Molecular Identification and Characterization of Hevein Antimicrobial Peptide Genes in Two-Row and Six-Row Cultivars of Barley (Hordeum vulgare L.)

Heveins are one of the most important groups of plant antimicrobial peptides. So far, various roles in plant growth and development and in response to biotic and abiotic stresses have reported for heveins. The present study aimed to identify and characterize the hevein genes in two-row and six-row cultivars of barley. In total, thirteen hevein genes were identified in the genome of two-row and six-row cultivars of barley. The identified heveins were identical in two-row and six-row cultivars of barley and showed a high similarity with heveins from other plant species. The hevein coding sequences produced open reading frames (ORFs) ranged from 342 to 1002 bp. Most of the identified hevein genes were intronless, and the others had only one intron. The hevein ORFs produced proteins ranged from 113 to 333 amino acids. Search for conserved functional domains showed CBD and LYZ domains in barley heveins. All barley heveins comprised extracellular signal peptides ranged from 19 to 35 amino acids. The phylogenetic analysis divided barley heveins into two groups. The promoter analysis showed regulatory elements with different frequencies between two-row and six-row cultivars. These cis-acting elements included elements related to growth and development, hormone response, and environmental stresses. The expression analysis showed high expression level of heveins in root and reproductive organs of both two-row and six-row cultivars. The expression analysis also showed that barley heveins is induced by both biotic and abiotic stresses. The results of antimicrobial activity prediction showed the highest antimicrobial activity in CBD domain of barley heveins. The findings of the current study can improve our knowledge about the role of hevein genes in plant and can be used for future studies.

Role of microRNAs and their putative mechanism in regulating potato (Solanum tuberosum L.) life cycle and response to various environmental stresses

The exponentially increasing population and the demand for food is inextricably linked. This has shifted global attention to improving crop plant traits to meet global food demands. Potato (Solanum tuberosum L.) is a major non-grain food crop that is grown all over the world. Currently, some of the major global potato research work focuses on the significance of microRNAs (miRNAs) in potato. miRNAs are a type of non-coding RNAs that regulate the gene expression of their target mRNA genes by cleavage and/or their translational inhibition. This suggests an essential role of miRNAs in a multitude of plant biological processes, including maintenance of genome integrity, plant growth, development and maturation, and initiation of responses to various stress conditions. Therefore, engineering miRNAs to generate stress-resistant varieties of potato may result in high yield and improved nutritional qualities. In this review, we discuss the potato miRNAs specifically known to play an essential role in the various stages of the potato life cycle, conferring stress-resistant characteristics, and modifying gene expression. This review highlights the significance of the miRNA machinery in plants, especially potato, encouraging further research into engineering miRNAs to boost crop yields and tolerance towards stress.

Harnessing root exudates for plant microbiome engineering and stress resistance in plants

A wide range of abiotic and biotic stresses adversely affect plant's growth and production. Under stress, one of the main responses of plants is the modulation of exudates excreted in the rhizosphere, which consequently leads to alterations in the resident microbiota. Thus, the exudates discharged into the rhizospheric environment play a preponderant role in the association and formation of plant-microbe interactions. In this review, we aimed to provide a synthesis of the latest and most pertinent literature on the diverse biochemical and structural compositions of plant root exudates. Also, this work investigates into their multifaceted role in microbial nutrition and intricate signaling processes within the rhizosphere, which includes quorum-sensing molecules. Specifically, it explores the contributions of low molecular weight compounds, such as carbohydrates, phenolics, organic acids, amino acids, and secondary metabolites, as well as the significance of high molecular weight compounds, including proteins and polysaccharides. It also discusses the state-of-the-art omics strategies that unveil the vital role of root exudates in plant-microbiome interactions, including defense against pathogens like nematodes and fungi. We propose multiple challenges and perspectives, including exploiting plant root exudates for host-mediated microbiome engineering. In this discourse, root exudates and their derived interactions with the rhizospheric microbiota should receive greater attention due to their positive influence on plant health and stress mitigation.

Genome-wide characterization of COMT family and regulatory role of CsCOMT19 in melatonin synthesis in Camellia sinensis

BACKGROUND

Caffeic acid O-methyltransferase (COMT) is a key enzyme that regulates melatonin synthesis and is involved in regulating the growth, development, and response to abiotic stress in plants. Tea plant is a popular beverage consumed worldwide, has been used for centuries for its medicinal properties, including its ability to reduce inflammation, improve digestion, and boost immune function. By analyzing genetic variation within the COMT family, while helping tea plants resist adversity, it is also possible to gain a deeper understanding of how different tea varieties produce and metabolize catechins, then be used to develop new tea cultivars with desired flavor profiles and health benefits.

RESULTS

In this study, a total of 25 CsCOMT genes were identified based on the high-quality tea (Camellia sinensis) plant genome database. Phylogenetic tree analysis of CsCOMTs with COMTs from other species showed that COMTs divided into four subfamilies (Class I, II, III, IV), and CsCOMTs was distributed in Class I, Class II, Class III. CsCOMTs not only undergoes large-scale gene recombination in pairs internally in tea plant, but also shares 2 and 7 collinear genes with Arabidopsis thaliana and poplar (Populus trichocarpa), respectively. The promoter region of CsCOMTs was found to be rich in cis-acting elements associated with plant growth and stress response. By analyzing the previously transcriptome data, it was found that some members of CsCOMT family exhibited significant tissue-specific expression and differential expression under different stress treatments. Subsequently, we selected six CsCOMTs to further validated their expression levels in different tissues organ using qRT-PCR. In addition, we silenced the CsCOMT19 through virus-induced gene silencing (VIGS) method and found that CsCOMT19 positively regulates the synthesis of melatonin in tea plant.

CONCLUSION

These results will contribute to the understanding the functions of CsCOMT gene family and provide valuable information for further research on the role of CsCOMT genes in regulating tea plant growth, development, and response to abiotic stress.

