OsGLYI3, a glyoxalase gene expressed in rice seed, contributes to seed longevity and salt stress tolerance

Integrated analysis of BSA-seq and RNA-seq identified the candidate genes for seed weight in Brassica juncea

Introduction

Brassica juncea is a major oilseed crop of Brassica. The seed weight is one of yield components in oilseed Brassica crops. Research on the genetic mechanism of seed weight is not only directly related to the yield and economic value of Brassica juncea but also can provide a theory foundation for studying other Brassica crops.

Methods

To map the genes for seed weight, the parental and F2 extreme bulks derived were constructed from the cross between the heavy-seeded accession 7981 and the light-seeded one Sichuan yellow (SY) of B. juncea, and used in bulk segregant sequencing (BSA-seq). Meanwhile, RNA-sequencing (RNA-seq) was performed for both parents at six seed development stages.

Results

Our results showed that a total of thirty five SNPs were identified in thirty two genes located on chromosomes A02 and A10, while fifty eight InDels in fifty one genes located on A01, A03, A05, A07, A09, A10, B01, B02 and B04. The 7,679 differentially expressed genes were identified in developing seeds between the parents. Furthermore, integrated analysis of BSA-seq and RNA-seq data revealed a cluster of nine genes on chromosome A10 and one gene on chromosome A05 that are putative candidate genes controlling seed weight in B. juncea.

Discussion

This study provides a new reference for research on Brassica seed weight and lays a solid foundation for the examination of seed in other Brassica crops.

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.

Integration Linkage Mapping and Comparative Transcriptome Analysis to Dissect the Genetic Basis of Rice Salt Tolerance Associated with the Germination Stage

Soil salinity poses a serious threat to rice production. The salt tolerance of rice at the germination stage is one of the major determinants of stable stand establishment, which is very important for direct seeding in saline soil. The complexity and polygenic nature of salt tolerance have limited the efficiency of discovering and cloning key genes in rice. In this study, an RIL population with an ultra-high-density genetic map was employed to investigate the salt-tolerant genetic basis in rice, and a total of 20 QTLs were detected, including a major and stable QTL (qRCL3-1). Subsequently, salt-specific DEGs from a comparative transcriptome analysis were overlaid onto annotated genes located on a stable QTL interval, and eight putative candidate genes were further identified. Finally, from the sequence alignment and variant analysis, OsCam1-1 was confirmed to be the most promising candidate gene for regulating salinity tolerance in rice. This study provides important information for elucidating the genetic and molecular basis of rice salt tolerance at the germination stage, and the genes detected here will be useful for improvements in rice salt tolerance.

OsRAV1 Regulates Seed Vigor and Salt Tolerance During Germination in Rice

Seed vigor is a complex trait encompassing seed germination, seedling emergence, growth, seed longevity, and stress tolerance, all are crucial for direct seeding in rice. Here, we report that the AP2/ERF transcription factor OsRAV1 (RELATED TO ABI3 AND VP1) positively regulates seed germination, vigor, and salt tolerance. Additionally, OsRAV1 was differently expressed in embryo and endosperm, with the OsRAV1 localized in the nucleus. Transcriptomic analysis revealed that OsRAV1 modulates seed vigor through plant hormone signal transduction and phenylpropanoid biosynthesis during germination. Haplotype analysis showed that rice varieties carrying Hap3 displayed enhanced salt tolerance during seed germination. These findings suggest that OsRAV1 is a potential target in breeding rice varieties with high seed vigor suitable for direct seeding cultivation.

Methylglyoxal detoxifying gene families in tomato: Genome-wide identification, evolution, functional prediction, and transcript profiling

