Clustered metallothionein genes are co-regulated in rice and ectopic expression of OsMT1e-P confers multiple abiotic stress tolerance in tobacco via ROS scavenging

Metallothionein family genes in kiwifruit: characterization and determining their roles in plant's response to different stresses

Kiwifruit growth and development are severely affected by various biotic and abiotic stresses, especially cold stress and the bacterial disease caused by Pseudomonas syringae pv. actinidiae (Psa). Metallothioneins (MTs) are a group of cysteine-rich proteins that play crucial roles in stress response, metal detoxification, and homeostasis in plants. However, the protective role of these MTs in kiwifruit remains to be elucidated. In the present study, four AcMT genes were identified in the Hongyang kiwifruit genome, namely, two Type 2 isoforms (AcMT2 and AcMT2a) and two Type 3 isoforms (AcMT3a and AcMT3b) located separately on four different chromosomes. The hormones and stress response cis-elements within the promoter regions of these AcMTs were characterized. It was revealed that the four AcMT genes exhibited different expression patterns in different tissues: AcMT2 and AcMT2a were expressed at much higher levels in the fruit, male flower, female flower, root, and bark, while AcMT3a was expressed mainly in the fruit and AcMT3b was expressed highly in the bark. The expression patterns of these AcMT genes after exposure to Psa infection and different phytohormones, including gibberellic acid A3(GA3), ethylene (ET), and abscisic acid (ABA), were evaluated. It was revealed that in response to Psa infection, the main AcMTs in each tissue (those with expression levels higher compared to the other MTs in that tissue) were downregulated during the early stage in kiwifruits, followed by a recovery phase. In addition, most AcMTs were downregulated after exposure to ET and GA3, while type 2 AcMTs (AcMT2 and AcMT2a) were upregulated after treatment with ABA. The overexpression of AcMTs in Escherichia coli presented a higher tolerance to H2O2, heavy metals, low temperature, and high temperature. Collectively, these findings demonstrated the protective roles of AcMTs in terms of stress resistance conferred through plant hormone-related signal pathways.

Increasing resistance of lawn grasses to zinc and copper pollution

Coppe and zinc are priority pollutants in city soils. Copper and zinc are the limiting factors for lawn grasses. Cell selection can increase the resistance of lawn grasses to zinc and copper. The effect of zinc on the morphogenic ability of the callus was determined. The results of this study showed that zinc is less toxic to calli than copper. The method of obtaining lawn grass resistant to zinc has been developed. The results were used to develop the cell selection technology for obtaining plants resistant to the complex effect of zinc and copper. Concentrations of Copper (75 mg/l) and zinc (150 mg/L) were selected as selective. The author developed the cell selection scheme for obtaining plants resistant to the complex effect of Cu and Zn. The regenerants showed increased resistance to copper and zinc.

Heat-stress-induced ROS in maize silks cause late pollen tube growth arrest and sterility

The reproductive phase of plants is highly sensitive to ambient temperature stresses. To investigate sensitivity of female reproductive organs in grass crops during the pollination phase, we exposed the elongated stigma (silk) of maize to ambient environment at the silking stage. Moderate heat stress causes cell death of silk hair cells but did not affect early pollen tube growth inside the silk. Late pollen tube growth arrest was observed, leading to sterility. Heat stress causes elevated levels of reactive oxygen species (ROS) in silks, whose levels can be reduced by scavengers partly restoring pollen tube growth and fertility. A number of biological processes including hydrogen peroxide catabolic processes and bHLH transcription factor genes are downregulated by heat stress, while some NAC transcription factor genes are strongly upregulated. In conclusion, this study now provides a basis to select genes for engineering heat-stress-tolerant grass crops during the pollination phase.

Regulation of nitro-oxidative homeostasis: an effective approach to enhance salinity tolerance in plants

Soil salinity is a major constraint for sustainable agricultural productivity, which together with the incessant climate change may be transformed into a severe threat to the global food security. It is, therefore, a serious concern that needs to be addressed expeditiously. The overproduction and accumulation of reactive oxygen species (ROS) and reactive nitrogen species (RNS) are the key events occurring during salt stress, consequently employing nitro-oxidative stress and programmed cell death in plants. However, very sporadic studies have been performed concerning different aspects of nitro-oxidative stress in plants under salinity stress. The ability of plants to tolerate salinity is associated with their ability to maintain the cellular redox equilibrium mediated by both non-enzymatic and enzymatic antioxidant defense mechanisms. The present review emphasizes the mechanisms of ROS and RNS generation in plants, providing a detailed evaluation of how redox homeostasis is conserved through their effective removal. The uniqueness of this article stems from its incorporation of expression analyses of candidate genes for different antioxidant enzymes involved in ROS and RNS detoxification across various developmental stages and tissues of rice, utilizing publicly available microarray data. It underscores the utilization of modern biotechnological methods to improve salinity tolerance in crops, employing different antioxidants as markers. The review also explores how various transcription factors contribute to plants' ability to tolerate salinity by either activating or repressing the expression of stress-responsive genes. In summary, the review offers a thorough insight into the nitro-oxidative homeostasis strategy for extenuating salinity stress in plants.

Physiological and Proteome Analysis of the Effects of Chitosan Oligosaccharides on Salt Tolerance of Rice Seedlings

Rice (Oryza sativa L.) is an important social-economic crop, and rice seedlings are easily affected by salt stress. Chitosan oligosaccharide (COS) plays a positive role in promoting plant growth and development. To gain a better understanding of the salt tolerance mechanism of rice under the action of COS, Nipponbare rice seedlings were selected as the experimental materials, and the physiological and biochemical indexes of rice seedlings in three stages (normal growth, salt stress and recovery) were measured. Unlabelled quantitative proteomics technology was used to study differential protein and signaling pathways of rice seedlings under salt stress, and the mechanism of COS to improve rice tolerance to salt stress was elucidated. Results showed that after treatment with COS, the chlorophyll content of rice seedlings was 1.26 times higher than that of the blank group (CK). The root activity during the recovery stage was 1.46 times that of the CK group. The soluble sugar in root, stem and leaf increased by 53.42%, 77.10% and 9.37%, respectively. The total amino acid content increased by 77% during the stem recovery stage. Furthermore, the malondialdehyde content in root, stem and leaf increased by 21.28%, 26.67% and 32.69%, respectively. The activity of oxide dismutase (SOD), peroxidase (POD) and oxygenase (CAT) were increased. There were more differentially expressed proteins in the three parts of the experimental group than in the CK group. Gene Ontology (GO) annotation of these differentially expressed proteins revealed that the experimental group was enriched for more entries. Then, through the Kyoto Encyclopedia of Genes and Genomes (KEGG), the top ten pathways enriched with differentially expressed proteins in the two groups (COS and CK groups) were utilized, and a detailed interpretation of the glycolysis and photosynthesis pathways was provided. Five key proteins, including phosphofructokinase, fructose bisphosphate aldolases, glycer-aldehyde-3-phosphate dehydrogenase, enolase and pyruvate kinase, were identified in the glycolysis pathway. In the photosynthesis pathway, oxygen evolution enhancement proteins, iron redox proteins and ferredoxin-NADPH reductase were the key proteins. The addition of COS led to an increase in the abundance of proteins, a response of rice seedlings to salt stress. COS helped rice seedlings resist salt stress. Furthermore, using COS as biopesticides and biofertilizers can effectively increase the utilization of saline-affected farmland, thereby contributing to the alleviating of the global food crisis.

Ultrasonic treatment alleviated cadmium stress in sugarcane via improving antioxidant activity and physiological and biochemical status

Cadmium (Cd) is a toxic element that endangers crop growth and affects food safety and human health. Therefore, the study of Cd mitigation technology is important. Ultrasonic treatment can improve crop growth and enhance their ability to resist various abiotic stresses. In this study, the effect of ultrasonic treatment on alleviating sugarcane Cd stress was studied in a barrel experiment using sugarcane varieties 'ROC22' and 'LC05-136' as test materials. Sugarcane buds without ultrasonic treatment and with ultrasonic treatment (20-40 kHz mixed frequency ultrasound for 2 min, dry treatment) were planted in soil with Cd contents of 0, 50, 100, 250, and 500 mg·kg-1. Compared with non-ultrasonic treatment, Ultrasonic treatment significantly increased the activities of antioxidant enzymes in sugarcane, significantly increased the content of osmoregulation substances, significantly reduced the content of superoxide anion (the highest decreases reached 11.55%) and malondialdehyde (the highest decreases reached 20.59%), and significantly increased the expression level of metallothionein (MT)-related genes, with the expression of ScMT1 increased by 8.80-37.49% and the expression of ScMT2-1-5 increased by 1.55-69.33%. In addition, ultrasonic treatment significantly reduced the Cd contents in sugarcane roots, stems, leaves, bagasse, and juice (the highest reduction in Cd content was 49.18%). In general, ultrasonic treatment regulated the metabolism of reactive oxygen species and MT-related gene expression in sugarcane, increased the Cd tolerance of sugarcane, promoted photosynthesis in sugarcane leaves, improved root morphology, enhanced sugarcane growth, and increased cane and sugar yield.

