Genome-wide survey and expression analysis suggest diverse roles of glutaredoxin gene family members during development and response to various stimuli in rice

Hydrogen peroxide positively regulates ABA signaling via oxidative modification of the C2H2-type zinc finger protein ZFP36 in rice

The rice zinc finger protein ZFP36 serves as a pivotal regulator of the hydrogen peroxide (H2O2) signaling pathway in response to abscisic acid (ABA). Its role is crucial for integrating H2O2 signals with the plant defense mechanisms against water deficit and oxidative stress. However, it remains unclear whether ZFP36 directly modulates ABA-induced H2O2 signaling. This study explored the effects of oxidative post-translational modifications (OxiPTMs) on ZFP36 in rice, with an emphasis on the H2O2-induced oxidation through its cysteine (Cys) residues. We found that ZFP36 undergoes oxidative modification as a target of H2O2 in the presence of ABA, specifically at Cys32. Employing quantitative detection and fluorescence assays, we observed that ZFP36 oxidation enhances the expression and activity of genes encoding protective antioxidant enzymes. Moreover, our investigation into the thioredoxin (Trx) and glutaredoxin (Grx) families revealed that OsTrxh1 facilitates the reduction of oxidized ZFP36. Genetic evidence indicates that ZFP36 positively influences rice resilience to oxidative and water stress, while OsTrxh1 exerts an opposing effect. These insights reveal a distinctive pathway for plant cells to perceive ABA-induced H2O2 signaling, advance our comprehension of H2O2 signaling dynamics, and ABA-related plant responses, and lay a vital groundwork for enhancing crop stress tolerance.

A DUF966 gene family member OsDSR3 positively regulates alkali stress tolerance in rice

Rice growth and production are severely constrained by alkali stress. However, the mechanism underlying the rice tolerance to alkali stress is unclear. OsDSR3, a novel gene from the domains of unknown function 966 (DUF966) family, was identified and characterized for its function in the response of rice to alkali stress. The result of this study clearly showed that alkali stress significantly induced OsDSR3 expression level. Moreover, the expression of OsDSR3 was up-regulated by drought, salt, cold, H2O2 and abscisic acid (ABA), and down-regulated by gibberellic acid (GA3), and 2,4-Dichlorophenoxyacetic acid (2,4-D) treatments. Subcellular localization exhibited that OsDSR3 was detected in the nucleus and membrane. OsDSR3-overexpressing (OsDSR3-OE) plants showed higher tolerance to alkali stress than the wild-type (WT). In contrast, OsDSR3 knockout (OsDSR3-KO) mutants were more vulnerable to alkali stress. The differentially expressed genes (DEGs) among OsDSR3-OE and WT seedlings were mainly enriched in porphyrin and chlorophyll, starch and sucrose, and carotenoid metabolic pathways. Among these DEGs, 26 were identified as potential alkali stress-responsive genes, including several up-regulated genes like OsHAK5, OsGRX23 and OsNIR2. Consistent with the expression profiles of metabolic pathways-related genes, most of the metabolite contents and metabolite synthases activities were improved in OsDSR3-OE lines and decreased in OsDSR3-KO lines compared to WT. This may explain the higher tolerance of OE lines and lower tolerance of KO lines to alkali stress. These findings suggested that OsDSR3 positively regulates rice tolerance to alkali stress, which will help to elucidate the molecular mechanism underlying rice alkali tolerance.

The integration of TRX/GRX systems and phytohormonal signalling pathways in plant stress and development

Plant acclimation to changing environmental conditions involves the interaction of different signalling molecules, including reactive oxygen species and hormones. Redox regulation exerted by thioredoxin (TRX) and glutaredoxin (GRX), two oxidoreductases, is emerging as a specific point of control mediating signal transduction pathways associated with plant growth and stress response. Phytohormones are messengers that coordinate plant cell activities to regulate growth, defence, and productivity, although their cross-talk with components of the redox system is less known. The present review focuses on our current knowledge of the interplay that occurs between TRX and GRX systems and phytohormonal signalling pathways in connection with the control of plant development and stress responses. Here, we consider the regulation that phytohormones exert on TRX and GRX systems, as well as the involvement of these redox proteins in the control of phytohormone-mediated signalling pathways.

Development of Single-Segment Substitution Lines and Fine-Mapping of qSPP4 for Spikelets Per Panicle and qGW9 for Grain Width Based on Rice Dual-Segment Substitution Line Z783

Single segment substitution line (SSSL) libraries are an ideal platform for breeding by design. To develop SSSLs-Xihui18 covering the whole genome, a novel rice chromosome segment substitution line (CSSL), Z783, carrying two substitution segments (average length of 6.55 Mb) on Chr.4 and Chr.9 was identified, which was a gap in the library previously. Z783 was developed from the progeny of recipient "Xihui18" (an indica restorer line) and donor "Huhan3" (a japonica cultivar) by advanced backcross combined molecular marker-assisted selection (MAS). It displayed multiple panicles and less spikelets and wide grains. Then, a F2 population derived from Xihui18/Z783 was used to map quantitative trait loci (QTLs) for yield-related traits by the mixed linear model method. Nine QTLs were detected (p < 0.05). Furthermore, three SSSLs were constructed by MAS, and all 9 QTLs could be validated, and 15 novel QTLs could be detected by these SSSLs by a one-way ANOVA analysis. The genetic analysis showed that qSSP4 for less spikelets and qGW9 for wide grain all displayed dominant gene action in their SSSLs. Finally, qSSP4 and qGW9 were fine-mapped to intervals of 2.75 Mb and 1.84 Mb, on Chromosomes 4 and 9, respectively. The results lay a solid foundation for their map cloning and molecular breeding by design.

Identification and adaptive evolution analysis of glutaredoxin genes in Populus spp

Glutaredoxin (GRX) is a class of small redox proteins widely involved in cellular redox homeostasis and the regulation of various cellular processes. The role of GRX gene in the differentiation of Populus spp. is rarely reported. We compared the similarities and differences of GRX genes among four sections of poplar using bioinformatics, corrected the annotations of some GRX genes, and focused on analysing their transcript profiling and adaptive evolution in Populus spp. A total of 219 GRX genes were identified in four sections of poplar, among which annotations for 13 genes were corrected. Differences in GRX genes were found between sect. Turanga, represented by P. euphratica, and other poplar sections. Most notably, P. euphratica had the smallest number of duplication events for GRX genes (n = 9) and no tandem duplications, whereas there were >25 duplication events for all other poplars. Furthermore, we detected 18 pairs of GRX genes under positive selection pressure in various sections of poplar, and identified two groups of GRX genes in the Salicaceae that potentially underwent positive selection. Expression profiling results showed that the PtrGRX34 and its orthologous genes were upregulated under stress treatments. In summary, the GRX gene family underwent expansion during poplar differentiation, and some genes underwent rapid evolution during this process, which may be beneficial for Populus spp. to adapt to environmental changes. This study may provide more insights into the molecular mechanisms of Populus spp. adaptation to environmental changes and the adaptive evolution of GRX genes.

Glutaredoxin in Rice Growth, Development, and Stress Resistance: Mechanisms and Research Advances

Rice (Oryza sativa L.) is a staple food for more than half of the global population. Various abiotic and biotic stresses lead to accumulation of reactive oxygen species in rice, which damage macromolecules and signaling pathways. Rice has evolved a variety of antioxidant systems, including glutaredoxin (GRX), that protect against various stressors. A total of 48 GRX gene loci have been identified on 11 of the 12 chromosomes of the rice genome; none were found on chromosome 9. GRX proteins were classified into four categories according to their active sites: CPYC, CGFS, CC, and GRL. In this paper, we summarized the recent research advances regarding the roles of GRX in rice development regulation and response to stresses, and discussed future research perspectives related to rice production. This review could provide information for rice researchers on the current status of the GRX and serve as guidance for breeding superior varieties.

The Mining of Genetic Loci and the Analysis of Candidate Genes to Identify the Physical and Chemical Markers of Anti-Senescence in Rice

Premature senescence is a common occurrence in rice production, and seriously affects rice plants' nutrient utilization and growth. A total of 120 recombinant inbred lines (RILs) were obtained from successive self-crossing of F12 generations derived from Huazhan and Nekken2. The superoxide dismutase (SOD) activity, malondialdehyde (MDA), content and catalase (CAT) activity related to the anti-senescence traits and enzyme activity index of rice were measured for QTL mapping using 4858 SNPs. Thirteen QTLs related to anti-senescence were found, among which the highest LOD score was 5.70. Eighteen anti-senescence-related genes were found in these regions, and ten of them differed significantly between the parents. It was inferred that LOC_Os01g61500, LOC_Os01g61810, and LOC_Os04g40130 became involved in the regulation of the anti-senescence molecular network upon upregulation of their expression levels. The identified anti-senescence-related QTLs and candidate genes provide a genetic basis for further research on the mechanism of the molecular network that regulates premature senescence.

