s, mutation breeding to select varieties with desirable traits using spontaneous mutation was actively conducted around the world, including Japan. In rice, the number of fixed mutations per generation was estimated to be 1.38-2.25. Although this low mutation rate was a major problem for breeding in those days, in the modern era with the development of next-generation sequencing (NGS) technology, it was conversely considered to be an advantage for efficient gene identification. In this paper, we proposed an in silico approach using NGS to compare the whole genome sequence of a spontaneous mutant with that of a closely related strain with a nearly identical genome, to find polymorphisms that differ between them, and to identify the causal gene by predicting the functional variation of the gene caused by the polymorphism. Using this approach, we found four causal genes for the dwarf mutation, the round shape grain mutation and the awnless mutation. Three of these genes were the same as those previously reported, but one was a novel gene involved in awn formation. The novel gene was isolated from Bozu-Aikoku, a mutant of Aikoku with the awnless trait, in which nine polymorphisms were predicted to alter gene function by their whole-genome comparison. Based on the information on gene function and tissue-specific expression patterns of these candidate genes, Os03g0115700/LOC_Os03g02460, annotated as a short-chain dehydrogenase/reductase SDR family protein, is most likely to be involved in the awnless mutation. Indeed, complementation tests by transformation showed that it is involved in awn formation. Thus, this method is an effective way to accelerate genome breeding of various crop species by enabling the identification of useful genes that can be used for crop breeding with minimal effort for NGS analysis.

Insight into the relationship between metabolic enzymes and oxadiazon degradation in Oryza sativa for reducing environmental risks

Oxadiazon (ODZ) is extensively utilized in agricultural fields for weed control owing to its strong effectiveness. However, excessive loading of ODZ in water bodies and agricultural soils can lead to various environmental concerns. Therefore, it is crucial to understand the ODZ metabolic process and associated mechanisms in crops to assess the likelihood of ODZ contamination in the environment. This study aimed to assess the effects of ODZ on the growth and toxicological responses of rice (Oryza sativa). The growth of rice tissues was notably compromised with the increase in ODZ concentrations. RNA sequencing in combination with liquid chromatography-quadrupole-time-of-flight-high-resolution mass spectrometry/mass spectrometry (LC-Q-TOF-HRMS/MS) analysis allowed for the identification of numerous transcriptional components associated with ODZ metabolism. Four libraries comprising rice roots and shoots exposed to ODZ were RNA-sequenced in triplicate. The application of environmentally realistic ODZ concentrations upregulated the expression of 844 genes in shoots and 1476 genes in roots. Gene enrichment analysis revealed the presence of multiple enzymes involved in ODZ metabolism and detoxification. These enzymes play a critical role in mitigating environmental stress and facilitating xenobiotic metabolism. Notably, among differentially expressed genes, several key enzymes were identified, including cytochrome P450s, protein kinases, aminotransferases, and ATP-binding cassette transporters involved in the metabolic process. Using LC-Q-TOF-HRMS/MS, 3 metabolites and 13 conjugates were identified in multiple metabolic pathways involving oxidation, hydrolysis, glycosylation, acetylation, and methylation. This study successfully established a potential link between the specific metabolic products of ODZ and increased activities of their corresponding enzymes. Moreover, this study considerably elucidates the detailed pathways and mechanisms involved in ODZ metabolism. The study findings provide valuable insights into the development of genotypes for reducing ODZ residues in paddy fields and minimizing their accumulation in rice crops.

Truncation of the calmodulin binding domain in rice glutamate decarboxylase 4 (OsGAD4) leads to accumulation of γ-aminobutyric acid and confers abiotic stress tolerance in rice seedlings

GABA (Gamma-aminobutyric acid) is a non-protein amino acid widely known as major inhibitory neurotransmitter. It is synthesized from glutamate via the enzyme glutamate decarboxylase (GAD). GAD is ubiquitous in all organisms, but only plant GAD has ability to bind Ca2+/calmodulin (CaM). This kind of binding suppresses the auto-inhibition of Ca2+/calmodulin binding domain (CaMBD) when the active site of GAD is unfolded resulting in stimulated GAD activity. OsGAD4 is one of the five GAD genes in rice genome. It was confirmed that OsGAD4 has ability to bind to Ca2+/CaM. Moreover, it exhibits strongest expression against several stress conditions among the five OsGAD genes. In this study, CRISPR/Cas9-mediated genome editing was performed to trim the coding region of CaMBD from the OsGAD4 gene, to remove its autoinhibitory function. DNA sequence analysis of the genome edited rice plants revealed the truncation of CaMBD (216 bp). Genome edited line (#14-1) produced 11.26 mg GABA/100 g grain, which is almost nine-fold in comparison to wild type. Short deletion in the coding region for CaMBD yielded in mutant (#14-6) with lower GABA content than wild type counterpart. Abiotic stresses like salinity, flooding and drought significantly enhanced GABA accumulation in #14-1 at various time points compared to wild-type and #14-6 under the same stress conditions. Moreover, upregulated mRNA expression in vegetative tissues seems correlated with the stress-responsiveness of OsGAD4 when exposed to the above-mentioned stresses. Stress tolerance of OsGAD4 genome edited lines was evidenced by the higher survival rate indicating the gene may induce tolerance against abiotic stresses in rice. This is the first report on abiotic stress tolerance in rice modulated by endogenous GABA.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-024-01460-1.

Uptake, translocation, accumulation, and metabolism of fluroxypyr-meptyl and oxidative stress induction in rice seedling

Fluroxypyr-meptyl (FLUME) is heterocyclic herbicide with internal absorption and transmission characteristics. Owing to its low cost and rapid efficacy, it has been widely used to control broad-leaved weeds in wheat, corn, and rice fields. However, the uptake, translocation, accumulation, and metabolism of FLUME in rice seedlings and the extent of oxidative stress induced by it remain largely unknown, which consequently restricts the comprehensive risk assessment of FLUME residues in the environment during rice production. Hence, we systematically investigated the growth and physiological responses of rice to FLUME and analyzed its uptake, translocation, accumulation, and metabolism in rice seedlings. The results indicated that under 0-0.12 mg/L FLUME treatment, only a small proportion of FLUME was translocated upward and accumulated in rice shoots following absorption via roots, with all the translocation factor values being < 1. Moreover, the distribution and enrichment ability of FLUME in rice seedlings were greater in roots than in shoots. Furthermore, we revealed that FLUME accumulation in rice seedlings evidently inhibited their growth and activated the defense system against oxidative stress, with an increase in the activity of antioxidant and detoxifying enzymes. In addition, multiple metabolic reactions of FLUME were observed in rice seedlings, including dehalogenation, hydroxylation, glycosylation, acetylation, and malonylation. Our study provides systematic insights into the uptake, translocation, accumulation, and metabolism of FLUME in rice seedlings as well as the oxidative stress induced by FLUME accumulation, which can help improve FLUME applications and environmental risk assessments in crops.

