Systematic Analysis of the Maize OSCA Genes Revealing ZmOSCA Family Members Involved in Osmotic Stress and ZmOSCA2.4 Confers Enhanced Drought Tolerance in Transgenic Arabidopsis

Genome-wide identification of the papaya-like cysteine protease family in poplar and determination of the functional role of PeRD19A in conferring salt tolerance

Papain-like cysteine proteases (PLCPs) are a large class of proteolytic enzymes involved in plant growth and development as well as plant responses to biological and abiotic stresses. However, there is no detailed characterization of PLCPs genes in poplar. In this study, a genome-wide analysis of the poplar PtrPLCPs family revealed 47 PtrPLCPs, which were classified into nine subfamilies according to their phylogeny: RD21, CEP, XCP, XBCP3, SAG12, RD19 (5), ALP, CTB, and the lost THI subgroups. SAG12 was the largest subfamily, with 22 members, and had the largest number of tandem repeats and homologous gene pairs. The PtrPLCPs family seems to have undergone whole-genome duplication (WGD), with the SAG12 subfamily as the main driving force in evolutionary amplification. An analysis of the abiotic stress expression profile showed that the 47 PtrPLCPs genes were induced by stresses such as cold, drought, and, especially, salt. Overexpression of the PeRD19A gene enhanced the scavenging ability of reactive oxygen species (ROS) in poplar, regulated several major metabolic pathways such as glyoxylate and dicarboxylate metabolic pathways, and provided energy for the synthesis of flavonoids and lignin compounds, thereby improving the antioxidant capacity of cells and increasing the mechanical strength of cell wall to prevent cell damage, and further helping poplar to cope with stress and improve the salt tolerance of poplar. Our study provides valuable insights that can be applied in future functional genome studies of poplar, and specifically studies of the PtrPLCPs gene family.

The homeostasis of ions and reactive oxygen species in root and shoot play crucial roles in the tolerance of alfalfa to salt alkali stress

High pH saline-alkali stress, mainly NaHCO3, limited the development of animal husbandry in Songnen Plain. Ion imbalance and reactive oxygen species (ROS) metabolism disorder caused by saline-alkali stress inhibited plant growth. In this study, we compared the differences in ion absorption, transport and ROS metabolism between saline-tolerant alfalfa (ZD) and saline-sensitive alfalfa (ZM) under NaHCO3 stress using physiology and transcripomics techniques. WGCNA analysis identified key genes associated with NaHCO3 stress-induced changes. NaHCO3 stress inhibited the absorption of K+ and Mg2+, but activated Ca2+ signal. Furthermore, ZD maintained higher K+, Mg2+ and Ca2+ contents and the K+/Na+ ratio than ZM, this is mainly related to the higher expression of proteins or channel-encoding genes involved in ion absorption and transport in ZD. Antioxidant enzyme systems can be activated in response to NaHCO3 stress. Peroxidase (EC 1.11.1.6), catalase (EC 1.11.1.7) and glutathione transferase (EC 2.5.1.18) activities were higher in ZD than ZM, and most genes encoding the relevant enzymes also demonstrated a stronger up-regulation trend in ZD. Although NaHCO3 stress inhibited Trx-Prx pathway, ZD related enzymes and their genes were also inhibited less than ZM. WGCNA results identified many genes involved in ion absorption, transport and antioxidant systems that play an important role in NaHCO3 stress adaptation. Collectively, ZD has the stronger ion homeostasis regulation and ROS scavenging ability, so it's more resistant to NaHCO3. The results provide theoretical guidance for further understanding of the molecular mechanism of NaHCO3 resistance and provide potential genes for research to improve saline-alkali tolerance in alfalfa.

Genetic, molecular and physiological crosstalk during drought tolerance in maize (Zea mays): pathways to resilient agriculture

MAIN CONCLUSION

This review comprehensively elucidates maize drought tolerance mechanisms, vital for global food security. It highlights genetic networks, key genes, CRISPR-Cas applications, and physiological responses, guiding resilient variety development. Maize, a globally significant crop, confronts the pervasive challenge of drought stress, impacting its growth and yield significantly. Drought, an important abiotic stress, triggers a spectrum of alterations encompassing maize's morphological, biochemical, and physiological dimensions. Unraveling and understanding these mechanisms assumes paramount importance for ensuring global food security. Approaches like developing drought-tolerant varieties and harnessing genomic and molecular applications emerge as effective measures to mitigate the negative effects of drought. The multifaceted nature of drought tolerance in maize has been unfolded through complex genetic networks. Additionally, quantitative trait loci mapping and genome-wide association studies pinpoint key genes associated with drought tolerance, influencing morphophysiological traits and yield. Furthermore, transcription factors like ZmHsf28, ZmNAC20, and ZmNF-YA1 play pivotal roles in drought response through hormone signaling, stomatal regulation, and gene expression. Genes, such as ZmSAG39, ZmRAFS, and ZmBSK1, have been reported to be pivotal in enhancing drought tolerance through diverse mechanisms. Integration of CRISPR-Cas9 technology, targeting genes like gl2 and ZmHDT103, emerges as crucial for precise genetic enhancement, highlighting its role in safeguarding global food security amid pervasive drought challenges. Thus, decoding the genetic and molecular underpinnings of drought tolerance in maize sheds light on its resilience and paves the way for cultivating robust and climate-smart varieties, thus safeguarding global food security amid climate challenges. This comprehensive review covers quantitative trait loci mapping, genome-wide association studies, key genes and functions, CRISPR-Cas applications, transcription factors, physiological responses, signaling pathways, offering a nuanced understanding of intricate mechanisms involved in maize drought tolerance.