Whole genome identification of olive flounder (Paralichthys olivaceus) cathepsin genes: Provides insights into its regulation on biotic and abiotic stresses response

Cathepsins are major lysosomal enzymes involved in essential physiological processes, including protein degradation, tissue differentiation, and innate or adaptive responses. Several kinds of cathepsins have been reported in teleost fishes, but no characterization have been performed for the inflammatory response of cathepsin family in olive flounder until now. In our current study, a total of 17 cathepsins in olive flounder were systematically identified and characterized. Phylogenetic analysis clearly indicated that the cathepsin genes was highly conserved. Analysis of structure and motifs exhibited high sequence similarity of cathepsin genes in olive flounder. Expression profiles of cathepsin genes in different tissues and developmental stages showed that cathepsins were temporally and spatially specific. RNA-seq analysis of bacteria and temperature stresses revealed that members of cathepsin were involved in inflammatory responses. Collectively, our findings would provide a further reference for understanding the molecular mechanisms of cathepsins in olive flounder.

Insights into Endophytic and Rhizospheric Bacteria of Five Sugar Beet Hybrids in Terms of Their Diversity, Plant-Growth Promoting, and Biocontrol Properties

Sugar beet is the most important crop for sugar production in temperate zones. The plant microbiome is considered an important factor in crop productivity and health. Here, we investigated the bacterial diversity of seeds, roots, and rhizosphere of five sugar beet hybrids named Eduarda (ED), Koala (KO), Tibor (T), Tajfun (TF), and Cercospora-resistant (C). A culture-independent next-generation sequencing approach was used for the further investigation of seed-borne endophytes. Hybrid-associated bacteria were evaluated for their plant growth-promoting (PGP) characteristics, antagonistic activity towards Cercospora beticola and several Fusarium strains in dual culture assays, and drought and salinity tolerance. High-throughput sequencing revealed that the Proteobacteria phylum was most dominant in the seeds of all hybrids, followed by Cyanobacteria and Actinobacteriota. The predominant genus in all hybrids was Pantoea, followed by Pseudomonas, Acinetobacter, Chalicogloea, Corynebacterium, Enterobacter, Enterococcus, Glutamicibacter, Kosakonia, and Marinilactibacillus. Unique genera in the hybrids were Pleurocapsa and Arthrobacter (T), Klebsiella (TF), Apibacter (ED), and Alloscardovia (KO). The genera that were most represented in one hybrid were Weissella and Staphylococcus (TF); Streptococcus (T); Gardnerella, Prevotella, and Rothia (KO); and Gilliamella, Lactobacillus, and Snodgrassella (ED). Thirty-two bacteria out of 156 isolates from the rhizosphere, roots, and seeds were selected with respect to various plant growth-promoting activities in vitro, i.e., nitrogen fixation, phosphate solubilization, siderophore production, indole-3-acetic acid production, 1-aminocyclopropane-1-carboxylic acid deaminase activity, hydrogen cyanide production, exoenzymatic activity (amylase, protease, lipase, cellulase, xylanase, mannanases, gelatinase, and pectinase), mitigation of environmental stresses, and antifungal activity. Mixta theicola KO3-44, Providencia vermicola ED3-10, Curtobacterium pusillum ED2-6, and Bacillus subtilis KO3-18 had the highest potential to promote plant growth due to their multiple abilities (nitrogen fixation, phosphate solubilization, production of siderophores, and IAA). The best antagonistic activity towards phytopathogenic fungi was found for Bacillus velezensis C3-19, Paenibacillus polymyxa C3-36 and Bacillus halotolerans C3-16/2.1. Only four isolates B. velezensis T2-23, B. subtilis T3-4, B. velezensis ED2-2, and Bacillus halotolerans C3-16/2.1 all showed enzymatic activity, with the exception of xylanase production. B. halotolerans C3-16/2.1 exhibited the greatest tolerance to salinity, while two B. subtilis strains (C3-62 and TF2-1) grew successfully at the maximum concentration of PEG. The current study demonstrates that sugar beet-associated bacteria have a wide range of beneficial traits and are therefore highly promising for the formulation of biological control and PGP agents.

The role and pathway of VQ family in plant growth, immunity, and stress response

MAIN CONCLUSION

This review provides a detailed description of the function and mechanism of VQ family gene, which is helpful for further research and application of VQ gene resources to improve crops. Valine-glutamine (VQ) motif-containing proteins are a large class of transcriptional regulatory cofactors. VQ proteins have their own unique molecular characteristics. Amino acids are highly conserved only in the VQ domain, while other positions vary greatly. Most VQ genes do not contain introns and the length of their proteins is less than 300 amino acids. A majority of VQ proteins are predicted to be localized in the nucleus. The promoter of many VQ genes contains stress or growth related elements. Segment duplication and tandem duplication are the main amplification mechanisms of the VQ gene family in angiosperms and gymnosperms, respectively. Purification selection plays a crucial role in the evolution of many VQ genes. By interacting with WRKY, MAPK, and other proteins, VQ proteins participate in the multiple signaling pathways to regulate plant growth and development, as well as defense responses to biotic and abiotic stresses. Although there have been some reports on the VQ gene family in plants, most of them only identify family members, with little functional verification, and there is also a lack of complete, detailed, and up-to-date review of research progress. Here, we comprehensively summarized the research progress of VQ genes that have been published so far, mainly including their molecular characteristics, biological functions, importance of VQ motif, and working mechanisms. Finally, the regulatory network and model of VQ genes were drawn, a precise molecular breeding strategy based on VQ genes was proposed, and the current problems and future prospects were pointed out, providing a powerful reference for further research and utilization of VQ genes in plant improvement.