Genome-wide analysis of the P450 gene family in tea plant (Camellia sinensis) reveals functional diversity in abiotic stress

BACKGROUND

Cytochrome P450 (Cytochrome P450s) genes are involved in the catalysis of various reactions, including growth, development, and secondary metabolite biosynthetic pathways. However, little is known about the characteristics and functions of the P450 gene family in Camellia sinensis (C. sinensis).

RESULTS

To reveal the mechanisms of tea plant P450s coping with abiotic stresses, analyses of the tea plant P450 gene family were conducted using bioinformatics-based methods. In total, 273 putative P450 genes were identified from the genome database of C. sinensis. The results showed that P450s were well-balanced across the chromosomes I to XV of entire genome, with amino acid lengths of 268-612 aa, molecular weights of 30.95-68.5 kDa, and isoelectric points of 4.93-10.17. Phylogenetic analysis divided CsP450s into 34 subfamilies, of which CYP71 was the most abundant. The predicted subcellular localization results showed that P450 was distributed in a variety of organelles, with chloroplasts, plasma membrane,,and cytoplasm localized more frequently. The promoter region of CsP450s contained various cis-acting elements related to phytohormones and stress responses. In addition, ten conserved motifs (Motif1-Motif10) were identified in the CsP450 family proteins, with 27 genes lacking introns and only one exon. The results of genome large segment duplication showed that there were 37 pairs of genes with tandem duplication. Interaction network analysis showed that CsP450 could interact with multiple types of target genes, and there are protein interactions within the family. Tissue expression analysis showed that P450 was highly expressed in roots and stems. Moreover, qPCR analysis of the relative expression level of the gene under drought and cold stress correlated with the sequencing results.

CONCLUSIONS

This study lays the foundation for resolving the classification and functional study of P450 family genes and provides a reference for the molecular breeding of C. sinensis.

Cadmium accumulation regulated by a rice heavy-metal importer is harmful for host plant and leaf bacteria

INTRODUCTION

Cadmium (Cd), one of the major toxic heavy metals, causes severe deleterious effects on all living organisms from prokaryotes to eukaryotes. Cadmium deposition affects bacterial diversity and bacterial population in soil. Cadmium accumulation in plants is mainly controlled by transporters and the resulting Cd enrichment gives rise to phytotoxicity.

OBJECTIVE

This study aimed to mine transporters that control Cd import or accumulation in rice and uncover the underlying mechanisms that how accumulated Cd poses risks to host plant and leaf bacteria.

METHODS

RNA-seq analysis, histochemical assays, and elemental quantification were carried out to reveal the biological roles of OsABCG43 for Cd import. Pathogen inoculation, IC₅₀ value, and bacterial virulence assays were conducted to disclose the effects of Cd on leaf bacteria.

RESULTS

OsABCG43 is characterized as a Cd importer controlling Cd accumulation in rice. OsABCG43 was induced under Cd stress and specifically expressed in the vasculature of leaves and roots. Overexpression of OsABCG43 caused Cd accumulation which inhibits photosynthesis and development and alters the antioxidant system, resulting in phytotoxicity. Moreover, overexpression of OsABCG43 resulted in retarded plant growth and enhanced rice sensitivity to Cd stress. Numerous differentially expressed genes were identified via RNA-seq analysis between the OsABCG43-overexpressing plants and wild type, which functioned in Cd or reactive oxygen species (ROS) homeostasis. In addition, OsABCG43 transcripts were induced by leaf bacteria Xanthomonas oryzae pv. oryzicola (Xoc) and X. oryzae pv. oryzae (Xoo). The enriched Cd directly impaired the formation of virulence factors for the leaf bacteria, preventing colonization or proliferation of Xoc or Xoo in rice leaves.

CONCLUSION

This work reveals that OsABCG43 is expressed specifically in the vascular and plasma membrane-localized OsABCG43 functions as a Cd importer. OsABCG43-mediated import of Cd is harmful for both rice and the corresponding leaf bacteria.

Molecular bases of rice grain size and quality for optimized productivity

The accomplishment of further optimization of crop productivity in grain yield and quality is a great challenge. Grain size is one of the crucial determinants of rice yield and quality; all of these traits are typical quantitative traits controlled by multiple genes. Research advances have revealed several molecular and developmental pathways that govern these traits of agronomical importance. This review provides a comprehensive summary of these pathways, including those mediated by G-protein, the ubiquitin-proteasome system, mitogen-activated protein kinase, phytohormone, transcriptional regulators, and storage product biosynthesis and accumulation. We also generalize the excellent precedents for rice variety improvement of grain size and quality, which utilize newly developed gene editing and conventional gene pyramiding capabilities. In addition, we discuss the rational and accurate breeding strategies, with the aim of better applying molecular design to breed high-yield and superior-quality varieties.

Application of RNA sequencing to understand the response of rice seedlings to salt-alkali stress

BACKGROUND

Salt-alkali stress represents one of the most stressful events with deleterious consequences for plant growth and crop productivity. Despite studies focusing on the effects of salt-alkali stress on morphology and physiology, its molecular mechanisms remain unclear. Here, we employed RNA-sequencing (RNA-seq) to understand how Na₂CO₃ stress inhibits rice seedling growth.

RESULTS

Na₂CO₃ stress significantly inhibited the growth of rice seedlings. Through RNA-seq, many differentially expressed genes (DEGs) were shown to be potentially involved in the rice seedling response to salt-alkali stress. After 1-day and 5-day treatments, RNA-seq identified 1780 and 2315 DEGs in the Na₂CO₃-treated versus -untreated rice seedling shoots, respectively. According to the gene ontology enrichment and the Kyoto Encylopedia of Genes and Genomes annotation of DEGs, the growth-inhibition processes associated with salt-alkali stress involve a myriad of molecular events, including biosynthesis and metabolism, enzyme activity, and binding, etc. CONCLUSION: Collectively, the transcriptome analyses in the present work revealed several potential key regulators of plant response to salt-alkali stress, and might pave a way to improve salt-alkali stress tolerance in rice.

Global identification of quantitative trait loci and candidate genes for cold stress and chilling acclimation in rice through GWAS and RNA-seq

Associated analysis of GWAS with RNA-seq had detected candidate genes responsible for cold stress and chilling acclimation in rice. Haplotypes of two candidate genes and geographic distribution were analyzed. To explore new candidate genes and genetic resources for cold tolerance improvement in rice, genome-wide association study (GWAS) mapping experiments with 351 rice core germplasms was performed for three traits (survival rate, shoot length and chlorophyll content) under three temperature conditions (normal temperature, cold stress and chilling acclimation), yielding a total of 134 QTLs, of which 54, 59 and 21 QTLs were responsible for normal temperature, cold stress and chilling acclimation conditions, respectively. Integrated analysis of significant SNPs in 134 QTLs further identified 116 QTLs for three temperature treatments, 53, 43 and 18 QTLs responsible for normal temperature, cold stress and chilling acclimation, respectively, and 2 QTLs were responsible for both cold stress and chilling acclimation. Matching differentially expressed genes from RNA-seq to 43 and 18 QTLs for cold stress and chilling acclimation, we identified 69 and 44 trait-associated candidate genes, respectively, to be classified into six and five groups, particularly involved in metabolisms, reactive oxygen species scavenging and hormone signaling. Interestingly, two candidate genes LOC_Os01g04814, encoding a vacuolar protein sorting-associating protein 4B, and LOC_Os01g48440, encoding glycosyltransferase family 43 protein, showed the highest expression levels under chilling acclimation. Haplotype analysis revealed that both genes had a distinctive differentiation with subpopulation. Haplotypes of both genes with more japonica accessions have higher latitude distribution and higher chilling tolerance than the chilling sensitive indica accessions. These findings reveal the new insight into the molecular mechanism and candidate genes for cold stress and chilling acclimation in rice.

Genome-wide identification, characterization and expression analysis of glutaredoxin gene family (Grxs) in Phaseolus vulgaris

Glutaredoxins (Grxs) are ubiquitous oxidoreductase proteins implicated in development and abiotic stress response mainly through maintaining redox homoeostasis. Here, we conducted the first systematic analysis of the Grx gene family (PvGrx) in the most popular legume Phaseolus vulgaris (common bean). A total of 50 PvGrx genes were identified, and divided into four classes (CC-type, CGFS-type, CPYC-type and Grl-type) based on the phylogenetic analysis. The different classes have different introns-exons structures and conserved motifs, indicating functional divergence in the PvGrx family. Both tandem and segmental duplications were found to be involved in the expansion of PvGrx family that underwent a purifying selection by excluding the deleterious loss-of-function mutations. Cis-acting regulatory elements and gene ontology analyses predicted their role of distinctive members in abiotic stress response and hormonal signalling. RNA-seq based expression analysis revealed their differential expression pattern during plant development. On the other hand, RT q-PCR analysis revealed that target PvGrx isoforms were associated with nodule organogenesis and symbiosis based on their expression profiles. In addition, a battery of PvGrx candidates were markedly upregulated by different abiotic stressors suggesting their broad spectrum of functions. These findings serve as a reference for functional analysis and genetic improvement in P. vulgaris and related legume species.