Function analysis of transcription factor OSR1 regulating osmotic stress resistance in maize

BACKGROUND

Maize is a major cereal crop world widely, however, the yield of maize is frequently limited by dehydration and even death of plants, which resulted from osmotic stress such as drought and salinity. Dissection of molecular mechanisms controlling stress tolerance will enable plant scientists and breeders to increase crops yield by manipulating key regulatory components.

METHODS

The candidate OSR1 gene was identified by map-based cloning. The expression level of OSR1 was verified by qRT-PCR and digital PCR in WT and osr1 mutant. Electrophoretic mobility shift assay, transactivation activity assay, subcellular localization, transcriptome analysis and physiological characters measurements were conducted to analyze the function of OSR1 in osmotic stress resistance in maize.

RESULTS

The osr1 mutant was significantly less sensitive to osmotic stress than the WT plants and displayed stronger water-holding capacity, and the OSR1 homologous mutant in Arabidopsis showed a phenotype similar with maize osr1 mutant. Differentially expressed genes (DEGs) were identified between WT and osr1 under osmotic stress by transcriptome analysis, the expression levels of many genes, such as LEA, auxin-related factors, PPR family members, and TPR family members, changed notably, which may primarily involve in osmotic stress or promote root development.

CONCLUSIONS

OSR1 may serve as a negative regulatory factor in response to osmotic stress in maize. The present study sheds new light on the molecular mechanisms of osmotic stress in maize.

Domain of unknown function (DUF) proteins in plants: function and perspective

Domains of unknown function (DUFs), which are deposited in the protein family database (Pfam), are protein domains with conserved amino acid sequences and uncharacterized functions. Proteins with the same DUF were classified as DUF families. Although DUF families are generally not essential for the survival of plants, they play roles in plant development and adaptation. Characterizing the functions of DUFs is important for deciphering biological puzzles. DUFs were generally studied through forward and reverse genetics. Some novelty approaches, especially the determination of crystal structures and interaction partners of the DUFs, should attract more attention. This review described the identification of DUF genes by genome-wide and transcriptome-wide analyses, summarized the function of DUF-containing proteins, and addressed the prospects for future studies in DUFs in plants.

Structure of mechanically activated ion channel OSCA2.3 reveals mobile elements in the transmembrane domain

Members of the OSCA/TMEM63 family are mechanically activated ion channels and structures of some OSCA members have revealed the architecture of these channels and structural features that are potentially involved in mechanosensation. However, these structures are all in a similar state and information about the motion of different elements of the structure is limited, preventing a deeper understanding of how these channels work. Here, we used cryoelectron microscopy to determine high-resolution structures of Arabidopsis thaliana OSCA1.2 and OSCA2.3 in peptidiscs. The structure of OSCA1.2 matches previous structures of the same protein in different environments. Yet, in OSCA2.3, the TM6a-TM7 linker adopts a different conformation that constricts the pore on its cytoplasmic side. Furthermore, coevolutionary sequence analysis uncovered a conserved interaction between the TM6a-TM7 linker and the beam-like domain (BLD). Our results reveal conformational heterogeneity and differences in conserved interactions between the TMD and BLD among members of the OSCA family.

An Integrated Multilevel Approach Unveils Complex Seed-Nanoparticle Interactions and Their Implications for Seed Priming

Nanotechnology has the potential to revolutionize agriculture with the introduction of engineered nanomaterials. However, their use is hindered by high cost, marginal knowledge of their interactions with plants, and unpredictable effects related to massive use in crop cultivation. Nanopriming is an innovative seed priming technology able to match economic, agronomic, and environmental needs in agriculture. The present study was focused on unveiling, by a multilevel integrated approach, undisclosed aspects of seed priming mediated by iron oxide magnetic nanoparticles in pepper seeds (Capsicum annuum), one of the most economically important crops worldwide. Inductively coupled plasma atomic emission mass spectrometry and scanning electron microscopy were used to quantify the MNP uptake and assess seed surface changes. Magnetic resonance imaging mapped the distribution of MNPs prevalently in the seed coat. The application of MNPs significantly enhanced the root and vegetative growth of pepper plants, whereas seed priming with equivalent Fe concentrations supplied as FeCl3 did not yield these positive effects. Finally, global gene expression by RNA-sequencing identified more than 2,200 differentially expressed genes, most of them involved in plant developmental processes and defense mechanisms. Collectively, these data provide evidence on the link between structural seed changes and an extensive transcriptional reprogramming, which boosts the plant growth and primes the embryo to cope with environmental challenges that might occur during the subsequent developmental and growth stages.