Where the wild things are: genetic associations of environmental adaptation in the Oryza rufipogon species complex

Crop wild relatives host unique adaptation strategies that enable them to thrive across a wide range of habitats. As pressures from a changing climate mount, a more complete understanding of the genetic variation that underlies this adaptation could enable broader utilization of wild materials for crop improvement. Here, we carry out environmental association analyses (EAA) in the Oryza rufipogon species complex (ORSC), the wild progenitor of cultivated Asian rice, to identify genomic regions associated with environmental adaptation characterized by variation in bioclimatic and soil variables. We further examine regions for colocalizations with phenotypic associations within the same collection. EAA results indicate that significant regions tend to associate with single environmental variables, although 2 significant loci on chromosomes 3 and 5 are detected as common across multiple variable types (i.e. precipitation, temperature, and/or soil). Distributions of allele frequencies at significant loci across subpopulations of cultivated Oryza sativa indicate that, in some cases, adaptive variation may already be present among cultivars, although evaluation in cultivated populations is needed to empirically test this. This work has implications for the potential utility of wild genetic resources in pre-breeding efforts for rice improvement.

Transcriptomic, osmoregulatory and translocation changes modulates Ni toxicity in Theobroma cacao

Nickel is one of the most released trace elements in the environment and in the case of bioaccumulation in foods and beverages derived from cocoa beans can cause risk to human health. It is very important to understand how plants respond to toxic metals and which are the defense strategies they adopt to mitigate their effects. In the present study we used young plants of T. cacao, submitted to increasing Ni doses (0, 100, 200, 300, 400 and 500 mg Ni kg^-1 soil) and evaluated them for a period of 30 days. Doses of Ni, from 300 mg of Ni kg^-1 onwards in the soil, promoted changes in photosynthetic, antioxidant, osmoregulatory, transcriptomic and translocation levels, evidenced by the increase in the activity of antioxidant enzymes, proline, glycine betaine, upregulation of the metallothionein 2B gene (Mt2b), and lipid peroxidation of the cell membranes. Foliar gas exchange was severely affected at higher doses of Ni. In addition, reduced levels of stomatal conductivity and transpiration rate were observed from 300 mg Ni kg^-1 dose onwards in the soil, which consequently affected CO₂ assimilation. Phytostabilization and exclusion mechanisms control the translocation of Ni from the root to the shoot and reduce harmful effects on plant metabolism. Our results highlighted the toxicity of Ni, a trace element often underestimated in T. cacao. In particular, it was noted that doses of 100 and 200 Ni kg^-1 soil, although high, do not induce toxicity in T. cacao plants. But Ni toxicity is observed from 300 mg Ni kg^-1 soil onwards. This study contributed to the understanding of the harmful effects of higher doses of Ni in cacao plants and the biochemical processes the plant uses to mitigate the effects of this metal.

Drought stress tolerance mechanisms and their potential common indicators to salinity, insights from the wild watermelon (Citrullus lanatus): A review

Climate change has escalated the effect of drought on crop production as it has negatively altered the environmental condition. Wild watermelon grows abundantly in the Kgalagadi desert even though the environment is characterized by minimal rainfall, high temperatures and intense sunshine during growing season. This area is also characterized by sandy soils with low water holding capacity, thus bringing about drought stress. Drought stress affects crop productivity through its effects on development and physiological functions as dictated by molecular responses. Not only one or two physiological process or genes are responsible for drought tolerance, but a combination of various factors do work together to aid crop tolerance mechanism. Various studies have shown that wild watermelon possess superior qualities that aid its survival in unfavorable conditions. These mechanisms include resilient root growth, timely stomatal closure, chlorophyll fluorescence quenching under water deficit as key physiological responses. At biochemical and molecular level, the crop responds through citrulline accumulation and expression of genes associated with drought tolerance in this species and other plants. Previous salinity stress studies involving other plants have identified citrulline accumulation and expression of some of these genes (chloroplast APX, Type-2 metallothionein), to be associated with tolerance. Emerging evidence indicates that the upstream of functional genes are the transcription factor that regulates drought and salinity stress responses as well as adaptation. In this review we discuss the drought tolerance mechanisms in watermelons and some of its common indicators to salinity at physiological, biochemical and molecular level.

DNA methylation dynamics in a coastal foundation seagrass species under abiotic stressors

DNA methylation (DNAm) has been intensively studied in terrestrial plants in response to environmental changes, but its dynamic changes in a temporal scale remain unexplored in marine plants. The seagrass Posidonia oceanica ranks among the slowest-growing and longest-living plants on Earth, and is particularly vulnerable to sea warming and local anthropogenic pressures. Here, we analysed the dynamics of DNAm changes in plants collected from coastal areas differentially impacted by eutrophication (i.e. oligotrophic, Ol; eutrophic, Eu) and exposed to abiotic stressors (nutrients, temperature increase and their combination). Levels of global DNAm (% 5-mC) and the expression of key genes involved in DNAm were assessed after one, two and five weeks of exposure. Results revealed a clear differentiation between plants, depending on environmental stimuli, time of exposure and plants' origin. % 5-mC levels were higher during the initial stress exposure especially in Ol plants, which upregulated almost all genes involved in DNAm. Contrarily, Eu plants showed lower expression levels, which increased under chronic exposure to stressors, particularly to temperature. These findings show that DNAm is dynamic in P. oceanica during stress exposure and underlined that environmental epigenetic variations could be implicated in the regulation of acclimation and phenotypic differences depending on local conditions.

Walking through crossroads-rice responses to heat and biotic stress interactions

Rice, the most important source of calories for humans is prone to severe yield loss due to changing climate including heat stress. Additionally, rice encounters biotic stresses in conjunction with heat stress, which exacerbates the adverse effects, and exponentially increase such losses. Several investigations have identified biotic and heat stress-related quantitative trait loci (QTLs) that may contribute to improved tolerance to these stresses. However, a significant knowledge gap exists in identifying the genomic regions imparting tolerance against combined biotic and heat stress. Hereby, we are presenting a conceptual meta-analysis identifying genomic regions that may be promising candidates for enhancing combined biotic and heat stress tolerance in rice. Fourteen common genomic regions were identified along chromosomes 1, 2, 3, 4, 6, 10 and 12, which harbored 1265 genes related to heat stress and defense responses in rice. Further, the meta expression analysis revealed 24 differentially expressed genes (DEGs) involved in calcium-mediated stress signaling including transcription factors Myb, bHLH, ROS signaling, molecular chaperones HSP110 and pathogenesis related proteins. Additionally, we also proposed a hypothetical model based on GO and MapMan analysis representing the pathways intersecting heat and biotic stresses. These DEGs can be potential candidate genes for improving tolerance to combined biotic and heat stress in rice. We present a framework highlighting plausible connecting links (QTLs/genes) between rice response to heat stress and different biotic factors associated with yield, that can be extended to other crops.

Genomics and transcriptomics to protect rice (Oryza sativa. L.) from abiotic stressors: -pathways to achieving zero hunger

More over half of the world's population depends on rice as a major food crop. Rice (Oryza sativa L.) is vulnerable to abiotic challenges including drought, cold, and salinity since it grown in semi-aquatic, tropical, or subtropical settings. Abiotic stress resistance has bred into rice plants since the earliest rice cultivation techniques. Prior to the discovery of the genome, abiotic stress-related genes were identified using forward genetic methods, and abiotic stress-tolerant lines have developed using traditional breeding methods. Dynamic transcriptome expression represents the degree of gene expression in a specific cell, tissue, or organ of an individual organism at a specific point in its growth and development. Transcriptomics can reveal the expression at the entire genome level during stressful conditions from the entire transcriptional level, which can be helpful in understanding the intricate regulatory network relating to the stress tolerance and adaptability of plants. Rice (Oryza sativa L.) gene families found comparatively using the reference genome sequences of other plant species, allowing for genome-wide identification. Transcriptomics via gene expression profiling which have recently dominated by RNA-seq complements genomic techniques. The identification of numerous important qtl,s genes, promoter elements, transcription factors and miRNAs involved in rice response to abiotic stress was made possible by all of these genomic and transcriptomic techniques. The use of several genomes and transcriptome methodologies to comprehend rice (Oryza sativa, L.) ability to withstand abiotic stress have been discussed in this review.