Methylglyoxal (MG) is a highly cytotoxic molecule produced in all biological systems, which could be converted into non-toxic D-lactate by an evolutionarily conserved glyoxalase pathway. Glutathione-dependent glyoxalase I (GLYI) and glyoxalase II (GLYII) are responsible for the detoxification of MG into D-lactate in sequential reactions, while DJ-1 domain containing glyoxalase III (GLYIII) catalyzes the same reaction in a single step without glutathione dependency. Afterwards, D-lactate dehydrogenase (D-LDH) converts D-lactate into pyruvate, a metabolically usable intermediate. In the study, a comprehensive genome-wide investigation has been performed in one of the important vegetable plants, tomato to identify 13 putative GLYI, 4 GLYII, 3 GLYIII (DJ-1), and 4 D-LDH genes. Expression pattern analysis using microarray data confirmed their ubiquitous presence in different tissues and developmental stages. Moreover, stress treatment of tomato seedlings and subsequent qRT-PCR demonstrated upregulation of SlGLYI-2, SlGLYI-3, SlGLYI-6A, SlGLYII-1A, SlGLYII-3B, SlDJ-1A, SlDLDH-1 and SlDLDH-4 in response to different abiotic stresses, whereas SlGLYI-6B, SlGLYII-1B, SlGLYII-3A, SlDJ-1D and SlDLDH-2 were downregulated. Expression data also revealed SlGLYII-1B, SlGLYI-1A, SlGLYI-2, SlDJ-1D, and SlDLDH-4 were upregulated in response to various pathogenic infections, indicating the role of MG detoxifying enzymes in both plant defence and stress modulation. The functional characterization of each of these members could lay the foundation for the development of stress and disease-resistant plants promoting sustainable agriculture and production.

MpNAC1, a transcription factor from the mangrove associate Millettia pinnata, confers salt and drought stress tolerance in transgenic Arabidopsis and rice

Pongamia (Millettia pinnata Syn. Pongamia pinnata), a mangrove associate plant, exhibits good stress tolerance, making it a treasure of genetic resources for crop improvement. NAC proteins are plant-specific transcription factors, which have been elucidated to participate in the regulation and tolerance of abiotic stresses (such as salt and drought). Here, we identified a salt-induced gene from Pongamia, MpNAC1, which encodes an NAC factor sharing five highly conserved domains with other NACs and exhibits close homology to AtNAC19/AtNAC55/AtNAC72 in Arabidopsis. MpNAC1 showed nuclear localization and transcriptional activator activity. MpNAC1-overexpressing Arabidopsis exhibited significantly stronger salt and drought tolerance compared with wild-type plants. The expression levels of stress-responsive genes were activated in transgenic Arabidopsis. Furthermore, the heterologous expression of MpNAC1 also enhanced the salt and drought tolerance of transgenic rice. The major agronomic traits, such as plant height and tiller number, panicle length, grain size, and yield, were similar between the transgenic lines and wild type under normal field growth conditions. RNA-Seq analysis revealed that MpNAC1 significantly up-regulated stress-responsive genes and activated the biosynthesis of secondary metabolites such as flavonoids, resulting in increased stress tolerance. Taken together, the MpNAC1 increased salt and drought stress tolerance in transgenic plants and did not retard the plant growth and development under normal growth conditions, suggesting the potential of MpNAC1 in breeding stress-resilient crops.

The association of protein-bound methionine sulfoxide with proteomic basis for aging in beech seeds

BACKGROUND

European beech (Fagus sylvatica L.) trees produce seeds irregularly; therefore, it is necessary to store beech seeds for forestation. Despite the acquisition of desiccation tolerance during development, beech seeds are classified as intermediate because they lose viability during long-term storage faster than typical orthodox seeds. In this study, beech seeds stored for short (3 years) or long (20 years) periods under optimal conditions and displaying 92 and 30% germination capacity, respectively, were compared.

RESULTS

Aged seeds displayed increased membrane damage, manifested as electrolyte leakage and lipid peroxidation levels. Analyses have been based on embryonic axes, which contained higher levels of reactive oxygen species (ROS) and higher levels of protein-bound methionine sulfoxide (MetO) in aged seeds. Using label-free quantitative proteomics, 3,949 proteins were identified, of which 2,442 were reliably quantified pointing to 24 more abundant proteins and 35 less abundant proteins in beech seeds under long-term storage conditions. Functional analyses based on gene ontology annotations revealed that nucleic acid binding activity (molecular function), ribosome organization or biogenesis and transmembrane transport (cellular processes), translational proteins (protein class) and membranous anatomical entities (cellular compartment) were affected in aged seeds. To verify whether MetO, the oxidative posttranslational modification of proteins that can be reversed via the action of methionine sulfoxide reductase (Msr) enzymes, is involved in the aging of beech seeds, we identified and quantified 226 MetO-containing proteins, among which 9 and 19 exhibited significantly up- and downregulated MetO levels, respectively, in beech seeds under long-term storage conditions. Several Msr isoforms were identified and recognized as MsrA1-like, MsrA4, MsrB5 and MsrB5-like in beech seeds. Only MsrA1-like displayed decreased abundance in aged seeds.

