Comprehensive analyses of the annexin gene family in wheat

The Evolution, Expression Patterns, and Domestication Selection Analysis of the Annexin Gene Family in the Barley Pan-Genome

Plant annexins constitute a conserved protein family that plays crucial roles in regulating plant growth and development, as well as in responses to both biotic and abiotic stresses. In this study, a total of 144 annexin genes were identified in the barley pan-genome, comprising 12 reference genomes, including cultivated barley, landraces, and wild barley. Their chromosomal locations, physical-chemical characteristics, gene structures, conserved domains, and subcellular localizations were systematically analyzed to reveal the certain differences between wild and cultivated populations. Through a cis-acting element analysis, co-expression network, and large-scale transcriptome analysis, their involvement in growth, development, and responses to various stressors was highlighted. It is worth noting that HvMOREXann5 is only expressed in pistils and anthers, indicating its crucial role in reproductive development. Based on the resequencing data from 282 barley accessions worldwide, genetic variations in thefamily were investigated, and the results showed that 5 out of the 12 identified HvMOREXanns were affected by selection pressure. Genetic diversity and haplotype frequency showed notable reductions between wild and domesticated barley, suggesting that a genetic bottleneck occurred on the annexin family during the barley domestication process. Finally, qRT-PCR analysis confirmed the up-regulation of HvMOREXann7 under drought stress, along with significant differences between wild accessions and varieties. This study provides some insights into the genome organization and genetic characteristics of the annexin gene family in barley at the pan-genome level, which will contribute to better understanding its evolution and function in barley and other crops.

Genome-Wide Identification of the GhANN Gene Family and Functional Validation of GhANN11 and GhANN4 under Abiotic Stress

Annexins (ANNs) are a structurally conserved protein family present in almost all plants. In the present study, 27 GhANNs were identified in cotton and were unevenly distributed across 14 chromosomes. Transcriptome data and RT-qPCR results revealed that multiple GhANNs respond to at least two abiotic stresses. Similarly, the expression levels of GhANN4 and GhANN11 were significantly upregulated under heat, cold, and drought stress. Using virus-induced gene silencing (VIGS), functional characterization of GhANN4 and GhANN11 revealed that, compared with those of the controls, the leaf wilting of GhANN4-silenced plants was more obvious, and the activities of catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD) were lower under NaCl and PEG stress. Moreover, the expression of stress marker genes (GhCBL3, GhDREB2A, GhDREB2C, GhPP2C, GhRD20-2, GhCIPK6, GhNHX1, GhRD20-1, GhSOS1, GhSOS2 and GhSnRK2.6) was significantly downregulated in GhANN4-silenced plants after stress. Under cold stress, the growth of the GHANN11-silenced plants was significantly weaker than that of the control plants, and the activities of POD, SOD, and CAT were also lower. However, compared with those of the control, the elasticity and orthostatic activity of the GhANN11-silenced plants were greater; the POD, SOD, and CAT activities were higher; and the GhDREB2C, GhHSP, and GhSOS2 expression levels were greater under heat stress. These results suggest that different GhANN family members respond differently to different types of abiotic stress.

Comprehensive analysis of annexin gene family and its expression in response to branching architecture and salt stress in crape myrtle

BACKGROUND

Annexin (ANN) is calcium (Ca2+)-dependent and phospholipid binding protein family, which is involved in plant growth and development and response to various stresses. However, little known about ANN genes were identified from crape myrtle, an ornamental horticultural plant widely cultivated in the world.

RESULTS

Here, 9 LiANN genes were identified from Lagerstroemia indica, and their characterizations and functions were investigated in L. indica for the first time. The LiANN genes were divided into 2 subfamilies. The gene structure, chromosomal location, and collinearity relationship were also explored. In addition, the GO annotation analysis of these LiANNs indicated that they are enriched in molecular functions, cellular components, and biological processes. Moreover, transcription factors (TFs) prediction analysis revealed that bHLH, MYB, NAC, and other TFs can interact with the LiANN promoters. Interestingly, the LiANN2/4/6-9 were demonstrated to play critical roles in the branching architecture of crape myrtle. Furthermore, the LiANN2/6/8/9 were differentially expressed under salt treatment, and a series of TFs regulating LiANN2/6/8/9 expression were predicted to play essential roles in salt resistance.

