Determining arsenic stress tolerance genes in rice (Oryza sativa L.) via genomic insights and QTL mapping with double haploid lines.

Arsenic, a hazardous heavy metal with potent carcinogenic properties, significantly affects key rice-producing regions worldwide. In this study, we present a quantitative trait locus (QTL) mapping investigation designed to identify candidate genes responsible for conferring tolerance to arsenic toxicity in rice (Oryza sativa L.) during the seedling stage. This study identified 17 QTLs on different chromosomes, including qCHC-1 and qCHC-3 on chromosome 1 and 3 related to chlorophyll content and qRFW-12 on chromosome 12 related to root fresh weight. Gene expression analysis revealed eight candidate genes exhibited significant upregulation in the resistant lines, OsGRL1, OsDjB1, OsZIP2, OsMATE12, OsTRX29, OsMADS33, OsABCG29, and OsENODL24. These genes display sequence alignment and phylogenetic tree similarities with other species and engaging in protein-protein interactions with significant proteins. Advanced gene-editing techniques such as CRISPR-Cas9 to precisely target and modify the candidate genes responsible for arsenic tolerance will be explore. This approach may expedite the development of arsenic-resistant rice cultivars, which are essential for ensuring food security in regions affected by arsenic-contaminated soil and water.

Unveiling the protective role of anthocyanin in rice: insights into drought-induced oxidative stress and metabolic regulation.

This study investigates the impact of anthocyanin treatment on rice plants under drought stress, focusing on phenotypic, molecular, and biochemical responses. Anthocyanin were treated to one month old plants one week before the droughtexposure. Drought stress was imposed by using 10% polyethylene glycol (PEG 6000). Anthocyanin-treated plants exhibited significant enhancements in various traits, including growth parameters and reproductive characteristics, under normal conditions. When subjected to drought stress, these plants displayed resilience, maintaining or improving essential morphological and physiological features compared to non-treated counterparts. Notably, anthocyanin application mitigated drought-induced oxidative stress, as evidenced by reduced levels of reactive oxygen species (ROS) and lipid membrane peroxidation. The study also elucidates the regulatory role of anthocyanins in the expression of flavonoid biosynthetic genes, leading to increased levels of key secondary metabolites. Furthermore, anthocyanin treatment influenced the levels of stress-related signaling molecules, including melatonin, proline, abscisic acid (ABA), and salicylic acid (SA), contributing to enhanced stress tolerance. The enzymatic activity of antioxidants and the expression of drought-responsive genes were modulated by anthocyanins, emphasizing their role in antioxidant defense and stress response. Additionally, anthocyanin treatment positively influenced macronutrient concentrations, particularly calcium ion (Ca+), potassium ion (K+), and sodium ion (Na+), essential for cell wall and membrane stability. The findings collectively highlight the multifaceted protective effects of anthocyanins, positioning them as potential key players in conferring resilience to drought stress in rice plants. The study provides valuable insights into the molecular and physiological mechanisms underlying anthocyanin-mediated enhancement of drought stress tolerance, suggesting promising applications in agricultural practices for sustainable crop production.

Genetic characterization and phylogenetic analysis of the Nigella sativa (black seed) plastome.

In this study, the complete plastome sequence of Nigella sativa (black seed), was analyzed for the first time. The plastome spans approximately 154,120 bp, comprising four sections: the Large Single-Copy (LSC) (85,538 bp), the Small Single-Copy (SSC) (17,984 bp), and two Inverted Repeat (IR) regions (25,299 bp). A comparative study of N. sativa's plastome with ten other species from various genera in the Ranunculaceae family reveals substantial structural variations. The contraction of the inverted repeat region in N. sativa influences the boundaries of single-copy regions, resulting in a shorter plastome size than other species. When comparing the plastome of N. sativa with those of its related species, significant divergence is observed, particularly except for N. damascena. Among these, the plastome of A. glaucifolium displays the highest average pairwise sequence divergence (0.2851) with N. sativa, followed by A. raddeana (0.2290) and A. coerulea (0.1222). Furthermore, the study identified 12 distinct hotspot regions characterized by elevated Pi values (> 0.1). These regions include trnH-GUG-psbA, matK-trnQ-UUG, psbK-trnR-UCU, atpF-atpI, rpoB-psbD, ycf3-ndhJ, ndhC-cemA, petA-psaJ, trnN-GUU-ndhF, trnV-GAC-rps12, ycf2-trnI-CAU, and ndhA-ycf1. Approximately, 24 tandem and 48 palindromic and forward repeats were detected in N. sativa plastome. The analysis revealed 32 microsatellites with the majority being mononucleotide repeats. In the N. sativa plastome, phenylalanine had the highest number of codons (1982 codons), while alanine was the least common amino acid with 260 codons. A phylogenetic tree, constructed using protein-coding genes, revealed a distinct monophyletic clade comprising N. sativa and N. damascene, closely aligned with the Cimicifugeae tribe and exhibiting robust support. This plastome provides valuable genetic information for precise species identification, phylogenetic resolution, and evolutionary studies of N. sativa.