The basic leucine zipper transcription factor OsbZIP83 and the glutaredoxins OsGRX6 and OsGRX9 facilitate rice iron utilization under the control of OsHRZ ubiquitin ligases

Under low iron availability, plants induce the expression of various genes for iron uptake and translocation. The rice (Oryza sativa) ubiquitin ligases OsHRZ1 and OsHRZ2 cause overall repression of these iron-related genes at the transcript level, but their protein-level regulation is unclear. We conducted a proteome analysis to identify key regulators whose abundance was regulated by OsHRZs at the protein level. In response to iron deficiency or OsHRZ knockdown, many genes showed differential regulation between the transcript and protein levels, including the TGA-type basic leucine zipper transcription factor OsbZIP83. We also identified two glutaredoxins, OsGRX6 and OsGRX9, as OsHRZ-interacting proteins in yeast and plant cells. OsGRX6 also interacted with OsbZIP83. Our in vitro degradation assay suggested that OsbZIP83, OsGRX6 and OsGRX9 proteins are subjected to 26S proteasome- and OsHRZ-dependent degradation. Proteome analysis and our in vitro degradation assay also suggested that OsbZIP83 protein was preferentially degraded under iron-deficient conditions in rice roots. Transgenic rice lines overexpressing OsGRX9 and OsbZIP83 showed improved tolerance to iron deficiency. Expression of iron-related genes was affected in the OsGRX9 and OsGRX6 knockdown lines, suggesting disturbed iron utilization and signaling. OsbZIP83 overexpression lines showed enhanced expression of OsYSL2 and OsNAS3, which are involved in internal iron translocation, in addition to OsGRX9 and genes related to phytoalexin biosynthesis and the salicylic acid pathway. The results suggest that OsbZIP83, OsGRX6 and OsGRX9 facilitate iron utilization downstream of the OsHRZ pathway.

Genomic insights on the contribution of introgressions from Xian/Indica to the genetic improvement of Geng/Japonica rice cultivars

Hybridization between Xian/indica (XI) and Geng/japonica (GJ) rice combined with utilization of plant ideotypes has greatly contributed to yield improvements in modern GJ rice in China over the past 50 years. To explore the genomic basis of improved yield and disease resistance in GJ rice, we conducted a large-scale genomic landscape analysis of 816 elite GJ cultivars representing multiple eras of germplasm from China. We detected consistently increasing introgressions from three XI subpopulations into GJ cultivars since the 1980s and found that the XI genome introgressions significantly increased the grain number per panicle (GN) and decreased the panicle number per plant. This contributed to the improvement of plant type during modern breeding, changing multi-tiller plants to moderate tiller plants with a large panicle size and increasing the blast resistance. Notably, we found that key gene haplotypes controlling plant architecture, yield components, and pest and disease resistance, including IPA1, SMG1, DEP3, Pib, Pi-d2, and Bph3, were introduced from XI rice by introgression. By GWAS analysis, we detected a GN-related gene Gnd5, which had been consistently introgressed from XI into GJ cultivars since the 1980s. Gnd5 is a GRAS transcription factor gene, and Gnd5 knockout mutants showed a significant reduction in GN. The estimated genetic effects of genes varied among different breeding locations, which explained the distinct introgression levels of XI gene haplotypes, including Gnd5, DEP3, etc., to these GJ breeding pedigrees. These findings reveal the genomic contributions of introgressions from XI to the trait improvements of GJ rice cultivars and provide new insights for future rice genomic breeding.

OsTGAL1 suppresses the resistance of rice to bacterial blight disease by regulating the expression of salicylic acid glucosyltransferase OsSGT1

Many TGA transcription factors participate in immune responses in the SA-mediated signaling pathway in Arabidopsis. This study identified a transcription factor OsTGAL1, which is induced upon infection by Xoo. Overexpression of OsTGAL1 increased the susceptibility of rice to Xoo. Plants overexpressing OsTGAL1 could affect the expression of many SA signaling-related genes. OsTGAL1 was able to interact with the promoter of OsSGT1, which encodes a key enzyme for SA metabolism. The transcript of OsSGT1 was induced by Xoo and this responsive expression was further increased in plants overexpressing OsTGAL1. OsSGT1 knockout lines had enhanced resistance to Xoo, and knocking out OsSGT1 in plants overexpressing OsTGAL1 blocked the susceptibility caused by OsTGAL1. Altered expression levels of several OsPRs in all the transgenic plants demonstrated that SA-mediated signaling had been affected. Furthermore, we identified an oxidoreductase of CC-type glutaredoxin, OsGRX17, which interacted with OsTGAL1. OsGRX17 reduced the regulation of OsTGAL1 on OsSGT1, and this may be due to its redox modulation. Thus, our results demonstrate that OsTGAL1 negatively regulates resistance to Xoo by its effects on SA metabolism via the activation of OsSGT1, which provides valuable targets for plant breeders in developing new cultivars that are resistant to Xoo.

Identification, In Silico Characterization, and Differential Expression Profiles of Carotenoid, Xanthophyll, Apocarotenoid Biosynthetic Pathways Genes, and Analysis of Carotenoid and Xanthophyll Accumulation in Heracleum moellendorffii Hance

Heracleum moellendorffii Hance is a non-woody forest plant widely used in China, Korea, and Japan because of its various therapeutic properties. However, the genetic details of the carotenoid pathway (CP), xanthophyll pathway (XP), and apocarotenoid pathway (AP) genes have not been studied. Thus, the CP, XP, and AP genes of H. moellendorffii were detected and analyzed. A total of fifteen genes were identified, of which eight, four, and three belonged to CP, XP, and AP, respectively. All identified genes possessed full open reading frames. Phylogenetic characterization of the identified gene sequences showed the highest similarity with other higher plants. Multiple alignments and 3D dimensional structures showed several diverse conserved motifs, such as the carotene-binding motif, dinucleotide-binding motif, and aspartate or glutamate residues. The results of real-time PCR showed that the CP, XP, and AP genes were highly expressed in leaves, followed by the stems and roots. In total, eight different individual carotenoids were identified using HPLC analysis. The highest individual and total carotenoid content were achieved in the leaves, followed by the stems and roots. This study will provide more information on the gene structure of the CP, XP, and AP genes, which may help to increase the accumulation of carotenoids in H. moellendorffii through genetic engineering. These results could be helpful for further molecular and functional studies of CP, XP, and AP genes.

The rice heavy-metal transporter OsNRAMP1 regulates disease resistance by modulating ROS homoeostasis

Crop diseases threaten food security and sustainable agriculture. Consumption of crops containing nonessential toxic metals leads to health risks for humans. Therefore, cultivation of disease-resistant and toxic metal-safe crops is a double-gain strategy that can contribute to food security. Here, we show that rice heavy-metal transporter OsNRAMP1 plays an important role in plant immunity by modulating metal ion and reactive oxygen species (ROS) homoeostasis. OsNRAMP1 expression was induced after pathogenic bacteria and fungi infections. The osnramp1 mutants had an increased content of H₂ O₂ and activity of superoxide dismutase, but decreased activity of catalase, showing enhanced broad-spectrum resistance against bacterial and fungal pathogens. RNA-seq analysis identified a number of differentially expressed genes that were involved in metal ion and ROS homoeostasis. Altered expression of metal ion-dependent ROS-scavenging enzymes genes and lower accumulation of cations such as Mn together induced compromised metal ion-dependent enzyme-catalysing activity and modulated ROS homoeostasis, which together contributed towards disease resistance in osnramp1 mutants. Furthermore, the osnramp1 mutants contained lower levels of toxic heavy metals Cd and Pb and micronutrients Ni and Mn in leaves and grains. Taken together, a proof of concept was achieved that broad-spectrum disease-resistant and toxic heavy-metal-safe rice was engineered by removal of the OsNRAMP1 gene.

Divergence of active site motifs among different classes of Populus glutaredoxins results in substrate switches

Enzymes are essential components of all biological systems. The key characteristics of proteins functioning as enzymes are their substrate specificities and catalytic efficiencies. In plants, most genes encoding enzymes are members of large gene families. Within such families, the contributions of active site motifs to the functional divergence of duplicate genes have not been well elucidated. In this study, we identified 41 glutaredoxin (GRX) genes in the Populus trichocarpa genome. GRXs are ubiquitous enzymes in plants that play important roles in developmental and stress tolerance processes. In poplar, GRX genes were divided into four classes based on clear differences in gene structure and expression pattern, subcellular localization, enzymatic activity, and substrate specificity of the encoded proteins. Using site-directed mutagenesis, this study revealed that the divergence of the active site motif among different classes of GRX proteins resulted in substrate switches and thus provided new insights into the molecular evolution of these important plant enzymes.