Plant-beneficial Streptomyces dioscori SF1 potential biocontrol and plant growth promotion in saline soil within the arid and semi-arid areas

Environmental challenges like salinity, drought, fungal phytopathogens, and pesticides directly or/and indirectly influence the environment and agricultural yields. Certain beneficial endophytic Streptomyces sp. can ameliorate environmental stresses and be utilized as crop growth promoters under adverse conditions. Herein, Streptomyces dioscori SF1 (SF1) isolated from seeds of Glycyrrhiza uralensis tolerated fungal phytopathogens and abiotic stresses (drought, salt, and acid base). Strain SF1 showed multifarious plant growth promotion characteristics, including the production of indole acetic acid (IAA), ammonia, siderophores, ACC deaminase, extracellular enzymes, the ability of potassium solubilization, and nitrogen fixation. The dual plate assay showed that strain SF1 inhibited 63.21 ± 1.53%, 64.84 ± 1.35%, and 74.19 ± 2.88% of Rhizoctonia solani, Fusarium acuminatum, and Sclerotinia sclerotiorum, respectively. The detached root assays showed that strain SF1 significantly reduced the number of rotten sliced roots, and the biological control effect on sliced roots of Angelica sinensis, Astragalus membranaceus, and Codonopsis pilosula was 93.33%, 86.67%, and 73.33%, respectively. Furthermore, the strain SF1 significantly increased the growth parameters and biochemical indicators of adversity in G. uralensis seedlings under drought and/or salt conditions, including radicle length and diameter, hypocotyl length and diameter, dry weight, seedling vigor index, antioxidant enzyme activity, and non-enzymatic antioxidant content. In conclusion, the strain SF1 can be used to develop environmental protection biological control agents, improve the anti-disease activity of plants, and promote plant growth in salinity soil within arid and semi-arid regions.

Phylogeny of the plant receptor-like kinase (RLK) gene family and expression analysis of wheat RLK genes in response to biotic and abiotic stresses

BACKGROUND

The receptor-like kinase (RLK) gene families in plants contains a large number of members. They are membrane proteins with an extracellular receptor domain and participate in biotic and abiotic stress responses.

RESULTS

In this study, we identified RLKs in 15 representative plant genomes, including wheat, and classified them into 64 subfamilies by using four types of phylogenetic trees and HMM models. Conserved exon‒intron structures with conserved exon phases in the kinase domain were found in many RLK subfamilies from Physcomitrella patens to Triticum aestivum. Domain distributions of RLKs were also diagrammed. Collinearity events and tandem gene clusters suggested that polyploidization and tandem duplication events contributed to the member expansions of T. aestivum RLKs. Global expression pattern analysis was performed by using public transcriptome data. These analyses were involved in T. aestivum, Aegilops tauschii and Brachypodium distachyon RLKs under biotic and abiotic stresses. We also selected 9 RLKs to validate the transcriptome prediction by using qRT‒PCR under drought treatment and with Fusarium graminearum infection. The expression trends of these 9 wheat RLKs from public transcriptome data were consistent with the results of qRT‒PCR, indicating that they might be stress response genes under drought or F. graminearum treatments.

CONCLUSION

In this study, we identified, classified, evolved, and expressed RLKs in wheat and related plants. Thus, our results will provide insights into the evolutionary history and molecular mechanisms of wheat RLKs.

Optimistic contributions of plant growth-promoting bacteria for sustainable agriculture and climate stress alleviation

Global climate change is the major cause of abiotic and biotic stresses that have adverse effects on agricultural productivity to an irreversible level, thus threatening to limit gains in production and imperil sustainable agriculture. These climate change-induced abiotic stresses, especially saline, drought, extreme temperature, and so on affect plant morphological, physiological, biochemical, and metabolic characteristics through various pathways and mechanisms, ultimately hindering plant growth, development, and productivity. However, overuse and other inappropriate uses of agrochemicals are not conducive to the protection of natural resources and the environment, thus hampering sustainable agricultural development. With the vigorous development of modern agriculture, the application of plant growth-promoting bacteria (PGPB) can better ensure sustainable agriculture, due to their ability to improve soil properties and confer stress tolerance in plants. This review deciphered the underlying mechanisms of PGPB involved in enhancing plant stress tolerance and performance under various abiotic and biotic stresses. Moreover, the recent advancements in PGPB inoculation techniques, the commercialization of PGPB-based technology and the current applications of PGPB in sustainable agriculture were extensively discussed. Finally, an outlook on the future directions of microbe-aided agriculture was pointed out. Providing insights into plant-PGPB interactions under biotic and abiotic stresses and offering evidence and strategies for PGPB better commercialization and implementation can inspire the development of innovative solutions exploiting PGPB under climatological conditions.

Crosstalk of nitro-oxidative stress and iron in plant immunity

Accumulation of oxygen and nitrogen radicals and their derivatives, known as reactive oxygen species (ROS) and reactive nitrogen species (RNS), occurs throughout various phases of plant growth in association with biotic and abiotic stresses. One of the consequences of environmental stresses is disruption of homeostasis between production and scavenging of ROS and RNS, which leads to nitro-oxidative burst and affects other defense-related mechanisms, such as polyamines levels, phenolics, lignin and callose as defense components related to plant cell wall reinforcement. Although this subject has attracted huge interest, the cross-talk between these signaling molecules and iron, as a main metal element involved in the activity of various enzymes and numerous vital processes in the living cells, remains largely unexplored. Therefore, it seems necessary to pay more in depth attention to the mechanisms of plant resistance against various environmental stimuli for designing novel and effective plant protection strategies. This review is focused on advances in recent knowledge related to the role of ROS, RNS, and association of these signaling molecules with iron in plant immunity. Furthermore, the role of cell wall fortification as a main physical barrier involved in plant defense have been discussed in association with reactive species and iron ions.