Genome-wide investigation and expression analysis of OSCA gene family in response to abiotic stress in alfalfa

Alfalfa is an excellent leguminous forage crop that is widely cultivated worldwide, but its yield and quality are often affected by drought and soil salinization. Hyperosmolality-gated calcium-permeable channel (OSCA) proteins are hyperosmotic calcium ion (Ca2+) receptors that play an essential role in regulating plant growth, development, and abiotic stress responses. However, no systematic analysis of the OSCA gene family has been conducted in alfalfa. In this study, a total of 14 OSCA genes were identified from the alfalfa genome and classified into three groups based on their sequence composition and phylogenetic relationships. Gene structure, conserved motifs and functional domain prediction showed that all MsOSCA genes had the same functional domain DUF221. Cis-acting element analysis showed that MsOSCA genes had many cis-regulatory elements in response to abiotic or biotic stresses and hormones. Tissue expression pattern analysis demonstrated that the MsOSCA genes had tissue-specific expression; for example, MsOSCA12 was only expressed in roots and leaves but not in stem and petiole tissues. Furthermore, RT-qPCR results indicated that the expression of MsOSCA genes was induced by abiotic stress (drought and salt) and hormones (JA, SA, and ABA). In particular, the expression levels of MsOSCA3, MsOSCA5, MsOSCA12 and MsOSCA13 were significantly increased under drought and salt stress, and MsOSCA7, MsOSCA10, MsOSCA12 and MsOSCA13 genes exhibited significant upregulation under plant hormone treatments, indicating that these genes play a positive role in drought, salt and hormone responses. Subcellular localization results showed that the MsOSCA3 protein was localized on the plasma membrane. This study provides a basis for understanding the biological information and further functional analysis of the MsOSCA gene family and provides candidate genes for stress resistance breeding in alfalfa.

Deciphering the role of mechanosensitive channels in plant root biology: perception, signaling, and adaptive responses

MAIN CONCLUSION

Mechanosensitive channels are integral membrane proteins that rapidly translate extrinsic or intrinsic mechanical tensions into biological responses. They can serve as potential candidates for developing smart-resilient crops with efficient root systems. Mechanosensitive (MS) calcium channels are molecular switches for mechanoperception and signal transduction in all living organisms. Although tremendous progress has been made in understanding mechanoperception and signal transduction in bacteria and animals, this remains largely unknown in plants. However, identification and validation of MS channels such as Mid1-complementing activity channels (MCAs), mechanosensitive-like channels (MSLs), and Piezo channels (PIEZO) has been the most significant discovery in plant mechanobiology, providing novel insights into plant mechanoperception. This review summarizes recent advances in root mechanobiology, focusing on MS channels and their related signaling players, such as calcium ions (Ca2+), reactive oxygen species (ROS), and phytohormones. Despite significant advances in understanding the role of Ca2+ signaling in root biology, little is known about the involvement of MS channel-driven Ca2+ and ROS signaling. Additionally, the hotspots connecting the upstream and downstream signaling of MS channels remain unclear. In light of this, we discuss the present knowledge of MS channels in root biology and their role in root developmental and adaptive traits. We also provide a model highlighting upstream (cell wall sensors) and downstream signaling players, viz., Ca2+, ROS, and hormones, connected with MS channels. Furthermore, we highlighted the importance of emerging signaling molecules, such as nitric oxide (NO), hydrogen sulfide (H2S), and neurotransmitters (NTs), and their association with root mechanoperception. Finally, we conclude with future directions and knowledge gaps that warrant further research to decipher the complexity of root mechanosensing.

Maize ZmHSP90 plays a role in acclimation to salt stress

Background

Maize is sensitive to salt stress, especially during the germination and seedling stages.

Methods

We conducted germination experiments on 60 maize materials under salt stress, and screened out the most salt-tolerant and salt-sensitive varieties based on germination indicators. Afterwards, transcriptome analysis was performed to screen for key regulators in the plumule and flag leaf at the germination and seedling stages, respectively. Following that, transgenic tobacco was developed to expose the roles and mechanisms of the candidate genes, enabling a deeper investigation of their functions.

Results

Out of the 60 inbred lines of maize, "975-12" exhibits the highest level of salt tolerance, while "GEMS64" displays the lowest. The application of salt stress resulted in a significant increase in the levels of antioxidant enzymes in both "975-12" and "GEMS64". ABA signal transduction and jasmonic acid pathways were the pathways that mainly affected by salt stress. In addition, a significant finding has been made indicating that when exposed to high levels of salt stress, the expression of ZmHSP90 in '975-12' increased while in 'GEMS64' decreased. Furthermore, in tobacco plants overexpressing ZmHSP90, there was an increase in antioxidant enzyme activity associated with salt tolerance. ZmHSP90 enhanced the expression levels of NtSOS1, NtHKT1, and NtNHX1 as compared to those in the salt treatment, causing the maintenance of Na+ and K+ homeostasis, suggesting that high expression of ZmHSP90 was conducive to regulate Na+ transporters to maintain K+/Na+ balanced in tobacco.