CRISPR/Cas9-mediated genome editing techniques and new breeding strategies in cereals - current status, improvements, and perspectives

Cereal crops, including triticeae species (barley, wheat, rye), as well as edible cereals (wheat, corn, rice, oat, rye, sorghum), are significant suppliers for human consumption, livestock feed, and breweries. Over the past half-century, modern varieties of cereal crops with increased yields have contributed to global food security. However, presently cultivated elite crop varieties were developed mainly for optimal environmental conditions. Thus, it has become evident that taking into account the ongoing climate changes, currently a priority should be given to developing new stress-tolerant cereal cultivars. It is necessary to enhance the accuracy of methods and time required to generate new cereal cultivars with the desired features to adapt to climate change and keep up with the world population expansion. The CRISPR/Cas9 system has been developed as a powerful and versatile genome editing tool to achieve desirable traits, such as developing high-yielding, stress-tolerant, and disease-resistant transgene-free lines in major cereals. Despite recent advances, the CRISPR/Cas9 application in cereals faces several challenges, including a significant amount of time required to develop transgene-free lines, laboriousness, and a limited number of genotypes that may be used for the transformation and in vitro regeneration. Additionally, developing elite lines through genome editing has been restricted in many countries, especially Europe and New Zealand, due to a lack of flexibility in GMO regulations. This review provides a comprehensive update to researchers interested in improving cereals using gene-editing technologies, such as CRISPR/Cas9. We will review some critical and recent studies on crop improvements and their contributing factors to superior cereals through gene-editing technologies.

The rice SnRK family: biological roles and cell signaling modules

Stimulus-activated signaling pathways orchestrate cellular responses to control plant growth and development and mitigate the effects of adverse environmental conditions. During this process, signaling components are modulated by central regulators of various signal transduction pathways. Protein phosphorylation by kinases is one of the most important events transmitting signals downstream, via the posttranslational modification of signaling components. The plant serine and threonine kinase SNF1-related protein kinase (SnRK) family, which is classified into three subgroups, is highly conserved in plants. SnRKs participate in a wide range of signaling pathways and control cellular processes including plant growth and development and responses to abiotic and biotic stress. Recent notable discoveries have increased our understanding of how SnRKs control these various processes in rice (Oryza sativa). In this review, we summarize current knowledge of the roles of OsSnRK signaling pathways in plant growth, development, and stress responses and discuss recent insights. This review lays the foundation for further studies on SnRK signal transduction and for developing strategies to enhance stress tolerance in plants.

Non-edible fruit seeds: nutritional profile, clinical aspects, and enrichment in functional foods and feeds

Nowadays, fruits are gaining high demand due to their promising advantages on human health. Astonishingly, their by-products, that is, seeds and peels, account for 10-35% of fruit weight and are usually thrown as waste after consumption or processing. But it is neglected that fruit seeds also have functional properties and nutritional value, and thus could be utilized for dietary and therapeutic purposes, ultimately reducing the waste burden on the environment. Owing to these benefits, researchers have started to assess the nutritional value of different fruits seeds, in addition to the chemical composition in various bioactive constituents, like carotenoids (lycopene), flavonoids, proteins (bioactive peptides), vitamins, etc., that have substantial health benefits and can be used in formulating different types of food products with noteworthy functional and nutraceutical potential. The current review aims to comprehend the known information of nutritional and phytochemical profiling of non-edible fruits seeds, viz. apple, apricot, avocado, cherry, date, jamun, litchi, longan, mango, and papaya. Additionally, clinical studies conducted on these selected non-edible fruit seed extracts, their safety issues and their enrichment in food products as well as animal feed has also been discussed. This review aims to highlight the potential applications of the non-edible fruit seeds in developing new food products and also provide a viable alternative to reduce the waste disposal issue faced by agro-based industries.

CRISPR-Cas System, a Possible "Savior" of Rice Threatened by Climate Change: An Updated Review

Climate change has significantly affected agriculture production, particularly the rice crop that is consumed by almost half of the world's population and contributes significantly to global food security. Rice is vulnerable to several abiotic and biotic stresses such as drought, heat, salinity, heavy metals, rice blast, and bacterial blight that cause huge yield losses in rice, thus threatening food security worldwide. In this regard, several plant breeding and biotechnological techniques have been used to raise such rice varieties that could tackle climate changes. Nowadays, gene editing (GE) technology has revolutionized crop improvement. Among GE technology, CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein) system has emerged as one of the most convenient, robust, cost-effective, and less labor-intensive system due to which it has got more popularity among plant researchers, especially rice breeders and geneticists. Since 2013 (the year of first application of CRISPR/Cas-based GE system in rice), several trait-specific climate-resilient rice lines have been developed using CRISPR/Cas-based GE tools. Earlier, several reports have been published confirming the successful application of GE tools for rice improvement. However, this review particularly aims to provide an updated and well-synthesized brief discussion based on the recent studies (from 2020 to present) on the applications of GE tools, particularly CRISPR-based systems for developing CRISPR rice to tackle the current alarming situation of climate change, worldwide. Moreover, potential limitations and technical bottlenecks in the development of CRISPR rice, and prospects are also discussed.

Genetic modification strategies for enhancing plant resilience to abiotic stresses in the context of climate change

Enhancing the resilience of plants to abiotic stresses, such as drought, salinity, heat, and cold, is crucial for ensuring global food security challenge in the context of climate change. The adverse effects of climate change, characterized by rising temperatures, shifting rainfall patterns, and increased frequency of extreme weather events, pose significant threats to agricultural systems worldwide. Genetic modification strategies offer promising approaches to develop crops with improved abiotic stress tolerance. This review article provides a comprehensive overview of various genetic modification techniques employed to enhance plant resilience. These strategies include the introduction of stress-responsive genes, transcription factors, and regulatory elements to enhance stress signaling pathways. Additionally, the manipulation of hormone signaling pathways, osmoprotectant accumulation, and antioxidant defense mechanisms is discussed. The use of genome editing tools, such as CRISPR-Cas9, for precise modification of target genes related to stress tolerance is also explored. Furthermore, the challenges and future prospects of genetic modification for abiotic stress tolerance are highlighted. Understanding and harnessing the potential of genetic modification strategies can contribute to the development of resilient crop varieties capable of withstanding adverse environmental conditions caused by climate change, thereby ensuring sustainable agricultural productivity and food security.