A Comprehensive Review of High Throughput Phenotyping and Machine Learning for Plant Stress Phenotyping

During the last decade, there has been rapid adoption of ground and aerial platforms with multiple sensors for phenotyping various biotic and abiotic stresses throughout the developmental stages of the crop plant. High throughput phenotyping (HTP) involves the application of these tools to phenotype the plants and can vary from ground-based imaging to aerial phenotyping to remote sensing. Adoption of these HTP tools has tried to reduce the phenotyping bottleneck in breeding programs and help to increase the pace of genetic gain. More specifically, several root phenotyping tools are discussed to study the plant's hidden half and an area long neglected. However, the use of these HTP technologies produces big data sets that impede the inference from those datasets. Machine learning and deep learning provide an alternative opportunity for the extraction of useful information for making conclusions. These are interdisciplinary approaches for data analysis using probability, statistics, classification, regression, decision theory, data visualization, and neural networks to relate information extracted with the phenotypes obtained. These techniques use feature extraction, identification, classification, and prediction criteria to identify pertinent data for use in plant breeding and pathology activities. This review focuses on the recent findings where machine learning and deep learning approaches have been used for plant stress phenotyping with data being collected using various HTP platforms. We have provided a comprehensive overview of different machine learning and deep learning tools available with their potential advantages and pitfalls. Overall, this review provides an avenue for studying various HTP platforms with particular emphasis on using the machine learning and deep learning tools for drawing legitimate conclusions. Finally, we propose the conceptual challenges being faced and provide insights on future perspectives for managing those issues.

Characterization of silicon transporter gene family in Saccharum and functional analysis of the ShLsi6 gene in biotic stress

Silicon, one of the most prevalent elements in the soil, is beneficial for plant growth and defense against different stresses. The silicon transporter gene (Lsi) plays an important role in the uptake and transport of silicon in higher plants. In this study, a total of 32 Lsi genes, including 20 SsLsi in sugarcane wild species Saccharum spontaneum, 5 ShLsi in Saccharum hybrid cultivar R570 and 7 SbLsi in sugarcane related species Sorghum bicolor, were identified and classified into three groups. Bioinformatics analysis showed that instability, hydrophobicity, localization of cell membranes and vacuoles were the main features of the Lsi proteins. Whole genome and segmental duplication contributed to the main expansion of Lsi gene family. Collinearity analysis of the Lsi genes showed that S. spontanum and R570 had a collinear relationship with monocotyledonous plants S. bicolor and Oryza sativa, but not with dicotyledonous plants Arabidopsis thaliana and Vitis vinifera. The replicated Lsi genes were mainly subjected to strong selection pressure for purification. The diverse cis-regulatory elements in the promoter of SsLsi, ShLsi and SbLsi genes suggested that they were widely involved in the response of plants to various stresses and the regulation of the growth and development. Transcriptome data and real time quantitative PCR analysis showed that the Lsi genes exhibited different expression profiles in sugarcane tissues and under Sporisorium scitamineum, drought and cold stresses. In addition, the cDNA and genomic DNA sequences of ShLsi6 that was homologous to SsLsi1b gene was cloned from Saccharum hybrid cultivar ROC22. Transient expression analysis showed that, compared with the control, Nicotiana benthamiana leaves which overexpressed the ShLsi6 gene showed a high sensitivity after inoculation with tobacco pathogens Ralstonia solanacearum and Fusarium solani var. coeruleum. This study provides important information for further functional analysis of Lsi genes and resistant breeding in sugarcane.

Genome-wide identification, characterization of expansin gene family of banana and their expression pattern under various stresses

Expansin, a cell wall-modifying gene family, has been well characterized and its role in biotic and abiotic stress resistance has been proven in many monocots, but not yet studied in banana, a unique model crop. Banana is one of the staple food crops in developing countries and its production is highly influenced by various biotic and abiotic factors. Characterizing the expansin genes of the ancestor genome (M. acuminata and M. balbisiana) of present day cultivated banana will enlighten their role in growth and development, and stress responses. In the present study, 58 (MaEXPs) and 55 (MbaEXPs) putative expansin genes were identified in A and B genome, respectively, and were grouped in four subfamilies based on phylogenetic analysis. Gene structure and its duplications revealed that EXPA genes are highly conserved and are under negative selection whereas the presence of more number of introns in other subfamilies revealed that they are diversifying. Expression profiling of expansin genes showed a distinct expression pattern for biotic and abiotic stress conditions. This study revealed that among the expansin subfamilies, EXPAs contributed significantly towards stress-resistant mechanism. The differential expression of MaEXPA18 and MaEXPA26 under drought stress conditions in the contrasting cultivar suggested their role in drought-tolerant mechanism. Most of the MaEXPA genes are differentially expressed in the root lesion nematode contrasting cultivars which speculated that this expansin subfamily might be the susceptible factor. The downregulation of MaEXPLA6 in resistant cultivar during Sigatoka leaf spot infection suggested that by suppressing this gene, resistance may be enhanced in susceptible cultivar. Further, in-depth studies of these genes will lead to gain insight into their role in various stress conditions in banana.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-021-03106-x.

Specialized metabolites: Physiological and biochemical role in stress resistance, strategies to improve their accumulation, and new applications in crop breeding and management

Specialized plant metabolites (SPMs), traditionally referred to as 'secondary metabolites', are chemical compounds involved in a broad range of biological functions, including plant responses to abiotic and biotic stresses. Moreover, some of them have a role in end-product quality with potential health benefits in humans. For this reason, they became an important target of studies focusing on their mechanisms of action and use in crop breeding and management. In this review we summarize the specific role of SPMs in physiological processes and in plant resistance to abiotic and biotic stresses, and the different strategies to enhance their production/accumulation in plant tissues under stress, including genetic approaches (marker-assisted selection and biotechnological tools) and agronomic management (fertilizer applications, cultivation method and beneficial microorganisms). New crop management strategies based on the direct application of the most promising compounds in form of plant residuals or liquid formulations are also described.