The tomato calcium-permeable channel 4.1 (SlOSCA4.1) is a susceptibility factor for pepino mosaic virus

The hyperosmolality-gated calcium permeable channel 4.1 (OSCA4.1) belongs to an evolutionarily conserved small family of mechano-sensitive channels. OSCA members may represent key players in plant resistance to drought and to pathogen infection but are scarcely studied. After screening for resistance to pepino mosaic virus (PepMV) a collection of 1000 mutagenized tomato families, we identified a mutant showing no symptoms and reduced virus accumulation. Resistance was mapped to chromosome 2 between positions 46 309 531 to 47 044 163, where a missense mutation caused the putative truncation of the OSCA4.1 protein. A CRISPR/Cas9 slosca4.1 mutant was resistant to PepMV, but not to tobacco mosaic virus or potato virus X. Inoculation of mutant and wild type tomato protoplasts showed that resistance was expressed in single cells, suggesting a role for SlOSCA4.1 in early viral function(s); congruently, SlOSCA4.1 re-localized to structures reminiscent of viral replication complexes. We propose that SlOSCA4.1 contributes to the correct regulation of the Ca2+ homeostasis necessary for optimal PepMV infection. PepMV is a pandemic virus that causes significant losses in tomato crops worldwide. In spite of its importance, no tomato-resistant varieties have been deployed yet; the mutant identified here has great potential to breed tomato varieties resistant to PepMV.

Abiotic Stress in Crop Production

The vast majority of agricultural land undergoes abiotic stress that can significantly reduce agricultural yields. Understanding the mechanisms of plant defenses against stresses and putting this knowledge into practice is, therefore, an integral part of sustainable agriculture. In this review, we focus on current findings in plant resistance to four cardinal abiotic stressors—drought, heat, salinity, and low temperatures. Apart from the description of the newly discovered mechanisms of signaling and resistance to abiotic stress, this review also focuses on the importance of primary and secondary metabolites, including carbohydrates, amino acids, phenolics, and phytohormones. A meta-analysis of transcriptomic studies concerning the model plant Arabidopsis demonstrates the long-observed phenomenon that abiotic stressors induce different signals and effects at the level of gene expression, but genes whose regulation is similar under most stressors can still be traced. The analysis further reveals the transcriptional modulation of Golgi-targeted proteins in response to heat stress. Our analysis also highlights several genes that are similarly regulated under all stress conditions. These genes support the central role of phytohormones in the abiotic stress response, and the importance of some of these in plant resistance has not yet been studied. Finally, this review provides information about the response to abiotic stress in major European crop plants—wheat, sugar beet, maize, potatoes, barley, sunflowers, grapes, rapeseed, tomatoes, and apples.

Genome-wide analysis of hyperosmolality-gated calcium-permeable channel (OSCA) family members and their involvement in various osmotic stresses in Brassica napus

Plant hyperosmolality-gated calcium-permeable channel (OSCA) is a calcium permeable cation channel that responds to hyperosmotic stress and plays a pivotal role in plant growth, development and stress response. Through a genome-wide survey, 41 OSCA genes were identified from the genome of Brassica napus. The OSCA family genes were unevenly distributed over 14 chromosomes of B. napus and phylogenetic analysis separated the OSCA family into four clades. Motif analyses indicated that OSCA proteins in the same clade were highly conserved and the protein conserved motifs shared similar composition patterns. The OSCA promoter regions contained many hormone-related elements and stress response elements. Gene duplication analysis elucidated that WGD/segmental duplication was the main driving force for the expansion of OSCA genes during evolution and these genes mainly underwent purifying selection. RNA-seq and qRT-PCR analysis of different tissues showed that OSCA genes are expressed and function mainly in the root. Among these genes, BnOSCA3.1a and BnOSCA3.1c had relatively high expression levels under osmotic stresses and cold stress and were highly expressed in different tissues. Protein interaction network analysis showed that a total of 5802 proteins might interact with OSCAs in B. napus, while KEGG/GO enrichment analysis indicated that OSCAs and their interacting proteins were mainly involved in plant response to abiotic stress. This systematic analysis of the OSCAs in B. napus identified gene structures, evolutionary features, expression patterns and related biological processes. These findings will facilitate further functional and evolutionary analysis of OSCAs in B. napus for breeding of osmotic-stress-resistant plants.

