Cellulose synthase-like protein OsCSLD4 plays an important role in the response of rice to salt stress by mediating abscisic acid biosynthesis to regulate osmotic stress tolerance

Coexpression Regulation of New and Ancient Genes in the Dynamic Transcriptome Landscape of Stem and Rhizome Development in "Bainianzhe"-An Ancient Chinese Sugarcane Variety Ratooned for Nearly 300 Years

The sucrose yield in sugarcane largely depends on stem morphology, including length, diameter and sugar content, making sugarcane stem a key trait in breeding. The "Bainianzhe" variety from Songxi County, Fujian Province, possesses both aerial stems and rhizomes, providing a unique model for studying stem development. We performed a spatiotemporal transcriptomic analysis of the base, middle and apical sections of both aerial stems and rhizomes. The analysis categorized transcriptomes by developmental stage-base, middle and apical-rather than environmental differences. Apical segments were enriched with genes related to cell proliferation, while base segments were linked to senescence and fibrosis. Gene regulatory networks revealed key TFs involved in stem development. Orphan genes may be involved in rhizome development through coexpression networks. Plant hormones, especially genes involved in ABA and GAs synthesis, were highly expressed in rhizomes. Thiamine-related genes were also more prevalent in rhizomes. Furthermore, the apical segments of rhizomes enriched in photosynthesis-related genes suggest adaptations to light exposure. Low average temperatures in Songxi have led to unique cold acclimation in Bainianzhe, with rhizomes showing higher expression of genes linked to unsaturated fatty acid synthesis and cold-responsive calcium signalling. This indicates that rhizomes may have enhanced cold tolerance, aiding in the plant's overwintering success.

Cellulose synthase-like OsCSLD4: a key regulator of agronomic traits, disease resistance, and metabolic indices in rice

KEY MESSAGE

Cellulose synthase-like OsCSLD4 plays a pivotal role in regulating diverse agronomic traits, enhancing resistance against bacterial leaf blight, and modulating metabolite indices based on the multi-omics analysis in rice. To delve deeper into this complex network between agronomic traits and metabolites in rice, we have compiled a dataset encompassing genome, phenome, and metabolome, including 524 diverse accessions, 11 agronomic traits, and 841 metabolites, enabling us to pinpoint eight hotspots through GWAS. We later discovered four distinct metabolite categories, encompassing 15 metabolites that are concurrently present on the QTL qC12.1, associated with leaf angle of flag and spikelet length, and finally focused the cellulose synthase-like OsCSLD4, which was pinpointed through a rigorous process encompassing sequence variation, haplotype, ATAC, and differential expression across diverse tissues. Compared to the wild type, csld4 exhibited significant reductions in the plant height, flag leaf length, leaf width, spikelet length, 1000-grain weight, grain width, grain thickness, fertility, yield per plant, and bacterial blight resistance. However, there were significant increase in tiller numbers, degree of leaf rolling, flowering period, growth period, grain length, and empty kernel rate. Furthermore, the content of four polyphenol metabolites, excluding metabolite N-feruloyltyramine (mr1268), notably rose, whereas the levels of the other three polyphenol metabolites, smiglaside C (mr1498), 4-coumaric acid (mr1622), and smiglaside A (mr1925) decreased significantly in mutant csld4. The content of amino acid L-tyramine (mr1446) exhibited a notable increase, whereas the alkaloid trigonelline (mr1188) displayed a substantial decrease among the mutants. This study offered a comprehensive multi-omics perspective to analyze the genetic mechanism of OsCSLD4, and breeders can potentially enhance rice's yield, bacterial leaf blight resistance, and metabolite content, leading to more sustainable and profitable rice production.

Small GTPase PvARFR2 interacts with cytosolic ABA receptor kinase 3 to enhance alkali tolerance in switchgrass

Soil alkalization has become a serious problem that limits plant growth through osmotic stress, ionic imbalance, and oxidative stress. Understanding how plants resist alkali stress has practical implications for alkaline-land utilization. In this study, we identified a small GTPase, PvARFR2 (ADP ribosylation factors related 2), that positively regulates alkali tolerance in switchgrass (Panicum virgatum) and uncovered its potential mode of action. Overexpressing PvARFR2 in switchgrass and Arabidopsis (Arabidopsis thaliana) conferred transformant tolerance to alkali stress, demonstrated by alleviated leaf wilting, less oxidative injury, and a lower Na+/K+ ratio under alkali conditions. Conversely, switchgrass PvARFR2-RNAi and its homolog mutant atgb1 in Arabidopsis displayed alkali sensitives. Transcriptome sequencing analysis showed that cytosolic abscisic acid (ABA) receptor kinase PvCARK3 transcript levels were higher in PvARFR2 overexpression lines compared to the controls and were strongly induced by alkali treatment in shoots and roots. Phenotyping analysis revealed that PvCARK3-OE × atgb1 lines were sensitive to alkali similar to the Arabidopsis atgb1 mutant, indicating that PvARFR2/AtGB1 functions in the same pathway as PvCARK3 under alkaline stress conditions. Application of ABA on PvARFR2-OE and PvCARK3-OE switchgrass transformants resulted in ABA sensitivity. Moreover, we determined that PvARFR2 physically interacts with PvCARK3 in vitro and in vivo. Our results indicate that a small GTPase, PvARFR2, positively responds to alkali stress by interacting with the cytosolic ABA receptor kinase PvCARK3, connecting the alkaline stress response to ABA signaling.

Physiological and Molecular Mechanisms of Rice Tolerance to Salt and Drought Stress: Advances and Future Directions

Rice, a globally important food crop, faces significant challenges due to salt and drought stress. These abiotic stresses severely impact rice growth and yield, manifesting as reduced plant height, decreased tillering, reduced biomass, and poor leaf development. Recent advances in molecular biology and genomics have uncovered key physiological and molecular mechanisms that rice employs to cope with these stresses, including osmotic regulation, ion balance, antioxidant responses, signal transduction, and gene expression regulation. Transcription factors such as DREB, NAC, and bZIP, as well as plant hormones like ABA and GA, have been identified as crucial regulators. Utilizing CRISPR/Cas9 technology for gene editing holds promise for significantly enhancing rice stress tolerance. Future research should integrate multi-omics approaches and smart agriculture technologies to develop rice varieties with enhanced stress resistance, ensuring food security and sustainable agriculture in the face of global environmental changes.