Transgenic tobacco co-expressing flavodoxin and betaine aldehyde dehydrogenase confers cadmium tolerance through boosting antioxidant capacity

Excessive heavy metal (HM) levels in soil have become a source of concern due to their adverse effects on human health and the agriculture industry. Soil contamination by HMs leads to an accumulation of reactive oxygen species (ROSs) within the plant cell and disruption of photosynthesis-related proteins. The response of tobacco lines overexpressing flavodoxin (Fld) and betaine aldehyde dehydrogenase (BADH) to cadmium (Cd) toxicity was investigated in this study. PCR results demonstrated the expected amplicon length of each gene in the transgenic lines. Absolute qRT-PCR demonstrates a single copy of T-DNA integration into each transgenic line. Relative qRT-PCR confirmed overexpression of Fld and BADH in transgenic lines. The maximum quantum yield of photosystem II (Fv/Fm) was measured under Cd toxicity stress and revealed that transgenic lines had a higher Fv/Fm than wild-type (WT) plants. Accumulation of proline, glycine betaine (GB), and higher activity of antioxidant enzymes alongside lower levels of malondialdehyde (MDA) and hydrogen peroxide (H2O2) was indicative of a robust antioxidant system in transgenic plants. Therefore, performing a loop in reducing the ROS produced in the photosynthesis electron transport chain and stimulating the ROS scavenger enzyme activity improved the plant tolerance to Cd stress.

Identification of Candidate Genes for Salinity and Anaerobic Tolerance at the Germination Stage in Rice by Genome-Wide Association Analyses

Multiple stress tolerance at the seed germination stage is crucial for better crop establishment in the direct-seeded rice ecosystem. Therefore, identifying rice genes/quantitative trait loci (QTLs) associated with salinity and anaerobic tolerance at the germination stage is a prerequisite for adaptive breeding. Here, we studied 498 highly diverse rice accessions Xian (Indica) and Geng (Japonica), and six traits that are highly associated with salinity and anaerobic tolerance at germination stage were measured. A high-density 2.8M Single Nucleotide Polymorphisms (SNP) genotype map generated from the 3,000 Rice Genomes Project (3KRGP) was used for mapping through a genome-wide association study. In total, 99 loci harboring 117 QTLs were detected in different populations, 54, 21, and 42 of which were associated with anaerobic, salinity, and combined (anaerobic and salinity) stress tolerance. Nineteen QTLs were close to the reported loci for abiotic stress tolerance, whereas two regions on chromosome 4 (qSGr4a/qCL4c/qRI4d and qAGr4/qSGr4b) and one region on chromosome 10 (qRI10/qCL10/ qSGr10b/qBM10) were associated with anaerobic and salinity related traits. Further haplotype analysis detected 25 promising candidates genes significantly associated with the target traits. Two known genes (OsMT2B and OsTPP7) significantly associated with grain yield and its related traits under saline and anaerobic stress conditions were identified. In this study, we identified the genes involved in auxin efflux (Os09g0491740) and transportation (Os01g0976100), whereas we identified multistress responses gene OsMT2B (Os01g0974200) and a major gene OsTPP7 (Os09g0369400) involved in anaerobic germination and coleoptile elongation on chromosome 9. These promising candidates provide valuable resources for validating potential salt and anaerobic tolerance genes and will facilitate direct-seeded rice breeding for salt and anaerobic tolerance through marker-assisted selection or gene editing.

OsCyp2-P, an auxin-responsive cyclophilin, regulates Ca2+ calmodulin interaction for an ion-mediated stress response in rice

OsCYP2-P is an active cyclophilin (having peptidyl-prolyl cis/trans-isomerase activity, PPIase) isolated from the wild rice Pokkali having a natural capacity to grow and yield seeds in coastal saline regions of India. Transcript abundance analysis in rice seedlings showed the gene is inducible by multiple stresses, including salinity, drought, high temperature, and heavy metals. To dissect the role of OsCYP2-P gene in stress response, we raised overexpression (OE) and knockdown (KD) transgenic rice plants with >2-3 folds higher and approximately 2-fold lower PPIase activity, respectively. Plants overexpressing this gene had more favorable physiological and biochemical parameters (K⁺ /Na⁺ ratio, electrolytic leakage, membrane damage, antioxidant enzymes) than wild type, and the reverse was observed in plants that were knocked down for this gene. We propose that OsCYP2-P contributes to stress tolerance via maintenance of ion homeostasis and thus prevents toxic cellular ion buildup and membrane damage. OE plants were found to have a higher harvest index and higher number of filled grains under salinity and drought stress than wild type. OsCYP2-P interacts with calmodulin, indicating it functions via the Ca-CaM pathway. Compared to the WT, the germinating OE seeds exhibited a substantially higher auxin level, and this hormone was below the detection limits in the WT and KD lines. These observations strongly indicate that OsCyp2-P affects the signaling and transport of auxin in rice.

Identification and characterization of eight metallothionein genes involved in heavy metal tolerance from the ectomycorrhizal fungus Laccaria bicolor

Metallothioneins (MTs) are small, cysteine-rich, heavy metal-binding proteins involved in metal homeostasis and detoxification. The increasing numbers of available genomic sequences of ectomycorrhizal (ECM) fungi enable deeper insights into the characteristics of MT genes in these fungi that form the most important symbiosis with the host trees in forest ecosystems. The aim of this study was to establish a comprehensive, genome-wide inventory of MT genes from the ECM fungus Laccaria bicolor. Eight MT genes in L. bicolor were cloned, and the expression patterns of their transcripts at various developmental stages based on expressed sequence tag (EST) counts were analyzed. The expression levels of four MTs were significantly increased during symbiosis stages. Quantitative real-time PCR (qRT-PCR) analysis revealed that transcripts of LbMT1 were dominant in free-living mycelia and strongly induced by excessive copper (Cu), cadmium (Cd), and hydrogen peroxide (H2O2). To determine whether these eight MTs functioned as metal chelators, we expressed them in the Cu- and Cd-sensitive yeast mutants, cup1∆ and yap1∆, respectively. All LbMT proteins provided similar levels of Cu(II) or Cd(II) tolerance, but did not affect by H2O2. Our findings provide novel data on the evolution and diversification of fungal MT gene duplicates, a valuable resource for understanding the vast array of biological processes in which these proteins are involved.

Genome-wide analysis of metallothionein gene family in maize to reveal its role in development and stress resistance to heavy metal

BACKGROUND

Maize (Zea mays L.) is a widely cultivated cereal and has been used as an optimum heavy metal phytoremediation crop. Metallothionein (MT) proteins are small, cysteine-rich, proteins that play important roles in plant growth and development, and the regulation of stress response to heavy metals. However, the MT genes for maize have not been fully analyzed so far.

METHODS

The putative ZmMT genes were identified by HMMER.The heat map of ZmMT genes spatial expression analysis was generated by using R with the log2 (FPKM + 1).The expression profiles of ZmMT genes under three kinds of heavy metal stresses were quantified by using qRT-PCR. The metallothionein proteins was aligned using MAFFT and phylogenetic analysis were constructed by ClustalX 2.1. The protein theoretical molecular weight and pI, subcellular localization, TFs binding sites, were predicted using ProtParam, PSORT, PlantTFDB, respectively.

RESULTS

A total of 9 ZmMT genes were identified in the whole genome of maize. The results showed that eight of the nine ZmMT proteins contained one highly conserved metallothio_2 domain, while ZmMT4 contained a Metallothio_PEC domain. All the ZmMT proteins could be classified into three major groups and located on five chromosomes. The ZmMT promoters contain a large number of hormone regulatory elements and hormone-related transcription factor binding sites. The ZmMT genes exhibited spatiotemporal specific expression patterns in 23 tissues of maize development stages and showed the different expression patterns in response to Cu, Cd, and Pb heavy metal stresses.

CONCLUSIONS

We identified the 9 ZmMT genes, and explored their conserved motif, tissue expression patterns, evolutionary relationship. The expression profiles of ZmMT genes under three kinds of heavy metal stresses (Cu, Cd, Pb) were analyzed. In summary, the expression of ZmMTs have poteintial to be regulated by hormones. The specific expression of ZmMTs in different tissues of maize and the response to different heavy metal stresses are revealed that the role of MT in plant growth and development, and stress resistance to heavy metals.