Crop root system plasticity for improved yields in saline soils

Crop yields must increase to meet the demands of a growing world population. Soil salinization is increasing due to the impacts of climate change, reducing the area of arable land for crop production. Plant root systems are plastic, and their architecture can be modulated to (1) acquire nutrients and water for growth, and (2) respond to hostile soil environments. Saline soils inhibit primary root growth and alter root system architecture (RSA) of crop plants. In this review, we explore how crop root systems respond and adapt to salinity, focusing predominately on the staple cereal crops wheat, maize, rice, and barley, that all play a major role in global food security. Cereal crops are classified as glycophytes (salt-sensitive) however salt-tolerance can differ both between species and within a species. In the past, due to the inherent difficulties associated with visualising and measuring root traits, crop breeding strategies have tended to focus on optimising shoot traits. High-resolution phenotyping techniques now make it possible to visualise and measure root traits in soil systems. A steep, deep and cheap root ideotype has been proposed for water and nitrogen capture. Changes in RSA can be an adaptive strategy to avoid saline soils whilst optimising nutrient and water acquisition. In this review we propose a new model for designing crops with a salt-tolerant root ideotype. The proposed root ideotype would exhibit root plasticity to adapt to saline soils, root anatomical changes to conserve energy and restrict sodium (Na⁺) uptake, and transport mechanisms to reduce the amount of Na⁺ transported to leaves. In the future, combining high-resolution root phenotyping with advances in crop genetics will allow us to uncover root traits in complex crop species such as wheat, that can be incorporated into crop breeding programs for yield stability in saline soils.

OSCA Genes in Bread Wheat: Molecular Characterization, Expression Profiling, and Interaction Analyses Indicated Their Diverse Roles during Development and Stress Response

The hyperosmolality-gated calcium-permeable channels (OSCA) are pore-forming transmembrane proteins that function as osmosensors during various plant developmental processes and stress responses. In our analysis, through in silico approaches, a total of 42 OSCA genes are identified in the Triticum aestivum genome. A phylogenetic analysis reveals the close clustering of the OSCA proteins of Arabidopsis thaliana, Oryza sativa, and T. aestivum in all the clades, suggesting their origin before the divergence of dicots and monocots. Furthermore, evolutionary analyses suggest the role of segmental and tandem duplication events (Des) and purifying selection pressure in the expansion of the OSCA gene family in T. aestivum. Expression profiling in various tissue developmental stages and under abiotic and biotic stress treatments reveals the probable functioning of OSCA genes in plant development and the stress response in T. aestivum. In addition, protein-protein and protein-chemical interactions reveal that OSCA proteins might play a putative role in Ca²⁺-mediated developmental processes and adaptive responses. The miRNA interaction analysis strengthens the evidence for their functioning in various biological processes and stress-induced signaling cascades. The current study could provide a foundation for the functional characterization of TaOSCA genes in future studies.

Structure, Function, and Applications of Soybean Calcium Transporters

Glycine max is a calcium-loving crop. The external application of calcium fertilizer is beneficial to the increase of soybean yield. Indeed, calcium is a vital nutrient in plant growth and development. As a core metal ion in signaling transduction, calcium content is maintained in dynamic balance under normal circumstances. Now, eight transporters were found to control the uptake and efflux of calcium. Though these calcium transporters have been identified through genome-wide analysis, only a few of them were functionally verified. Therefore, in this study, we summarized the current knowledge of soybean calcium transporters in structural features, expression characteristics, roles in stress response, and prospects. The above results will be helpful in understanding the function of cellular calcium transport and provide a theoretical basis for elevating soybean yield.

Preliminary Expression Analysis of the OSCA Gene Family in Maize and Their Involvement in Temperature Stress

Hyperosmolality-gated calcium-permeable channels (OSCA) are characterized as an osmosensor in plants; they are able to recognize and respond to exogenous and endogenous osmotic changes, and play a vital role in plant growth and adaptability to environmental stress. To explore the potential biological functions of OSCAs in maize, we performed a bioinformatics and expression analysis of the ZmOSCA gene family. Using bioinformatics methods, we identified twelve OSCA genes from the genome database of maize. According to their sequence composition and phylogenetic relationship, the maize OSCA family was classified into four groups (Ⅰ, Ⅱ, Ⅲ, and Ⅳ). Multiple sequence alignment analysis revealed a conserved DUF221 domain in these members. We modeled the calcium binding sites of four OSCA families using the autodocking technique. The expression profiles of ZmOSCA genes were analyzed in different tissues and under diverse abiotic stresses such as drought, salt, high temperature, and chilling using quantitative real-time PCR (qRT-PCR). We found that the expression of twelve ZmOSCA genes is variant in different tissues of maize. Furthermore, abiotic stresses such as drought, salt, high temperature, and chilling differentially induced the expression of twelve ZmOSCA genes. We chose ZmOSCA2.2 and ZmOSCA2.3, which responded most strongly to temperature stress, for prediction of protein interactions. We modeled the calcium binding sites of four OSCA families using autodocking tools, obtaining a number of new results. These results are helpful in understanding the function of the plant OSCA gene family for study of the molecular mechanism of plant osmotic stress and response, as well as exploration of the interaction between osmotic stress, high-temperature stress, and low-temperature stress signal transduction mechanisms. As such, they can provide a theoretical basis for crop breeding.