Genome-wide identification and expression analysis of the coronatine-insensitive 1 (COI1) gene family in response to biotic and abiotic stresses in Saccharum

Background

The coronatine insensitive 1 (COI1) gene is the core member of jasmonate signaling pathway, which is closely related to plant biotic and abiotic resistance. However, there have been no reports on COI1 in sugarcane (Sacharum spp.). Hence, systematically investigating the characteristics of the COI1 multigene family in sugarcane can provide a means to study and manipulate the jasmonic acid signaling pathway.

Results

A total of 156 COI1 proteins were obtained from the genomes of 19 land plants, while none were obtained from five algae species. A phylogenetic tree demonstrated that these COI1 proteins were classified into four groups, while 31 proteins of SsCOI1 from Saccharum spontaneum, SbCOI1 from Sorghum bicolor, and ShCOI1 from Saccharum spp. hybrid cultivar R570 clustered into three groups. Synteny analysis and duplication patterns revealed that COI1 genes expanded through various genome replication events and could have experienced strong purifying selective pressure during evolution in S. spontaneum, S. bicolor, and R570. An investigation of cis-acting elements suggests that COI1 genes may be involved in plant growth and development and response to various stresses. Expression analysis implied that 21 SsCOI1 genes were constitutively expressed, and had positive responses to drought, cold, and Sporisorium scitamineum stresses with different expression patterns. Among them, seven SsCOI1 haplotype genes may play different roles in response to methyl jasmonate. Furthermore, the ShCOI1–4, ShCOI1–5, and ShCOI1–6 genes were cloned from Saccharum spp. hybrid cultivar ROC22. Real-time quantitative PCR (RT-qPCR) analysis demonstrated that these three ShCOI1 genes had divergent expression profiles in response to salicylic acid, abscisic acid, polyethylene glycol, cold, and S. scitamineum.

Conclusions

These results suggest that COI1 genes may act in sugarcane growth, development, and response to various stresses via different regulatory mechanisms, which laying a foundation for the functional identification of the sugarcane COI1 gene.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08255-0.

HD2-type histone deacetylases: unique regulators of plant development and stress responses

Plants have developed sophisticated and complex epigenetic regulation-based mechanisms to maintain stable growth and development under diverse environmental conditions. Histone deacetylases (HDACs) are important epigenetic regulators in eukaryotes that are involved in the deacetylation of lysine residues of histone H3 and H4 proteins. Plants have developed a unique HDAC family, HD2, in addition to the RPD3 and Sir2 families, which are also present in other eukaryotes. HD2s are well conserved plant-specific HDACs, which were first identified as nucleolar phosphoproteins in maize. The HD2 family plays important roles not only in fundamental developmental processes, including seed germination, root and leaf development, floral transition, and seed development but also in regulating plant responses to biotic and abiotic stresses. Some of the HD2 members coordinate with each other to function. The HD2 family proteins also show functional association with RPD3-type HDACs and other transcription factors as a part of repression complexes in gene regulatory networks involved in environmental stress responses. This review aims to analyse and summarise recent research progress in the HD2 family, and to describe their role in plant growth and development and in response to different environmental stresses.

Microbiome for sustainable agriculture: a review with special reference to the corn production system

Microbial diversity formed by ages of evolution in soils plays an important role in sustainability of crop production by enriching soil and alleviating biotic and abiotic stresses. This diversity is as an essential part of the agro-ecosystems, which is being pushed to edges by pumping agrochemicals and constant soil disturbances. Consequently, efficiency of cropping system has been decreasing, aggravated further by the increased incidence of abiotic stresses due to changes in climatic patterns. Thus, the sustainability of agriculture is at stake. Understanding the microbiota inhabiting phyllosphere, endosphere, spermosphere, rhizosphere, and non-rhizosphere, and its utilization could be a sustainable crop production strategy. This review explores the available information on diversity of beneficial microbes in agricultural ecosystem and synthesizes their commercial uses in agriculture. Microbiota in agro-ecosystem works by nutrient acquisition, enhancing nutrient availability, water uptake, and amelioration of abiotic and abiotic stresses. External application of such beneficial microbiota or microbial consortia helps in boosting plant growth and provides resistance to drought, salinity, heavy metal, high-temperature and radiation stress in various crop plants. These have been instrumental in enhancing tolerance to diseases, insect pest and nematodes in various cropping system. However, studies on the microbiome in revolutionary production systems like conservation agriculture and protected cultivation, which use lesser agrochemicals, are limited and if exploited can provide valuable input in sustainable agriculture production.

Genome-wide investigation and expression analysis of membrane-bound fatty acid desaturase genes under different biotic and abiotic stresses in sunflower (Helianthus annuus L.)

Membrane-bound fatty acid desaturase (FAD) gene family plays crucial roles in regulation of fatty acid (FA) compositions in plants. Sunflower (Helianthus annuus L.) is an important oilseed crop in the world; however, no comprehensive study on exploring the role of FAD family in relation to stress tolerance in sunflower has been performed yet. In this study, we identified 40 putative FAD genes in H. annuus (HaFAD), which were unevenly distributed across 13 of the total 17 chromosomes. Phylogenetic analysis indicated that HaFAD genes were divided into four subfamilies, as supported by highly conserved gene structures and motifs. Collinearity analysis showed that tandem duplication events played a crucial role in the expansion of HaFAD gene family. In addition, tissue-specific expression showed that 32 HaFAD genes were widely expressed in various tissues or organs of sunflower. Furthermore, qRT-PCR results revealed significant expression changes of HaFAD genes in response to abiotic (cadmium, drought) and biotic (Orobanche cumana) stresses, suggesting their important functions in response to different stresses. Therefore, our results provide insights into HaFAD gene family in response to different stresses, and some specific up-regulated genes such as HaFAD3.2, HaADS8, HaFAD2.1, and HaADS9 would be the potential candidate genes for the sunflower tolerance breeding.