The complete plastome sequences of invasive weed Parthenium hysterophorus: genome organization, evolutionary significance, structural features, and comparative analysis.

Parthenium hysterophorus, a globally widespread weed, poses a significant threat to agricultural ecosystems due to its invasive nature. We investigated the chloroplast genome of P. hysterophorus in this study. Our analysis revealed that the chloroplast genome of P. hysterophorus spans a length of 151,881 base pairs (bp). It exhibits typical quadripartite structure commonly found in chloroplast genomes, including inverted repeat regions (IR) of 25,085 bp, a small single copy (SSC) region of 18,052 bp, and a large single copy (LSC) region of 83,588 bp. A total of 129 unique genes were identified in P. hysterophorus chloroplast genomes, including 85 protein-coding genes, 36 tRNAs, and eight rRNAs genes. Comparative analysis of the P. hysterophorus plastome with those of related species from the tribe Heliantheae revealed both conserved structures and intriguing variations. While many structural elements were shared among the species, we identified a rearrangement in the large single-copy region of P. hysterophorus. Moreover, our study highlighted notable gene divergence in several specific genes, namely matK, ndhF, clpP, rps16, ndhA, rps3, and ndhD. Phylogenetic analysis based on the 72 shared genes placed P. hysterophorus in a distinct clade alongside another species, P. argentatum. Additionally, the estimated divergence time between the Parthenium genus and Helianthus (sunflowers) was approximately 15.1 million years ago (Mya). These findings provide valuable insights into the evolutionary history and genetic relationships of P. hysterophorus, shedding light on its divergence and adaptation over time.

Plastome diversity and evolution in mosses: Insights from structural characterization, comparative genomics, and phylogenetic analysis.

Mosses play a significant role in ecology, evolution, and the economy. They belong to the nonvascular plant kingdom and are considered the closest living relatives of the first terrestrial plants. The circular chloroplast DNA molecules (plastomes) of mosses contain all the genetic information essential for chloroplast functions and represent the source of the evolutionary history of these organisms. This study comprehensively analyzed the plastomes of 47 moss species belonging to 14 orders, focusing on their size, GC content, gene loss, gene content, synteny, and evolution. The findings revealed great differences among plastome sizes, with Takakia lepidozioides (Takakiopsida) and Funaria hygrometrica (Funariales) having the largest and smallest plastomes, respectively. Moss plastomes included 69 to 89 protein-coding genes, 8 rRNA genes, and 34 to 42 tRNA genes, resulting in the total number of genes in a plastome ranging between 115 and 138. Various genes have been lost from the plastomes of different moss species, with Atrichum angustatum lacking the highest number of genes. This study also examined plastome synteny and moss evolution using comparative genomics and repeat sequence analysis. The results demonstrated that synteny and similarity levels varied across the 47 moss examined species, with some exhibiting structure similarity and others displaying structural inversions. Maximum likelihood and Bayesian approaches were used to construct a phylogenetic tree using 36 concatenated protein-coding genes, and the results revealed that the genera Sphagnum and Takakia are sister groups to the other mosses. Additionally, it was found that Tetraphidales, Polytrichales, Buxbaumiales, and Diphysciales are closely related. This research describes the evolutionary diversity of mosses and offers guidelines for future studies in this field. The findings also highlight the need for more investigations into the factors regulating plastome size variation in these plants.