Regulation of ammonium acquisition and use in Oryza longistaminata ramets under nitrogen source heterogeneity

Oryza longistaminata, a wild rice, vegetatively reproduces and forms a networked clonal colony consisting of ramets connected by rhizomes. Although water, nutrients, and other molecules can be transferred between ramets via the rhizomes, inter-ramet communication in response to spatially heterogeneous nitrogen availability is not well understood. We studied the response of ramet pairs to heterogeneous nitrogen availability using a split hydroponic system that allowed each ramet root to be exposed to different conditions. Ammonium uptake was compensatively enhanced in the sufficient-side root when roots of the ramet pairs were exposed to ammonium-sufficient and ammonium-deficient conditions. Comparative transcriptome analysis revealed that a gene regulatory network for effective ammonium assimilation and amino acid biosynthesis was activated in the sufficient-side roots. Allocation of absorbed nitrogen from the nitrogen-sufficient to the nitrogen-deficient ramets was rather limited. Nitrogen was preferentially used for newly growing axillary buds on the sufficient-side ramets. Biosynthesis of trans-zeatin (tZ), a cytokinin, was upregulated in response to the nitrogen supply, but tZ appeared not to target the compensatory regulation. Our results also implied that the O. longistaminata putative ortholog of rice (Oryza sativa) C-terminally encoded peptide1 plays a role as a nitrogen-deficient signal in inter-ramet communication, providing compensatory upregulation of nitrogen assimilatory genes. These results provide insights into the molecular basis for efficient growth strategies of asexually proliferating plants growing in areas where the distribution of ammonium ions is spatially heterogeneous.

Genome-Wide Association Analysis for Salt-Induced Phenotypic and Physiologic Responses in Rice at Seedling and Reproductive Stages

Salinity is one of the main adverse environmental factors severely inhibiting rice growth and decreasing grain productivity. Developing rice varieties with salt tolerance (ST) is one of the most economical approaches to cope with salinity stress. In this study, the salt tolerance of 220 rice accessions from rice diversity panel l (RDP1), representing five subpopulations, were evaluated based on 16 ST indices at both seedling and reproductive stages under salt stress. An apparent inconsistency was found for ST between the two stages. Through a gene-based/tightly linked genome-wide association study with 201,332 single nucleotide polymorphisms (SNPs) located within genes and their flanking regions were used, a total of 214 SNPs related to 251 genes, significantly associated with 16 ST-related indices, were detected at both stages. Eighty-two SNPs with low frequency favorable (LFF) alleles in the population were proposed to hold high breeding potential in improving rice ST. Fifty-four rice accessions collectively containing all these LFF alleles were identified as donors of these alleles. Through the integration of meta-quantitative trait locus (QTL) for ST and the response patterns of differential expression genes to salt stress, thirty-eight candidate genes were suggested to be involved in the regulation of rice ST. In total, the present study provides valuable information for further characterizing ST-related genes and for breeding ST varieties across whole developmental stages through marker-assisted selection (MAS).

Identification, Characterization, and Expression Analysis of Carotenoid Biosynthesis Genes and Carotenoid Accumulation in Watercress (Nasturtium officinale R. Br.)

Watercress (Nasturtium officinale R. Br.) is an important aquatic herb species belonging to the Brassicaceae family. It has various medicinal properties and has been utilized for the treatment of cancer and other diseases; however, currently available genomic information regarding this species is limited. Here, we performed the first comprehensive analysis of the carotenoid biosynthesis pathway (CBP) genes of N. officinale, which were identified from next-generation sequencing data. We identified and characterized 11 putative carotenoid pathway genes; among these, nine full and two partial open reading frames were determined. These genes were closely related to CBP genes of the other higher plants in the phylogenetic tree. Three-dimensional structure analysis and multiple alignments revealed several distinct conserved motifs, including aspartate or glutamate residues, carotene-binding motifs, and dinucleotide-binding motifs. Quantitative reverse transcription-polymerase chain reaction results showed that the CBP was expressed in a tissue-specific manner: expression levels of NoPSY, NoPDS, NoZDS-p, NoCrtISO, NoLCYE, NoCHXE-p, and NoCCD were highest in the flower, whereas NoLCYB, NoCHXB, NoZEP, and NoNCED were highest in the leaves. Stems, roots, and seeds did not show a significant change in the expression compared to the leaves and flowers. High-performance liquid chromatography analysis of the same organs showed the presence of seven distinct carotenoid compounds. The total carotenoid content was highest in the leaves followed by flowers, seeds, stems, and roots. Among the seven individual carotenoids, the levels of six carotenoids (i.e., 13-Z-β-carotene, 9-Z-β-carotene, E-β-carotene, lutein, violaxanthin, and β-cryptoxanthin) were highest in the leaves. The highest content was observed for lutein, followed by E-β-carotene, and 9-Z-β-carotene; these carotenoids were much higher in the leaves compared to the other organs. The results will be useful references for further molecular genetics and functional studies involving this species and other closely related species.

CGFS-type glutaredoxin mutations reduce tolerance to multiple abiotic stresses in tomato

Sessile organisms such as plants have adopted diverse reactive oxygen species (ROS) scavenging mechanisms to mitigate damage under abiotic stress conditions. Though CGFS-type glutaredoxin (GRX) genes are important regulators of ROS homeostasis, each of their functions in crop plants have not yet been well understood. We performed a targeted mutagenesis analysis of four CGFS-type GRXs (SlGRXS14, SlGRXS15, SlGRXS16, and SlGRXS17) in tomato plants (Solanum lycopersicum) using a multiplex clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system and found that Slgrxs mutants were more sensitive to various abiotic stresses compared with the wild-type tomatoes. Slgrxs15 mutants were embryonic lethal. Single, double, and triple combinations of Slgrxs14, 16, and 17 mutants were examined under heat, chilling, drought, heavy metal toxicity, nutrient deficiency, and short photoperiod stresses. Slgrxs14 and 17 mutants showed hypersensitivity to almost all stresses while Slgrxs16 mutants were affected by chilling stress and showed milder sensitivity to other stresses. Additionally, Slgrxs14 and 17 mutants showed delayed flowering time. Our results indicate that the CGFS-type SlGRXs have specific roles against abiotic stresses, providing valuable resources to develop tomato and, possibly, other crop species that are tolerant to multiple abiotic stresses by genetic engineering.

Molecular Characterization, Expression Analysis of Carotenoid, Xanthophyll, Apocarotenoid Pathway Genes, and Carotenoid and Xanthophyll Accumulation in Chelidonium majus L

Chelidonium majus L. is a perennial herbaceous plant that has various medicinal properties. However, the genomic information about its carotenoid biosynthesis pathway (CBP), xanthophyll biosynthesis pathway (XBP), and apocarotenoid biosynthesis pathway (ABP) genes were limited. Thus, the CBP, XBP, and ABP genes of C. majus were identified and analyzed. Among the 15 carotenoid pathway genes identified, 11 full and 4 partial open reading frames were determined. Phylogenetic analysis of these gene sequences showed higher similarity with higher plants. Through 3D structural analysis and multiple alignments, several distinct conserved motifs were identified, including dinucleotide binding motif, carotene binding motif, and aspartate or glutamate residues. Quantitative RT-PCR showed that CBP, XBP, and ABP genes were expressed in a tissue-specific manner; the highest expression levels were achieved in flowers, followed by those in leaves, roots, and stems. The HPLC analysis of the different organs showed the presence of eight different carotenoids. The highest total carotenoid content was found in leaves, followed by that in flowers, stems, and roots. This study provides information on the molecular mechanisms involved in CBP, XBP, and ABP genes, which might help optimize the carotenoid production in C. majus. The results could also be a basis of further studies on the molecular genetics and functional analysis of CBP, XBP, and ABP genes.

Identification of rice (Oryza sativa L.) genes involved in sheath blight resistance via a genome-wide association study

Rice sheath blight (RSB) is an economically significant disease affecting rice yield worldwide. Genetic resistance to RSB is associated with multiple minor genes, with each providing a minor phenotypic effect, but the underlying dominant resistance genes remain unknown. A genome-wide association study (GWAS) of 259 diverse rice varieties, with genotypes based on a single nucleotide polymorphism (SNP) and haplotype, was conducted to assess their sheath blight reactions at three developmental stages (seedlings, tillering and booting). A total of 653 genes were correlated with sheath blight resistance, of which the disease resistance protein RPM1 (OsRSR1) and protein kinase domain-containing protein (OsRLCK5) were validated by overexpression and knockdown assays. We further found that the coiled-coil (CC) domain of OsRSR1 (OsRSR1-CC) and full-length OsRLCK5 interacted with serine hydroxymethyltransferase 1 (OsSHM1) and glutaredoxin (OsGRX20), respectively. It was found that OsSHM1, which has a role in the reactive oxygen species (ROS) burst, and OsGRX20 enhanced the antioxidation ability of plants. A regulation model of the new RSB resistance though the glutathione (GSH)-ascorbic acid (AsA) antioxidant system was therefore revealed. These results enhance our understanding of RSB resistance mechanisms and provide better gene resources for the breeding of disease resistance in rice.

Genome-wide association study and transcriptome analysis discover new genes for bacterial leaf blight resistance in rice (Oryza sativa L.)

BACKGROUND

Rice (Oryza sativa) bacterial leaf blight (BLB), caused by the hemibiotrophic Xanthomonas oryzae pv. oryzae (Xoo), is one of the most devastating diseases affecting the production of rice worldwide. The development and use of resistant rice varieties or genes is currently the most effective strategy to control BLB.