Genome-Wide Identification, Evolution and Expressional Analysis of OSCA Gene Family in Barley (Hordeum vulgare L.)

The hyperosmolality-gated calcium-permeable channel gene family (OSCA) is one kind of conserved osmosensors, playing a crucial role in maintaining ion and water homeostasis and protecting cellular stability from the damage of hypertonic stress. Although it has been systematically characterized in diverse plants, it is necessary to explore the role of the OSCA family in barley, especially its importance in regulating abiotic stress response. In this study, a total of 13 OSCA genes (HvOSCAs) were identified in barley through an in silico genome search method, which were clustered into 4 clades based on phylogenetic relationships with members in the same clade showing similar protein structures and conserved motif compositions. These HvOSCAs had many cis-regulatory elements related to various abiotic stress, such as MBS and ARE, indicating their potential roles in abiotic stress regulation. Furthermore, their expression patterns were systematically detected under diverse stresses using RNA-seq data and qRT-PCR methods. All of these 13 HvOSCAs were significantly induced by drought, cold, salt and ABA treatment, demonstrating their functions in osmotic regulation. Finally, the genetic variations of the HvOSCAs were investigated using the re-sequencing data, and their nucleotide diversity in wild barley and landrace populations were 0.4966 × 10-3 and 0.391 × 10-3, respectively, indicating that a genetic bottleneck has occurred in the OSCA family during the barley evolution process. This study evaluated the genomic organization, evolutionary relationship and genetic expression of the OSCA family in barley, which not only provides potential candidates for further functional genomic study, but also contributes to genetically improving stress tolerance in barley and other crops.

Systematic Characterization of the OSCA Family Members in Soybean and Validation of Their Functions in Osmotic Stress

Since we discovered OSCA1, a hyperosmolarity-gated calcium-permeable channel that acted as an osmosensor in Arabidopsis, the OSCA family has been identified genome-wide in several crops, but only a few OSCA members' functions have been experimentally demonstrated. Osmotic stress seriously restricts the yield and quality of soybean. Therefore, it is essential to decipher the molecular mechanism of how soybean responds to osmotic stress. Here, we first systematically studied and experimentally demonstrated the role of OSCA family members in the osmotic sensing of soybean. Phylogenetic relationships, gene structures, protein domains and structures analysis revealed that 20 GmOSCA members were divided into four clades, of which members in the same cluster may have more similar functions. In addition, GmOSCA members in clusters III and IV may be functionally redundant and diverged from those in clusters I and II. Based on the spatiotemporal expression patterns, GmOSCA1.6, GmOSCA2.1, GmOSCA2.6, and GmOSCA4.1 were extremely low expressed or possible pseudogenes. The remaining 16 GmOSCA genes were heterologously overexpressed in an Arabidopsis osca1 mutant, to explore their functions. Subcellular localization showed that most GmOSCA members could localize to the plasma membrane (PM). Among 16 GmOSCA genes, only overexpressing GmOSCA1.1, GmOSCA1.2, GmOSCA1.3, GmOSCA1.4, and GmOSCA1.5 in cluster I could fully complement the reduced hyperosmolality-induced [Ca²⁺]_i increase (OICI) in osca1. The expression profiles of GmOSCA genes against osmotic stress demonstrated that most GmOSCA genes, especially GmOSCA1.1, GmOSCA1.2, GmOSCA1.3, GmOSCA1.4, GmOSCA1.5, GmOSCA3.1, and GmOSCA3.2, strongly responded to osmotic stress. Moreover, overexpression of GmOSCA1.1, GmOSCA1.2, GmOSCA1.3, GmOSCA1.4, GmOSCA1.5, GmOSCA3.1, and GmOSCA3.2 rescued the drought-hypersensitive phenotype of osca1. Our findings provide important clues for further studies of GmOSCA-mediated calcium signaling in the osmotic sensing of soybean and contribute to improving soybean drought tolerance through genetic engineering and molecular breeding.

Mechanotransduction in the spotlight of mechano-sensitive channels

The study of mechanosensitive channels (MS) in living organisms has progressed considerably over the past two decades. The understanding of their roles in mechanosensation and mechanotransduction was consecrated by the awarding of the Nobel Prize in 2021 to A. Patapoutian for his discoveries on the role of MS channels in mechanoperception in humans. In this review, we first summarize the fundamental properties of MS channels and their mode of operation. Then in a second step, we provide an update on the knowledge on the families of MS channels identified in plants and the roles and functions that have been attributed to them.