Novel Insights into Exogenous Phytohormones: Central Regulators in the Modulation of Physiological, Biochemical, and Molecular Responses in Rice under Metal(loid) Stress.

Rice (Oryza sativa) is a research model for monocotyledonous plants. Rice is also one of the major staple foods and the primary crop for more than half of the world's population. Increasing industrial activities and the use of different fertilizers and pesticides containing heavy metals (HMs) contribute to the contamination of agriculture fields. HM contamination is among the leading causes that affect the health of rice plants by limiting their growth and causing plant death. Phytohormones have a crucial role in stress-coping mechanisms and in determining a range of plant development and growth aspects during heavy metal stress. This review summarizes the role of different exogenous applications of phytohormones including auxin, cytokinin, gibberellins, ethylene, abscisic acid, strigolactones, jasmonates, brassinosteroids, and salicylic acids in rice plants for mitigating heavy metal stress via manipulation of their stress-related physiological and biochemical processes, and alterations of signaling and biosynthesis of genes. Exogenous administration of phytohormones and regulation of endogenous levels by targeting their biosynthesis/signaling machineries is a potential strategy for protecting rice from HM stress. The current review primarily emphasizes the key mechanistic phytohormonal-mediated strategies for reducing the adverse effects of HM toxicity in rice. Herein, we have provided comprehensive evidence for the effective role of exogenous phytohormones in employing defense responses and tolerance in rice to the phytotoxic effects of HM toxicity along with endogenous hormonal crosstalk for modulation of subcellular mechanisms and modification of stress-related signaling pathways, and uptake and translocation of metals. Altogether, this information offers a systematic understanding of how phytohormones modulate a plant's tolerance to heavy metals and may assist in directing the development of new approaches to strengthen rice plant resistance to HM toxicity.

Halotolerant endophytic bacteria alleviate salinity stress in rice (oryza sativa L.) by modulating ion content, endogenous hormones, the antioxidant system and gene expression.

Excessive salinity reduces crop production and negatively impacts agriculture worldwide. We previously isolated endophytic bacterial strains from two halophytic species: Artemisia princeps and Chenopodium ficifolium. We used three bacterial isolates: ART-1 (Lysinibacillus fusiformis), ART-10 (Lysinibacillus sphaericus), and CAL-8 (Brevibacterium pityocampae) to alleviate the impact of salinity stress on rice. The impact of 160 mM NaCl salinity on rice was significantly mitigated following inoculation with these bacterial strains, resulting in increased growth and chlorophyll content. Furthermore, OsNHX1, OsAPX1, OsPIN1 and OsCATA expression was increased, but OsSOS expression was decreased. Inductively coupled plasma mass spectrometry (ICP-MS) revealed reduced K+ and Na+ levels in shoots of bacteria-inoculated plants, whereas that of Mg2+ was increased. Bacterial inoculation reduced the content of total flavonoids in rice leaves. Salinized plants inoculated with bacteria showed reduced levels of endogenous salicylic acid (SA) and abscisic acid (ABA) but increased levels of jasmonic acid (JA). In conclusion, the bacterial isolates ART-1, ART-10, and CAL-8 alleviated the adverse effect of salinity on rice growth, which justifies their use as an eco-friendly agricultural practice.

Exploring the potential of halotolerant bacteria from coastal regions to mitigate salinity stress in wheat: physiological, molecular, and biochemical insights.