RESULTS

Here, we used 259 rice accessions, which are genotyped with 2 888 332 high-confidence single nucleotide polymorphisms (SNPs). Combining resistance variation data of 259 rice lines for two Xoo races observed in 2 years, we conducted a genome-wide association study (GWAS) to identify quantitative trait loci (QTL) conferring plant resistance against BLB. The expression levels of genes, which contains in GWAS results were also identified between the resistant and susceptible rice lines by transcriptome analysis at four time points after pathogen inoculation. From that 109 candidate resistance genes showing significant differential expression between resistant and susceptible rice lines were uncovered. Furthermore, the haplotype block structure analysis predicted 58 candidate genes for BLB resistance based on Chr. 7_707158 with a minimum P-value (-log 10 P = 9.72). Among them, two NLR protein-encoding genes, LOC_Os07g02560 and LOC_Os07g02570, exhibited significantly high expression in the resistant line, but had low expression in the susceptible line of rice.

CONCLUSIONS

Together, our results reveal novel BLB resistance gene resources, and provide important genetic basis for BLB resistance breeding of rice crops.

Advances in Sensing, Response and Regulation Mechanism of Salt Tolerance in Rice

Soil salinity is a serious menace in rice production threatening global food security. Rice responses to salt stress involve a series of biological processes, including antioxidation, osmoregulation or osmoprotection, and ion homeostasis, which are regulated by different genes. Understanding these adaptive mechanisms and the key genes involved are crucial in developing highly salt-tolerant cultivars. In this review, we discuss the molecular mechanisms of salt tolerance in rice—from sensing to transcriptional regulation of key genes—based on the current knowledge. Furthermore, we highlight the functionally validated salt-responsive genes in rice.

CC-type glutaredoxin, OsGrx_C7 plays a crucial role in enhancing protection against salt stress in rice

Soil salinity is one of the critical issue worldwide that adversely affect soil fertility. Salt stress significantly limits crop yield and grain quality; therefore, there is an urgent need to develop a strategy to improve salt stress tolerance. In present study, we reported that rice glutaredoxin (OsGrx_C7) plays a positive response in salt induced stress. Gene expression analysis, silencing, and overexpression of OsGrx_C7 gene were used to discover the role of OsGrx_C7 in response to salt stress. Gene expression analysis suggested that OsGrx_C7 expression was induced under salt stress and ubiquitously expressed in rice including root and shoot. The silencing of osgrx_c7 gene leads to increased sensitivity to salt stress, indicating its importance in salt stress tolerance. A gain-of-function approach showed that OsGrx_C7 may act as an important determinant in salt stress, compared with WT, and revealed higher biomass accumulation, improved root and plant growth under salt stress. Under salt stress condition, OsGrx_C7 overexpressing rice plants showed lower level of lipid peroxidation and Na⁺/K⁺ ratio, while proline accumulation, soluble sugar content and GSH/GSSG ratio was higher compared to WT. Furthermore, expression analysis suggested that OsGrx_C7 acted as positive regulator of salt tolerance by reinforcing the expression of transporters (OsHKT2;1, OsHKT1;5 and OsSOS1) engaged in Na⁺ homeostasis in overexpressing plants. Overall our study revealed that OsGrx_C7 emerged as a key mediator in response to salt stress in rice and could be used for engineering tolerance against salt stress in rice and other crops.

Genome-wide identification, characterization and expression profile of glutaredoxin gene family in relation to fruit ripening and response to abiotic and biotic stresses in banana (Musa acuminata)

Glutaredoxins (GRXs) are disulfide oxidoreductases that are involved in various biological processes. However, little information on the role of GRXs in the regulation of fruit ripening and the response to stress is available. In this study, we isolated 64 GRX genes from banana genome. Their encoded GRX proteins could be classified into four classes: CC, CGFS, CPYC and GRL types. The distribution and synteny of these GRXs on chromosomes, the gene structures, the promoter sequences, and the possible protein subcellular localizations were characterized. Molecular interaction network analysis suggested that MaGRX might interact with glutathione reductase (GR), sulfiredoxin, peroxiredoxin (Prx), and NADPH-dependent thioredoxin reductase C (NTRC), contributing to the antioxidative defense of banana fruit. MicroRNA prediction showed that MaGRX genes might be targeted by different miRNAs. Transcriptome analysis characterized the expression profiles of different MaGRX genes during banana fruit ripening, and in response to different storage stresses. The results suggested that CC-type, CPYC-type and GRL-type MaGRXs might be more active than CGFS-type MaGRXs during banana fruit ripening and the response to stress. Moreover, MaGRX6/7/9/11/17/23/28 and MaGRL3/16/19 might play important roles in regulating fruit ripening or in response to low and high temperature, or Fusarium proliferatum infection.

Iron-Sulfur Cluster Protein NITROGEN FIXATION S-LIKE1 and Its Interactor FRATAXIN Function in Plant Immunity

Iron-sulfur (Fe-S) clusters are inorganic cofactors that are present in all kingdoms of life as part of a large number of proteins involved in several cellular processes, including DNA replication and metabolism. In this work, we demonstrate an additional role for two Fe-S cluster genes in biotic stress responses in plants. Eleven Fe-S cluster genes, including the NITROGEN FIXATION S-LIKE1 (NFS1) and its interactor FRATAXIN (FH), when silenced in Nicotiana benthamiana, compromised nonhost resistance to Pseudomonas syringae pv. tomato T1. NbNFS1 expression was induced by pathogens and salicylic acid. Arabidopsis (Arabidopsis thaliana) atnfs and atfh mutants, with reduced AtNFS1 or AtFH gene expression, respectively, showed increased susceptibility to both host and nonhost pathogen infection. Arabidopsis AtNFS1 and AtFH overexpressor lines displayed decreased susceptibility to infection by host pathogen P syringae pv. tomato DC3000. The AtNFS1 overexpression line exhibited constitutive upregulation of several defense-related genes and enrichment of gene ontology terms related to immunity and salicylic acid responses. Our results demonstrate that NFS1 and its interactor FH are involved not only in nonhost resistance but also in basal resistance, suggesting a new role of the Fe-S cluster pathway in plant immunity.

Overexpression of rice glutaredoxin genes LOC_Os02g40500 and LOC_Os01g27140 regulate plant responses to drought stress

Glutaredoxins (Grxs) are small (10-15 kDa) glutathione (GSH) - dependent redox proteins. The role of Grxs are well documented in tolerance to heavy metal stress in prokaryotic and mammalian systems and a few plant genera, but is poorly understood in plants against drought. In the present study, two rice glutaredoxin (Osgrx) genes (LOC_Os02g40500 and LOC_Os01g27140) responsible for tolerance against heavy metal stress have been studied for investigating their role against drought. Each glutaredoxin gene was over-expressed in Arabidopsis thaliana to reveal their role in drought stress. The relative expression of both Osgrx genes was higher in the transgenic lines. Transgenic lines of both Osgrxs showed longer roots, higher seed germination, and survival efficiency during drought stress. The physiological parameters (P_N, g_s, E, WUE, qP, NPQ and ETR), antioxidant enzymes (GRX, GR, GPX, GST, APX, POD, SOD, CAT, DHAR, and MDHAR), antioxidant molecules (ascorbate and GSH) and stress-responsive amino acids (cysteine and proline) levels were additionally increased in transgenic lines of both Osgrxs to provide drought tolerance. The outcomes from this study strongly determined that each Osgrx gene participated in the moderation of drought and might be utilized in biological engineering strategies to overcome drought conditions in different crops.

A rice glutaredoxin regulate the expression of aquaporin genes and modulate root responses to provide arsenic tolerance

Rice is the most consumed food crop and essential determinant in global food security program. Currently, arsenic (As) accumulation in rice is a critical concern in terms of both crop productivity and grain quality; therefore, it is an urgent need to reduce As accumulation. Here, we selected a glutaredoxin (OsGrx_C7) gene that plays an essential role in AsIII tolerance in rice. To explore the mechanism, we raised OsGrx_C7 overexpression (OE) rice lines, which showed improved plant AsIII tolerance and lowered its accumulation in grains. Arsenic accumulation in husk, unpolished, and polished rice reduced by ca. 65%, 67%, and 85%, respectively, in OE lines, compared to wild-type (WT) plants. To know the rationale, expression of AsIII transporters (aquaporins) in root and shoot tissues were examined, and revealed that OsGrx_C7 regulates the expression of these genes, which ultimately reduces root to shoot AsIII translocation. Additionally, OsGrx_C7 improves root growth by regulating the expression of oxidative stress-induced root expansion related genes, promote root growth and plant health. Overall, current study suggested that AsIII induced OsGrx_C7 markedly enhanced tolerance to AsIII with reduced accumulation in grains by regulating root expansion and controlling root to shoot As transport by altered expression of AsIII aquaporins.