Identification and Expression Profile Analysis of the OSCA Gene Family Related to Abiotic and Biotic Stress Response in Cucumber

Simple Summary

Hyperosmolality-gated calcium-permeable channels (OSCAs) are calcium nonselective cation channel proteins involved in multiple biological processes. In this work, the members of the OSCA family in cucumber were systematically analyzed, including their sequence characteristics, phylogenetic relationships, conserved motifs, gene structures, promoter regions, and tissue expression patterns. In addition, the effects of different osmotic-related abiotic stresses [salt (NaCl), drought (PEG), and abscisic acid (ABA)] and three biotic stresses [powdery mildew (PM), downy mildew (DM), and root-knot nematode (RKN)] on OSCA family genes were also determined. The results indicated that cucumber OSCA genes play important roles in response to osmotic-related abiotic stresses and pathogen invasion. Overall, this study lays a foundation for research on the biological function and evolutionary process of OSCA family genes in cucumber.

Abstract

Calcium ions are important second messengers, playing an important role in the signal transduction pathways. Hyperosmolality gated calcium-permeable channels (OSCA) gene family members play critical modulating roles in response to osmotic-related abiotic stress as well as other abiotic and biotic stresses, which has been reported in many plant species such as Arabidopsis, rice, maize, and wheat. However, there has been no report about the identification and expression profile of the OSCA genes in cucumber. In this study, a total of nine OSCA genes were identified, which are unevenly distributed on the six chromosomes of cucumber. Phylogenetic analysis revealed that the OSCAs of cucumber, Arabidopsis, rice and maize were clustered into four clades. The motif arrangement of CsOSCAs was strongly conserved, and the CsOSCA genes in each group had similar genetic structure. A total of 11 and 10 types of cis-elements related to hormone and stress, respectively, were identified in the promoter regions of CsOSCA genes. Gene expression analysis indicated that the CsOSCA genes have different expression patterns in various tissues, and some of them were regulated by three osmotic-related abiotic stresses (salt, drought and ABA) and three biotic stresses (powdery mildew, downy mildew, and root-knot nematode). As the first genome-wide identification and characterization of the OSCA gene family in cucumber, this study lays a foundation for research on the biological function and evolutionary process of this gene family, which is of great significance for exploiting stress resistant cucumber varieties.

Plant cell mechanobiology: Greater than the sum of its parts

The ability to sense and respond to physical forces is critical for the proper function of cells, tissues, and organisms across the evolutionary tree. Plants sense gravity, osmotic conditions, pathogen invasion, wind, and the presence of barriers in the soil, and dynamically integrate internal and external stimuli during every stage of growth and development. While the field of plant mechanobiology is growing, much is still poorly understood-including the interplay between mechanical and biochemical information at the single-cell level. In this review, we provide an overview of the mechanical properties of three main components of the plant cell and the mechanoperceptive pathways that link them, with an emphasis on areas of complexity and interaction. We discuss the concept of mechanical homeostasis, or "mechanostasis," and examine the ways in which cellular structures and pathways serve to maintain it. We argue that viewing mechanics and mechanotransduction as emergent properties of the plant cell can be a useful conceptual framework for synthesizing current knowledge and driving future research.

Between Stress and Response: Function and Localization of Mechanosensitive Ca2+ Channels in Herbaceous and Perennial Plants

Over the past three decades, how plants sense and respond to mechanical stress has become a flourishing field of research. The pivotal role of mechanosensing in organogenesis and acclimation was demonstrated in various plants, and links are emerging between gene regulatory networks and physical forces exerted on tissues. However, how plant cells convert physical signals into chemical signals remains unclear. Numerous studies have focused on the role played by mechanosensitive (MS) calcium ion channels MCA, Piezo and OSCA. To complement these data, we combined data mining and visualization approaches to compare the tissue-specific expression of these genes, taking advantage of recent single-cell RNA-sequencing data obtained in the root apex and the stem of Arabidopsis and the Populus stem. These analyses raise questions about the relationships between the localization of MS channels and the localization of stress and responses. Such tissue-specific expression studies could help to elucidate the functions of MS channels. Finally, we stress the need for a better understanding of such mechanisms in trees, which are facing mechanical challenges of much higher magnitudes and over much longer time scales than herbaceous plants, and we mention practical applications of plant responsiveness to mechanical stress in agriculture and forestry.

Genome-wide identification, genomic organization, and expression profiling of the CONSTANS-like (COL) gene family in petunia under multiple stresses

Background

CONSTANS-like (CO-like, COL) are putative zinc-finger transcription factors known to play vital role in various plant biological processes such as control of flowering time, regulation of plant growth and development and responses to stresses. However, no systematic analysis of COL family gene regarding the plant development and stress response has been previously performed in any solanaceous crop. In the present study, a comprehensive genome-wide analysis of COL family genes in petunia has been conducted to figure out their roles in development of organs and stress response.

Results

A total of 33 COL genes, 15 PaCOL genes in P. axillaris and 18 PiCOL genes in P. inflata, were identified in petunia. Subsequently, a genome-wide systematic analysis was performed in 15 PaCOL genes. Considering the domain composition and sequence similarity the 15 PaCOL and 18 PiCOL genes were phylogenetically classified into three groups those are conserved among the flowering plants. Moreover, all of the 15 PaCOL proteins were localized in nucleus. Furthermore, differential expression patterns of PaCOL genes were observed at different developmental stages of petunia. Additionally, transcript expression of 15 PaCOL genes under various abiotic and phytohormone treatments showed their response against stresses. Moreover, several cis-elements related to stress, light-responsive, hormone signaling were also detected in different PaCOL genes.