Salinity stress, a significant global abiotic stress, is caused by various factors such as irrigation with saline water, fertilizer overuse, and drought conditions, resulting in reduced agricultural production and sustainability. In this study, we investigated the use of halotolerant bacteria from coastal regions characterized by high salinity as a solution to address the major environmental challenge of salinity stress. To identify effective microbial strains, we isolated and characterized 81 halophilic bacteria from various sources, such as plants, rhizosphere, algae, lichen, sea sediments, and sea water. We screened these bacterial strains for their plant growth-promoting activities, such as indole acetic acid (IAA), phosphate solubilization, and siderophore production. Similarly, the evaluation of bacterial isolates through bioassay revealed that approximately 22% of the endophytic isolates and 14% of rhizospheric isolates exhibited a favorable influence on seed germination and seedling growth. Among the tested isolates, GREB3, GRRB3, and SPSB2 displayed a significant improvement in all growth parameters compared to the control. As a result, these three isolates were utilized to evaluate their efficacy in alleviating the negative impacts of salt stress (150 mM, 300 mM, and seawater (SW)) on the growth of wheat plants. The result showed that shoot length significantly increased in plants inoculated with bacterial isolates up to 15% (GREB3), 16% (GRRB3), and 24% (SPSB2), respectively, compared to the control. The SPSB2 strain was particularly effective in promoting plant growth and alleviating salt stress. All the isolates exhibited a more promotory effect on root length than shoot length. Under salt stress conditions, the GRRB3 strain significantly impacted root length, leading to a boost of up to 6%, 5%, and 3.8% at 150 mM, 300 mM, and seawater stress levels, respectively. The bacterial isolates also positively impacted the plant's secondary metabolites and antioxidant enzymes. The study also identified the WDREB2 gene as highly upregulated under salt stress, whereas DREB6 was downregulated. These findings demonstrate the potential of beneficial microbes as a sustainable approach to mitigate salinity stress in agriculture.

Enhanced Physiological and Biochemical Performance of Mung Bean and Maize under Saline and Heavy Metal Stress through Application of Endophytic Fungal Strain SL3 and Exogenous IAA.

Modern irrigation practices and industrial pollution can contribute to the simultaneous occurrence of salinity and heavy metal contamination in large areas of the world, resulting in significant negative effects on crop productivity and sustainability. This study aimed to investigate the growth-promoting potentials of an important endophytic fungal strain SL3 and to compare its potential with exogenous IAA (indole-3-acetic acid) in the context of salt and heavy metal stress. The strain was assessed for plant growth-promoting traits such as the production of indole-3-acetic acid, gibberellins (GA), and siderophore. We selected two important crops, mung bean and maize, and examined various physiological and biochemical characteristics under 300 mM NaCl and 2.5 mM Pb stress conditions, with and without the application of IAA and SL3. This study's results demonstrated that both IAA and SL3 positively impacted the growth and development of plants under normal and stressed conditions. In NaCl and Pb-induced stress conditions, the growth of mung bean and maize plants was significantly reduced. However, the application of IAA and SL3 helped to alleviate stress, leading to a significant increase in shoot/root length and weight compared to IAA and SL3 non-treated plants. The results revealed that photosynthetic pigments, accumulation of catalase (CAT), phenolic contents, polyphenol oxidase, and flavanols are higher in the IAA and SL3-treated plants than in the non-inoculated plants. This study's findings revealed that applying the SL3 fungal strain positively influenced various physiological and biochemical processes in tested plant species under normal and stress conditions of NaCl and Pb. These findings also suggested that SL3 could be a potential replacement for widely used IAA to promote plant growth by improving photosynthetic efficiency, reducing oxidative stress, and enhancing metabolic activities in plants, including mung and maize. Moreover, this study highlights that SL3 has synergistic effects with IAA in enhancing resilience to salt and heavy stress and offers a promising avenue for future agricultural applications in salt and heavy metal-affected regions.

Dynamic interplay of WRKY, GRAS, and ERF transcription factor families in tomato-endophytic fungal symbiosis: insights from transcriptome and genome-wide analysis.