Map-based cloning and CRISPR/Cas9-based editing uncover BoNA1 as the causal gene for the no-anthocyanin-accumulation phenotype in curly kale (Brassica oleracea var. sabellica)

Brassica oleracea comprises several important vegetable and ornamental crops, including curly kale, ornamental kale, cabbage, broccoli, and others. The accumulation of anthocyanins, important secondary metabolites valuable to human health, in these plants varies widely and is responsible for their pink to dark purple colors. Some curly kale varieties lack anthocyanins, making these plants completely green. The genetic basis of this trait is still unknown. We crossed the curly kale inbred line BK2019 (without anthocyanins) with the cabbage inbred line YL1 (with anthocyanins) and the Chinese kale inbred line TO1000 (with anthocyanins) to generate segregating populations. The no-anthocyanin trait was genetically controlled by a recessive gene, bona1. We generated a linkage map and mapped bona1 to a 256-kb interval on C09. We identified one candidate gene, Bo9g058630, in the target genomic region; this gene is homologous to AT5G42800, which encodes a dihydroflavonol-4-reductase-like (DFR-like) protein in Arabidopsis. In BK2019, a 1-bp insertion was observed in the second exon of Bo9g058630 and directly produced a stop codon. To verify the candidate gene function, CRISPR/Cas9 gene editing technology was applied to knock out Bo9g058630. We generated three bona1 mutants, two of which were completely green with no anthocyanins, confirming that Bo9g058630 corresponds to BoNA1. Different insertion/deletion mutations in BoNA1 exons were found in all six of the other no-anthocyanin kale varieties examined, supporting that independent disruption of BoNA1 resulted in no-anthocyanin varieties of B. oleracea. This study improves the understanding of the regulation mechanism of anthocyanin accumulation in B. oleracea subspecies.

Breakthrough in CRISPR/Cas system: Current and future directions and challenges

Targeted genome editing (GE) technology has brought a significant revolution in fictional genomic research and given hope to plant scientists to develop desirable varieties. This technology involves inducing site-specific DNA perturbations that can be repaired through DNA repair pathways. GE products currently include CRISPR-associated nuclease DNA breaks, prime editors generated DNA flaps, single nucleotide-modifications, transposases, and recombinases. The discovery of double-strand breaks, site-specific nucleases (SSNs), and repair mechanisms paved the way for targeted GE, and the first-generation GE tools, ZFNs and TALENs, were successfully utilized in plant GE. However, CRISPR-Cas has now become the preferred tool for GE due to its speed, reliability, and cost-effectiveness. Plant functional genomics has benefited significantly from the widespread use of CRISPR technology for advancements and developments. This review highlights the progress made in CRISPR technology, including multiplex editing, base editing (BE), and prime editing (PE), as well as the challenges and potential delivery mechanisms.

Recent Developments in CRISPR/Cas9 Genome-Editing Technology Related to Plant Disease Resistance and Abiotic Stress Tolerance

The revolutionary CRISPR/Cas9 genome-editing technology has emerged as a powerful tool for plant improvement, offering unprecedented precision and efficiency in making targeted gene modifications. This powerful and practical approach to genome editing offers tremendous opportunities for crop improvement, surpassing the capabilities of conventional breeding techniques. This article provides an overview of recent advancements and challenges associated with the application of CRISPR/Cas9 in plant improvement. The potential of CRISPR/Cas9 in terms of developing crops with enhanced resistance to biotic and abiotic stresses is highlighted, with examples of genes edited to confer disease resistance, drought tolerance, salt tolerance, and cold tolerance. Here, we also discuss the importance of off-target effects and the efforts made to mitigate them, including the use of shorter single-guide RNAs and dual Cas9 nickases. Furthermore, alternative delivery methods, such as protein- and RNA-based approaches, are explored, and they could potentially avoid the integration of foreign DNA into the plant genome, thus alleviating concerns related to genetically modified organisms (GMOs). We emphasize the significance of CRISPR/Cas9 in accelerating crop breeding processes, reducing editing time and costs, and enabling the introduction of desired traits at the nucleotide level. As the field of genome editing continues to evolve, it is anticipated that CRISPR/Cas9 will remain a prominent tool for crop improvement, disease resistance, and adaptation to challenging environmental conditions.

Current insights and advances into plant male sterility: new precision breeding technology based on genome editing applications

Plant male sterility (MS) represents the inability of the plant to generate functional anthers, pollen, or male gametes. Developing MS lines represents one of the most important challenges in plant breeding programs, since the establishment of MS lines is a major goal in F1 hybrid production. For these reasons, MS lines have been developed in several species of economic interest, particularly in horticultural crops and ornamental plants. Over the years, MS has been accomplished through many different techniques ranging from approaches based on cross-mediated conventional breeding methods, to advanced devices based on knowledge of genetics and genomics to the most advanced molecular technologies based on genome editing (GE). GE methods, in particular gene knockout mediated by CRISPR/Cas-related tools, have resulted in flexible and successful strategic ideas used to alter the function of key genes, regulating numerous biological processes including MS. These precision breeding technologies are less time-consuming and can accelerate the creation of new genetic variability with the accumulation of favorable alleles, able to dramatically change the biological process and resulting in a potential efficiency of cultivar development bypassing sexual crosses. The main goal of this manuscript is to provide a general overview of insights and advances into plant male sterility, focusing the attention on the recent new breeding GE-based applications capable of inducing MS by targeting specific nuclear genic loci. A summary of the mechanisms underlying the recent CRISPR technology and relative success applications are described for the main crop and ornamental species. The future challenges and new potential applications of CRISPR/Cas systems in MS mutant production and other potential opportunities will be discussed, as generating CRISPR-edited DNA-free by transient transformation system and transgenerational gene editing for introducing desirable alleles and for precision breeding strategies.

A method for generating genome edited plant lines from CRISPR-transformed Shanxin poplar plants

Due to the reason of low efficiency of mutation in CRISPR-editing, a high frequency of CRISPR transformed plant lines failing in mutation had been generated and had to be discarded. In the present study, we built a method to increase the efficiency of CRISPR-editing. We used Shanxin poplar (Populus davidiana×P. bolleana) as the study material, and CRISPR-editing system was first built to generate the CRISPR-transformed lines. The line that failed in CRISPR-editing was used for improving the efficiency of mutation, which was treated with heat (37 °C) to improve the cleaving activity of Cas9, leading to increased frequency of the cleaved DNA. Our results indicated that 87-100% of cells in CRISPR-transformed plants whose DNA had been cleaved by heat treatment, and the heat treatment plants were then cut into explants to differentiate adventitious buds. Each differentiated bud can be considered as an independent line. Twenty independent lines were randomly selected for analysis, and all of them had been mutated by CRISPR editing, displaying 4 types of mutation. Our results indicated that heat treatment combined with re-differentiation can generate CRISPR-edited plants efficiently. This method could conquer the problem of low mutation efficiency of CRISPR-editing in Shanxin poplar, and will have a wide application in plant CRISPR-editing. DATA AVAILABILITY: The genome sequence of Populus davidiana × P. bolleana had been submitted to GenBank with the BioProject Accession number of PRJNA867039 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA867039).