Integrative Analyses Reveal the Physiological and Molecular Role of Prohexadione Calcium in Regulating Salt Tolerance in Rice

Salinity stress severely restricts rice growth. Prohexadione calcium (Pro-Ca) modulation can effectively alleviate salt stress in rice. In this study, we explored the effects of Pro-Ca on enhancing salt tolerance in two rice varieties, IR29 and HD96-1. The results revealed that Pro-Ca markedly enhanced root and shoot morphological traits and improved plant biomass under salt stress. Chlorophyll a and b content were significantly increased, which improved photosynthetic capacity. Transcriptomic and metabolomic data showed that Pro-Ca significantly up-regulated the expression of genes involved in E3 ubiquitin ligases in IR29 and HD96-1 by 2.5-fold and 3-fold, respectively, thereby maintaining Na+ and K+ homeostasis by reducing Na+. Moreover, Pro-Ca treatment significantly down-regulated the expression of Lhcb1, Lhcb2, Lhcb3, Lhcb5, and Lhcb6 in IR29 under salt stress, which led to an increase in photosynthetic efficiency. Furthermore, salt stress + Pro-Ca significantly increased the A-AAR of IR29 and HD96-1 by 2.9-fold and 2.5-fold, respectively, and inhibited endogenous cytokinin synthesis and signal transduction, which promoted root growth. The current findings suggested that Pro-Ca effectively alleviated the harmful effects of salt stress on rice by maintaining abscisic acid content and by promoting oxylipin synthesis. This study provides a molecular basis for Pro-Ca to alleviate salt stress in rice.

OsG6PGH1 affects various grain quality traits and participates in the salt stress response of rice

Cytoplasmic 6-phosphogluconate dehydrogenase (G6PGH) is a key enzyme in the pentose phosphate pathway that is involved in regulating various biological processes such as material metabolism, and growth and development in plants. However, it was unclear if OsG6PGH1 affected rice grain quality traits. We perform yeast one-hybrid experiments and reveal that OsG6PGH1 may interact with OsAAP6. Subsequently, yeast in vivo point-to-point experiments and local surface plasmon resonance experiments verified that OsG6PGH1 can bind to OsAAP6. OsG6PGH1 in rice is a constitutive expressed gene that may be localized in the cytoplasm. OsAAP6 and protein-synthesis metabolism-related genes are significantly upregulated in OsG6PGH1 overexpressing transgenic positive endosperm, corresponding to a significant increase in the number of protein bodies II, promoting accumulation of related storage proteins, a significant increase in grain protein content (GPC), and improved rice nutritional quality. OsG6PGH1 positively regulates amylose content, negatively regulates chalkiness rate and taste value, significantly affects grain quality traits such as appearance, cooking, and eating qualities of rice, and is involved in regulating the expression of salt stress related genes, thereby enhancing the salt-stress tolerance of rice. Therefore, OsG6PGH1 represents an important genetic resource to assist in the design of high-quality and multi-resistant rice varieties.

Candidate Genes and Favorable Haplotypes Associated with Iron Toxicity Tolerance in Rice

Iron (Fe) toxicity is a major issue adversely affecting rice production worldwide. Unfortunately, the physiological and genetic mechanisms underlying Fe toxicity tolerance in rice remain relatively unknown. In this study, we conducted a genome-wide association study using a diverse panel consisting of 551 rice accessions to identify genetic mechanisms and candidate genes associated with Fe toxicity tolerance. Of the 29 quantitative trait loci (QTL) for Fe toxicity tolerance detected on chromosomes 1, 2, 5, and 12, five (qSH_Fe5, qSFW_Fe2.3, qRRL5.1, qRSFW1.1, and qRSFW12) were selected to identify candidate genes according to haplotype and bioinformatics analyses. The following five genes were revealed as promising candidates: LOC_Os05g40160, LOC_Os05g40180, LOC_Os12g36890, LOC_Os12g36900, and LOC_Os12g36940. The physiological characteristics of rice accessions with contrasting Fe toxicity tolerance reflected the importance of reactive oxygen species-scavenging antioxidant enzymes and Fe homeostasis for mitigating the negative effects of Fe toxicity on rice. Our findings have clarified the genetic and physiological mechanisms underlying Fe toxicity tolerance in rice. Furthermore, we identified valuable genetic resources for future functional analyses and the development of Fe toxicity-tolerant rice varieties via marker-assisted selection.

Genome-wide identification and expression analysis of the KNOX family and its diverse roles in response to growth and abiotic tolerance in sweet potato and its two diploid relatives

KNOXs, a type of homeobox genes that encode atypical homeobox proteins, play an essential role in the regulation of growth and development, hormonal response, and abiotic stress in plants. However, the KNOX gene family has not been explored in sweet potato. In this study, through sequence alignment, genomic structure analysis, and phylogenetic characterization, 17, 12 and 11 KNOXs in sweet potato (I. batatas, 2n = 6x = 90) and its two diploid relatives I. trifida (2n = 2x = 30) and I. triloba (2n = 2x = 30) were identified. The protein physicochemical properties, chromosome localization, phylogenetic relationships, gene structure, protein interaction network, cis-elements of promoters, tissue-specific expression and expression patterns under hormone treatment and abiotic stresses of these 40 KNOX genes were systematically studied. IbKNOX4, -5, and - 6 were highly expressed in the leaves of the high-yield varieties Longshu9 and Xushu18. IbKNOX3 and IbKNOX8 in Class I were upregulated in initial storage roots compared to fibrous roots. IbKNOXs in Class M were specifically expressed in the stem tip and hardly expressed in other tissues. Moreover, IbKNOX2 and - 6, and their homologous genes were induced by PEG/mannitol and NaCl treatments. The results showed that KNOXs were involved in regulating growth and development, hormone crosstalk and abiotic stress responses between sweet potato and its two diploid relatives. This study provides a comparison of these KNOX genes in sweet potato and its two diploid relatives and a theoretical basis for functional studies.