Plant-microbe interactions play a crucial role in shaping plant growth and development, as well as in mediating plant responses to biotic and abiotic stresses. In this study, we used RNA-seq data to examine the expression profiles of SlWRKY, SlGRAS, and SlERF genes during the symbiotic association of Curvularia lunata SL1 with tomato (Solanum lycopersicum) plants. We also conducted functional annotation analysis by comparative genomics studies of their paralogs and orthologs genes, as well as other approaches, such as gene analysis and protein interaction networks, to identify and characterize the regulatory roles of these TFs in the development of the symbiotic association. We found that more than half of the investigated SlWRKY genes exhibited significant upregulation during symbiotic association, including SlWRKY38, SlWRKY46, SlWRKY19, and SlWRKY51. Several SlGRAS and SlERF genes were upregulated, such as SlGLD2, SlGLD1, SlERF.C.5, ERF16, and SlERF.B12. Conversely, a smaller proportion of SlWRKY, SlGRAS, and SlERF genes were significantly downregulated during symbiotic association. Furthermore, we investigated the possible roles of SlWRKY, SlGRAS, and SlERF genes in hormonal regulation during plant-microbe interactions. We identified several upregulated candidate transcripts likely to be involved in plant hormone signaling pathways. Our findings are consistent with previous studies on these genes, providing further evidence of their involvement in hormonal regulation during plant-microbe interactions. To validate the RNA-seq data accuracy, we performed RT-qPCR analyses of selected SlWRKY, SlGRAS, and SlERF genes, which showed similar expression patterns to those observed in the RNA-seq data. These results confirmed the accuracy of our RNA-seq data and provided additional support for the differential expression of these genes during plant-microbe interactions. Taken together, our study provides new insights into the differential expression profiles of SlWRKY, SlGRAS, and SlERF genes during symbiotic association with C. lunata, as well as their potential roles in hormonal regulation during plant-microbe interactions. These findings could be useful for guiding future research on the ways in which plants and microbes interact, and may ultimately lead to the creation of better approaches for promoting plant growth under stressful conditions.

Seed Bio-priming of wheat with a novel bacterial strain to modulate drought stress in Daegu, South Korea.

Wheat is one of the major cereal crop grown food worldwide and, therefore, plays has a key role in alleviating the global hunger crisis. The effects of drought stress can reduces crop yields by up to 50% globally. The use of drought-tolerant bacteria for biopriming can improve crop yields by countering the negative effects of drought stress on crop plants. Seed biopriming can reinforce the cellular defense responses to stresses via the stress memory mechanism, that its activates the antioxidant system and induces phytohormone production. In the present study, bacterial strains were isolated from rhizospheric soil taken from around the Artemisia plant at Pohang Beach, located near Daegu, in the South Korea Republic of Korea. Seventy-three isolates were screened for their growth-promoting attributes and biochemical characteristics. Among them, the bacterial strain SH-8 was selected preferred based on its plant growth-promoting bacterial traits, which are as follows: abscisic acid (ABA) concentration = 1.08 ± 0.05 ng/mL, phosphate-solubilizing index = 4.14 ± 0.30, and sucrose production = 0.61 ± 0.13 mg/mL. The novel strain SH-8 demonstrated high tolerance oxidative stress. The antioxidant analysis also showed that SH-8 contained significantly higher levels of catalase (CAT), superoxide dismutase (SOD), and ascorbic peroxidase (APX). The present study also quantified and determined the effects of biopriming wheat (Triticum aestivum) seeds with the novel strain SH-8. SH-8 was highly effective in enhancing the drought tolerance of bioprimed seeds; their drought tolerance and germination potential (GP) were increased by up to 20% and 60%, respectively, compared with those in the control group. The lowest level of impact caused by drought stress and the highest germination potential, seed vigor index (SVI), and germination energy (GE) (90%, 2160, and 80%, respectively), were recorded for seeds bioprimed with with SH-8. These results show that SH-8 enhances drought stress tolerance by up to 20%. Our study suggests that the novel rhizospheric bacterium SH-8 (gene accession number OM535901) is a valuable biostimulant that improves drought stress tolerance in wheat plants and has the potential to be used as a biofertilizer under drought conditions.

Comparative plastome genomics, taxonomic delimitation and evolutionary divergences of Tetraena hamiensis var. qatarensis and Tetraena simplex (Zygophyllaceae).