Acetyltransferase OsACE2 acts as a regulator to reduce the environmental risk of oxyfluorfen to rice production

The constant use of the pesticide oxyfluorfen (OFF) in farmland contaminates the soil, posing threats to crop growth and human health. To avoid the contamination of food crops with OFF, it is critically important to understand its absorption and degradation mechanisms. In this study, we characterized a new functional locus encoding an acetyltransferase (OsACE2) that can facilitate OFF degradation in rice. OsACE2 was drastically induced by OFF at 0.04-0.2 mg L^-1 for 6 days and the rice growth was significantly inhibited. To demonstrate the regulatory role of OsACE2 in resistance to OFF toxicity, we generated OsACE2 overexpression (OE) and knockout mutant using genetic transformation and gene-editing technologies (CRISPR/Cas9). The OE plants grown in the hydroponic medium showed improved growth (plant elongation and biomass), increased chlorophyll content, and reduced OFF-induced oxidative stress. The OsACE2-improved growth phenotypes of rice were attributed to the significantly lower OFF accumulation in OE plants. Conversely, knocking out OsACE2 resulted in compromised growth phenotypes compared to the wild-type (WT). Using LC-LTQ-HRMS/MS, five mono-metabolites and eleven conjugates of OFF were characterized through various canonical pathways, such as hydrolysis, oxidation, reduction, glycosylation, acetylation, malonylation, and interaction with amino acids. These metabolites increased in the OE plants, and five acetylated conjugates were reported for the first time. Collectively, OsACE2 plays a primary role in catabolizing OFF residues in rice through multiple degradation pathways and reducing OFF in its growth environment.

A fast breeding strategy creates fragrance- and anthocyanin-enriched rice lines by marker-free gene-editing and hybridization

As rice is a staple food for nearly half of the world's population, rice varieties with excellent agronomic traits as well as high flavor and nutritional quality such as fragrant rice and purple rice are naturally favored by the market. In the current study, we adopt a fast breeding strategy to improve the aroma and anthocyanin content in the excellent rice inbred line, F25. The strategy skillfully used the advantages of obtaining editing pure lines in T0 generation of CRISPR/Cas9 editing system and easy observation of purple character and grain shape, integrated the subsequent screening of non-transgenic lines, and the elimination of undesirable edited variants from gene-editing and cross-breeding at the same time as the separation of the progeny from the purple cross, thus expediting the breeding process. Compared with conventional breeding strategies, this strategy saves about 6-8 generations and reduces breeding costs. Firstly, we edited the OsBADH2 gene associated with rice flavor using an Agrobacterium-mediated CRISPR/Cas9 system to improve the aroma of F25. In the T0 generation, a homozygous OsBADH2-edited F25 line (F25B) containing more of the scented substance 2-AP was obtained. Then, we crossed F25B (♀) with a purple rice inbred line, P351 (♂), with high anthocyanin enrichment to improve the anthocyanin content of F25. After nearly 2.5 years of screening and identification over five generations, the undesirable variation characteristics caused by gene-editing and hybridization and the transgenic components were screened out. Finally, the improved F25 line with highly stable aroma component, 2-AP, increased anthocyanin content and no exogenous transgenic components were obtained. This study not only provides high-quality aromatic anthocyanin rice lines that meet the market demand, but also offers a reference for the comprehensive use of CRISPR/Cas9 editing technology, hybridization, and marker-assisted selection to accelerate multi-trait improvement and breeding process.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01369-1.

Improvement of Salinity Tolerance in Water-Saving and Drought-Resistance Rice (WDR)

Rice is one of the most economically important staple food crops in the world. Soil salinization and drought seriously restrict sustainable rice production. Drought aggravates the degree of soil salinization, and, at the same time, increased soil salinity also inhibits water absorption, resulting in physiological drought stress. Salt tolerance in rice is a complex quantitative trait controlled by multiple genes. This review presents and discusses the recent research developments on salt stress impact on rice growth, rice salt tolerance mechanisms, the identification and selection of salt-tolerant rice resources, and strategies to improve rice salt tolerance. In recent years, the increased cultivation of water-saving and drought-resistance rice (WDR) has shown great application potential in alleviating the water resource crisis and ensuring food and ecological security. Here, we present an innovative germplasm selection strategy of salt-tolerant WDR, using a population that is developed by recurrent selection based on dominant genic male sterility. We aim to provide a reference for efficient genetic improvement and germplasm innovation of complex traits (drought and salt tolerance) that can be translated into breeding all economically important cereal crops.

Advancement in the Breeding, Biotechnological and Genomic Tools towards Development of Durable Genetic Resistance against the Rice Blast Disease

Rice production needs to be sustained in the coming decades, as the changeable climatic conditions are becoming more conducive to disease outbreaks. The majority of rice diseases cause enormous economic damage and yield instability. Among them, rice blast caused by Magnaportheoryzae is a serious fungal disease and is considered one of the major threats to world rice production. This pathogen can infect the above-ground tissues of rice plants at any growth stage and causes complete crop failure under favorable conditions. Therefore, management of blast disease is essentially required to sustain global food production. When looking at the drawback of chemical management strategy, the development of durable, resistant varieties is one of the most sustainable, economic, and environment-friendly approaches to counter the outbreaks of rice blasts. Interestingly, several blast-resistant rice cultivars have been developed with the help of breeding and biotechnological methods. In addition, 146 R genes have been identified, and 37 among them have been molecularly characterized to date. Further, more than 500 loci have been identified for blast resistance which enhances the resources for developing blast resistance through marker-assisted selection (MAS), marker-assisted backcross breeding (MABB), and genome editing tools. Apart from these, a better understanding of rice blast pathogens, the infection process of the pathogen, and the genetics of the immune response of the host plant are very important for the effective management of the blast disease. Further, high throughput phenotyping and disease screening protocols have played significant roles in easy comprehension of the mechanism of disease spread. The present review critically emphasizes the pathogenesis, pathogenomics, screening techniques, traditional and molecular breeding approaches, and transgenic and genome editing tools to develop a broad spectrum and durable resistance against blast disease in rice. The updated and comprehensive information presented in this review would be definitely helpful for the researchers, breeders, and students in the planning and execution of a resistance breeding program in rice against this pathogen.