ABA-mediated regulation of rice grain quality and seed dormancy via the NF-YB1-SLRL2-bHLH144 Module

Abscisic acid (ABA) plays a crucial role in promoting plant stress resistance and seed dormancy. However, how ABA regulates rice quality remains unclear. This study identifies a key transcription factor SLR1-like2 (SLRL2), which mediates the ABA-regulated amylose content (AC) of rice. Mechanistically, SLRL2 interacts with NF-YB1 to co-regulate Wx, a determinant of AC and rice quality. In contrast to SLR1, SLRL2 is ABA inducible but insensitive to GA. In addition, SLRL2 exhibits DNA-binding activity and directly regulates the expression of Wx, bHLH144 and MFT2. SLRL2 competes with NF-YC12 for interaction with NF-YB1. NF-YB1 also directly represses SLRL2 transcription. Genetic validation supports that SLRL2 functions downstream of NF-YB1 and bHLH144 in regulating rice AC. Thus, an NF-YB1-SLRL2-bHLH144 regulatory module is successfully revealed. Furthermore, SLRL2 regulates rice dormancy by modulating the expression of MFT2. In conclusion, this study revealed an ABA-responsive regulatory cascade that functions in both rice quality and seed dormancy.

Neem Leaf Extract Exhibits Anti-Aging and Antioxidant Effects from Yeast to Human Cells

Neem leaves have long been used in traditional medicine for promoting longevity. However, the precise mechanisms underlying their anti-aging effects remain elusive. In this study, we investigated the impact of neem leaf extract (NLE) extracted from a 50% ethanol solution on the chronological lifespan of Saccharomyces cerevisiae, revealing an extension in lifespan, heightened oxidative stress resistance, and a reduction in reactive oxygen species. To discern the active compounds in NLE, LC/MS and the GNPS platform were employed. The majority of identified active compounds were found to be flavonoids. Subsequently, compound-target pharmacological networks were constructed using the STP and STITCH platforms for both S. cerevisiae and Homo sapiens. GOMF and KEGG enrichment analyses of the predicted targets revealed that "oxidoreductase activity" was among the top enriched terms in both yeast and human cells. These suggested a potential regulation of oxidative stress response (OSR) by NLE. RNA-seq analysis of NLE-treated yeast corroborated the anti-oxidative effect, with "oxidoreductase activity" and "oxidation-reduction process" ranking high in enriched GO terms. Notably, CTT1, encoding catalase, emerged as the most significantly up-regulated gene within the "oxidoreductase activity" cluster. In a ctt1 null mutant, the enhanced oxidative stress resistance and extended lifespan induced by NLE were nullified. For human cells, NLE pretreatment demonstrated a decrease in reactive oxygen species levels and senescence-associated β-galactosidase activity in HeLa cells, indicative of anti-aging and anti-oxidative effects. This study unveils the anti-aging and anti-oxidative properties of NLE while delving into their mechanisms, providing novel insights for pharmacological interventions in aging using phytochemicals.

The MsDHN1-MsPIP2;1-MsmMYB module orchestrates the trade-off between growth and survival of alfalfa in response to drought stress

Dehydrins and aquaporins play crucial roles in plant growth and stress responses by acting as protector and controlling water transport across membranes, respectively. MsDHN1 (dehydrin) and MsPIP2;1 (aquaporin) were demonstrated to interact with a membrane-anchored MYB protein, MsmMYB (as mMYB) in plasma membrane under normal condition. MsDHN1, MsPIP2;1 and MsDHN1-MsPIP2;1 positively regulated alfalfa tolerance to water deficiency. Water deficiency caused phosphorylation of MsPIP2;1 at Ser 272, which led to release C terminus of mMYB (mMYBΔ83) from plasma membrane and translocate to nucleus, where C terminus of MsDHN1 interacted with mMYBΔ83, and promoted mMYBΔ83 transcriptional activity in response to water deficiency. Overexpression of mMYB and mMYBΔ83 down-regulated the expression of MsCESA3, but up-regulated MsCESA7 expression by directly binding to their promoters, and resulted in high drought tolerance in transgenic hairy roots. These results indicate that the MsDHN1-MsPIP2;1-MsMYB module serves as a key regulator in alfalfa against drought stress.

The rice LATE ELONGATED HYPOCOTYL enhances salt tolerance by regulating Na+/K+ homeostasis and ABA signalling

The circadian clock plays multiple functions in the regulation of plant growth, development and response to various abiotic stress. Here, we showed that the core oscillator component late elongated hypocotyl (LHY) was involved in rice response to salt stress. The mutations of OsLHY gene led to reduced salt tolerance in rice. Transcriptomic analyses revealed that the OsLHY gene regulates the expression of genes related to ion homeostasis and the abscisic acid (ABA) signalling pathway, including genes encoded High-affinity K+ transporters (OsHKTs) and the stress-activated protein kinases (OsSAPKs). We demonstrated that OsLHY directly binds the promoters of OsHKT1;1, OsHKT1;4 and OsSAPK9 to regulate their expression. Moreover, the ossapk9 mutants exhibited salt tolerance under salt stress. Taken together, our findings revealed that OsLHY integrates ion homeostasis and the ABA pathway to regulate salt tolerance in rice, providing insights into our understanding of how the circadian clock controls rice response to salt stress.

Caffeic Acid O-Methyltransferase Gene Family in Mango (Mangifera indica L.) with Transcriptional Analysis under Biotic and Abiotic Stresses and the Role of MiCOMT1 in Salt Tolerance

Caffeic acid O-methyltransferase (COMT) participates in various physiological activities in plants, such as positive responses to abiotic stresses and the signal transduction of phytohormones. In this study, 18 COMT genes were identified in the chromosome-level reference genome of mango, named MiCOMTs. A phylogenetic tree containing nine groups (I-IX) was constructed based on the amino acid sequences of the 71 COMT proteins from seven species. The phylogenetic tree indicated that the members of the MiCOMTs could be divided into four groups. Quantitative real-time PCR showed that all MiCOMT genes have particularly high expression levels during flowering. The expression levels of MiCOMTs were different under abiotic and biotic stresses, including salt and stimulated drought stresses, ABA and SA treatment, as well as Xanthomonas campestris pv. mangiferaeindicae and Colletotrichum gloeosporioides infection, respectively. Among them, the expression level of MiCOMT1 was significantly up-regulated at 6-72 h after salt and stimulated drought stresses. The results of gene function analysis via the transient overexpression of the MiCOMT1 gene in Nicotiana benthamiana showed that the MiCOMT1 gene can promote the accumulation of ABA and MeJA, and improve the salt tolerance of mango. These results are beneficial to future researchers aiming to understand the biological functions and molecular mechanisms of MiCOMT genes.