CONCLUSIONS

We demonstrated that the loss of membrane integrity reflected in the elevated abundance of membrane proteins had a higher impact on seed aging progress than the MetO/Msr system. Proteome analyses enabled us to propose protein Sec61 and glyceraldehyde-3-phosphate dehydrogenase as potential longevity modulators in beech seeds.

Role of methylglyoxal and glyoxalase in the regulation of plant response to heavy metal stress

KEY MESSAGE

Methylglyoxal and glyoxalase function a significant role in plant response to heavy metal stress. We update and discuss the most recent developments of methylglyoxal and glyoxalase in regulating plant response to heavy metal stress. Methylglyoxal (MG), a by-product of several metabolic processes, is created by both enzymatic and non-enzymatic mechanisms. It plays an important role in plant growth and development, signal transduction, and response to heavy metal stress (HMS). Changes in MG content and glyoxalase (GLY) activity under HMS imply that they may be potential biomarkers of plant stress resistance. In this review, we summarize recent advances in research on the mechanisms of MG and GLY in the regulation of plant responses to HMS. It has been discovered that appropriate concentrations of MG assist plants in maintaining a balance between growth and development and survival defense, therefore shielding them from heavy metal harm. MG and GLY regulate plant physiological processes by remodeling cellular redox homeostasis, regulating stomatal movement, and crosstalking with other signaling molecules (including abscisic acid, gibberellic acid, jasmonic acid, cytokinin, salicylic acid, melatonin, ethylene, hydrogen sulfide, and nitric oxide). We also discuss the involvement of MG and GLY in the regulation of plant responses to HMS at the transcriptional, translational, and metabolic levels. Lastly, considering the current state of research, we present a perspective on the future direction of MG research to elucidate the MG anti-stress mechanism and offer a theoretical foundation and useful advice for the remediation of heavy metal-contaminated environments in the future.

A glutathione-independent DJ-1/Pfp1 domain containing glyoxalase III, OsDJ-1C, functions in abiotic stress adaptation in rice

MAIN CONCLUSION

Overexpression of OsDJ-1C in rice improves root architecture, photosynthesis, yield and abiotic stress tolerance through modulating methylglyoxal levels, antioxidant defense, and redox homeostasis. Exposure to abiotic stresses leads to elevated methylglyoxal (MG) levels in plants, impacting seed germination and root growth. In response, the activation of NADPH-dependent aldo-keto reductase and glutathione (GSH)-dependent glyoxalase enzymes helps to regulate MG levels and reduce its toxic effects. However, detoxification may not be carried out effectively due to the limitation of GSH and NADPH in plants under stress. Recently, a novel enzyme called glyoxalase III (GLY III) has been discovered which can detoxify MG in a single step without needing GSH. To understand the physiological importance of this pathway in rice, we overexpressed the gene encoding GLYIII enzyme (OsDJ-1C) in rice. It was observed that OsDJ-1C overexpression in rice regulated MG levels under stress conditions thus, linked well with plants' abiotic stress tolerance potential. The OsDJ-1C overexpression lines displayed better root architecture, improved photosynthesis, and reduced yield penalty compared to the WT plants under salinity, and drought stress conditions. These plants demonstrated an improved GSH/GSSG ratio, reduced level of reactive oxygen species, increased antioxidant capacity, and higher anti-glycation activity thereby indicating that the GLYIII mediated MG detoxification plays a significant role in plants' ability to reduce the impact of abiotic stress. Furthermore, these findings imply the potential of OsDJ-1C in crop improvement programs.

Methylglyoxal metabolism is altered during defence response in pigeonpea (Cajanus cajan (L.) Millsp.) against the spotted pod borer (Maruca vitrata)