The Zygophyllum and Tetraena genera are intriguingly important ecologically and medicinally. Based on morphological characteristics, T. hamiensis var. qatarensis, and T. simplex were transferred from Zygophyllum to Tetraena with the least genomic datasets available. Hence, we sequenced the T. hamiensis and T. simplex and performed in-depth comparative genomics, phylogenetic analysis, and estimated time divergences. The complete plastomes ranged between 106,720 and 106,446 bp-typically smaller than angiosperms plastomes. The plastome circular genomes are divided into large single-copy regions (~ 80,964 bp), small single-copy regions (~ 17,416 bp), and two inverted repeats regions (~ 4170 bp) in both Tetraena species. An unusual shrinkage of IR regions 16-24 kb was identified. This resulted in the loss of 16 genes, including 11 ndh genes which encode the NADH dehydrogenase subunits, and a significant size reduction of Tetraena plastomes compared to other angiosperms. The inter-species variations and similarities were identified using genome-wide comparisons. Phylogenetic trees generated by analyzing the whole plastomes, protein-coding genes, matK, rbcL, and cssA genes exhibited identical topologies, indicating that both species are sisters to the genus Tetraena and may not belong to Zygophyllum. Similarly, based on the entire plastome and proteins coding genes datasets, the time divergence of Zygophyllum and Tetraena was 36.6 Ma and 34.4 Ma, respectively. Tetraena stem ages were 31.7 and 18.2 Ma based on full plastome and protein-coding genes. The current study presents the plastome as a distinguishing and identification feature among the closely related Tetraena and Zygophyllum species. It can be potentially used as a universal super-barcode for identifying plants.

Silicon-Induced Morphological, Biochemical and Molecular Regulation in Phoenix dactylifera L. under Low-Temperature Stress.

Climate changes abruptly affect optimum growth temperatures, leading to a negative influence on plant physiology and productivity. The present study aimed to investigate the extent of low-temperature stress effects on date palm growth and physiological indicators under the exogenous application of silicon (Si). Date palm seedlings were treated with Si (1.0 mM) and exposed to different temperature regimes (5, 15, and 30 °C). It was observed that the application of Si markedly improved fresh and dry biomass, photosynthetic pigments (chlorophyll and carotenoids), plant morphology, and relative water content by ameliorating low-temperature-induced oxidative stress. Low-temperature stress (5 and 15 °C), led to a substantial upregulation of ABA-signaling-related genes (NCED-1 and PyL-4) in non Si treated plants, while Si treated plants revealed an antagonistic trend. However, jasmonic acid and salicylic acid accumulation were markedly elevated in Si treated plants under stress conditions (5 and 15 °C) in comparison with non Si treated plants. Interestingly, the upregulation of low temperature stress related plant plasma membrane ATPase (PPMA3 and PPMA4) and short-chain dehydrogenases/reductases (SDR), responsible for cellular physiology, stomatal conductance and nutrient translocation under silicon applications, was observed in Si plants under stress conditions in comparison with non Si treated plants. Furthermore, a significant expression of LSi-2 was detected in Si plants under stress, leading to the significant accumulation of Si in roots and shoots. In contrast, non Si plants demonstrated a low expression of LSi-2 under stress conditions, and thereby, reduced level of Si accumulation were observed. Less accumulation of oxidative stress was evident from the expression of superoxide dismutase (SOD) and catalase (CAT). Additionally, Si plants revealed a significant exudation of organic acids (succinic acid and citric acid) and nutrient accumulation (K and Mg) in roots and shoots. Furthermore, the application of Si led to substantial upregulation of the low temperature stress related soybean cold regulated gene (SRC-2) and ICE-1 (inducer of CBF expression 1), involved in the expression of CBF/DREB (C-repeat binding factor/dehydration responsive element binding factor) gene family under stress conditions in comparison with non Si plants. The current research findings are crucial for exploring the impact on morpho-physio-biochemical attributes of date palms under low temperature and Si supplementation, which may provide an efficient strategy for growing plants in low-temperature fields.

Corrigendum: Microbiome variation across populations of desert halophyte Zygophyllum qatarensis.

[This corrects the article DOI: 10.3389/fpls.2022.841217.].

Characterization of the Seed Biopriming, Plant Growth-Promoting and Salinity-Ameliorating Potential of Halophilic Fungi Isolated from Hypersaline Habitats.