Hydrogen sulfide (H(2)S) signaling in plant development and stress responses

ABSTRACT

Hydrogen sulfide (H₂S) was initially recognized as a toxic gas and its biological functions in mammalian cells have been gradually discovered during the past decades. In the latest decade, numerous studies have revealed that H₂S has versatile functions in plants as well. In this review, we summarize H₂S-mediated sulfur metabolic pathways, as well as the progress in the recognition of its biological functions in plant growth and development, particularly its physiological functions in biotic and abiotic stress responses. Besides direct chemical reactions, nitric oxide (NO) and hydrogen peroxide (H₂O₂) have complex relationships with H₂S in plant signaling, both of which mediate protein post-translational modification (PTM) to attack the cysteine residues. We also discuss recent progress in the research on the three types of PTMs and their biological functions in plants. Finally, we propose the relevant issues that need to be addressed in the future research.

GRAPHIC ABSTRACT

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s42994-021-00035-4.

ScAOC1, an allene oxide cyclase gene, confers defense response to biotic and abiotic stresses in sugarcane

KEY MESSAGE

An allene oxide cyclase gene which is involved in defense against biotic and abiotic stresses was cloned and characterized in sugarcane. Allene oxide cyclase (AOC), a key enzyme in jasmonate acid (JA) biosynthesis, affects the stereoisomerism and biological activity of JA molecules, and plays an important role in plant stress resistance. In this study, four SsAOC alleles (SsAOC1-SsAOC4), which shared similar gene structure and were located on Chr1A, Chr1B, Chr1C, and Chr1D, respectively, were mined from sugarcane wild species Saccharum spontaneum, and a homologous gene ScAOC1 (GenBank Accession Number: MK674849) was cloned from sugarcane hybrid variety Yacheng05-179 inoculated with Sporisorium scitamineum for 48 h. ScAOC1 and SsAOC1-SsAOC4 were alkaline, unstable, hydrophilic, and non-secretory proteins, which possess the same set of conserved motifs and were clustered into one group in the phylogenetic analysis. ScAOC1 was expressed in all sugarcane tissues, but with different levels. After infection by S. scitamineum, the transcripts of ScAOC1 were increased significantly both in the smut-susceptible (ROC22) and resistant (Yacheng05-179) varieties, but its transcripts were more accumulated and lasted for a longer period in the smut-resistant variety than in the smut-susceptible one. ScAOC1 was down-regulated under MeJA and NaCl treatments, but up-regulated under SA, ABA, PEG, and cold stresses. Transiently overexpressing ScAOC1 gene into Nicotiana benthamiana leaves regulated the responses of N. benthamiana to two pathogens Ralstonia solanacearum and Fusarium solani var. coeruleum. Furthermore, prokaryotic expression analysis showed overexpression of ScAOC1 in Escherichia coli BL21 could enhance its tolerance to NaCl, mannitol, and cold stimuli. These results indicated that ScAOC1 may play an active role in response to biotic and abiotic stresses in sugarcane.

Mechanisms of Sugar Beet Response to Biotic and Abiotic Stresses

Sugar beet is used not only in the sugar production, but also in a wide range of industries including the production of bioethanol as a source of renewable energy, extraction of pectin and production of molasses. The red beetroot has attracted much attention as health-promoting and disease-preventing functional food. The negative effects of environmental stresses, including abiotic and biotic ones, significantly decrease the cash crop sugar beet productivity. In this paper, we outline the mechanisms of sugar beet response to biotic and abiotic stresses at the levels of physiological change, the genes' functions, transcription and translation. Regarding the physiological changes, most research has been carried out on salt and drought stress. The functions of genes from sugar beet in response to salt, cold and heavy metal stresses were mainly investigated by transgenic technologies. At the transcriptional level, the transcriptome analysis of sugar beet in response to salt, cold and biotic stresses were conducted by RNA-Seq or SSH methods. At the translational level, more than 800 differentially expressed proteins in response to salt, K⁺/Na⁺ ratio, iron deficiency and resupply and heavy metal (zinc) stress were identified by quantitative proteomics techniques. Understanding how sugar beet respond and tolerate biotic and abiotic stresses is important for boosting sugar beet productivity under these challenging conditions. In order to minimize the negative impact of these stresses, studying how the sugar beet has evolved stress coping mechanisms will provide new insights and lead to novel strategies for improving the breeding of stress-resistant sugar beet and other crops.

Tomato MYB49 enhances resistance to Phytophthora infestans and tolerance to water deficit and salt stress

MYB49-overexpressing tomato plants showed significant resistance to Phytophthora infestans and tolerance to drought and salt stresses. This finding reveals the potential application of tomato MYB49 in future molecular breeding. Biotic and abiotic stresses severely reduce the productivity of tomato worldwide. Therefore, it is necessary to find key genes to simultaneously improve plant resistance to pathogens and tolerance to various abiotic stresses. In this study, based on homologous relationships with Arabidopsis R2R3-MYBs (AtMYBs) involved in responses to biotic and abiotic stresses, we identified a total of 24 R2R3-MYB transcription factors in the tomato genome. Among these tomato R2R3-MYBs, MYB49 (Solyc10g008700.1) was clustered into subgroup 11 by phylogenetic analysis, and its expression level was significantly induced after treatment with P. infestans, NaCl and PEG6000. Overexpression of MYB49 in tomato significantly enhanced the resistance of tomato to P. infestans, as evidenced by decreases in the number of necrotic cells, sizes of lesion, abundance of P. infestans, and disease index. Likewise, MYB49-overexpressing transgenic tomato plants also displayed increased tolerance to drought and salt stresses. Compared to WT plants, the accumulation of reactive oxygen species (ROS), malonaldehyde content, and relative electrolyte leakage was decreased, and peroxidase activity, superoxide dismutase activity, chlorophyll content, and photosynthetic rate were increased in MYB49-overexpressing tomato plants under P. infestans, salt or drought stress. These results suggested that tomato MYB49, as a positive regulator, could enhance the capacity to scavenge ROS, inhibit cell membrane damage and cell death, and protect chloroplasts, resulting in an improvement in resistance to P. infestans and tolerance to salt and drought stresses, and they provide a candidate gene for tomato breeding to enhance biotic stress resistance and abiotic stress tolerance.