Potential use of arbuscular mycorrhizal fungi for simultaneous mitigation of arsenic and cadmium accumulation in rice

Rice polluted by metal(loid)s, especially arsenic (As) and cadmium (Cd), imposes serious health risks. Numerous studies have demonstrated that the obligate plant symbionts arbuscular mycorrhizal fungi (AMF) can reduce As and Cd concentrations in rice. The behaviours of metal(loid)s in the soil-rice-AMF system are of significant interest for scientists in the fields of plant biology, microbiology, agriculture, and environmental science. We review the mechanisms of As and Cd accumulation in rice with and without the involvement of AMF. In the context of the soil-rice-AMF system, we assess and discuss the role of AMF in affecting soil ion mobility, chemical forms, transport pathways (including the symplast and apoplast), and genotype variation. A potential strategy for AMF application in rice fields is considered, followed by future research directions to improve theoretical understanding and encourage field application.

Unraveling the contribution of OsSOS2 in conferring salinity and drought tolerance in a high-yielding rice

Abiotic stresses are emerging as a potential threat to sustainable agriculture worldwide. Soil salinity and drought will be the major limiting factors for rice productivity in years to come. The Salt Overly Sensitive (SOS) pathway plays a key role in salinity tolerance by maintaining the cellular ion homeostasis, with SOS2, a S/T kinase, being a vital component. The present study investigated the role of the OsSOS2, a SOS2 homolog from rice, in improving salinity and drought tolerance. Transgenic plants with either overexpression (OE) or knockdown (KD) of OsSOS2 were raised in one of the high-yielding cultivars of rice-IR64. Using a combined approach based on physiological, biochemical, anatomical, microscopic, molecular, and agronomic assessment, the evidence presented in this study advocates the role of OsSOS2 in improving salinity and drought tolerance in rice. The OE plants were found to have favorable ion and redox homeostasis when grown in the presence of salinity, while the KD plants showed the reverse pattern. Several key stress-responsive genes were found to work in an orchestrated manner to contribute to this phenotype. Notably, the OE plants showed tolerance to stress at both the seedling and the reproductive stages, addressing the two most sensitive stages of the plant. Keeping in mind the importance of developing crops plants with tolerance to multiple stresses, the present study established the potential of OsSOS2 for biotechnological applications to improve salinity and drought stress tolerance in diverse cultivars of rice.

A Comprehensive Review on the Heavy Metal Toxicity and Sequestration in Plants

Heavy metal (HM) toxicity has become a global concern in recent years and is imposing a severe threat to the environment and human health. In the case of plants, a higher concentration of HMs, above a threshold, adversely affects cellular metabolism because of the generation of reactive oxygen species (ROS) which target the key biological molecules. Moreover, some of the HMs such as mercury and arsenic, among others, can directly alter the protein/enzyme activities by targeting their -SH group to further impede the cellular metabolism. Particularly, inhibition of photosynthesis has been reported under HM toxicity because HMs trigger the degradation of chlorophyll molecules by enhancing the chlorophyllase activity and by replacing the central Mg ion in the porphyrin ring which affects overall plant growth and yield. Consequently, plants utilize various strategies to mitigate the negative impact of HM toxicity by limiting the uptake of these HMs and their sequestration into the vacuoles with the help of various molecules including proteins such as phytochelatins, metallothionein, compatible solutes, and secondary metabolites. In this comprehensive review, we provided insights towards a wider aspect of HM toxicity, ranging from their negative impact on plant growth to the mechanisms employed by the plants to alleviate the HM toxicity and presented the molecular mechanism of HMs toxicity and sequestration in plants.

A comprehensive review of adaptations in plants under arsenic toxicity: Physiological, metabolic and molecular interventions

Arsenic (As) is recognized as a toxic metalloid and a severe threat to biodiversity due to its contamination. Soil and groundwater contamination with this metalloid has become a major concern. Large fractions of cultivable lands are becoming infertile gradually due to the irrigation of As contaminated water released from various sources. The toxicity of As causes the generation of free radicals, which are harmful to cellular metabolism and functions of plants. It alters the growth, metabolic, physiological, and molecular functions of the plants due to oxidative burst. Plants employ different signaling mechanisms to face the As toxicity like phosphate cascade, MAPK (Mitogen-Activated Protein Kinase), Ca-calmodulin, hormones, and ROS-signaling. The toxicity of As may significantly be reduced through various remediation techniques. Among them, the microbial-assisted remediation technique is cost-effective and eco-friendly. It breaks down the metalloid into less harmful species through various processes viz. biovolatilization, biomethylation, and transformation. Moreover, the adaptation strategies towards As toxicity are vacuolar sequestration, involvement of plant defense mechanism, and restricting its uptake from plant roots to above-ground parts. The speciation, uptake, transport, metabolism, ion dynamics, signaling pathways, crosstalk with phytohormones and gaseous molecules, as well as harmful impacts of the As on physiological processes, overall development of plants and remediation techniques are summarized in this review.

How do rice seedlings of landrace Pokkali survive in saline fields after transplantation? Physiology, biochemistry, and photosynthesis

Rice, one of the most important staple food crops in the world, is highly sensitive to soil salinity at the seedling stage. The ultimate yield of this crop is a function of the number of seedlings surviving after transplantation in saline water. Oryza sativa cv. IR64 is a high-yielding salinity-sensitive variety, while Pokkali is a landrace traditionally cultivated by the local farmers in the coastal regions in India. However, the machinery responsible for the seedling-stage tolerance in Pokkali is not understood. To bridge this gap, we subjected young seedlings of these contrasting genotypes to salinity and performed detailed investigations about their growth parameters, ion homeostasis, biochemical composition, and photosynthetic parameters after every 24 h of salinity for three days. Taken together, all the physiological and biochemical indicators, such as proline accumulation, K⁺/Na⁺ ratio, lipid peroxidation, and electrolyte leakage, clearly revealed significant differences between IR64 and Pokkali under salinity, establishing their contrasting nature at this stage. In response to salinity, the F_v/F_m ratio (maximum quantum efficiency of Photosystem II as inferred from Chl a fluorescence) and the energy conserved for the electron transport after the reduction of Q_A (the primary electron acceptor of PSII), to Q_A^-, and reduction of the end electron acceptor molecules towards the PSI (Photosystem I) electron acceptor side was higher in Pokkali than IR64 plants. These observations reflect a direct contribution of photosynthesis towards seedling-stage salinity tolerance in rice. These findings will help to breed high-yielding crops for salinity prone agricultural lands.

Nickel stress-tolerance in plant-bacterial associations

Nickel (Ni) is an essential element for plant growth and is a constituent of several metalloenzymes, such as urease, Ni-Fe hydrogenase, Ni-superoxide dismutase. However, in high concentrations, Ni is toxic and hazardous to plants, humans and animals. High levels of Ni inhibit plant germination, reduce chlorophyll content, and cause osmotic imbalance and oxidative stress. Sustainable plant-bacterial native associations are formed under Ni-stress, such as Ni hyperaccumulator plants and rhizobacteria showed tolerance to high levels of Ni. Both partners (plants and bacteria) are capable to reduce the Ni toxicity and developed different mechanisms and strategies which they manifest in plant-bacterial associations. In addition to physical barriers, such as plants cell walls, thick cuticles and trichomes, which reduce the elevated levels of Ni entrance, plants are mitigating the Ni toxicity using their own antioxidant defense mechanisms including enzymes and other antioxidants. Bacteria in its turn effectively protect plants from Ni stress and can be used in phytoremediation. PGPR (plant growth promotion rhizobacteria) possess various mechanisms of biological protection of plants at both whole population and single cell levels. In this review, we highlighted the current understanding of the bacterial induced protective mechanisms in plant-bacterial associations under Ni stress.

Genome-Wide Identification and Analysis of the Metallothionein Genes in Oryza Genus

Metallothionein (MT) proteins are low molecular mass, cysteine-rich, and metal-binding proteins that play an important role in maintaining metal homeostasis and stress response. However, the evolutionary relationships and functional differentiation of MT in the Oryza genus remain unclear. Here we identified 53 MT genes from six Oryza genera, including O. sativa ssp. japonica, O. rufipogon, O. sativa ssp. indica, O. nivara, O. glumaepatula, and O. barthii. The MT genes were clustered into four groups based on phylogenetic analysis. MT genes are unevenly distributed on chromosomes; almost half of the MT genes were clustered on chromosome 12, which may result from a fragment duplication containing the MT genes on chromosome 12. Five pairs of segmental duplication events and ten pairs of tandem duplication events were found in the rice MT family. The Ka/Ks values of the fifteen duplicated MT genes indicated that the duplicated MT genes were under a strong negative selection during evolution. Next, combining the promoter activity assay with gene expression analysis revealed different expression patterns of MT genes. In addition, the expression of OsMT genes was induced under different stresses, including NaCl, CdCl₂, ABA, and MeJ treatments. Additionally, we found that OsMT genes were mainly located in chloroplasts. These results imply that OsMT genes play different roles in response to these stresses. All results provide important insights into the evolution of the MT gene family in the Oryza genus, and will be helpful to further study the function of MT genes.