A Tos17 transposon insertion in OsCesA9 causes brittle culm in rice

The mechanical strength of rice stalks plays an important role in rice growth and development. In this study, the brittle culm mutant bc26 was identified from a tissue culture-derived line of the japonica rice cultivar 'ZH15'. bc26 plants showed fragile leaves and stalks and reduced plant height and spike number compared with wild-type 'ZH15'. Analysis of cell wall components revealed that the cellulose content of stems, leaves, roots and spikes of bc26 plants was significantly lower than that of the wild type, while the hemicellulose content in these tissues of bc26 plants was significantly higher than that of the wild type. Further sequencing using a mixed pool bulked segregant analysis sequencing (BSA-Seq) of brittle plants from the F2 populations localized the bc26 gene to chromosome 9, and a Tos17 transposon insertion in the bc6 gene near the highest SNP-index point was associated with a loss of gene function. Therefore, the bc26 gene was tentatively identified as a new allele of the Bc6 gene, resulting in the brittle culm trait caused by the insertion of the Tos17 transposon.

Insights into plant salt stress signaling and tolerance

Soil salinization is an essential environmental stressor, threatening agricultural yield and ecological security worldwide. Saline soils accumulate excessive soluble salts which are detrimental to most plants by limiting plant growth and productivity. It is of great necessity for plants to efficiently deal with the adverse effects caused by salt stress for survival and successful reproduction. Multiple determinants of salt tolerance have been identified in plants, and the cellular and physiological mechanisms of plant salt response and adaption have been intensely characterized. Plants respond to salt stress signals and rapidly initiate signaling pathways to re-establish cellular homeostasis with adjusted growth and cellular metabolism. This review summarizes the advances in salt stress perception, signaling, and response in plants. A better understanding of plant salt resistance will contribute to improving crop performance under saline conditions using multiple engineering approaches. The rhizosphere microbiome-mediated plant salt tolerance as well as chemical priming for enhanced plant salt resistance are also discussed in this review.

Comparative analysis of the carrot miRNAome in response to salt stress

Soil salinity adversely affects the yield and quality of crops, including carrot. During salt stress, plant growth and development are impaired by restricted water uptake and ion cytotoxicity, leading to nutrient imbalance and oxidative burst. However, the molecular mechanisms of the carrot plant response to salt stress remain unclear. The occurrence and expression of miRNAs that are potentially involved in the regulation of carrot tolerance to salinity stress were investigated. The results of small RNA sequencing revealed that salt-sensitive (DH1) and salt-tolerant (DLBA) carrot varieties had different miRNA expression profiles. A total of 95 miRNAs were identified, including 71 novel miRNAs, of which 30 and 23 were unique to DH1 and DLBA, respectively. The comparison of NGS and qPCR results allowed identification of two conserved and five novel miRNA involved in carrot response to salt stress, and which differentiated the salt-tolerant and salt-sensitive varieties. Degradome analysis supported by in silico-based predictions and followed by expression analysis of exemplary target genes pointed at genes related to proline, glutathione, and glutamate metabolism pathways as potential miRNA targets involved in salt tolerance, and indicated that the regulation of osmoprotection and antioxidant protection, earlier identified as being more efficient in the tolerant variety, may be controlled by miRNAs. Furthermore, potential miRNA target genes involved in chloroplast protection, signal transduction and the synthesis and modification of cell wall components were indicated in plants growing in saline soil.

SMALL PLANT AND ORGAN 1 (SPO1) Encoding a Cellulose Synthase-like Protein D4 (OsCSLD4) Is an Important Regulator for Plant Architecture and Organ Size in Rice

Plant architecture and organ size are considered as important traits in crop breeding and germplasm improvement. Although several factors affecting plant architecture and organ size have been identified in rice, the genetic and regulatory mechanisms remain to be elucidated. Here, we identified and characterized the small plant and organ 1 (spo1) mutant in rice (Oryza sativa), which exhibits narrow and rolled leaf, reductions in plant height, root length, and grain width, and other morphological defects. Map-based cloning revealed that SPO1 is allelic with OsCSLD4, a gene encoding the cellulose synthase-like protein D4, and is highly expressed in the roots at the seedling and tillering stages. Microscopic observation revealed the spo1 mutant had reduced number and width in leaf veins, smaller size of leaf bulliform cells, reduced cell length and cell area in the culm, and decreased width of epidermal cells in the outer glume of the grain. These results indicate the role of SPO1 in modulating cell division and cell expansion, which modulates plant architecture and organ size. It is showed that the contents of endogenous hormones including auxin, abscisic acid, gibberellin, and zeatin tested in the spo1 mutant were significantly altered, compared to the wild type. Furthermore, the transcriptome analysis revealed that the differentially expressed genes (DEGs) are significantly enriched in the pathways associated with plant hormone signal transduction, cell cycle progression, and cell wall formation. These results indicated that the loss of SPO1/OsCSLD4 function disrupted cell wall cellulose synthase and hormones homeostasis and signaling, thus leading to smaller plant and organ size in spo1. Taken together, we suggest the functional role of SPO1/OsCSLD4 in the control of rice plant and organ size by modulating cell division and expansion, likely through the effects of multiple hormonal pathways on cell wall formation.

PacBio Full-Length Transcriptome Sequencing Reveals the Mechanism of Salt Stress Response in Sonneratia apetala

Sonneratia apetala is an essential mangrove wetland restoration tree species. Studying its molecular mechanism for salt tolerance could lay a foundation for further cultivating excellent resistant germplasm. This study used a combination of PacBio isoform sequencing (Iso-seq) and BGISEQ RNA sequencing (RNA-seq) to analyze the molecular mechanism to salt stress response of one-year-old S. apetala leaves. The growth and physiological analysis showed that physiological indexes such as growth rate, net photosynthetic rate and antioxidant enzyme activity all exhibit significant changes under salt stress. From Iso-seq, a total of 295,501 full-length transcripts, with an average length of 1418 bp, were obtained. RNA-seq produced 4712 differentially expressed genes (DEGs) as compared to a control group. Of these, 930 were identified to be co-expressed during the STEM time sequence analysis. Further, 715 and 444 co-expressed DEGs were annotated by GO and KEGG analyses, respectively. Moreover, 318 of the co-expressed DEGs were annotated as essential genes that were implicated in salt stress response of S. apetala, which were involved in transcription factors, signal transduction, hormone response, ROS homeostasis, osmotic balance, cell wall synthesis or modification. These results provide candidate targets for further characterization and offer insights into the salt-tolerant mechanism of S. apetala.