Conclusion

The phylogenetic clustering, organ specific expression pattern and stress responsive expression profile of conserved petunia COL genes indicating their involvement in plant growth and development and stress response mechanism. This work provide a significant foundation for understanding the biological roles of petunia COL genes in plant growth, development and in stress response.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08019-w.

Transcriptional regulatory networks in response to drought stress and rewatering in maize (Zea mays L.)

Drought severely affects the growth and development of maize, but there is a certain degree of compensation effect after rewatering. This study intends to elaborate the response mechanism of maize at the physiological and molecular level as well as excavating potential genes with strong drought resistance and recovery ability. Physiological indexes analysis demonstrated that stomata conductance, transpiration rate, photosynthesis rate, antioxidant enzymes, and proline levels in maize were significantly altered in response to drought for 60 and 96 h and rewatering for 3 days. At 60 h, 96 h, and R3d, we detected 3095, 1941, and 5966 differentially expressed genes (DEGs) and 221, 226, and 215 differentially expressed miRNAs. Weighted correlation network analysis (WGCNA) showed that DEGs responded to maize drought and rewatering through participating in photosynthesis, proline metabolism, ABA signaling, and oxidative stress. Joint analysis of DEGs, miRNA, and target genes showed that zma-miR529, miR5072, zma-miR167e, zma-miR167f, zma-miR167j, miR397, and miR6214 were involved to regulate SBPs, MYBs, ARFs, laccases, and antioxidant enzymes, respectively. Hundreds of differentially expressed DNA methylation-related 24-nt siRNA clusters overlap with DEGs, indicating that DNA methylation is involved in responses under drought stress. These results provide new insights into the molecular mechanisms of drought tolerance, and may identify new targets for breeding drought-tolerant maize lines.

Genome-wide analysis of OSCA gene family members in Vigna radiata and their involvement in the osmotic response

BACKGROUND

Mung bean (Vigna radiata) is a warm-season legume crop and belongs to the papilionoid subfamily of the Fabaceae family. China is the leading producer of mung bean in the world. Mung bean has significant economic and health benefits and is a promising species with broad adaptation ability and high tolerance to environmental stresses. OSCA (hyperosmolality-gated calcium-permeable channel) gene family members play an important role in the modulation of hypertonic stress, such as drought and salinity. However, genome-wide analysis of the OSCA gene family has not been conducted in mung bean.

RESULTS

We identified a total of 13 OSCA genes in the mung bean genome and named them according to their homology with AtOSCAs. All the OSCAs were phylogenetically split into four clades. Phylogenetic relationship and synteny analyses showed that the VrOSCAs in mung bean and soybean shared a relatively conserved evolutionary history. In addition, three duplicated VrOSCA gene pairs were identified, and the duplicated VrOSCAs gene pairs mainly underwent purifying selection pressure during evolution. Protein domain, motif and transmembrane analyses indicated that most of the VrOSCAs shared similar structures with their homologs. The expression pattern showed that except for VrOSCA2.1, the other 12 VrOSCAs were upregulated under treatment with ABA, PEG and NaCl, among which VrOSCA1.4 showed the largest increased expression levels. The duplicated genes VrOSCA2.1/VrOSCA2.2 showed divergent expression, which might have resulted in functionalization during subsequent evolution. The expression profiles under ABA, PEG and NaCl stress revealed a functional divergence of VrOSCA genes, which agreed with the analysis of cis-acting regulatory elements in the promoter regions of VrOSCA genes.

CONCLUSIONS

Collectively, the study provided a systematic analysis of the VrOSCA gene family in mung bean. Our results establish an important foundation for functional and evolutionary analysis of VrOSCAs and identify genes for further investigation of their ability to confer abiotic stress tolerance in mung bean.

Systematic analysis of differentially expressed ZmMYB genes related to drought stress in maize

MYB transcription factors play pivotal roles in hormone conduction signaling and abiotic stress response. In this study, 54 differentially expressed ZmMYB genes were identified and comprehensive analyses were conducted including gene's structure, chromosomal localization, phylogenetic tree, motif prediction, cis-elements and expression patterns. The results showed that 54 genes were unevenly distributed on 10 chromosomes and classified into eleven main subgroups by phylogenetic analysis, supported by motif and exon/intron analyses. The mainly stress-related cis-elements were ABRE, ARE, MBS and DRE-core. In addition, 8 core ZmMYB genes were identified by co-expression network. qRT-PCR results showed that the 8 ZmMYB genes exhibited different expression levels under different abiotic stresses, indicating that they were responsive to various abiotic stress. These results will provide insight for further functional investigation of ZmMYB genes.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01013-2.