Genome-wide identification and analysis of WD40 proteins in wheat (Triticum aestivum L.)

BACKGROUND

WD40 domains are abundant in eukaryotes, and they are essential subunits of large multiprotein complexes, which serve as scaffolds. WD40 proteins participate in various cellular processes, such as histone modification, transcription regulation, and signal transduction. WD40 proteins are regarded as crucial regulators of plant development processes. However, the systematic identification and analysis of WD40 proteins have yet to be reported in wheat.

RESULTS

In this study, a total of 743 WD40 proteins were identified in wheat, and they were grouped into 5 clusters and 11 subfamilies. Their gene structures, chromosomal locations, and evolutionary relationships were analyzed. Among them, 39 and 46 pairs of TaWD40s were distinguished as tandem duplication and segmental duplication genes. The 123 OsWD40s were identified to exhibit synteny with TaWD40s. TaWD40s showed the specific characteristics at the reproductive developmental stage, and numerous TaWD40s were involved in responses to stresses, including cold, heat, drought, and powdery mildew infection pathogen, based on the result of RNA-seq data analysis. The expression profiles of some TaWD40s in wheat seed development were confirmed through qRT-PCR technique.

CONCLUSION

In this study, 743 TaWD40s were identified from the wheat genome. As the main driving force of evolution, duplication events were observed, and homologous recombination was another driving force of evolution. The expression profiles of TaWD40s revealed their importance for the growth and development of wheat and their response to biotic and abiotic stresses. Our study also provided important information for further functional characterization of some WD40 proteins in wheat.

Combinatorial Interactions of Biotic and Abiotic Stresses in Plants and Their Molecular Mechanisms: Systems Biology Approach

Plants are continually facing biotic and abiotic stresses, and hence, they need to respond and adapt to survive. Plant response during multiple and combined biotic and abiotic stresses is highly complex and varied than the individual stress. These stresses resulted alteration of plant behavior through regulating the levels of microRNA, heat shock proteins, epigenetic variations. These variations can cause many adverse effects on the growth and development of the plant. Further, in natural conditions, several abiotic stresses causing factors make the plant more susceptible to pathogens infections and vice-versa. A very intricate and multifaceted interactions of various biomolecules are involved in metabolic pathways that can direct towards a cross-tolerance and improvement of plant's defence system. Systems biology approach plays a significant role in the investigation of these molecular interactions. The valuable information obtained by systems biology will help to develop stress-resistant plant varieties against multiple stresses. Thus, this review aims to decipher various multilevel interactions at the molecular level under combinatorial biotic and abiotic stresses and the role of systems biology to understand these molecular interactions.

Characterization and Alternative Splicing Profiles of the Lipoxygenase Gene Family in Tea Plant (Camellia sinensis)

Oxylipins, including jasmonic acid (JA) and volatiles, are important for signaling in plants, and these are formed by the lipoxygenase (LOX) enzyme family. There is a large gap in understanding of the underlying molecular basis of their roles in tea plants. Here, we identified 11 CsLOX genes from the tea plant (Camellia sinensis), and characterized their phylogeny, gene structure and protein features into three subclasses. We then examined their enzymatic activities, LOX expression and alternative splicing of transcripts during development and in response to abiotic or biotic stresses in tea plants. In vitro expressed protein assays showed that the CsLOX2, 3 and 9 enzymatically function to produce 9/13-HPOT, 13-HPOT and 9-HPOT, respectively. CsLOX2 and CsLOX9 green fluorescent protein (GFP) fusion proteins localized to chloroplasts and the cytoplasm, respectively. RNA sequencing, quantitative reverse transcription-PCR and Northern blot analysis suggested that CsLOX5, 6 and 9 were predominantly expressed in seeds, flowers and roots, respectively. CsLOX2, 3, 4, 6 and 7 were up-regulated after attack by the insect Ectropis oblique, while CsLOX1 was induced after infection with the pathogen Glomerella cingulata. CsLOX3, 7 and 10 were up-regulated by JA but not ABA or salicylic acid. Long-term cold stress down-regulated CsLOX expression while a short duration of cold induced the expression of CsLOX1, 6 and 7. Alternatively spliced transcripts of six CsLOX genes were dynamically regulated through time and varied in relative abundances under the investigated stresses; we propose a mechanism of competing or compensating regulation between isoforms. This study improves our understanding of evolution of LOXs and regulation of their diverse functions in plants.

Silicon (Si): Review and future prospects on the action mechanisms in alleviating biotic and abiotic stresses in plants

In the era present, due to increasing incidences of a large number of different biotic and abiotic stresses all over the world, the growth of plants (principal crops) may be restrained by these stresses. In addition to beneficial microorganisms, use of silicon (Si)-fertilizer is known as an ecologically compatible and environmentally friendly technique to stimulate plant growth, alleviate various biotic and abiotic stresses in plants, and enhance the plant resistance to multiple stresses, because Si is not harmful, corrosive, and polluting to plants when presents in excess. Here, we reviewed the action mechanisms by which Si alleviates abiotic and biotic stresses in plants. The use of Si (mostly as industrial slags and rice straw) is predicted to become a sustainable strategy and an emerging trend in agriculture to enhance crop growth and alleviate abiotic and biotic stresses in the not too distant future. In this review article, the future research needs on the use of Si under the conditions of abiotic and biotic stresses are also highlighted.