OsSTS, a Novel Allele of Mitogen-Activated Protein Kinase Kinase 4 (OsMKK4), Controls Grain Size and Salt Tolerance in Rice

Soil salinization is one of the most common abiotic stresses of rice, which seriously affects the normal growth of rice. Breeding salt-tolerant varieties have become one of the important ways to ensure food security and sustainable agricultural development. However, the mechanisms underlying salt tolerance control still need to be clarified. In this study, we identified a mutant, termed salt-tolerant and small grains(sts), with salt tolerance and small grains. Gene cloning and physiological and biochemical experiments reveal that sts is a novel mutant allele of Mitogen-activated protein Kinase Kinase 4 (OsMKK4), which controls the grain size, and has recently been found to be related to salt tolerance in rice. Functional analysis showed that OsSTS is constitutively expressed throughout the tissue, and its proteins are localized to the nucleus, cell membrane, and cytoplasm. It was found that the loss of OsSTS function enhanced the salt tolerance of rice seedlings, and further studies showed that the loss of OsSTS function increased the ROS clearance rate of rice seedlings, independent of ionic toxicity. In order to explore the salt tolerance mechanism of sts, we found that the salt tolerance of sts is also regulated by ABA through high-throughput mRNA sequencing. Salt and ABA treatment showed that ABA might alleviate the inhibitory effect of salt stress on root length in sts. These results revealed new functions of grain size gene OsMKK4, expanded new research ideas related to salt tolerance mechanism and hormone regulation network, and provided a theoretical basis for salt-tolerant rice breeding.

Physicochemical Properties of the Rice Flour and Structural Features of the Isolated Starches from Saline-Tolerant Rice Grown at Different Levels of Soil Salinity

Three varieties of saline-tolerant indica rice were grown in soils with salinities of 0.0-0.6% (w/w). The rice grown at salinities of 0.3 and 0.6% had a smaller grain dimension than its counterpart. Salinity stress altered the physiology of plants, leading to changes in the basic chemical compositions for all rice varieties, e.g., increasing the soil salinity improved the content of rice protein (RP). The pasting and rheological properties of the rice flour highly depended on its chemical compositions. An increase of RP inhibited the swelling of starch granules and accordingly decreased the peak viscosity of rice flour, while the aggregation of RP weakened the gel structure of the cooked rice flour. The isolated starches showed polyhedral granules, and they all had an A-type crystalline structure with relative crystallinity varying from 34.16 to 45.40%. Moreover, increasing the soil salinity enhanced the lamellar order and periodic length of the isolated starches.

The salt-activated CBF1/CBF2/CBF3-GALS1 module fine-tunes galactan-induced salt hypersensitivity in Arabidopsis

Plant growth and development are significantly hampered in saline environments, limiting agricultural productivity. Thus, it is crucial to unravel the mechanism underlying plant responses to salt stress. β-1,4-Galactan (galactan), which forms the side chains of pectic rhamnogalacturonan I, enhances plant sensitivity to high-salt stress. Galactan is synthesized by GALACTAN SYNTHASE1 (GALS1). We previously showed that NaCl relieves the direct suppression of GALS1 transcription by the transcription factors BPC1 and BPC2 to induce the excess accumulation of galactan in Arabidopsis (Arabidopsis thaliana). However, how plants adapt to this unfavorable environment remains unclear. Here, we determined that the transcription factors CBF1, CBF2, and CBF3 directly interact with the GALS1 promoter and repress its expression, leading to reduced galactan accumulation and enhanced salt tolerance. Salt stress enhances the binding of CBF1/CBF2/CBF3 to the GALS1 promoter by inducing CBF1/CBF2/CBF3 transcription and accumulation. Genetic analysis suggested that CBF1/CBF2/CBF3 function upstream of GALS1 to modulate salt-induced galactan biosynthesis and the salt response. CBF1/CBF2/CBF3 and BPC1/BPC2 function in parallel to regulate GALS1 expression, thereby modulating the salt response. Our results reveal a mechanism in which salt-activated CBF1/CBF2/CBF3 inhibit BPC1/BPC2-regulated GALS1 expression to alleviate galactan-induced salt hypersensitivity, providing an activation/deactivation fine-tune mechanism for dynamic regulation of GALS1 expression under salt stress in Arabidopsis.

Multi-Omics Pipeline and Omics-Integration Approach to Decipher Plant's Abiotic Stress Tolerance Responses

The present day's ongoing global warming and climate change adversely affect plants through imposing environmental (abiotic) stresses and disease pressure. The major abiotic factors such as drought, heat, cold, salinity, etc., hamper a plant's innate growth and development, resulting in reduced yield and quality, with the possibility of undesired traits. In the 21st century, the advent of high-throughput sequencing tools, state-of-the-art biotechnological techniques and bioinformatic analyzing pipelines led to the easy characterization of plant traits for abiotic stress response and tolerance mechanisms by applying the 'omics' toolbox. Panomics pipeline including genomics, transcriptomics, proteomics, metabolomics, epigenomics, proteogenomics, interactomics, ionomics, phenomics, etc., have become very handy nowadays. This is important to produce climate-smart future crops with a proper understanding of the molecular mechanisms of abiotic stress responses by the plant's genes, transcripts, proteins, epigenome, cellular metabolic circuits and resultant phenotype. Instead of mono-omics, two or more (hence 'multi-omics') integrated-omics approaches can decipher the plant's abiotic stress tolerance response very well. Multi-omics-characterized plants can be used as potent genetic resources to incorporate into the future breeding program. For the practical utility of crop improvement, multi-omics approaches for particular abiotic stress tolerance can be combined with genome-assisted breeding (GAB) by being pyramided with improved crop yield, food quality and associated agronomic traits and can open a new era of omics-assisted breeding. Thus, multi-omics pipelines together are able to decipher molecular processes, biomarkers, targets for genetic engineering, regulatory networks and precision agriculture solutions for a crop's variable abiotic stress tolerance to ensure food security under changing environmental circumstances.