Pigeonpea (Cajanus cajan ) production can be affected by the spotted pod borer (Maruca vitrata ). Here, we identified biochemical changes in plant parts of pigeonpea after M. vitrata infestation. Two pigeonpea genotypes (AL 1747, moderately resistant; and MN 1, susceptible) were compared for glyoxalase and non-glyoxalase enzyme systems responsible for methylglyoxal (MG) detoxification, γ-glutamylcysteine synthetase (γ-GCS), glutathione-S-transferase (GST) and glutathione content in leaves, flowers and pods under control and insect-infested conditions. MN 1 had major damage due to M. vitrata infestation compared to AL 1747. Lower accumulation of MG in AL 1747 was due to higher activities of enzymes of GSH-dependent (glyoxylase I, glyoxylase II), GSH-independent (glyoxalase III) pathway, and enzyme of non-glyoxalase pathway (methylglyoxal reductase, MGR), which convert MG to lactate. Decreased glyoxylase enzymes and MGR activities in MN 1 resulted in higher accumulation of MG. Higher lactate dehydrogenase (LDH) activity in AL 1747 indicates utilisation of MG detoxification pathway. Higher glutathione content in AL 1747 genotype might be responsible for efficient working of MG detoxification pathway under insect infestation. Higher activity of γ-GCS in AL 1747 maintains the glutathione pool, necessary for the functioning of glyoxylase pathway to carry out the detoxification of MG. Higher activities of GST and GPX in AL 1747 might be responsible for detoxification of toxic products that accumulates following insect infestation, and elevated activities of glyoxylase and non-glyoxylase enzyme systems in AL 1747 after infestation might be responsible for reducing reactive cabanoyl stress. Our investigation will help the future development of resistant cultivars.

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.

Identification and molecular evolution of the GLX genes in 21 plant species: a focus on the Gossypium hirsutum

BACKGROUND

The glyoxalase system includes glyoxalase I (GLXI), glyoxalase II (GLXII) and glyoxalase III (GLXIII), which are responsible for methylglyoxal (MG) detoxification and involved in abiotic stress responses such as drought, salinity and heavy metal.

RESULTS

In this study, a total of 620 GLX family genes were identified from 21 different plant species. The results of evolutionary analysis showed that GLX genes exist in all species from lower plants to higher plants, inferring that GLX genes might be important for plants, and GLXI and GLXII account for the majority. In addition, motif showed an expanding trend in the process of evolution. The analysis of cis-acting elements in 21 different plant species showed that the promoter region of the GLX genes were rich in phytohormones and biotic and abiotic stress-related elements, indicating that GLX genes can participate in a variety of life processes. In cotton, GLXs could be divided into two groups and most GLXIs distributed in group I, GLXIIs and GLXIIIs mainly belonged to group II, indicating that there are more similarities between GLXII and GLXIII in cotton evolution. The transcriptome data analysis and quantitative real-time PCR analysis (qRT-PCR) show that some members of GLX family would respond to high temperature treatment in G.hirsutum. The protein interaction network of GLXs in G.hirsutum implied that most members can participate in various life processes through protein interactions.

CONCLUSIONS

The results elucidated the evolutionary history of GLX family genes in plants and lay the foundation for their functions analysis in cotton.

Elevated methylglyoxal levels inhibit tomato fruit ripening by preventing ethylene biosynthesis

Methylglyoxal (MG), a toxic compound produced as a by-product of several cellular processes, such as respiration and photosynthesis, is well known for its deleterious effects, mainly through glycation of proteins during plant stress responses. However, very little is known about its impact on fruit ripening. Here, we found that MG levels are maintained at high levels in green tomato (Solanum lycopersicum L.) fruits and decline during fruit ripening despite a respiratory burst during this transition. We demonstrate that this decline is mainly mediated through a glutathione-dependent MG detoxification pathway and primarily catalyzed by a Glyoxalase I enzyme encoded by the SlGLYI4 gene. SlGLYI4 is a direct target of the MADS-box transcription factor RIPENING INHIBITOR (RIN), and its expression is induced during fruit ripening. Silencing of SlGLYI4 leads to drastic MG overaccumulation at ripening stages of transgenic fruits and interferes with the ripening process. MG most likely glycates and inhibits key enzymes such as methionine synthase and S-adenosyl methionine synthase in the ethylene biosynthesis pathway, thereby indirectly affecting fruit pigmentation and cell wall metabolism. MG overaccumulation in fruits of several nonripening or ripening-inhibited tomato mutants suggests that the tightly regulated MG detoxification process is crucial for normal ripening progression. Our results underpin a SlGLYI4-mediated regulatory mechanism by which MG detoxification controls fruit ripening in tomato.