Transcription activation of β-carotene biosynthetic genes at the initial stage of stresses as an indicator of the increased β-carotene accumulation in isolated Dunaliella salina strain GY-H13

β-carotene is an efficient antioxidant and its accumulation is an oxidative response to stressors. Dunaliella salina strain GY-H13 is rich in β-carotene under environmental stresses, which was selected as material to understand the molecular mechanism underlying β-carotene biosynthesis. Seven full length cDNA sequences in β-carotene biosynthesis pathway were cloned, including geranylgeranyl pyrophosphate synthase (GGPS), phytoene synthase (PSY), phytoene desaturase (PDS), 15-cis-zeta-carotene isomerase (ZISO), zeta-carotene desaturase (ZDS), prolycopene isomerase (CRTISO), lycopene beta-cyclase (LCYb). The seven protein sequences from the strain GY-H13 showed the highest similarity with other D. salina strains. Especially, PSY, PDS and LCYb protein sequences shared 100 % identity. Phylogenetic analysis indicated all proteins from GY-H13 firstly clustered with those from other D. salina strains with a bootstrap of 100 %. Multiple alignment indicated several distinct conserved motifs such as aspartate-rich domain (ARD), dinucleotide binding domain (DBD), and carotene binding domain (CBD). These motifs are located near ligand-binding pocket, which may be required for the activity of enzyme. Expression levels of these genes and β-carotene content were measured over 24-h cycle, showing clear daily dynamics. All genes were dramatically up-regulated in the morning but the highest accumulation of β-carotene was observed at noon, suggesting a lag-effect between gene transcription and biological response. Furthermore, the accumulation of β-carotene increased under nitrogen deficiency, Cd exposure and high light and decreased under high salinity in a time-dependent manner. No gene of β-carotene biosynthesis was up-regulated by high salinity while most genes were activated by the other stresses at the beginning stage of exposure. Growth inhibition and oxidative damage were also observed under high salinity. Overall, transcription activation of β-carotene biosynthetic genes at the initial stage of stress exposure is a determinant of the increased accumulation of β-carotene in microalgae, which help their survive under harsh environments. The newly isolated D. salina strain GY-H13 would be a promising microalgae model for investigating the molecular mechanism of stress-induced β-carotene biosynthesis.

Over-expression of chickpea glutaredoxin (CaGrx) provides tolerance to heavy metals by reducing metal accumulation and improved physiological and antioxidant defence system

Glutaredoxins (Grxs) are small multifunctional redox proteins. Grxs have glutathione-dependent oxidoreductase activity in the presence of glutathione reductase and NADPH. The role of Grxs is well studied in heavy metal tolerance in prokaryotic and mammalian systems but not in plant genera. In the present study, a chickpea glutaredoxin (CaGrx) gene (LOC101493651) has been investigated against metal stress based on its primary screening in chickpea which revealed higher up-regulation of CaGrx gene under various heavy metals (AsIII-25 μM, AsV-250 μM, Cr(VI)-300 μM, and Cd-500 μM) stress. This CaGrx gene was overexpressed in Arabidopsis thaliana and investigated various biochemical and physiological performances under each metal stress. Transgenic plants showed significant up-regulation of the CaGrx gene during qRT-PCR analysis as well as longer roots, higher seed germination, and survival efficiency during each metal stress. The levels of stress markers, TBARS, H₂O_2, and electrolyte leakage were found to be less in transgenic lines as compared to WT revealed less toxicity in transgenics. The total accumulation of AsIII, AsV, and Cr(VI) were significantly reduced in all transgenic lines except Cd, which was slightly reduced. The physiological parameters such as net photosynthetic rate (P_N), stomatal conductance (g_s), transpiration (E), water use efficiency (WUE), photochemical quenching (qP), and electron transport rate (ETR), were maintained in transgenic lines during metal stress. Various antioxidant enzymes such as glutaredoxin (GRX), glutathione reductase (GR), glutathione peroxidase (GPX), glutathione-S-transferase (GST), ascorbate peroxidase (APX), superoxide dismutase (SOD), catalase (CAT), dehydroascorbate reductase (DHAR), monodehydroascorbate reductase (MDHAR), antioxidant molecules (ascorbate, GSH) and stress-responsive amino acids (proline and cysteine) levels were significantly increased in transgenic lines which provide metal tolerance. The outcome of this study strongly indicates that the CaGrx gene participates in the moderation of metal stress in Arabidopsis, which can be utilized in biotechnological interventions to overcome heavy metal stress conditions in different crops.

Genome-wide expression analysis suggests glutaredoxin genes response to various stresses in cotton

Oxidative stress reflects an imbalance between the systemic manifestation of reactive oxygen species (ROS) and a biological system's ability to readily detoxify the reactive intermediates or to repair the resulting damage. Glutaredoxins (GRXs) are ubiquitous oxidoreductase enzymes involved in diverse cellular processes and play a key role in oxidative stress responsive mechanisms. This study was aimed to explore the structure-function relationship and to provide a framework for functional validation and biochemical characterization of various GRX members. In this study, our analysis revealed the presence of 127 genes encoding GRX proteins in G. hirsutum. A total of 758 genes from two typical monocot and nine dicot species were naturally divided into four classes based on phylogenetic analysis. The classification was supported with organization of conserved protein motifs and sequence logos comparison between cotton, rice and Arabidopsis. Cotton GRX gene family has underwent strong purifying selection with limited functional divergence. A good collinearity was observed in the synteny analysis of four Gossypium species. Majority of cotton GRXs were influenced by various phytohormones and abiotic stress conditions during expression analysis, suggesting an important role of GRX proteins in response to oxidative stress. Cis-regulatory elements, gene enrichments and co-expression network analysis also support their predicted role against various abiotic stresses. Whole genome and segmental duplication were determined to be the two major impetuses for the expansion of gene numbers during the evolution. The identification of GRX genes showing differential expression in specific tissues or in response to environmental stimuli provides a new avenue for in-depth characterization of selected genes of importance. This study will further broaden our insights into the evolution and functional elucidation of GRX gene family in cotton.

In Silico Identification of QTL-Based Polymorphic Genes as Salt-Responsive Potential Candidates through Mapping with Two Reference Genomes in Rice

Recent advances in next generation sequencing have created opportunities to directly identify genetic loci and candidate genes for abiotic stress responses in plants. With the objective of identifying candidate genes within the previously identified QTL-hotspots, the whole genomes of two divergent cultivars for salt responses, namely At 354 and Bg 352, were re-sequenced using Illumina Hiseq 2500 100PE platform and mapped to Nipponbare and R498 genomes. The sequencing results revealed approximately 2.4 million SNPs and 0.2 million InDels with reference to Nipponbare while 1.3 million and 0.07 million with reference to R498 in two parents. In total, 32,914 genes were reported across all rice chromosomes of this study. Gene mining within QTL hotspots revealed 1236 genes, out of which 106 genes were related to abiotic stress. In addition, 27 abiotic stress-related genes were identified in non-QTL regions. Altogether, 32 genes were identified as potential genes containing polymorphic non-synonymous SNPs or InDels between two parents. Out of 10 genes detected with InDels, tolerant haplotypes of Os01g0581400, Os10g0107000, Os11g0655900, Os12g0622500, and Os12g0624200 were found in the known salinity tolerant donor varieties. Our findings on different haplotypes would be useful in developing resilient rice varieties for abiotic stress by haplotype-based breeding studies.

Identification of Maize CC-Type Glutaredoxins That Are Associated with Response to Drought Stress

Global maize cultivation is often adversely affected by drought stress. The CC-type glutaredoxin (GRX) genes form a plant-specific subfamily that regulate plant growth and respond to environmental stresses. However, how maize CC-type GRX (ZmGRXCC) genes respond to drought stress remains unclear. We performed a TBLASTN search to identify ZmGRXCCs in the maize genome and verified the identified sequences using the NCBI conservative domain database (CDD). We further established a phylogenetic tree using Mega7 and surveyed known cis-elements in the promoters of ZmGRXCCs using the PlantCARE database. We found twenty-one ZmGRXCCs in the maize genome by a genome-wide investigation and compared their phylogenetic relationships with rice, maize, and Arabidopsis. The analysis of their redox active sites showed that most of the 21 ZmGRXCCs share similar structures with their homologs. We assessed their expression at young seedlings and adult leaves under drought stress and their expression profiles in 15 tissues, and found that they were differentially expressed, indicating that different ZmGRXCC genes have different functions. Notably, ZmGRXCC14 is up-regulated at seedling, V12, V14, V16, and R1 stages. Importantly, significant associations between genetic variation in ZmGRXCC14 and drought tolerance are found at the seedling stage. These results will help to advance the study of the function of ZmGRXCCs genes under drought stress and understand the mechanism of drought resistance in maize.