Exploring the significant contribution of silicon in regulation of cellular redox homeostasis for conferring stress tolerance in plants

Silicon (Si), a bioactive metalloid is beneficial for plant growth and development. It also plays a key role in the amelioration of different abiotic and biotic stresses. Extensive studies have elucidated the morpho-physiological, biochemical and molecular background of Si-mediated stress tolerance in plants. However, the mechanism acquired by Si to enhance stress tolerance in plants is still unheeded. Present review summarized the prospective mechanisms of Si in acquisition of stress tolerance with emphasis on its interactions with secondary messengers. Silicon usually modulates the different gene expressions in plants under stress conditions rather than acting as a direct signal or secondary messengers. Silicon regulates the production and accumulation of reactive oxygen species (ROS) and reactive nitrogen species (RNS) in plants under stress conditions. Furthermore, Si also activates the antioxidant defence system in plants; thereby, maintaining the cellular redox homeostasis and preventing the oxidative damage of cells. Silicon also up-regulates the synthesis of hydrogen sulfide (H₂S) or acts synergistically with nitric oxide (NO), consequently conferring stress tolerance in plants. Overall, the review may provide a progressive understanding of the role of Si in conservation of the redox homeostasis in plants.

High-resolution genome-wide association study pinpoints metal transporter and chelator genes involved in the genetic control of element levels in maize grain

Despite its importance to plant function and human health, the genetics underpinning element levels in maize grain remain largely unknown. Through a genome-wide association study in the maize Ames panel of nearly 2,000 inbred lines that was imputed with ∼7.7 million SNP markers, we investigated the genetic basis of natural variation for the concentration of 11 elements in grain. Novel associations were detected for the metal transporter genes rte2 (rotten ear2) and irt1 (iron-regulated transporter1) with boron and nickel, respectively. We also further resolved loci that were previously found to be associated with one or more of five elements (copper, iron, manganese, molybdenum, and/or zinc), with two metal chelator and five metal transporter candidate causal genes identified. The nas5 (nicotianamine synthase5) gene involved in the synthesis of nicotianamine, a metal chelator, was found associated with both zinc and iron and suggests a common genetic basis controlling the accumulation of these two metals in the grain. Furthermore, moderate predictive abilities were obtained for the 11 elemental grain phenotypes with two whole-genome prediction models: Bayesian Ridge Regression (0.33–0.51) and BayesB (0.33–0.53). Of the two models, BayesB, with its greater emphasis on large-effect loci, showed ∼4–10% higher predictive abilities for nickel, molybdenum, and copper. Altogether, our findings contribute to an improved genotype-phenotype map for grain element accumulation in maize.

Redox imbalance impedes photosynthetic activity in rice by disrupting cellular membrane integrity and induces programmed cell death under submergence

Climate change negatively impacts the global hydrological resources leading to detrimental flood events. Submergence impedes the cellular membrane integrity, consequently affecting the membrane fluidity. Different abiotic stresses influence membrane lipid composition. Therefore, the remodeling of membrane lipids plays a major role in stress adaptation. Submergence-induced membrane lipid peroxidation is well established in plants. However, dynamic changes in lipid composition for regulating submergence tolerance in rice remain so far unexplored. The present study explored the effect of submergence on the lipidomic profile of the Sub1 near-isogenic lines (NILs) of rice, viz. Swarna, and Swarna Sub1 with contrasting submergence tolerance. The study also examined the association of lipidomic alteration with the membrane integrity and submergence tolerance. Submergence caused increased accumulation of reactive oxygen species (ROS), which was significantly higher in Swarna than Swarna Sub1. The lipid profile was also considerably altered under submergence. Following submergence, Swarna exhibited a significant decrease in phospholipid content accompanied by increased lipid peroxidation and electrolyte leakage. Furthermore, the disintegration of the thylakoid membrane resulted in a significant decrease in the chlorophyll content and photosynthesis rate under submergence. Submergence-induced hypoxic condition also promoted starch depletion to fulfill the energy requirement. In contrast, submergence acclimation in Swarna Sub1 was associated with the shift to anaerobic respiration mediated by increased alcohol dehydrogenase (ADH) activity. Effective ROS detoxification in Swarna Sub1 facilitated by increased antioxidant enzyme activities contributed to the submergence tolerance by maintaining membrane integrity and photosynthetic activity. The present study established the direct association of lipid remodeling with membrane integrity, cell viability, and photosynthesis and also devised a crop model to reveal the molecular background of submergence tolerance in plants.

Elucidating the Response of Crop Plants towards Individual, Combined and Sequentially Occurring Abiotic Stresses

In nature, plants are exposed to an ever-changing environment with increasing frequencies of multiple abiotic stresses. These abiotic stresses act either in combination or sequentially, thereby driving vegetation dynamics and limiting plant growth and productivity worldwide. Plants' responses against these combined and sequential stresses clearly differ from that triggered by an individual stress. Until now, experimental studies were mainly focused on plant responses to individual stress, but have overlooked the complex stress response generated in plants against combined or sequential abiotic stresses, as well as their interaction with each other. However, recent studies have demonstrated that the combined and sequential abiotic stresses overlap with respect to the central nodes of their interacting signaling pathways, and their impact cannot be modelled by swimming in an individual extreme event. Taken together, deciphering the regulatory networks operative between various abiotic stresses in agronomically important crops will contribute towards designing strategies for the development of plants with tolerance to multiple stress combinations. This review provides a brief overview of the recent developments in the interactive effects of combined and sequentially occurring stresses on crop plants. We believe that this study may improve our understanding of the molecular and physiological mechanisms in untangling the combined stress tolerance in plants, and may also provide a promising venue for agronomists, physiologists, as well as molecular biologists.

Elucidating the Response of Crop Plants towards Individual, Combined and Sequentially Occurring Abiotic Stresses

In nature, plants are exposed to an ever-changing environment with increasing frequencies of multiple abiotic stresses. These abiotic stresses act either in combination or sequentially, thereby driving vegetation dynamics and limiting plant growth and productivity worldwide. Plants' responses against these combined and sequential stresses clearly differ from that triggered by an individual stress. Until now, experimental studies were mainly focused on plant responses to individual stress, but have overlooked the complex stress response generated in plants against combined or sequential abiotic stresses, as well as their interaction with each other. However, recent studies have demonstrated that the combined and sequential abiotic stresses overlap with respect to the central nodes of their interacting signaling pathways, and their impact cannot be modelled by swimming in an individual extreme event. Taken together, deciphering the regulatory networks operative between various abiotic stresses in agronomically important crops will contribute towards designing strategies for the development of plants with tolerance to multiple stress combinations. This review provides a brief overview of the recent developments in the interactive effects of combined and sequentially occurring stresses on crop plants. We believe that this study may improve our understanding of the molecular and physiological mechanisms in untangling the combined stress tolerance in plants, and may also provide a promising venue for agronomists, physiologists, as well as molecular biologists.

Methods for metal chelation in plant homeostasis: Review

Metal uptake, transport and storage in plants depend on specialized ligands with closely related functions. Individual studies differing by species, nutrient availability, tissue type, etc. are not comprehensive enough to understand plant metal homeostasis in its entirety. A thorough review is required that distinguishes the role of ligands directly involved in chelation from the myriad of plant responses to general stress. Distinguishing between the functions of metal chelating compounds is the primary focus of this review; reactive oxygen species mediation and other aspects of metal homeostasis are also discussed. High molecular weight ligands (polysaccharides, phytochelatin, metallothionein), low molecular weight ligands (nicotianamine, histidine, secondary metabolites) and select studies which demonstrate the complex nature of plant metal homeostasis are explored.

Nitro-oxidative stress induces the formation of roots' cortical aerenchyma in rice under osmotic stress

Drought stress induces the formation of cortical aerenchyma in roots, providing drought tolerance by reducing respiration. However, unrestricted aerenchyma formation impedes the radial transport of water through the root's central cylinder; thereby decreasing the water uptake under drought stress. Therefore, exploring the root architectural and anatomical alterations in rice under drought is essential for targeting crop improvement. Drought stress-induced accumulation of reactive oxygen species (ROS) plays a key role in the lysigenous aerenchyma development. However, the influence of nitric oxide (NO) and reactive nitrogen species (RNS) in the development of lysigenous aerenchyma under drought has never been studied in rice. The present study examined the effect of ROS and RNS, generated by progressive drought stress, on the lysigenous aerenchyma formation in the roots of contrasting rice genotypes of the Eastern Indo-Gangetic plains (EIGP). As expected, the PEG-induced drought stress stimulated the expression of NADPH oxidase (NOX), thereby promoting the ROS generation in roots of the rice seedlings. Excessive ROS and RNS accumulations in roots affected the membrane lipids, promoting the tissue-specific programmed cell death (PCD) in rice. The activation of the antioxidant defense system played a major role in the ROS and RNS detoxification, thereby restricting the root aerenchyma formation in rice under drought stress. The results also displayed that drought tolerance in rice is associated with the formation of the Casparian strip, which limits the apoplastic flow of water in the water-deficient roots. Overall, our study revealed the association of nitro-oxidative metabolism with PCD and lysigenous aerenchyma formation in the cortical cells of root under drought stress in rice.