Recent Molecular Aspects and Integrated Omics Strategies for Understanding the Abiotic Stress Tolerance of Rice

Rice is an important staple food crop for over half of the world's population. However, abiotic stresses seriously threaten rice yield improvement and sustainable production. Breeding and planting rice varieties with high environmental stress tolerance are the most cost-effective, safe, healthy, and environmentally friendly strategies. In-depth research on the molecular mechanism of rice plants in response to different stresses can provide an important theoretical basis for breeding rice varieties with higher stress resistance. This review presents the molecular mechanisms and the effects of various abiotic stresses on rice growth and development and explains the signal perception mode and transduction pathways. Meanwhile, the regulatory mechanisms of critical transcription factors in regulating gene expression and important downstream factors in coordinating stress tolerance are outlined. Finally, the utilization of omics approaches to retrieve hub genes and an outlook on future research are prospected, focusing on the regulatory mechanisms of multi-signaling network modules and sustainable rice production.

The regulation of plant cell wall organisation under salt stress

Plant cell wall biosynthesis is a complex and tightly regulated process. The composition and the structure of the cell wall should have a certain level of plasticity to ensure dynamic changes upon encountering environmental stresses or to fulfil the demand of the rapidly growing cells. The status of the cell wall is constantly monitored to facilitate optimal growth through the activation of appropriate stress response mechanisms. Salt stress can severely damage plant cell walls and disrupt the normal growth and development of plants, greatly reducing productivity and yield. Plants respond to salt stress and cope with the resulting damage by altering the synthesis and deposition of the main cell wall components to prevent water loss and decrease the transport of surplus ions into the plant. Such cell wall modifications affect biosynthesis and deposition of the main cell wall components: cellulose, pectins, hemicelluloses, lignin, and suberin. In this review, we highlight the roles of cell wall components in salt stress tolerance and the regulatory mechanisms underlying their maintenance under salt stress conditions.

Comparison of Tomato Transcriptomic Profiles Reveals Overlapping Patterns in Abiotic and Biotic Stress Responses

Until a few years ago, many studies focused on the transcriptomic response to single stresses. However, tomato cultivations are often constrained by a wide range of biotic and abiotic stress that can occur singularly or in combination, and several genes can be involved in the defensive mechanism response. Therefore, we analyzed and compared the transcriptomic responses of resistant and susceptible genotypes to seven biotic stresses (Cladosporium fulvum, Phytophthora infestans, Pseudomonas syringae, Ralstonia solanacearum, Sclerotinia sclerotiorum, Tomato spotted wilt virus (TSWV) and Tuta absoluta) and five abiotic stresses (drought, salinity, low temperatures, and oxidative stress) to identify genes involved in response to multiple stressors. With this approach, we found genes encoding for TFs, phytohormones, or participating in signaling and cell wall metabolic processes, participating in defense against various biotic and abiotic stress. Moreover, a total of 1474 DEGs were commonly found between biotic and abiotic stress. Among these, 67 DEGs were involved in response to at least four different stresses. In particular, we found RLKs, MAPKs, Fasciclin-like arabinogalactans (FLAs), glycosyltransferases, genes involved in the auxin, ET, and JA pathways, MYBs, bZIPs, WRKYs and ERFs genes. Detected genes responsive to multiple stress might be further investigated with biotechnological approaches to effectively improve plant tolerance in the field.

Identification and Functional Characterization of WRKY, PHD and MYB Three Salt Stress Responsive Gene Families in Mungbean (Vigna radiata L.)

WRKY-, PHD-, and MYB-like proteins are three important types of transcription factors in mungbeans, and play an important role in development and stress resistance. The genes' structures and characteristics were clearly reported and were shown to contain the conservative WRKYGQK heptapeptide sequence, Cys4-His-cys3 zinc binding motif, and HTH (helix) tryptophan cluster W structure, respectively. Knowledge on the response of these genes to salt stress is largely unknown. To address this issue, 83 VrWRKYs, 47 VrPHDs, and 149 VrMYBs were identified by using comparative genomics, transcriptomics, and molecular biology methods in mungbeans. An intraspecific synteny analysis revealed that the three gene families had strong co-linearity and an interspecies synteny analysis showed that mungbean and Arabidopsis were relatively close in genetic relationship. Moreover, 20, 10, and 20 genes showed significantly different expression levels after 15 days of salt treatment (p < 0.05; Log2 FC > 0.5), respectively. Additionally, in the qRT-PCR analysis, VrPHD14 had varying degrees of response to NaCl and PEG treatments after 12 h. VrWRKY49 was upregulated by ABA treatment, especially in the beginning (within 24 h). VrMYB96 was significantly upregulated in the early stages of ABA, NaCl, and PEG stress treatments (during the first 4 h). VrWRKY38 was significantly upregulated by ABA and NaCl treatments, but downregulated by PEG treatment. We also constructed a gene network centered on the seven DEGs under NaCl treatment; the results showed that VrWRKY38 was in the center of the PPI network and most of the homologous Arabidopsis genes of the interacted genes were reported to have response to biological stress. Candidate genes identified in this study provide abundant gene resources for the study of salt tolerance in mungbeans.

Cell Wall Matrix Polysaccharides Contribute to Salt-Alkali Tolerance in Rice

Salt-alkali stress threatens the resilience to variable environments and thus the grain yield of rice. However, how rice responds to salt-alkali stress at the molecular level is poorly understood. Here, we report isolation of a novel salt-alkali-tolerant rice (SATR) by screening more than 700 germplasm accessions. Using 93-11, a widely grown cultivar, as a control, we characterized SATR in response to strong salt-alkali stress (SSAS). SATR exhibited SSAS tolerance higher than 93-11, as indicated by a higher survival rate, associated with higher peroxidase activity and total soluble sugar content but lower malonaldehyde accumulation. A transcriptome study showed that cell wall biogenesis-related pathways were most significantly enriched in SATR relative to 93-11 upon SSAS. Furthermore, higher induction of gene expression in the cell wall matrix polysaccharide biosynthesis pathway, coupled with higher accumulations of hemicellulose and pectin as well as measurable physio-biochemical adaptive responses, may explain the strong SSAS tolerance in SATR. We mapped SSAS tolerance to five genomic regions in which 35 genes were candidates potentially governing SSAS tolerance. The 1,4-β-D-xylan synthase gene OsCSLD4 in hemicellulose biosynthesis pathway was investigated in details. The OsCSLD4 function-disrupted mutant displayed reduced SSAS tolerance, biomass and grain yield, whereas the OsCSLD4 overexpression lines exhibited increased SSAS tolerance. Collectively, this study not only reveals the potential role of cell wall matrix polysaccharides in mediating SSAS tolerance, but also highlights applicable value of OsCSLD4 and the large-scale screening system in developing SSAS-tolerant rice.