Deep Learning Utilization in Agriculture: Detection of Rice Plant Diseases Using an Improved CNN Model

Rice is considered one the most important plants globally because it is a source of food for over half the world’s population. Like other plants, rice is susceptible to diseases that may affect the quantity and quality of produce. It sometimes results in anywhere between 20–40% crop loss production. Early detection of these diseases can positively affect the harvest, and thus farmers would have to be knowledgeable about the various disease and how to identify them visually. Even then, it is an impossible task for farmers to survey the vast farmlands on a daily basis. Even if this is possible, it becomes a costly task that will, in turn, increases the price of rice for consumers. Machine learning algorithms fitted to drone technology combined with the Internet of Things (IoT) can offer a solution to this problem. In this paper, we propose a Deep Convolutional Neural Network (DCNN) transfer learning-based approach for the accurate detection and classification of rice leaf disease. The modified proposed approach includes a modified VGG19-based transfer learning method. The proposed modified system can accurately detect and diagnose six distinct classes: healthy, narrow brown spot, leaf scald, leaf blast, brown spot, and bacterial leaf blight. The highest average accuracy is 96.08% using the non-normalized augmented dataset. The corresponding precision, recall, specificity, and F1-score were 0.9620, 0.9617, 0.9921, and 0.9616, respectively. The proposed modified approach achieved significantly better results compared with similar approaches using the same dataset or similar-size datasets reported in the extant literature.

Management of Post-Harvest Anthracnose: Current Approaches and Future Perspectives

Anthracnose is a severe disease caused by Colletotrichum spp. on several crop species. Fungal infections can occur both in the field and at the post-harvest stage causing severe lesions on fruits and economic losses. Physical treatments and synthetic fungicides have traditionally been the preferred means to control anthracnose adverse effects; however, the urgent need to decrease the use of toxic chemicals led to the investigation of innovative and sustainable protection techniques. Evidence for the efficacy of biological agents and vegetal derivates has been reported; however, their introduction into actual crop protection strategies requires the solutions of several critical issues. Biotechnology-based approaches have also been explored, revealing the opportunity to develop innovative and safe methods for anthracnose management through genome editing and RNA interference technologies. Nevertheless, besides the number of advantages related to their use, e.g., the putative absence of adverse effects due to their high specificity, a number of aspects remain to be clarified to enable their introduction into Integrated Pest Management (IPM) protocols against Colletotrichum spp. disease.

Increasing the level of resistant starch in 'Presidio' rice through multiplex CRISPR-Cas9 gene editing of starch branching enzyme genes

Rice (Oryza sativa L.) is an excellent source of starch, which is composed of amylopectin and amylose. Resistant starch (RS) is a starch product that is not easily digestible and absorbed in the stomach or small intestine and instead is passed on directly to the large intestine. Cereals high in RS may be beneficial to improve human health and reduce the risk of diet-related chronic diseases. It has been reported through chemical mutagenesis and RNA interference studies that starch branching enzymes (SBEs) play a major role in contributing to higher levels of RS in cereal crops. In this study, we used multiplex clustered regularly interspaced short palindromic repeat (CRISPR)-CRISPR associated protein 9 (Cas9) genome editing to simultaneously target all four SBE genes in rice using the endogenous transfer RNA (tRNA)-processing system for expressing the single-guide RNAs (sgRNAs) targeting these genes. The CRISPR-Cas9 vector construct with four SBE gene sgRNAs was transformed into the U.S. rice cultivar Presidio using Agrobacterium-mediated transformation. Knockout mutations were identified at all four SBE genes across eight transgene-positive T₀ plants. Transgene-free T₁ lines with different combinations of disrupted SBE genes were identified, with several SBE-edited lines showing significantly increased RS content up to 15% higher than the wild-type (WT) cultivar Presidio. Although further efforts are needed to fix all of the mutant alleles as homozygous, our study demonstrated the potential of multiplex genome editing to develop high-RS lines.

How Could the Use of Crop Wild Relatives in Breeding Increase the Adaptation of Crops to Marginal Environments?

Alongside the use of fertilizer and chemical control of weeds, pests, and diseases modern breeding has been very successful in generating cultivars that have increased agricultural production several fold in favorable environments. These typically homogeneous cultivars (either homozygous inbreds or hybrids derived from inbred parents) are bred under optimal field conditions and perform well when there is sufficient water and nutrients. However, such optimal conditions are rare globally; indeed, a large proportion of arable land could be considered marginal for agricultural production. Marginal agricultural land typically has poor fertility and/or shallow soil depth, is subject to soil erosion, and often occurs in semi-arid or saline environments. Moreover, these marginal environments are expected to expand with ongoing climate change and progressive degradation of soil and water resources globally. Crop wild relatives (CWRs), most often used in breeding as sources of biotic resistance, often also possess traits adapting them to marginal environments. Wild progenitors have been selected over the course of their evolutionary history to maintain their fitness under a diverse range of stresses. Conversely, modern breeding for broad adaptation has reduced genetic diversity and increased genetic vulnerability to biotic and abiotic challenges. There is potential to exploit genetic heterogeneity, as opposed to genetic uniformity, in breeding for the utilization of marginal lands. This review discusses the adaptive traits that could improve the performance of cultivars in marginal environments and breeding strategies to deploy them.

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.

The genetic editing of GS3 via CRISPR/Cas9 accelerates the breeding of three-line hybrid rice with superior yield and grain quality

Grain size is one of the major traits that determine rice grain yield and quality. The GS3 gene is the first major quantitative trait locus (QTL) that was identified in regulating rice grain length and weight. It was reported that the gs3 allele with a mutation in the organ size regulation (OSR) domain of the GS3 protein produced longer grains. In this study, we used the CRISPR/Cas9 gene editing technology to introduce an edited gs3 allele into our indica maintainer line, Mei1B, to enhance its grain yield and quality. Through molecular analysis and sequencing, a homologous edited-gs3 mutant line without any transgene was obtained in the T1 generation and was named Mei2B. A superior male sterile line Mei2A was generated by backcrossing the cytoplasmic male sterile (CMS) line Mei1A with Mei2B. Mei2B had a higher grain quality and yield compared to its wild-type Mei1B. Its grain length increased by 7.9%, its length/width ratio increased from 3.89 to 4.19, TGW increased by 6.7%, and grain yield per plant increased by 14.9%. In addition, genetic improvement of other quality traits including brown rice length (6.83 mm), brown rice grain length/width ratio (3.61), matched the appearance standards set for traditional Simiao (silk seedling) type cultivars. Two restorer lines were outcrossed to both Mei1A and Mei2A to produce hybrid rice. Compared to two hybrids of Mei1A, the hybrids of Mei2A had longer grains, higher length/width ratio, TGW, and yield per plant. In addition, the hybrids of Mei2A showed a better grain appearance including better translucency, a lower chalky rice rate, and degree of chalkiness than the hybrids of Mei1A. These results demonstrated that the introduction of an elite gs3 allele into Mei1A via CRISPR/Cas9 gene editing technology led to significant genetic improvement of the rice grain. The resultant CMS line Mei2A(gs3) displayed much higher grain quality and yield than the original Mei1A. Therefore, our study demonstrated that the targeted genetic improvement via gene editing technology can enhance rice breeding, especially the breeding of three-line hybrid rice.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-022-01290-z.