Silicon-mediated abiotic and biotic stress mitigation in plants: Underlying mechanisms and potential for stress resilient agriculture

Silicon (Si) is a beneficial macronutrient for plants. The Si supplementation to growth media mitigates abiotic and biotic stresses by regulating several physiological, biochemical and molecular mechanisms. The uptake of Si from the soil by root cells and subsequent transport are facilitated by Lsi1 (Low silicon1) belonging to nodulin 26-like major intrinsic protein (NIP) subfamily of aquaporin protein family, and Lsi2 (Low silicon 2) belonging to putative anion transporters, respectively. The soluble Si in the cytosol enhances the production of jasmonic acid, enzymatic and non-enzymatic antioxidants, secondary metabolites and induces expression of genes in plants under stress conditions. Silicon has been found beneficial in conferring tolerance against biotic and abiotic stresses by scavenging the reactive oxygen species (ROS) and regulation of different metabolic pathways. In the present review, Si transporters identified in various plant species and mechanisms of Si-mediated abiotic and biotic stress tolerance have been presented. In addition, role of Si in regulating gene expression under various abiotic and biotic stresses as revealed by transcriptome level studies has been discussed. This provides a deeper understanding of various mechanisms of Si-mediated stress tolerance in plants and may help in devising strategies for stress resilient agriculture.

Reassessing the role of ion homeostasis for improving salinity tolerance in crop plants

Soil salinity is a constraint for major agricultural crops leading to severe yield loss, which may increase with the changing climatic conditions. Disruption in the cellular ionic homeostasis is one of the primary responses induced by elevated sodium ions (Na⁺ ). Therefore, unraveling the mechanism of Na⁺ uptake and transport in plants along with the characterization of the candidate genes facilitating ion homeostasis is obligatory for enhancing salinity tolerance in crops. This review summarizes the current advances in understanding the ion homeostasis mechanism in crop plants, emphasizing the role of transporters involved in the regulation of cytosolic Na⁺ level along with the conservation of K⁺ /Na⁺ ratio. Furthermore, expression profiles of the candidate genes for ion homeostasis were also explored under various developmental stages and tissues of Oryza sativa based on the publicly available microarray data. The review also gives an up-to-date summary on the efforts to increase salinity tolerance in crops by manipulating selected stress-associated genes. Overall, this review gives a combined view on both the ionomic and molecular background of salt stress tolerance in plants.

The Rice GLYCINE-RICH PROTEIN 3 Confers Drought Tolerance by Regulating mRNA Stability of ROS Scavenging-Related Genes

BACKGROUND

Plant glycine-rich proteins are categorized into several classes based on their protein structures. The glycine-rich RNA binding proteins (GRPs) are members of class IV subfamily possessing N-terminus RNA-recognition motifs (RRMs) and proposed to be involved in post-transcriptional regulation of its target transcripts. GRPs are involved in developmental process and cellular stress responses, but the molecular mechanisms underlying these regulations are still elusive.

RESULTS

Here, we report the functional characterization of rice GLYCINE-RICH PROTEIN 3 (OsGRP3) and its physiological roles in drought stress response. Both drought stress and ABA induce the expression of OsGRP3. Transgenic plants overexpressing OsGRP3 (OsGRP3^OE) exhibited tolerance while knock-down plants (OsGRP3^KD) were susceptible to drought compared to the non-transgenic control. In vivo, subcellular localization analysis revealed that OsGRP3-GFP was transported from cytoplasm/nucleus into cytoplasmic foci following exposure to ABA and mannitol treatments. Comparative transcriptomic analysis between OsGRP3^OE and OsGRP3^KD plants suggests that OsGRP3 is involved in the regulation of the ROS related genes. RNA-immunoprecipitation analysis revealed the associations of OsGRP3 with PATHOGENESIS RELATED GENE 5 (PR5), METALLOTHIONEIN 1d (MT1d), 4,5-DOPA-DIOXYGENASE (DOPA), and LIPOXYGENASE (LOX) transcripts. The half-life analysis showed that PR5 transcripts decayed slower in OsGRP3^OE but faster in OsGRP3^KD, while MT1d and LOX transcripts decayed faster in OsGRP3^OE but slower in OsGRP3^KD plants. H₂O₂ accumulation was reduced in OsGRP3^OE and increased in OsGRP3^KD plants compared to non-transgenic plants (NT) under drought stress.

CONCLUSION

OsGRP3 plays a positive regulator in rice drought tolerance and modulates the transcript level and mRNA stability of stress-responsive genes, including ROS-related genes. Moreover, OsGRP3 contributes to the reduction of ROS accumulation during drought stress. Our results suggested that OsGRP3 alleviates ROS accumulation by regulating ROS-related genes' mRNA stability under drought stress, which confers drought tolerance.

Chromosomal introgressions from Oryza meridionalis into domesticated rice Oryza sativa result in iron tolerance

Iron (Fe) toxicity is one of the most common mineral disorders affecting rice (Oryza sativa) production in flooded lowland fields. Oryza meridionalis is indigenous to northern Australia and grows in regions with Fe-rich soils, making it a candidate for use in adaptive breeding. With the aim of understanding tolerance mechanisms in rice, we screened a population of interspecific introgression lines from a cross between O. sativa and O. meridionalis for the identification of quantitative trait loci (QTLs) contributing to Fe-toxicity tolerance. Six putative QTLs were identified. A line carrying one introgression from O. meridionalis on chromosome 9 associated with one QTL was highly tolerant despite very high shoot Fe concentrations. Physiological, biochemical, ionomic, and transcriptomic analyses showed that the tolerance of the introgression lines could partly be explained by higher relative Fe retention in the leaf sheath and culm. We constructed the interspecific hybrid genome in silico for transcriptomic analysis and identified differentially regulated introgressed genes from O. meridionalis that could be involved in shoot-based Fe tolerance, such as metallothioneins, glutathione S-transferases, and transporters from the ABC and MFS families. This work demonstrates that introgressions of O. meridionalis into the O. sativa genome can confer increased tolerance to excess Fe.

Recent progress in understanding salinity tolerance in plants: Story of Na+/K+ balance and beyond

High salt concentrations in the growing medium can severely affect the growth and development of plants. It is imperative to understand the different components of salt-tolerant network in plants in order to produce the salt-tolerant cultivars. High-affinity potassium transporter- and myelocytomatosis proteins have been shown to play a critical role for salinity tolerance through exclusion of sodium (Na⁺) ions from sensitive shoot tissues in plants. Numerous genes, that limit the uptake of salts from soil and their transport throughout the plant body, adjust the ionic and osmotic balance of cells in roots and shoots. In the present review, we have tried to provide a comprehensive report of major research advances on different mechanisms regulating plant tolerance to salinity stress at proteomics, metabolomics, genomics and transcriptomics levels. Along with the role of ionic homeostasis, a major focus was given on other salinity tolerance mechanisms in plants including osmoregulation and osmo-protection, cell wall remodeling and integrity, and plant antioxidative defense. Major proteins and genes expressed under salt-stressed conditions and their role in enhancing salinity tolerance in plants are discussed as well. Moreover, this manuscript identifies and highlights the key questions on plant salinity tolerance that remain to be discussed in the future.

Novel and Transgressive Salinity Tolerance in Recombinant Inbred Lines of Rice Created by Physiological Coupling-Uncoupling and Network Rewiring Effects

The phenomenon of transgressive segregation, where a small minority of recombinants are outliers relative to the range of parental phenotypes, is commonly observed in plant breeding populations. While this phenomenon has been attributed to complementation and epistatic effects, the physiological and developmental synergism involved have not been fully illuminated by the QTL mapping approach alone, especially for stress-adaptive traits involving highly complex interactions. By systems-level profiling of the IR29 × Pokkali recombinant inbred population of rice, we addressed the hypothesis that novel salinity tolerance phenotypes are created by reconfigured physiological networks due to positive or negative coupling-uncoupling of developmental and physiological attributes of each parent. Real-time growth and hyperspectral profiling distinguished the transgressive individuals in terms of stress penalty to growth. Non-parental network signatures that led to either optimal or non-optimal integration of developmental with stress-related mechanisms were evident at the macro-physiological, biochemical, metabolic, and transcriptomic levels. Large positive net gain in super-tolerant progeny was due to ideal complementation of beneficial traits while shedding antagonistic traits. Super-sensitivity was explained by the stacking of multiple antagonistic traits and loss of major beneficial traits. The synergism uncovered by the phenomics approach in this study supports the modern views of the Omnigenic Theory, emphasizing the synergy or lack thereof between core and peripheral components. This study also supports a breeding paradigm rooted on genomic modeling from multi-dimensional genetic, physiological, and phenotypic profiles to create novel adaptive traits for new crop varieties of the 21st century.