The Cell Wall Regeneration of Tobacco Protoplasts Based on Microfluidic System

The cell wall, serving as the exoskeleton of plants, is naturally a barrier to resist external stresses. Protoplasts can be obtained by dissolving the cell walls of plant cells without damaging the cell membrane, and are widely used in the rapid propagation, transgenic breeding, and somatic hybridization of plants. However, to regenerate the cell wall is a precondition for cell division. Therefore, to study the culture condition and influencing factors during the cell wall regeneration of protoplasts is vital. Traditionally, culture medium is used to cultivate protoplasts, but it has some disadvantages. Herein, a microfluidic system with crossed channels was constructed to isolate and cultivate the protoplasts of tobacco. Then, the cell wall regeneration of the tobacco protoplasts was also studied based on this microfluidic system. It was found that, compared with the control, benzo-(1, 2, 3)-thiadiazole-7-carbothioic acid S-methyl ester (BTH) could accelerate the regeneration of the cell wall, while Pseudomonas syringae pv. tomato DC3000 (Pst DC3000) could inhibit the regeneration of the cell wall within 24 h. To conclude, this study demonstrated that a crossed microfluidic chip could be an effective tool to study cell wall regeneration or other behavior of plant cells in situ with high resolution. In addition, this study revealed the rate of cell wall regeneration under BTH and Pst DC3000 treatment.

Genome-wide identification and functional analysis of Cellulose synthase gene superfamily in Fragaria vesca

The Cellulose synthase (CesA) and Cellulose synthase-like (Csl) gene superfamilies encode key enzymes involved in the synthesis of cellulose and hemicellulose, which are major components of plant cell walls, and play important roles in the regulation of fruit ripening. However, genome-wide identification and functional analysis of the CesA and Csl gene families in strawberry remain limited. In this study, eight CesA genes and 25 Csl genes were identified in the genome of diploid woodland strawberry (Fragaria vesca). The protein structures, evolutionary relationships, and cis-acting elements of the promoter for each gene were investigated. Transcriptome analysis and quantitative real-time PCR (qRT-PCR) results showed that the transcript levels of many FveCesA and FveCsl genes were significantly decreased during fruit ripening. Moreover, based on the transcriptome analysis, we found that the expression levels of many FveCesA/Csl genes were changed after nordihydroguaiaretic acid (NDGA) treatment. Transient overexpression of FveCesA4 in immature strawberry fruit increased fruit firmness and reduced fresh fruit weight, thereby delaying ripening. In contrast, transient expression of FveCesA4-RNAi resulted in the opposite phenotypes. These findings provide fundamental information on strawberry CesA and Csl genes and may contribute to the elucidation of the molecular mechanism by which FveCesA/Csl-mediated cell wall synthesis regulates fruit ripening. In addition, these results may be useful in strawberry breeding programs focused on the development of new cultivars with increased fruit shelf-life.

Rice cellulose synthase-like protein OsCSLD4 coordinates the trade-off between plant growth and defense

Plant cell wall is a complex and changeable structure, which is very important for plant growth and development. It is clear that cell wall polysaccharide synthases have critical functions in rice growth and abiotic stress, yet their role in plant response to pathogen invasion is poorly understood. Here, we describe a dwarf and narrowed leaf in Hejiang 19 (dnl19) mutant in rice, which shows multiple growth defects such as reduced plant height, enlarged lamina joint angle, curled leaf morphology, and a decrease in panicle length and seed setting. MutMap analysis, genetic complementation and gene knockout mutant show that cellulose synthase-like D4 (OsCSLD4) is the causal gene for DNL19. Loss function of OsCSLD4 leads to a constitutive activation of defense response in rice. After inoculation with rice blast and bacterial blight, dnl19 displays an enhanced disease resistance. Widely targeted metabolomics analysis reveals that disruption of OsCSLD4 in dnl19 resulted in significant increase of L-valine, L-asparagine, L-histidine, L-alanine, gentisic acid, but significant decrease of L-aspartic acid, malic acid, 6-phosphogluconic acid, glucose 6-phosphate, galactose 1-phosphate, gluconic acid, D-aspartic acid. Collectively, our data reveals the importance of OsCSLD4 in balancing the trade-off between rice growth and defense.

Combined transcriptomic and metabolomic analysis reveals a role for adenosine triphosphate-binding cassette transporters and cell wall remodeling in response to salt stress in strawberry

Strawberry (Fragaria × ananassa Duch) are sensitive to salt stress, and breeding salt-tolerant strawberry cultivars is the primary method to develop resistance to increased soil salinization. However, the underlying molecular mechanisms mediating the response of strawberry to salinity stress remain largely unknown. This study evaluated the salinity tolerance of 24 strawberry varieties, and transcriptomic and metabolomic analysis were performed of 'Sweet Charlie' (salt-tolerant) and 'Benihoppe' (salt-sensitive) to explore salt tolerance mechanisms in strawberry. Compared with the control, we identified 3412 differentially expressed genes (DEGs) and 209 differentially accumulated metabolites (DAMs) in 'Benihoppe,' and 5102 DEGs and 230 DAMs in 'Sweet Charlie.' DEGs Gene Ontology (GO) enrichment analyses indicated that the DEGs in 'Benihoppe' were enriched for ion homeostasis related terms, while in 'Sweet Charlie,' terms related to cell wall remodeling were over-represented. DEGs related to ion homeostasis and cell wall remodeling exhibited differential expression patterns in 'Benihoppe' and 'Sweet Charlie.' In 'Benihoppe,' 21 ion homeostasis-related DEGs and 32 cell wall remodeling-related DEGs were upregulated, while 23 ion homeostasis-related DEGs and 138 cell wall remodeling-related DEGs were downregulated. In 'Sweet Charlie,' 72 ion homeostasis-related DEGs and 275 cell wall remodeling-related DEGs were upregulated, while 11 ion homeostasis-related DEGs and 20 cell wall remodeling-related DEGs were downregulated. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed only four KEGG enriched pathways were shared between 'Benihoppe' and 'Sweet Charlie,' including flavonoid biosynthesis, phenylalanine metabolism, phenylpropanoid biosynthesis and ubiquinone, and other terpenoid-quinone biosynthesis. Integrating the results of transcriptomic and metabolomics analyses showed that adenosine triphosphate-binding cassette (ABC) transporters and flavonoid pathway genes might play important roles in the salt stress response in strawberry, and DAMs and DEGs related to ABC transporter and flavonoid pathways were differentially expressed or accumulated. The results of this study reveal that cell wall remodeling and ABC transporters contribute to the response to salt stress in strawberry, and that related genes showed differential expression patterns in varieties with different salt tolerances. These findings provide new insights into the underlying molecular mechanism of strawberry response to salt stress and suggest potential targets for the breeding of salt-tolerant strawberry varieties.