State-of-the-Art in CRISPR Technology and Engineering Drought, Salinity, and Thermo-tolerant crop plants

Our review has described principles and functional importance of CRISPR-Cas9 with emphasis on the recent advancements, such as CRISPR-Cpf1, base editing (BE), prime editing (PE), epigenome editing, tissue-specific (CRISPR-TSKO), and inducible genome editing and their potential applications in generating stress-tolerant plants. Improved agricultural practices and enhanced food crop production using innovative crop breeding technology is essential for increasing access to nutritious foods across the planet. The crop plants play a pivotal role in energy and nutrient supply to humans. The abiotic stress factors, such as drought, heat, and salinity cause a substantial yield loss in crop plants and threaten food security. The most sustainable and eco-friendly way to overcome these challenges are the breeding of crop cultivars with improved tolerance against abiotic stress factors. The conventional plant breeding methods have been highly successful in developing abiotic stress-tolerant crop varieties, but usually cumbersome and time-consuming. Alternatively, the CRISPR/Cas genome editing has emerged as a revolutionary tool for making efficient and precise genetic manipulations in plant genomes. Here, we provide a comprehensive review of the CRISPR/Cas genome editing (GE) technology with an emphasis on recent advances in the plant genome editing, including base editing (BE), prime editing (PE), epigenome editing, tissue-specific (CRISPR-TSKO), and inducible genome editing (CRISPR-IGE), which can be used for obtaining cultivars with enhanced tolerance to various abiotic stress factors. We also describe tissue culture-free, DNA-free GE technology, and some of the CRISPR-based tools that can be modified for their use in crop plants.

Multiple Abiotic Stresses Applied Simultaneously Elicit Distinct Responses in Two Contrasting Rice Cultivars

Rice crops are often subject to multiple abiotic stresses simultaneously in both natural and cultivated environments, resulting in yield reductions beyond those expected from single stress. We report physiological changes after a 4 day exposure to combined drought, salt and extreme temperature treatments, following a 2 day salinity pre-treatment in two rice genotypes—Nipponbare (a paddy rice) and IAC1131 (an upland landrace). Stomata closed after two days of combined stresses, causing intercellular CO2 concentrations and assimilation rates to diminish rapidly. Abscisic acid (ABA) levels increased at least five-fold but did not differ significantly between the genotypes. Tandem Mass Tag isotopic labelling quantitative proteomics revealed 6215 reproducibly identified proteins in mature leaves across the two genotypes and three time points (0, 2 and 4 days of stress). Of these, 987 were differentially expressed due to stress (cf. control plants), including 41 proteins that changed significantly in abundance in all stressed plants. Heat shock proteins, late embryogenesis abundant proteins and photosynthesis-related proteins were consistently responsive to stress in both Nipponbare and IAC1131. Remarkably, even after 2 days of stress there were almost six times fewer proteins differentially expressed in IAC1131 than Nipponbare. This contrast in the translational response to multiple stresses is consistent with the known tolerance of IAC1131 to dryland conditions.

Prospectus of Genomic Selection and Phenomics in Cereal, Legume and Oilseed Breeding Programs

The last decade witnessed an unprecedented increase in the adoption of genomic selection (GS) and phenomics tools in plant breeding programs, especially in major cereal crops. GS has demonstrated the potential for selecting superior genotypes with high precision and accelerating the breeding cycle. Phenomics is a rapidly advancing domain to alleviate phenotyping bottlenecks and explores new large-scale phenotyping and data acquisition methods. In this review, we discuss the lesson learned from GS and phenomics in six self-pollinated crops, primarily focusing on rice, wheat, soybean, common bean, chickpea, and groundnut, and their implementation schemes are discussed after assessing their impact in the breeding programs. Here, the status of the adoption of genomics and phenomics is provided for those crops, with a complete GS overview. GS’s progress until 2020 is discussed in detail, and relevant information and links to the source codes are provided for implementing this technology into plant breeding programs, with most of the examples from wheat breeding programs. Detailed information about various phenotyping tools is provided to strengthen the field of phenomics for a plant breeder in the coming years. Finally, we highlight the benefits of merging genomic selection, phenomics, and machine and deep learning that have resulted in extraordinary results during recent years in wheat, rice, and soybean. Hence, there is a potential for adopting these technologies into crops like the common bean, chickpea, and groundnut. The adoption of phenomics and GS into different breeding programs will accelerate genetic gain that would create an impact on food security, realizing the need to feed an ever-growing population.

CRISPR-Cas9 mediated mutation in GRAIN WIDTH and WEIGHT2 (GW2) locus improves aleurone layer and grain nutritional quality in rice

Enhancing crop productivity and their nutritional quality are the key components and primary focus of crop improvement strategy for fulfilling future food demand and improving human health. Grain filling and endosperm development are the key determinants of grain yield and nutritional quality. GRAIN WIDTH and WEIGHT2 (GW2) gene encodes a RING-type E3 ubiquitin ligase and determines the grain weight in cereal crops. Here we report GW2 knockout (KO) mutants in Indica (var. MTU1010) through CRISPR/Cas9 genome editing. The endosperm of GW2-KO mutant seed displays a thick aleurone layer with enhanced grain protein content. Further the loss of function of OsGW2 results in improved accumulation of essential dietary minerals (Fe, Zn, K, P, Ca) in the endosperm of rice grain. Additionally, the mutants displayed an early growth vigour phenotype with an improved root and shoot architecture. The hull morphology of GW2-KO lines also showed improved, grain filling thereby promoting larger grain architecture. Together, our findings indicate that GW2 may serve as a key regulator of improved grain architecture, grain nutritional quality and an important modulator of plant morphology. The study offers a strategy for the development of improved rice cultivars with enriched nutritional quality and its possible implementation in other cereals as well.

Multiplex Genome-Editing Technologies for Revolutionizing Plant Biology and Crop Improvement

Multiplex genome-editing (MGE) technologies are recently developed versatile bioengineering tools for modifying two or more specific DNA loci in a genome with high precision. These genome-editing tools have greatly increased the feasibility of introducing desired changes at multiple nucleotide levels into a target genome. In particular, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) [CRISPR/Cas] system-based MGE tools allow the simultaneous generation of direct mutations precisely at multiple loci in a gene or multiple genes. MGE is enhancing the field of plant molecular biology and providing capabilities for revolutionizing modern crop-breeding methods as it was virtually impossible to edit genomes so precisely at the single base-pair level with prior genome-editing tools, such as zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs). Recently, researchers have not only started using MGE tools to advance genome-editing applications in certain plant science fields but also have attempted to decipher and answer basic questions related to plant biology. In this review, we discuss the current progress that has been made toward the development and utilization of MGE tools with an emphasis on the improvements in plant biology after the discovery of CRISPR/Cas9. Furthermore, the most recent advancements involving CRISPR/Cas applications for editing multiple loci or genes are described. Finally, insights into the strengths and importance of MGE technology in advancing crop-improvement programs are presented.