Identification of a new function of metallothionein-like gene OsMT1e for cadmium detoxification and potential phytoremediation

Cadmium (Cd) is a biologically non-essential and toxic heavy metal leaking to the environment via natural emission or anthropogenic activities, thereby contaminating crops and threatening human health. Metallothioneins (MTs) are a group of metal-binding proteins playing critical roles in metal allocation and homeostasis. In this study, we identified a novel function of OsMT1e from rice plants. OsMT1e was dominantly expressed in roots at all developmental stages and, to less extent, expressed in leaves at vegetative and seed filling stages. OsMT1e was mainly targeted to the nucleus and substantially induced by Cd exposure. Expression of OsMT1e in a yeast Cd-sensitive strain ycf1 conferred cellular tolerance to Cd, even though the ycf1 + OsMT1e cells accumulated more Cd than the control cells (ycf1 + pYES2). Both transgenic rice overexpressing (OX) and repressing OsMT1e by RNA interference (RNAi) were developed. Phenotypic analysis revealed that OsMT1e overexpression enhanced the rice growth concerning the increased shoot or root elongation, dry weight and chlorophyll contents, whereas the RNAi lines displayed a sensitive growth phenotype compared to wild-type. Assessment with 0.5, 2 and 10 μM Cd for two weeks revealed that the RNAi lines accumulated less Cd, while the OX lines had an increased Cd accumulation in root and shoot tissues. The contrasting Cd accumulation phenotypes between the OX and RNAi lines were further confirmed by a long-term study with 0.5 μM Cd for one month. Overall, the study unveiled a new function of OsMT1e in rice, which can be potentially used for engineering genotypes for phytoremediation or minimizing Cd in rice crops.

Two metallothionein genes highly expressed in rice nodes are involved in distribution of Zn to the grain

A rice node is a hub for distribution of mineral elements; however, most genes highly expressed in the node have not been functionally characterized. Transcriptomic analysis of a rice node revealed that two metallothionein genes, OsMT2b and OsMT2c, were highly expressed in the node I. We functionally characterized these genes in terms of gene expression pattern, cellular and subcellular localization, phenotypic analysis of the single and double knockout mutants and metal-binding ability. Both OsMT2b and OsMT2c were mainly and constitutively expressed in the phloem region of enlarged and diffuse vascular bundles in the nodes and of the anther. Knockout of either OsMT2b or OsMT2c increased zinc (Zn) accumulation in the nodes, but decreased Zn distribution to the panicle, resulting in decreased grain yield. A double mutant, osmt2bmt2c, showed further negative effects on the Zn distribution and grain yield. By contrast, knockout of OsMT2b had a small effect on copper (Cu) accumulation. Both OsMT2b and OsMT2c showed binding ability with Zn, whereas only OsMT2b showed binding ability with Cu in yeast. Our results suggest that both OsMT2b and OsMT2c play an important role mainly in the distribution of Zn to grain through chelation and subsequent transport of Zn in the phloem in rice.

Genome-wide analysis and transcript profiling of PSKR gene family members in Oryza sativa

Peptide signalling is an integral part of cell-to-cell communication which helps to relay the information responsible for coordinating cell proliferation and differentiation. Phytosulfokine Receptor (PSKR) is a transmembrane LRR-RLK family protein with a binding site for small signalling peptide, phytosulfokine (PSK). PSK signalling through PSKR promotes normal growth and development and also plays a role in defense responses. Like other RLKs, these PSKRs might have a role in signal transduction pathways related to abiotic stress responses. Genome-wide analysis of phytosulfokine receptor gene family has led to the identification of fifteen putative members in the Oryza sativa genome. The expression analysis of OsPSKR genes done using RNA-seq data, showed that these genes were differentially expressed in different tissues and responded specifically to heat, salt, drought and cold stress. Furthermore, the real-time quantitative PCR for fifteen OsPSKR genes revealed temporally and spatially regulated gene expression corresponding to salinity and drought stress. Our results provide useful information for a better understanding of OsPSKR genes and provide the foundation for additional functional exploration of the rice PSKR gene family in development and stress response.

Ameliorative effects of Lanthanum(Ⅲ) on Copper(Ⅱ) stressed rice (Oryza sativa) and its molecular mechanism revealed by transcriptome profiling

Rare earth elements are known to alleviate heavy metal stress. However, the potential mechanisms of the alleviation remain unclear. This study compared the effects of La(NO3)3 and La(NO3)3-amino acid chelates (La (Ⅲ)-AA) on growth, oxidative stress, ultrastructure, bioaccumulation and gene expression in rice. Results demonstrated that 20 mg/L La (Ⅲ)-AA can effectively ameliorate CuSO4 (50 mg/L) stress in rice by reducing oxidative stress and increasing chlorophyll content, thus promoting growth. ICP and TEM revealed an antagonistic effect between La (Ⅲ) and Cu(Ⅱ). Exogenous La (Ⅲ)-AA decreased Cu(Ⅱ) content in rice leaves, stems and roots by 55.56%, 59.46% and 26.29%, and ameliorated Cu(Ⅱ) damage by maintaining the ultrastructure of mesophyll cells. RNA sequencing identified 7020 differentially expressed genes, and 8 were validated by qRT-PCR. Indole-3-acetic acid (IAA) concentration was detected by HPLC. Correlation analysis between OsGH3.4-IAA-Expansin revealed that IAA content is negatively correlated with OsGH3.4 (r = -0.82, P < 0.05), and positively correlated with Expansin (r = 0.78, P < 0.05). It's assumed that La (Ⅲ)-induced OsGH3.4 could inhibit IAA-dependent Expansin expression, thereby conferring resistance to Cu stress. This work provides novel insights into the molecular basis underlying La (Ⅲ)-induced Cu(Ⅱ) tolerance in rice.

Constitutive overexpression of rice metallothionein-like gene OsMT-3a enhances growth and tolerance of Arabidopsis plants to a combination of various abiotic stresses

Metallothioneins (MT) are primarily involved in metal chelation. Recent studies have shown that MT proteins are also involved in the responses of plants to various environmental stresses. The rice metallothionein-like gene OsMT-3a is upregulated by salinity and various abiotic stressors. A DNA construct containing the complete OsMT-3a coding sequence cloned downstream to the CaMV35S promoter was transformed into Arabidopsis and homozygous single-copy transgenic lines were produced. Compared to wild-type plants, transgenic plants showed substantially increased salinity tolerance (NaCl), drought tolerance (PEG), and heavy metal tolerance (CdCl₂) as individual stresses, as well as different combinations of these stresses. Relevantly, under unstressed control conditions, vegetative growth of transgenic plants was also improved. The shoot Na⁺ concentration and hydrogen peroxide in transgenic plants were lower than those in wild-type plants. OsMT-3a-overexpressing Arabidopsis lines accumulated higher levels of Cd²⁺ in both shoots and roots following CdCl₂ treatment. In the transgenic MT-3a lines, increased activity of two major antioxidant enzymes, catalase and ascorbate peroxidase, was observed. Thus, rice OsMT-3a is a valuable target gene for plant genetic improvement against multiple abiotic stresses.

Celery and Celeriac: A Critical View on Present and Future Breeding

Cultivated for the crispy petioles and round, fleshy, and flavored hypocotyl celery and celeriac have over two centuries of breeding history in Europe. In this review paper we summarized the most recent advances touching when necessary the historical context of celery and celeriac breeding. In the post genomic era of research, the genome sequence of celery is only partially available. We comprised however in this paper the most important aspects of celery genetics that are available today and have applicability in celery modern cultivars development. We discussed the problems and traits that drive the main celery and celeriac breeding goals, like hybrid seed production, disease resistance, and interesting enlarged hypocotyl and petiole characteristics. Besides the classical breeding traits we covered the potential of integration of existing cultivars as sources for consumer oriented traits like nutraceuticals and health promoting substances. Sustainability is a subject that is continuously growing in popularity and we looked at the genetic base of celery and celeriac that makes them sources for abiotic stress resistance and candidates for phytoremediation. We explored the fundamental concepts gained in various fields of celery and related species research, as resources for future improvement of celery and celeriac germplasm. We forecast what the next years will bring to Apium breeding.