Salinity stress is one of the major abiotic factors limiting crop yield in arid and semi-arid regions. Plant growth-promoting fungi can help plants thrive in stressful conditions. In this study, we isolated and characterized 26 halophilic fungi (endophytic, rhizospheric, and soil) from the coastal region of Muscat, Oman, for plant growth-promoting activities. About 16 out of 26 fungi were found to produce IAA, and about 11 isolates (MGRF1, MGRF2, GREF1, GREF2, TQRF4, TQRF5, TQRF5, TQRF6, TQRF7, TQRF8, TQRF2) out of 26 strains were found to significantly improve seed germination and seedling growth of wheat. To evaluate the effect of the above-selected strains on salt tolerance in wheat, we grew wheat seedlings in 150 mM, 300 mM NaCl and SW (100% seawater) treatments and inoculated them with the above strains. Our findings showed that fungal strains MGRF1, MGRF2, GREF2, and TQRF9 alleviate 150 mM salt stress and increase shoot length compared to their respective control plants. However, in 300 mM stressed plants, GREF1 and TQRF9 were observed to improve shoot length. Two strains, GREF2 and TQRF8, also promoted plant growth and reduced salt stress in SW-treated plants. Like shoot length, an analogous pattern was observed in root length, and different salt stressors such as 150 mM, 300 mM, and SW reduced root length by up to 4%, 7.5%, and 19.5%, respectively. Three strains, GREF1, TQRF7, and MGRF1, had higher catalase (CAT) levels, and similar results were observed in polyphenol oxidase (PPO), and GREF1 inoculation dramatically raised the PPO level in 150 mM salt stress. The fungal strains had varying effects, with some, such as GREF1, GREF2, and TQRF9, showing a significant increase in protein content as compared to their respective control plants. Under salinity stress, the expression of DREB2 and DREB6 genes was reduced. However, the WDREB2 gene, on the other hand, was shown to be highly elevated during salt stress conditions, whereas the opposite was observed in inoculated plants.

Identification of a Major Locus for Lodging Resistance to Typhoons Using QTL Analysis in Rice.

We detected a new target quantitative trait locus (QTL) for lodging resistance in rice by analyzing lodging resistance to typhoons (Maysak and Haishen) using a scale from 0 (no prostrating) to 1 (little prostrating or prostrating) to record the resistance score in a Cheongcheong/Nagdong double haploid rice population. Five quantitative trait loci for lodging resistance to typhoons were detected. Among them, qTyM6 and qTyH6 exhibited crucial effects of locus RM3343-RM20318 on chromosome 6, which overlaps with our previous rice lodging studies for the loci qPSLSA6-2, qPSLSB6-5, and qLTI6-2. Within the target locus RM3343-RM20318, 12 related genes belonging to the cytochrome P450 protein family were screened through annotation. Os06g0599200 (OsTyM/Hq6) was selected for further analysis. We observed that the culm and panicle lengths were positively correlated with lodging resistance to typhoons. However, the yield was negatively correlated with lodging resistance to typhoons. The findings of this study improve an understanding of rice breeding, particularly the culm length, early maturing, and heavy panicle varieties, and the mechanisms by which the plant's architecture can resist natural disasters such as typhoons to ensure food safety. These results also provide the insight that lodging resistance in rice may be associated with major traits such as panicle length, culm length, tiller number, and heading date, and thereby improvements in these traits can increase lodging resistance to typhoons. Moreover, rice breeding should focus on maintaining suitable varieties that can withstand the adverse effects of climate change in the future and provide better food security.

Diversity, Lifestyle, Genomics, and Their Functional Role of Cochliobolus, Bipolaris, and Curvularia Species in Environmental Remediation and Plant Growth Promotion under Biotic and Abiotic Stressors.