Potato biofortification: an effective way to fight global hidden hunger

Hidden hunger is leading to extensive health problems in the developing world. Several strategies could be used to reduce the micronutrient deficiencies by increasing the dietary uptake of essential micronutrients. These include diet diversification, pharmaceutical supplementation, food fortification and crop biofortification. Among all, crop biofortification is the most sustainable and acceptable strategy to overcome the global issue of hidden hunger. Since most of the people suffering from micronutrient deficiencies, have monetary issues and are dependent on staple crops to fulfil their recommended daily requirements of various essential micronutrients. Therefore, increasing the micronutrient concentrations in cost effective staple crops seems to be an effective solution. Potato being the world's most consumed non-grain staple crop with enormous industrial demand appears to be an ideal candidate for biofortification. It can be grown in different climatic conditions, provide high yield, nutrition and dry matter in lesser time. In addition, huge potato germplasm have natural variations related to micronutrient concentrations, which can be utilized for its biofortification. This review discuss the current scenario of micronutrient malnutrition and various strategies that could be used to overcome it. The review also shed a light on the genetic variations present in potato germplasm and suggest effective ways to incorporate them into modern high yielding potato varieties.

A method for determining the cutting efficiency of the CRISPR/Cas system in birch and poplar

Determination of Cas9 cutting efficiency to the target sites is important for genome editing. However, this determination can only be made via an in vitro method, as the purification of Cas protein and synthesis of gRNA are necessary. Here, we developed an in vivo method, called transient CRISPR/Cas editing in plants (TCEP) to determine Cas9 cutting efficiency. The CRISPR/Cas vector for plant transformation mediated by Agrobacterium tumefaciens was constructed as normal. Using the transient transformation method we built, the Cas9 protein and gRNA were transiently expressed and formed a complex to cut its target sites, resulting in dynamic DNA breakage. The broken DNA was quantified using qPCR to measure the efficiencies of Cas9 cutting. We studied the Cas9 cutting efficiencies to different target sites in Betula platyphylla and Populus davidiana×P. bolleana plants using TCEP and an in vitro method. The results of TCEP were consistent with those of the in vitro method, suggesting that the TCEP method is reliable in determining cutting efficiency. Additionally, using the TCEP method, we showed that both heat and sonication treatment significantly improved CRISPR/Cas efficiency. Therefore, the TCEP method has broad application value and can not only be used to analyze the CRISPR/Cas efficiency but also to determine the factors involved in Cas9 cutting.

Improving the Rice Photosynthetic Efficiency and Yield by Editing OsHXK1 via CRISPR/Cas9 System

Rice (Oryza sativa L.) is an important food crop species in China. Cultivating high-yielding rice varieties that have a high photosynthetic efficiency is an important goal of rice breeding in China. In recent years, due to the continual innovation of molecular breeding methods, many excellent genes have been applied in rice breeding, which is highly important for increasing rice yields. In this paper, the hexokinase gene OsHXK1 was knocked out via the CRISPR/Cas9 gene-editing method in the indica rice varieties Huanghuazhan, Meixiangzhan, and Wushansimiao, and OsHXK1-CRISPR/Cas9 lines were obtained. According to the results of a phenotypic analysis and agronomic trait statistics, the OsHXK1-CRISPR/Cas9 plants presented increased light saturation points, stomatal conductance, light tolerance, photosynthetic products, and rice yields. Moreover, transcriptome analysis showed that the expression of photosynthesis-related genes significantly increased. Taken together, our results revealed that knocking out OsHXK1 via the CRISPR/Cas9 gene-editing method could effectively lead to the cultivation of high-photosynthetic efficiency and high-yielding rice varieties. They also revealed the important roles of OsHXK1 in the regulation of rice yield and photosynthesis.

CRISPR Genome Editing Technology: A Powerful Tool Applied to Developing Agribusiness

The natural increase of the world's population implies boosting agricultural demand. In the current non-optimistic global scenario, where adverse climate changes come associated with substantial population growth, the main challenge in agribusiness is food security. Recently, the CRISPR/Cas system has emerged as a friendly gene editing biotechnological tool, enabling a precise manipulation of genomes and enhancement of desirable traits in several organisms. This review highlights the CRISPR/Cas system as a paramount tool for the improvement of agribusiness products and brings up-to-date findings showing its potential applications in improving agricultural-related traits in major plant crops and farm animals, all representing economic-relevant commodities responsible for feeding the world. Several applied pieces of research have successfully demonstrated the CRISPR/Cas ability in boosting interesting traits in agribusiness products, including animal productivity and welfare, crop yield growth, and seed quality, reflecting positive impacts in both socioeconomics and human health aspects. Hence, the CRISPR/Cas system has revolutionized bioscience and biotechnology, and its concrete application in agribusiness goods is on the horizon.

A single transcript CRISPR/Cas9 mediated mutagenesis of CaERF28 confers anthracnose resistance in chilli pepper (Capsicum annuum L.)

T-DNA-free homozygous mutant lines developed through a single transcript CRISPR/Cas9 system harboring the desired modification in the CaERF28 locus exhibited significantly enhanced resistance to the anthracnose pathogen Colletotrichum truncatum coupled with the improved expression of defense responsive genes. Anthracnose, caused by Colletotrichum species, is a major disease of chilli (Capsicum annuum) accounting for significant pre- and post-harvest yield losses across the tropical and subtropical regions of the world. Management of chilli anthracnose using traditional methods have not met with noticeable success. In the present study, we have demonstrated an enhanced anthracnose resistance through a single transcript unit CRISPR/Cas9 mediated alteration of the susceptibility gene CaERF28 in C. annuum. A construct with a single Pol II promoter-driven expression of Cas9, sgRNA and a hammerhead ribozyme (RZ) was designed to modify the CaERF28 gene in the susceptible chilli genotype Arka Lohit. Fourty-five C-ERF28-induced mutant lines (72.5%) were identified from 62 T₀ transgenic plants. Further, simultaneously targeted multiple sites within CaERF28 showed increased mutation (85.7%) efficiency. DNA sequence analysis showed that these plants harboured multiple InDels at the target site. The allelic mutants of C-ERF28 were transferred to the following generations by simple Mendelian inheritance. Segregation in the T₁ and T₂ generations resulted in the identification of T-DNA free and marker-free C-ERF28 mutant lines. Five homozygous mutants demonstrated enhanced resistance to anthracnose compared to wild type as demonstrated by reduced spore count and fungal growth as well as induced expression of defense-related genes. Our results demonstrated that the STU-CRISPR/Cas9 mediated editing of the CaERF28 gene is a rapid, safe and versatile approach for enhancing anthracnose resistance in chilli pepper and pave way for its utilization in the improvement of other solanaceous crops.