Halophyte Nitraria billardieri CIPK25 mitigates salinity-induced cell damage by alleviating H2O2 accumulation

The plant-specific module of calcineurin B-like proteins (CBLs) and CBL-interacting protein kinases (CIPKs) play a crucial role in plant adaptation to different biotic and abiotic stresses in various plant species. Despite the importance of the CBL-CIPK module in regulating plant salt tolerance, few halophyte CIPK orthologs have been studied. We identified NbCIPK25 in the halophyte Nitraria billardieri as a salt-responsive gene that may improve salt tolerance in glycophytes. Sequence analyses indicated that NbCIPK25 is a typical CIPK family member with a conserved NAF motif, which contains the amino acids: asparagine, alanine, and phenylalanine. NbCIPK25 overexpression in salt-stressed transgenic Arabidopsis seedlings resulted in enhanced tolerance to salinity, a higher survival rate, longer newly grown roots, more root meristem cells, and less damaged root cells in comparison to wild-type (WT) plants. H2O2 accumulation and malondialdehyde (MDA) content were both deceased in NbCIPK25-transgenic plants under salt treatment. Furthermore, their proline content, an important factor for scavenging reactive oxygen species, accumulated at a significantly higher level. In concordance, the transcription of genes related to proline accumulation was positively regulated in transgenic plants under salt condition. Finally, we observed a stronger auxin response in salt-treated transgenic roots. These results provide evidence for NbCIPK25 improving salt tolerance by mediating scavenging of reactive oxygen species, thereby protecting cells from oxidation and maintaining plant development under salt stress. These findings suggest the potential application of salt-responsive NbCIPK25 for cultivating glycophytes with a higher salt tolerance through genetic engineering.

H3K36 demethylase JMJ710 negatively regulates drought tolerance by suppressing MYB48-1 expression in rice

The homeostasis of histone methylation is maintained by histone methyltransferases and demethylases, which are important for the regulation of gene expression. Here, we report a histone demethylase from rice (Oryza sativa), Jumonji C domain-containing protein (JMJ710), which belongs to the JMJD6 group and plays an important role in the response to drought stress. Overexpression of JMJ710 causes a drought-sensitive phenotype, while RNAi and clustered regularly interspaced short palindromic repeats (CRISPR)-knockout mutant lines show drought tolerance. In vitro and in vivo assays showed that JMJ710 is a histone demethylase. It targets to MYB TRANSCRIPTION FACTOR 48 (MYB48-1) chromatin, demethylates H3K36me2, and negatively regulates the expression of MYB48-1, a positive regulator of drought tolerance. Under drought stress, JMJ710 is downregulated and the expression of MYB48-1 increases, and the subsequent activation of its downstream drought-responsive genes leads to drought tolerance. This research reports a negative regulator of drought stress-responsive genes, JMJ710, that ensures that the drought tolerance mechanism is not mis-activated under normal conditions but allows quick activation upon drought stress.

Phenotypic and Methylome Responses to Salt Stress in Arabidopsis thaliana Natural Accessions

Salt stress threatens plant growth, development and crop yields, and has become a critical global environmental issue. Increasing evidence has suggested that the epigenetic mechanism such as DNA methylation can mediate plant response to salt stress through transcriptional regulation and transposable element (TE) silencing. However, studies exploring genome-wide methylation dynamics under salt stress remain limited, in particular, for studies on multiple genotypes. Here, we adopted four natural accessions of the model species Arabidopsis thaliana and investigated the phenotypic and genome-wide methylation responses to salt stress through whole-genome bisulfite sequencing (WGBS). We found that salt stress significantly changed plant phenotypes, including plant height, rosette diameter, fruit number, and aboveground biomass, and the change in biomass tended to depend on accessions. Methylation analysis revealed that genome-wide methylation patterns depended primarily on accessions, and salt stress caused significant methylation changes in ∼ 0.1% cytosines over the genomes. About 33.5% of these salt-induced differential methylated cytosines (DMCs) were located to transposable elements (TEs). These salt-induced DMCs were mainly hypermethylated and accession-specific. TEs annotated to have DMCs (DMC-TEs) across accessions were found mostly belonged to the superfamily of Gypsy, a type II transposon, indicating a convergent DMC dynamic on TEs across different genetic backgrounds. Moreover, 8.0% of salt-induced DMCs were located in gene bodies and their proximal regulatory regions. These DMCs were also accession-specific, and genes annotated to have DMCs (DMC-genes) appeared to be more accession-specific than DMC-TEs. Intriguingly, both accession-specific DMC-genes and DMC-genes shared by multiple accessions were enriched in similar functions, including methylation, gene silencing, chemical homeostasis, polysaccharide catabolic process, and pathways relating to shifts between vegetative growth and reproduction. These results indicate that, across different genetic backgrounds, methylation changes may have convergent functions in post-transcriptional, physiological, and phenotypic modulation under salt stress. These convergent methylation dynamics across accession may be autonomous from genetic variation or due to convergent genetic changes, which requires further exploration. Our study provides a more comprehensive picture of genome-wide methylation dynamics under salt stress, and highlights the importance of exploring stress response mechanisms from diverse genetic backgrounds.