Overexpression of a CPYC-Type Glutaredoxin, OsGrxC2.2, Causes Abnormal Embryos and an Increased Grain Weight in Rice

Glutaredoxins (Grxs) are a ubiquitous group of oxidoreductase enzymes that are important in plant growth and development; however, the functions of rice Grxs have not been fully elucidated. In this paper, we showed that one of the Grxs, encoded by OsGrxC2.2, exhibited Grx activity. Furthermore, we demonstrated that OsGrxC2.2 was able to regulate embryo development during embryogenesis. Transgenic rice lines overexpressing OsGrxC2.2 unexpectedly exhibited degenerate embryos as well as embryoless seeds. Our data indicated that the embryonic abnormalities occurred at an early stage during embryogenesis. We found that the expression of several endodermal layer marker genes for embryo development, such as OSH1 (apical region marker), OsSCR (L2 ground tissue marker), and OsPNH1 (L3 vascular tissue marker), were significantly decreased in the OsGrxC2.2-overexpressed transgenic rice lines. In contrast, the transcript levels of the majority of protodermal layer markers, including HAZ1, ROC2, ROC3, and RAmy1A, and the shoot apical meristem marker HB, showed little change between the wild-type (WT) and OsGrxC2.2-overexpressing embryos. Surprisingly, the seed weight of the overexpressed transgenic rice was remarkably increased in comparison to that of the WT. These results indicate that the overexpression of OsGrxC2.2 interferes with the normal embryogenesis of rice embryos and leads to increased grain weight. To the best of our knowledge, this is the first report that OsGrxC2.2 is a rice embryo development-associated gene.

Transcriptome monitoring visualizes growth stage-dependent nutrient status dynamics in rice under field conditions

Crop plants undergo morpho-physiological changes throughout the growth process in response to both the internal and the external environment, and that eventually determine the yield. The system-level adjustment of the morpho-physiological changes has remained largely unclear, however, especially in field conditions. Here, we reveal changes in nutrient status associated with tiller development and soil conditions based on the leaf transcriptome profile of rice (Oryza sativa) throughout the entire period of growth. We performed gene co-expression network analysis and identified three gene sets as indicators for monitoring the internal nitrogen and phosphorus status. Expression profiling reveals that the phosphorus starvation response is expressed during the tillering stage and is then switched off with the transition to nitrogen deficiency. Coincident with phosphorus status dynamics, the level of phosphate in the leaf is demonstrated to be low during the tillering stage and subsequently increases drastically. The phosphorus dynamics are genetically validated by analysing mutants with a defect in phosphorus homeostasis. Notably, we show that nitrogen limitation directly suppresses the phosphorus starvation response. Finally, the phosphorus starvation response is demonstrated to be activated in soil with a high phosphate retention capacity, without the visible phenotypes associated with phosphorus starvation. Our results reveal a growth stage- and soil condition-dependent reaction that requires phosphorus, which is expressed to promote the phosphorus uptake required for developing tillers and is directly adjusted by nitrogen status. A molecular framework for elucidating nutrient status dynamics under field conditions would provide insights into improving crop productivity.

Transcriptomic response of durum wheat to cold stress at reproductive stage

Understanding the genetic basis of cold tolerance is a key step towards obtaining new and improved crop varieties. Current geographical distribution of durum wheat in Argentina exposes the plants to frost damage when spikes have already emerged. Biochemical pathways involved in cold tolerance are known to be early activated at above freezing temperatures. In this study we reported the transcriptome of CBW0101 spring durum wheat by merging data from untreated control and cold (5 °C) treated plant samples at reproductive stage. A total of 128,804 unigenes were predicted. Near 62% of the unigenes were annotated in at least one database. In total 876 unigenes were differentially expressed (DEGs), 562 were up-regulated and 314 down-regulated in treated samples. DEGs are involved in many critical processes including, photosynthetic activity, lipid and carbohydrate synthesis and accumulation of amino acids and seed proteins. Twenty-eight transcription factors (TFs) belonging to 14 families resulted differentially expressed from which eight families comprised of only TFs induced by cold. We also found 31 differentially expressed Long non-coding RNAs (lncRNAs), most of them up-regulated in treated plants. Two of these lncRNAs could operate via microRNAs (miRNAs) target mimic. Our results suggest a reprogramming of expression patterns in CBW0101 that affects a number of genes that is closer to the number reported in winter genotypes. These observations could partially explain its moderate tolerance (low proportion of frost-damaged spikes) when exposed to freezing days in the field.

Identification and Analysis of a CPYC-Type Glutaredoxin Associated with Stress Response in Rubber Trees

Glutaredoxins (GRXs) are a class of small oxidoreductases which modulate various biological processes in plants. Here, we isolated a GRX gene from the rubber tree (Hevea brasiliensis Müll. Arg.), named as HbSRGRX1, which encoded 107 amino acid residues with a CPYC active site. Phylogenetic analysis displayed that HbSRGRX1 was more correlated with GRXs from Manihot esculenta Crantz. and Ricinus communis L. HbSRGRX1 was localized in the nuclei of tobacco cells, and its transcripts were preferentially expressed in male flowers and in the high-yield variety Reyan 7-33-97 with strong resistance against cold. The expression levels of HbSRGRX1 significantly decreased in tapping panel dryness (TPD) trees. Furthermore, HbSRGRX1 was regulated by wounding, hydrogen peroxide (H2O2), and multiple hormones. Altogether, these results suggest important roles of HbSRGRX1 in plant development and defense response to TPD and multiple stresses.

Identification and characterization of drought-responsive CC-type glutaredoxins from cassava cultivars reveals their involvement in ABA signalling

BACKGROUND

CC-type glutaredoxins (GRXs) are plant-specific glutaredoxin, play regulatory roles in response of biotic and abiotic stress. However, it is not clear whether the CC-type GRXs are involve in drought response in cassava (Manihot esculenta), an important tropical tuber root crop.

RESULTS

Herein, genome-wide analysis identified 18 CC-type GRXs in the cassava genome, of which six (namely MeGRXC3, C4, C7, C14, C15, and C18) were induced by drought stress in leaves of two cassava cultivars Argentina 7 (Arg7) and South China 124 (SC124). Exogenous abscisic acid (ABA) application induced the expression of all the six CC-type GRXs in leaves of both Arg7 and SC124 plants. Overexpression of MeGRXC15 in Arabidopsis (Col-0) increases tolerance of ABA on the sealed agar plates, but results in drought hypersensitivity in soil-grown plants. The results of microarray assays show that MeGRXC15 overexpression affected the expression of a set of transcription factors which involve in stress response, ABA, and JA/ET signalling pathway. The results of protein interaction analysis show that MeGRXC15 can interact with TGA5 from Arabidopsis and MeTGA074 from cassava.

CONCLUSIONS

CC-type glutaredoxins play regulatory roles in cassava response to drought possibly through ABA signalling pathway.

A Rice CPYC-Type Glutaredoxin OsGRX20 in Protection against Bacterial Blight, Methyl Viologen and Salt Stresses

Glutaredoxins (GRXs) belong to the antioxidants involved in the cellular stress responses. In spite of the identification 48 GRX genes in rice genomes, the biological functions of most of them remain unknown. Especially, the biological roles of members of GRX family in disease resistance are still lacking. Our proteomic analysis found that OsGRX20 increased by 2.7-fold after infection by bacterial blight. In this study, we isolated and characterized the full-length nucleotide sequences of the rice OsGRX20 gene, which encodes a GRX family protein with CPFC active site of CPYC-type class. OsGRX20 protein was localized in nucleus and cytosol, and its transcripts were expressed predominantly in leaves. Several stress- and hormone-related motifs putatively acting as regulatory elements were found in the OsGRX20 promoter. Real-time quantitative PCR analysis indicated that OsGRX20 was expressed at a significantly higher level in leaves of a resistant or tolerant rice genotype, Yongjing 50A, than in a sensitive genotype, Xiushui 11, exposed to bacterial blight, methyl viologen, heat, and cold. Its expression could be induced by salt, PEG-6000, 2,4-D, salicylic acid, jasmonic acid, and abscisic acid treatments in Yongjing 50A. Overexpression of OsGRX20 in rice Xiushui 11 significantly enhanced its resistance to bacterial blight attack, and tolerance to methyl viologen and salt stresses. In contrast, interference of OsGRX20 in Yongjing 50A led to increased susceptibility to bacterial blight, methyl viologen and salt stresses. OsGRX20 restrained accumulation of superoxide radicals in aerial tissue during methyl viologen treatment. Consistently, alterations in OsGRX20 expression affect the ascorbate/dehydroascorbate ratio and the abundance of transcripts encoding four reactive oxygen species scavenging enzymes after methyl viologen-induced stress. Our results demonstrate that OsGRX20 functioned as a positive regulator in rice tolerance to multiple stresses, which may be of significant use in the genetic improvement of rice resistance.