Mechanistic insights of CRISPR/Cas-mediated genome editing towards enhancing abiotic stress tolerance in plants

Abiotic stresses such as temperature (high/low), drought, salinity, and others make the environment hostile to plants. Abiotic stressors adversely affect plant growth and development; and thereby makes a direct impact on overall plant productivity. Plants confront stress by developing an internal defense system orchestrated by compatible solutes, reactive oxygen species scavengers and phytohormones. However, routine exposure to unpredictable environmental stressors makes it essential to equip plants with a system that contributes to sustainable agricultural productivity, besides imparting multi-stress tolerance. The sustainable approach against abiotic stress is accomplished through breeding of tolerant cultivars. Though eco-friendly, tedious screening and crossing protocol limits its usage to overcome stress and in attaining the goal of global food security. Advancement on the technological front has enabled adoption of genomic engineering approaches to perform site-specific modification in the plant genome for improving adaptability, increasing the yield and in attributing resilience against different stressors. Of the different genome editing approaches, CRISPR/Cas has revolutionized biological research with wider applicability to crop plants. CRISPR/Cas emerged as a versatile tool in editing genomes for desired traits in highly accurate and precise manner. The present study summarizes advancement of the CRISPR/Cas genome editing tool in its adoption to manipulate plant genomes for novel traits towards developing high-yielding and climate-resilient crop varieties.

Base editing in rice: current progress, advances, limitations, and future perspectives

Base editing is one of the promising genome editing tools for generating single-nucleotide changes in rice genome. Rice (Oryza sativa L.) is an important staple food crop, feeding half of the population around the globe. Developing new rice varieties with desirable agronomic traits is necessary for sustaining global food security. The use of genome editing technologies for developing rice varieties is pre-requisite in the present scenario. Among the genome editing technologies developed for rice crop improvement, base editing technology has emerged as an efficient and reliable tool for precise genome editing in rice plants. Base editing technology utilizes either adenosine or cytidine base editor for precise editing at the target region. A base editor (adenosine or cytidine) is a fusion of catalytically inactive CRISPR/Cas9 domain and adenosine or cytidine deaminase domain. In this review, authors have discussed the different adenine and cytosine base editors developed so far for precise genome editing of rice via base editing technology. We address the current progress, advances, limitations, as well as future perspectives of the base editing technology for rice crop improvement.

Novel CRISPR-Cas Systems: An Updated Review of the Current Achievements, Applications, and Future Research Perspectives

According to Darwin's theory, endless evolution leads to a revolution. One such example is the Clustered Regularly Interspaced Palindromic Repeats (CRISPR)-Cas system, an adaptive immunity system in most archaea and many bacteria. Gene editing technology possesses a crucial potential to dramatically impact miscellaneous areas of life, and CRISPR-Cas represents the most suitable strategy. The system has ignited a revolution in the field of genetic engineering. The ease, precision, affordability of this system is akin to a Midas touch for researchers editing genomes. Undoubtedly, the applications of this system are endless. The CRISPR-Cas system is extensively employed in the treatment of infectious and genetic diseases, in metabolic disorders, in curing cancer, in developing sustainable methods for fuel production and chemicals, in improving the quality and quantity of food crops, and thus in catering to global food demands. Future applications of CRISPR-Cas will provide benefits for everyone and will save countless lives. The technology is evolving rapidly; therefore, an overview of continuous improvement is important. In this review, we aim to elucidate the current state of the CRISPR-Cas revolution in a tailor-made format from its discovery to exciting breakthroughs at the application level and further upcoming trends related to opportunities and challenges including ethical concerns.

CRISPR-Cas technology in corn: a new key to unlock genetic knowledge and create novel products

Since its inception in 2012, CRISPR-Cas technologies have taken the life science community by storm. Maize genetics research is no exception. Investigators around the world have adapted CRISPR tools to advance maize genetics research in many ways. The principle application has been targeted mutagenesis to confirm candidate genes identified using map-based methods. Researchers are also developing tools to more effectively apply CRISPR-Cas technologies to maize because successful application of CRISPR-Cas relies on target gene identification, guide RNA development, vector design and construction, CRISPR-Cas reagent delivery to maize tissues, and plant characterization, each contributing unique challenges to CRISPR-Cas efficacy. Recent advances continue to chip away at major barriers that prevent more widespread use of CRISPR-Cas technologies in maize, including germplasm-independent delivery of CRISPR-Cas reagents and production of high-resolution genomic data in relevant germplasm to facilitate CRISPR-Cas experimental design. This has led to the development of novel breeding tools to advance maize genetics and demonstrations of how CRISPR-Cas technologies might be used to enhance maize germplasm.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-021-01200-9.

Assessment of the roles of SPO11-2 and SPO11-4 in meiosis in rice using CRISPR/Cas9 mutagenesis

In Arabidopsis, chromosomal double-strand breaks at meiosis are presumably catalyzed by two distinct SPO11 transesterases, AtSPO11-1 and AtSPO11-2, together with M-TOPVIB. To clarify the roles of the SPO11 paralogs in rice, we used CRISPR/Cas9 mutagenesis to produce null biallelic mutants in OsSPO11-1, OsSPO11-2, and OsSPO11-4. Similar to Osspo11-1, biallelic mutations in the first exon of OsSPO11-2 led to complete panicle sterility. Conversely, all Osspo11-4 biallelic mutants were fertile. To generate segregating Osspo11-2 mutant lines, we developed a strategy based on dual intron targeting. Similar to Osspo11-1, the pollen mother cells of Osspo11-2 progeny plants showed an absence of bivalent formation at metaphase I, aberrant segregation of homologous chromosomes, and formation of non-viable tetrads. In contrast, the chromosome behavior in Osspo11-4 male meiocytes was indistinguishable from that in the wild type. While similar numbers of OsDMC1 foci were revealed by immunostaining in wild-type and Osspo11-4 prophase pollen mother cells (114 and 101, respectively), a surprisingly high number (85) of foci was observed in the sterile Osspo11-2 mutant, indicative of a divergent function between OsSPO11-1 and OsSPO11-2. This study demonstrates that whereas OsSPO11-1 and OsSPO11-2 are the likely orthologs of AtSPO11-1 and AtSPO11-2, OsSPO11-4 has no major role in wild-type rice meiosis.