Genome-wide analysis and expression profiling of glyoxalase gene families in oat (Avena sativa) indicate their responses to abiotic stress during seed germination

Abiotic stresses have deleterious effects on seed germination and seedling establishment, leading to significant crop yield losses. Adverse environmental conditions can cause the accumulation of methylglyoxal (MG) within plant cells, which can negatively impact plant growth and development. The glyoxalase system, which consists of the glutathione (GSH)-dependent enzymes glyoxalase I (GLX1) and glyoxalase II (GLX2), as well as the GSH-independent glyoxalase III (GLX3 or DJ-1), plays a crucial role in detoxifying MG. However, genome-wide analysis of glyoxalase genes has not been performed for one of the agricultural important species, oat (Avena sativa). This study identified a total of 26 AsGLX1 genes, including 8 genes encoding Ni²⁺-dependent GLX1s and 2 genes encoding Zn²⁺-dependent GLX1s. Additionally, 14 AsGLX2 genes were identified, of which 3 genes encoded proteins with both lactamase B and hydroxyacylglutathione hydrolase C-terminal domains and potential catalytic activity, and 15 AsGLX3 genes encoding proteins containing double DJ-1 domains. The domain architecture of the three gene families strongly correlates with the clades observed in the phylogenetic trees. The AsGLX1, AsGLX2, and AsGLX3 genes were evenly distributed in the A, C, and D subgenomes, and gene duplication of AsGLX1 and AsGLX3 genes resulted from tandem duplications. Besides the core cis-elements, hormone responsive elements dominated the promoter regions of the glyoxalase genes, and stress responsive elements were also frequently observed. The subcellular localization of glyoxalases was predicted to be primarily in the cytoplasm, chloroplasts, and mitochondria, with a few presents in the nucleus, which is consistent with their tissue-specific expression. The highest expression levels were observed in leaves and seeds, indicating that these genes may play important roles in maintaining leaf function and ensuring seed vigor. Moreover, based on in silico predication and expression pattern analysis, AsGLX1-7A, AsGLX2-5D, AsDJ-1-5D, AsGLX1-3D2, and AsGLX1-2A were suggested as promising candidate genes for improving stress resistance or seed vigor in oat. Overall, the identification and analysis of the glyoxalase gene families in this study can provide new strategies for improving oat stress resistance and seed vigor.

Seedling establishment: The neglected trait in the seed longevity field

Seed longevity is a central actor in plant germplasm resource conservation, species reproduction, geographical distribution, crop yield and quality and food processing and safety. Seed longevity and vigor decrease gradually during storage, which directly influences seed germination and post-germination seedling establishment. It is noted that seedling establishment is a key shift from heterotropism to autotropism and is fueled by the energy reserved in the seeds per se. Numerous studies have demonstrated that expedited catabolism of triacylglycerols, fatty acid and sugars during seed storage is closely related to seed longevity. Storage of farm-saved seeds of elite cultivars for use in subsequent years is a common practice and it is recognized that aged seed (especially those stored under less-than-ideal conditions) can lead to poor seed germination, but the significance of poor seedling establishment as a separate factor capable of influencing crop yield has been overlooked. This review article summarizes the relationship between seed germination and seedling establishment and the effect of different seed reserves on seed longevity. Based on this, we emphasize the importance of simultaneous scoring of seedling establishment and germination percentage from aged seeds and discuss the reasons.

The Potential of CRISPR/Cas Technology to Enhance Crop Performance on Adverse Soil Conditions

Worldwide food security is under threat in the actual scenery of global climate change because the major staple food crops are not adapted to hostile climatic and soil conditions. Significant efforts have been performed to maintain the actual yield of crops, using traditional breeding and innovative molecular techniques to assist them. However, additional strategies are necessary to achieve the future food demand. Clustered regularly interspaced short palindromic repeat/CRISPR-associated protein (CRISPR/Cas) technology, as well as its variants, have emerged as alternatives to transgenic plant breeding. This novelty has helped to accelerate the necessary modifications in major crops to confront the impact of abiotic stress on agriculture systems. This review summarizes the current advances in CRISPR/Cas applications in crops to deal with the main hostile soil conditions, such as drought, flooding and waterlogging, salinity, heavy metals, and nutrient deficiencies. In addition, the potential of extremophytes as a reservoir of new molecular mechanisms for abiotic stress tolerance, as well as their orthologue identification and edition in crops, is shown. Moreover, the future challenges and prospects related to CRISPR/Cas technology issues, legal regulations, and customer acceptance will be discussed.