Application of glycine reduces arsenic accumulation and toxicity in Oryza sativa L. by reducing the expression of silicon transporter genes

The present study was intended to investigate the role of amino acid glycine in detoxification of As in Oryza sativa L. The growth parameters such as, shoot length and fresh weight were decreased during As(III) and As(V) toxicity. However, the application of glycine recovered the growth parameters against As stress. The application of glycine reduced the As accumulation in all the treatments, and it was more effective against As(III) treatment and reduced the accumulation by 68% in root and 71% in shoot. Similarly, the translocation of As from root to shoot, was higher against As(III) and As(V) treatments, whereas, reduced upon glycine application. The translocation of Fe and Na was also affected by As, which was lower under As(III) and As(V) treatments. However, the application of glycine significantly enhanced the translocation of Fe and Na in the shoot. Besides, the expression of lower silicon transporters i.e. Lsi-1 and Lsi-2 was observed to be significantly suppressed in the root with the application of glycine against As treatment. Similarly, the expression of three GRX and two GST gene isoforms were found to be significantly increased with glycine application. Simultaneously, the activities of antioxidant enzymes i.e. l-arginine dependent NOS, SOD, NTR and GRX were found to be significantly enhanced in the presence of glycine. Increased activities of antioxidant enzymes coincided with the decreased level of TBARS and H₂O₂ in rice seedlings. Overall, the results suggested that the application of glycine reduces As accumulation through suppressing the gene expression of lower silicon transporters and ameliorates As toxicity by enhancing antioxidants defense mechanism in rice seedlings.

The calcium-dependent kinase OsCPK24 functions in cold stress responses in rice

Calcium-dependent protein kinases (CPKs) are serine/threonine protein kinases that function in plant stress responses. Although CPKs are recognized as key messengers in signal transduction, the specific roles of CPKs and the molecular mechanisms underlying their activity remain largely unknown. Here, we characterized the function of OsCPK24, a cytosol-localized calcium-dependent protein kinase in rice. OsCPK24 was universally and highly expressed in rice plants and was induced by cold treatment. Whereas OsCPK24 knockdown plants exhibited increased sensitivity to cold compared to wild type (WT), OsCPK24-overexpressing plants exhibited increased cold tolerance. Plants overexpressing OsCPK24 exhibited increased accumulation of proline (an osmoprotectant) and glutathione (an antioxidant) and maintained a higher GSH/GSSG (reduced glutathione to oxidized glutathione) ratio during cold stress compared to WT. In addition to these effects in response to cold stress, we observed the kinase activity of OsCPK24 varied under different calcium concentrations. Further, OsCPK24 phosphorylated OsGrx10, a glutathione-dependent thioltransferase, at rates modulated by changes in calcium concentration. Together, our results support the hypothesis that OsCPK24 functions as a positive regulator of cold stress tolerance in rice, a process mediated by calcium signaling and involving phosphorylation and the inhibition of OsGrx10 to sustain higher glutathione levels.

Enhanced resistance to rice blast and sheath blight in rice (oryza sativa L.) by expressing the oxalate decarboxylase protein Bacisubin from Bacillus subtilis

Oxalate decarboxylase (OxDC), catalyzing the degradation of oxalic acid, is widely distributed in varieties of organisms. In this study, an oxalate decarboxylase gene from Bacillus subtilis strain BS-916, Bacisubin, was transformed into rice variety Nipponbare to generate transgenic rice with increased OxDC activity. Pathogenicity test revealed that the transgenic rice showed enhanced resistance to rice blast and sheath blight. Further RNA-seq analysis between Nipponbare WT (wild type) and transgenic rice identified 1764 DEGs (Differentially expressed genes) including 723 up-regulated unigenes and 1041 down-regulated unigenes. Five GO terms including single-organism process and oxidation-reduction process were significantly enriched in the up-regulated genes. Interestingly, five genes encoding glutaredoxin and one gene encoding MADS box were up- and down-regulated in the transgenic rice, respectively. Collectively, our study advances the understanding of OxDC in resistance to rice disease and its possible mechanisms. Our results also suggest that OxDC would be an effective antifungal protein preventing fungal infection in transgenic rice.

Genome-wide association study and gene set analysis for understanding candidate genes involved in salt tolerance at the rice seedling stage

Salt is the major factor limiting crop productivity in saline soils and is controlled by various genes. The development of salt-tolerant rice through molecular breeding methods is important to meet the needs of rice breeding. We used 295 accessions to perform a genome-wide association study (GWAS) of salt tolerance-related phenotypes in rice at the seedling stage and obtained 93 candidate genes with high association peaks across six phenotypes. We constructed a protein interaction network using the candidate genes identified here, and 33 genes were associated. Based on the expression patterns, we found that most of these genes showed a different expression level under control and salt stress conditions. In addition, haplotype network and sequence analysis of one 'key' gene, a transcription factor (Os12g0176700) encoding a SWIRM domain-containing protein, in the interaction network was investigated to explore its possible role in the network. Our study revealed candidate salt tolerance-related genes in rice at the seedling stage, and demonstrated the feasibility of using GWAS to identify genetic architecture underlying salt tolerance. The data generated here may provide resources for molecular breeding and functional analysis of salt tolerance in rice seedlings.

Silencing of OsGRXS17 in rice improves drought stress tolerance by modulating ROS accumulation and stomatal closure

Glutaredoxins (GRXs) modulate redox-dependent signaling pathways and have emerged as key mediators in plant responses to environmental stimuli. Here we report that RNAi-mediated suppression of Oryza sativa GRXS17 (OsGRXS17) improved drought tolerance in rice. Gene expression studies showed that OsGRXS17 was present throughout the plant and that transcript abundance increased in response to drought stress and abscisic acid (ABA) treatment. Localization studies, utilizing GFP-OsGRXS17 fusion proteins, indicated that OsGRXS17 resides in both the cytoplasm and the nuclear envelope. Under drought stress conditions, rice plants with reduced OsGRXS17 expression showed lower rates of water loss and stomatal conductance, higher relative water content, and enhanced survival compared to wild-type controls. Further characterization of the OsGRXS17 down-regulated plants revealed an elevation in H₂O₂ production within the guard cells, increased sensitivity to ABA, and a reduction in stomatal apertures. The findings demonstrate a critical link between OsGRXS17, the modulation of guard cell H₂O₂ concentrations, and stomatal closure, expanding our understanding of the mechanisms governing plant responses to drought.

Genome-wide association study and gene set analysis for understanding candidate genes involved in salt tolerance at the rice seedling stage

Salt is the major factor limiting crop productivity in saline soils and is controlled by various genes. The development of salt-tolerant rice through molecular breeding methods is important to meet the needs of rice breeding. We used 295 accessions to perform a genome-wide association study (GWAS) of salt tolerance-related phenotypes in rice at the seedling stage and obtained 93 candidate genes with high association peaks across six phenotypes. We constructed a protein interaction network using the candidate genes identified here, and 33 genes were associated. Based on the expression patterns, we found that most of these genes showed a different expression level under control and salt stress conditions. In addition, haplotype network and sequence analysis of one 'key' gene, a transcription factor (Os12g0176700) encoding a SWIRM domain-containing protein, in the interaction network was investigated to explore its possible role in the network. Our study revealed candidate salt tolerance-related genes in rice at the seedling stage, and demonstrated the feasibility of using GWAS to identify genetic architecture underlying salt tolerance. The data generated here may provide resources for molecular breeding and functional analysis of salt tolerance in rice seedlings.

Genome-Wide Single-Nucleotide Polymorphisms in CMS and Restorer Lines Discovered by Genotyping Using Sequencing and Association with Marker-Combining Ability for 12 Yield-Related Traits in Oryza sativa L. subsp. Japonica

Heterosis or hybrid vigor is closely related with general combing ability (GCA) of parents and special combining ability (SCA) of combinations. The evaluation of GCA and SCA facilitate selection of parents and combinations in heterosis breeding. In order to improve combining ability (CA) by molecular marker assist selection, it is necessary to identify marker loci associated with the CA. To identify the single nucleotide polymorphisms (SNP) loci associated with CA in the parental genomes of japonica rice, genome-wide discovered SNP loci were tested for association with the CA of 18 parents for 12 yield-related traits. In this study, 81 hybrids were created and evaluated to calculate the CA of 18 parents. The parents were sequenced by genotyping by sequencing (GBS) method for identification of genome-wide SNPs. The analysis of GBS indicated that the successful mapping of 9.86 × 10⁶ short reads in the Nipponbare reference genome consists of 39,001 SNPs in parental genomes at 11,085 chromosomal positions. The discovered SNPs were non-randomly distributed within and among the 12 chromosomes of rice. Overall, 20.4% (8026) of the discovered SNPs were coding types, and 8.6% (3344) and 9.9% (3951) of the SNPs revealed synonymous and non-synonymous changes, which provide valuable knowledge about the underlying performance of the parents. Furthermore, the associations between SNPs and CA indicated that 362 SNP loci were significantly related to the CA of 12 parental traits. The identified SNP loci of CA in our study were distributed genome wide and caused a positive or negative effect on the CA of traits. For the yield-related traits, such as grain thickness, days to heading, panicle length, grain length and 1000-grain weight, a maximum number of positive SNP loci of CA were found in CMS A171 and in the restorers LC64 and LR27. On an individual basis, some of associated loci that resided on chromosomes 2, 5, 7, 9, and 11 recorded maximum positive values for the CA of traits. From our results, we suggest that heterosis in japonica rice would be improved by pyramiding the favorable SNP loci of CA and eliminating the unfavorable loci from parental genomes.