Cochliobolus, Bipolaris, and Curvularia genera contain various devastating plant pathogens that cause severe crop losses worldwide. The species belonging to these genera also perform a variety of diverse functions, including the remediation of environmental contaminations, beneficial phytohormone production, and maintaining their lifestyle as epiphytes, endophytes, and saprophytes. Recent research has revealed that despite their pathogenic nature, these fungi also play an intriguing role in agriculture. They act as phosphate solubilizers and produce phytohormones, such as indole acetic acid (IAA) and gibberellic acid (GAs), to accelerate the growth of various plants. Some species have also been reported to play a significant role in plant growth promotion during abiotic stresses, such as salinity stress, drought stress, heat stress, and heavy metal stress, as well as act as a biocontrol agent and a potential mycoherbicide. Similarly, these species have been reported in numerous industrial applications to produce different types of secondary metabolites and biotechnological products and possess a variety of biological properties, such as antibacterial, antileishmanial, cytotoxic, phytotoxic, and antioxidant activities. Additionally, some of the species have been utilized in the production of numerous valuable industrial enzymes and biotransformation, which has an impact on the growth of crops all over the world. However, the current literature is dispersed, and some of the key areas, such as taxonomy, phylogeny, genome sequencing, phytohormonal analysis, and diversity, are still being neglected in terms of the elucidation of its mechanisms, plant growth promotion, stress tolerance, and bioremediation. In this review, we highlighted the potential role, function, and diversity of Cochliobolus, Curvularia, and Bipolaris for improved utilization during environmental biotechnology.

Genome-wide annotation and expression analysis of WRKY and bHLH transcriptional factor families reveal their involvement under cadmium stress in tomato (Solanum lycopersicum L.).

The WRKY and bHLH transcription factors have been implicated in the regulation of gene expression during various physiological processes in plants, especially in plant stress responses. However, little information about the heavy metal-responsive SlWRKY and SlbHLH in tomato (Solanum lycopersicum) is available. We performed a genome-wide investigation for these two TF families in S. lycopersicum and determined their role in cadmium (Cd) stress tolerance. Furthermore, ortholog analysis with the Arabidopsis genome led to classifying WRKY and bHLH ortholog genes into nine and 11 clusters, respectively. The comparative phylogenetic analysis revealed duplication events and gene loss in Arabidopsis and S. lycopersicum, which occurred during evolution both before and after the last common ancestor of the two species. Orthologous relationships are also supported by additional evidence, such as gene structure, conserved motif compositions, and protein-protein interaction networks for the majority of genes, suggesting their similar functions. A comprehensive transcriptomics analysis revealed that both WRKY and bHLH genes were differentially expressed in response to cadmium stress as compared with control plants. A gene ontology analysis revealed that most WRKYs and bHLHs are DNA-binding essential proteins that regulate gene expression positively and negatively. Analyses of interaction networks revealed that both WRKYs and bHLHs mediate networks implicated in several stress-signaling pathways. The findings of this work may help us to comprehend the intricate transcriptional control of WRKY and bHLH genes and identify potential stress-responsive genes relevant to tomato genetic improvement. Moreover, identifying heavy metal stress-responsive WRKY and bHLH genes in S. lycopersicum will provide fundamental insights for developing new heavy metal stress-tolerant varieties of tomato crops.

Melatonin alleviates arsenic (As) toxicity in rice plants via modulating antioxidant defense system and secondary metabolites and reducing oxidative stress.

The Arsenic (As) load on the environment has increased immensely due to large-scale industrial and agricultural uses of As in several synthetic products, such as fertilizers, herbicides, and pesticides. Melatonin is a plant hormone that has a key role in abiotic stress inhibition, but the mechanism of resilience to As stress remains unexplored in rice plants. In this study, we determined how As affects rice plant and how melatonin facilitate As stress tolerance in rice. Here we investigated that, exogenous melatonin reduced As stress by inducing anthocyanin biosynthesis. Melatonin induced the expression of anthocyanin biosynthesis genes such as PAL, CHS, CHI, F3H, DFR, and ANS, which resulted in 1659% and 389% increases in cyanidin and delphinidin, respectively. Similarly, melatonin application significantly induced SA and ABA accumulation in response to As stress in rice plant. Application of melatonin also significantly reduced expression of PT-2 and PT-8 (transporter genes) and reduced uptake of As and its translocation to other compartments. Melatonin and As analysis revealed that melatonin application significantly reduced As contents in the melatonin-supplemented plants, suggesting that As uptake is largely dependent on either the melatonin basal level or anthocyanin in rice plants. In this study, we investigated new symptoms on leaves, which can severely damage leaves and impair photosynthesis. However, anthocyanin as a chelating agent, detoxifies As in vacuole and reduces oxidative stress induced by As.