The quest for osmosensors in plants

Osmotic stress has severe effects on crop productivity. Since climate change is predicted to exacerbate this problem, the development of new crops that are tolerant to osmotic stresses, especially drought and salinity stress, is required. However, only limited success has been achieved to date, primarily because of the lack of a clear understanding of the mechanisms that facilitate osmosensing. Here, we discuss the potential mechanisms of osmosensing in plants. We highlight the roles of proteins such as receptor-like kinases, which sense stress-induced cell wall damage, mechanosensitive calcium channels, which initiate a calcium-induced stress response, and phospholipase C, a membrane-bound enzyme that is integral to osmotic stress perception. We also discuss the roles of aquaporins and membrane-bound histidine kinases, which could potentially detect changes in extracellular osmolarity in plants, as they do in prokaryotes and lower eukaryotes. These putative osmosensors have the potential to serve as master regulators of the osmotic stress response in plants and could prove to be useful targets for the selection of osmotic stress-tolerant crops.

OsMSR3, a Small Heat Shock Protein, Confers Enhanced Tolerance to Copper Stress in Arabidopsis thaliana

Copper is a mineral element essential for the normal growth and development of plants; however, excessive levels can severely affect plant growth and development. Oryza sativa L. multiple stress-responsive gene 3 (OsMSR3) is a small, low-molecular-weight heat shock protein (HSP) gene. A previous study has shown that OsMSR3 expression improves the tolerance of Arabidopsis to cadmium stress. However, the role of OsMSR3 in the Cu stress response of plants remains unclear, and, thus, this study aimed to elucidate this phenomenon in Arabidopsis thaliana, to further understand the role of small HSPs (sHSPs) in heavy metal resistance in plants. Under Cu stress, transgenic A. thaliana expressing OsMSR3 showed higher tolerance to Cu, longer roots, higher survival rates, biomass, and relative water content, and accumulated more Cu, abscisic acid (ABA), hydrogen peroxide, chlorophyll, carotenoid, superoxide dismutase, and peroxidase than wild-type plants did. Moreover, OsMSR3 expression in A. thaliana increased the expression of antioxidant-related and ABA-responsive genes. Collectively, our findings suggest that OsMSR3 played an important role in regulating Cu tolerance in plants and improved their tolerance to Cu stress through enhanced activation of antioxidative defense mechanisms and positive regulation of ABA-responsive gene expression.

CO2 uptake and chlorophyll a fluorescence of Suaeda fruticosa grown under diurnal rhythm and after transfer to continuous dark

Although only 2-4% of absorbed light is emitted as chlorophyll (Chl) a fluorescence, its measurement provides valuable information on photosynthesis of the plant, particularly of Photosystem II (PSII) and Photosystem I (PSI). In this paper, we have examined photosynthetic parameters of Suaeda fruticosa L. (family: Amaranthaceae), surviving under extreme xerohalophytic conditions, as influenced by diurnal rhythm or continuous dark condition. We report here CO₂ gas exchange and the kinetics of Chl a fluorescence of S. fruticosa, made every 3 hours (hrs) for 3 days, using a portable infra-red gas analyzer and a Handy PEA fluorimeter. Our measurements on CO₂ gas exchange show the maximum rate of photosynthesis to be at 08:00 hrs under diurnal condition and at 05:00 hrs under continuous dark. From the OJIP phase of Chl a fluorescence transient, we have inferred that the maximum quantum yield of PSII photochemistry must have increased during the night under diurnal rhythm, and between 11:00 and 17:00 hrs under constant dark. Overall, our study has revealed novel insights into how photosynthetic reactions are affected by the photoperiodic cycles in S. fruticosa under high salinity. This study has further revealed a unique strategy operating in this xero-halophyte where the repair mechanism for damaged PSII operates during the dark, which, we suggest, contributes to its ecological adaptation and ability to survive and reproduce under extreme saline, high light, and drought conditions. We expect these investigations to help in identifying key genes and pathways for raising crops for saline and dry areas.

Identification of the metallothionein gene family from cucumber and functional characterization of CsMT4 in Escherichia coli under salinity and osmotic stress

Metallothionein (MT) proteins are low-molecular-weight, cysteine-rich and metal-binding proteins that play important roles in the maintenance of metal homeostasis and detoxification, but their roles in abiotic stress tolerance remain largely unknown. In this study, three MT family genes (CsMT2, CsMT3 and CsMT4) were identified in the cucumber genome. CsMT2, CsMT3 and CsMT4 possessed 14, 10, and 18 Cys residues, which were clustered into 2, 2, and 3 Cys-rich regions, respectively. Phylogenetic analysis of MTs from cucumber, Arabidopsis and soybean revealed that these MTs were clustered into four groups in accordance with the MT types (types 1-4). An analysis of the cis-acting regulatory elements revealed that a series of hormone-, stress-, and development-related cis-elements were present in the promoter regions of CsMT genes. Expression pattern analysis by RT-PCR showed that the CsMT genes exhibited different tissue expression patterns. CsMT2 showed relatively higher expression in stem, leaf, and flower; CsMT3 was mainly expressed in leaf, flower, and fruit, while CsMT4 was highly expressed in fruit and leaf. The qRT-PCR results showed that the CsMT genes were induced by various stress treatments including NaCl, PEG, and ABA, while CsMT4 displayed much higher expression levels in response to these stresses than CsMT2 and CsMT3. Escherichia coli cells expressing CsMT4 exhibited higher salinity and osmotic tolerance compared with control cells, indicating the significant function of CsMT4 to confer tolerance to these stresses. These results lay a foundation for further research on the function of MT family genes in plant stress responses.

Transcriptome profiles of soybean leaves and roots in response to zinc deficiency

Zinc (Zn) deficiency is a widespread agricultural problem in arable soils of the whole world. However, the molecular mechanisms underlying Zn-deficiency response are largely unknown. Here, we analyzed the transcriptomic profilings of soybean leaves and roots in response to Zn deficiency through Illumina's high-throughput RNA sequencing in order to understand the molecular basis of Zn-deficiency response in the plants. A total of 614 and 1011 gene loci were found to be differentially expressed in leaves and roots, respectively, and 88 loci were commonly found in both leaves and roots. Twelve differentially expressed genes (DEGs) were randomly selected for validation by quantitative reverse transcription polymerase chain reaction, and their fold changes were similar to those of RNA-seq. Gene ontology enrichment analysis showed that ion transport, nicotianamine (NA) biosynthetic process and queuosine biosynthetic process were enriched in the upregulated genes, while oxidation-reduction process and defense response were enriched in the downregulated genes. Among the DEGs, 20 DEGs are potentially involved in Zn homeostasis, including seven ZRT, IRT-related protein (ZIP) transporter genes, three NA synthase genes, and seven metallothionein genes; 40 DEGs are possibly involved in diverse hormonal signals such as auxin, cytokinin, ethylene and gibberellin; nine DEGs are putatively involved in calcium signaling; 85 DEGs are putative transcription factor genes. Nine DEGs were found to contain zinc-deficiency-response element in their promoter regions. These results could provide comprehensive insights into the soybean response to Zn deficiency and will be helpful for further elucidation of the molecular mechanisms of Zn-deficiency response and Zn-deficiency tolerance in plants.

Hyperaccumulation of Cu, Zn, Ni, and Cd in Azolla species inducing expression of methallothionein and phytochelatin synthase genes

Azolla is a floating aquatic fern, having amazing capacity for concentrating toxic heavy metals. Metallothioneins (MTs) and phytochelatins (PCs) are well-defined heavy metal-binding ligands in plants. Bioaccumulation potential of different Azolla species varies according to their heavy metal ions. Therefore, the accumulation of Ni, Zn, Cu, and Cd was studied in A. pinnata, A. filiculoides, and a sample taken from Anzali wetland. Moreover, the expression of metallothionein and phytochelatin synthase encoding genes was examined at different metal concentrations. The highest level of Cu and Cd absorption was detected in A. pinnata, while the maximum amount of Ni and Zn absorption was observed in A. filiculoides and the sample taken from Anzali, respectively. The MT2 and PCS1 gene expression patterns were significantly induced by the heavy metal treatments, confirming their roles in phytoremediation potential of Azolla. However, as the results concerning heavy metal accumulation and gene expression vary in different species, only specific species of Azolla can be used for special purposes. It can be concluded that the Azolla is a good candidate for phytoremediation purposes, and the formation of phytochelatin-heavy metal complexes and their sequestration in vacuole are the main processes influencing susceptibility of Azolla to heavy metals.