Genome-wide characterization and expression profiling of PDI family gene reveals function as abiotic and biotic stress tolerance in Chinese cabbage (Brassica rapa ssp. pekinensis)

Background

Protein disulfide isomerase (PDI) and PDI-like proteins contain thioredoxin domains that catalyze protein disulfide bond, inhibit aggregation of misfolded proteins, and function in isomerization during protein folding in endoplasmic reticulum and responses during abiotic stresses.Chinese cabbage is widely recognized as an economically important, nutritious vegetable, but its yield is severely hampered by various biotic and abiotic stresses. Because of, it is prime need to identify those genes whose are responsible for biotic and abiotic stress tolerance. PDI family genes are among of them.

Results

We have identified 32 PDI genes from the Br135K microarray dataset, NCBI and BRAD database, and in silico characterized their sequences. Expression profiling of those genes was performed using cDNA of plant samples imposed to abiotic stresses; cold, salt, drought and ABA (Abscisic Acid) and biotic stress; Fusarium oxysporum f. sp. conglutinans infection. The Chinese cabbage PDI genes were clustered in eleven groups in phylogeny. Among them, 15 PDI genes were ubiquitously expressed in various organs, while 24 PDI genes were up-regulated under salt and drought stress. By contrast, cold and ABA stress responsive gene number were ten and nine, respectively. In case of F. oxysporum f. sp. conglutinans infection 14 BrPDI genes were highly up-regulated. Interestingly, BrPDI1–1 gene was identified as putative candidate against abiotic (salt and drought) and biotic stresses, BrPDI5–2 gene for ABA stress, and BrPDI1–4, 6–1 and 9–2 were putative candidate genes for both cold and chilling injury stresses.

Conclusions

Our findings help to elucidate the involvement of PDI genes in stress responses, and they lay the foundation for functional genomics in future studies and molecular breeding of Brassica rapa crops. The stress-responsive PDI genes could be potential resources for molecular breeding of Brassica crops resistant to biotic and abiotic stresses.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4277-2) contains supplementary material, which is available to authorized users.

A sugarcane pathogenesis-related protein, ScPR10, plays a positive role in defense responses under Sporisorium scitamineum, SrMV, SA, and MeJA stresses

KEY MESSAGE

A pathogenesis-related gene, ScPR10 , was isolated from sugarcane and its bio-function was characterized, demonstrating that ScPR10 was involved in plant defense responses to Sporisorium scitamineum , SrMV, SA, and MeJA stresses. Plant fungal and viral diseases are the major concerns in sugarcane industry. Many anti-fungal and antivirus components, including pathogenesis-related (PR) proteins, have been identified. The pathogenesis-related protein 10 (PR10) is the dominant group in PR families, involved in the plant defense mechanism. In this study, ScPR10 (GenBank Acc. No. KT887884), a 701-bp-length PR10 gene with a 483 bp-length open reading frame, was isolated from sugarcane. Its transient expression in the leaves of Nicotiana benthamiana indicated that the function role of ScPR10 is likely in the nucleus, and it increased the level of H2O2 accumulation in leaf cells. Moreover, ScPR10 could also enhance the resistance of N. benthamiana leaves to infection by Pseudomonas solanacearum and Fusarium solani var. coeruleum. Quantitative real-time PCR analysis revealed that ScPR10 was not constitutively expressed in sugarcane tissues due to its high expression in the buds and scant presence in root tips. In addition, the transcript of ScPR10 could be induced by a pathogenic fungus (Sporisorium scitamineum) and a virus (Sorghum mosaic virus, SrMV) in the resistant sugarcane cultivars, while it was down-regulated in the susceptible ones. After exposure to salicylic acid (SA) and methyl jasmonate (MeJA), ScPR10 peaked at 6 and 12 h, respectively. These results suggest that ScPR10 can play a positive role in sugarcane defense responses to S. scitamineum, SrMV, SA, and MeJA stresses.

Characterization of triterpenoid profiles and triterpene synthase expression in the leaves of eight Vitis vinifera cultivars grown in the Upper Rhine Valley

Plant triterpenoids are a diverse group of secondary metabolites with wide distribution, high chemical diversity and interesting pharmacological and antimicrobial properties. The first step in the biosynthesis of all triterpenoids is the cyclization of the 2,3-oxidosqualene precursor, catalyzed by oxidosqualene cyclases (OSCs), which have characteristic product specificities. Biosynthesis and functions of pentacyclic triterpenes have been poorly studied in grapevine. In this study, we first investigated the profile of triterpenoids present in leaf cuticular waxes from eight Vitis vinifera cultivars cultivated in the Upper Rhine Valley. Further quantification of triterpenoids showed that these cultivars can be divided into two groups, characterized by high levels of lupeol (e.g., Pinot noir) or taraxerol (e.g., Gewurztraminer) respectively. We further analyzed the OSC family involved in the synthesis of pentacyclic triterpenes (called VvTTPSs) in the sequenced V. vinifera 40024 genome and found nine genes with similarity to previously characterized triterpene synthases. Phylogenetic analysis further showed that VvTTPS1-VvTTPS3 and VvTTPS5-VvTTPS9 belong to the β-amyrin synthase and multifunctional triterpene synthase clade, whereas VvTTPS10 belongs to the lupeol synthase clade. We studied the expression of several members of the VvTTPS family following biotic and abiotic stresses in V. vinifera 40024 as well as in the eight healthy cultivars. This study further revealed that one candidate gene, VvTTPS5, which does not belong to the lupeol synthase clade, is highly expressed in lupeol-rich cultivars. VvTTPS3, VvTTPS5, VvTTPS6, VvTTPS7 and VvTTPS10 were highly upregulated by UV stress, but only VvTTPS3, VvTTPS5, VvTTPS6 and VvTTPS10 were upregulated following downy mildew and gray mold infections respectively. These results suggest differential roles of VvTTPS against environmental stresses in grape leaves.