CONCLUSIONS

These results shed light on profile and function of the LiANN gene family, and lay a foundation for further studies of the LiANN genes.

Calcium Signaling and the Response to Heat Shock in Crop Plants

Climate change and the increasing frequency of high temperature (HT) events are significant threats to global crop yields. To address this, a comprehensive understanding of how plants respond to heat shock (HS) is essential. Signaling pathways involving calcium (Ca2+), a versatile second messenger in plants, encode information through temporal and spatial variations in ion concentration. Ca2+ is detected by Ca2+-sensing effectors, including channels and binding proteins, which trigger specific cellular responses. At elevated temperatures, the cytosolic concentration of Ca2+ in plant cells increases rapidly, making Ca2+ signals the earliest response to HS. In this review, we discuss the crucial role of Ca2+ signaling in raising plant thermotolerance, and we explore its multifaceted contributions to various aspects of the plant HS response (HSR).

The Wheat Annexin TaAnn12 Plays Positive Roles in Plant Disease Resistance by Regulating the Accumulation of Reactive Oxygen Species and Callose

(1) Annexins are proteins that bind phospholipids and calcium ions in cell membranes and mediate signal transduction between Ca2+ and cell membranes. They play key roles in plant immunity. (2) In this study, virus mediated gene silencing and the heterologous overexpression of TaAnn12 in Arabidopsis thaliana Col-0 trials were used to determine whether the wheat annexin TaAnn12 plays a positive role in plant disease resistance. (3) During the incompatible interaction between wheat cv. Suwon 11 and the Puccinia striiformis f. sp. tritici (Pst) race CYR23, the expression of TaAnn12 was significantly upregulated at 24 h post inoculation (hpi). Silencing TaAnn12 in wheat enhanced the susceptibility to Pst. The salicylic acid hormone contents in the TaAnn12-silenced plants were significantly reduced. The overexpression of TaAnn12 in A. thaliana significantly increased resistance to Pseudomonas syringae pv. tomato DC3000, and the symptoms of the wild-type plants were more serious than those of the transgenic plants; the amounts of bacteria were significantly lower than those in the control group, the accumulation of Reactive Oxygen Species (ROS)and callose deposition increased, and the expression of resistance-related genes (AtPR1, AtPR2, and AtPR5) significantly increased. (4) Our results suggest that wheat TaAnn12 resisted the invasion of pathogens by inducing the production and accumulation of ROS and callose.

Genome-wide analysis of annexin gene family in Schrenkiella parvula and Eutrema salsugineum suggests their roles in salt stress response

Annexins (Anns) play an important role in plant development, growth and responses to various stresses. Although Ann genes have been characterized in some plants, their role in adaptation mechanisms and tolerance to environmental stresses have not been studied in extremophile plants. In this study, Ann genes in Schrenkiella parvula and Eutrema salsugineum were identified using a genome-wide method and phylogenetic relationships, subcellular distribution, gene structures, conserved residues and motifs and also promoter prediction have been studied through bioinformatics analysis. We identified ten and eight encoding putative Ann genes in S. parvula and E. salsugineum genome respectively, which were divided into six subfamilies according to phylogenetic relationships. By observing conservation in gene structures and protein motifs we found that the majority of Ann members in two extremophile plants are similar. Furthermore, promoter analysis revealed a greater number of GATA, Dof, bHLH and NAC transcription factor binding sites, as well as ABRE, ABRE3a, ABRE4, MYB and Myc cis-acting elements in compare to Arabidopsis thaliana. To gain additional insight into the putative roles of candidate Ann genes, the expression of SpAnn1, SpAnn2 and SpAnn6 in S. parvula was studied in response to salt stress, which indicated that their expression level in shoot increased. Similarly, salt stress induced expression of EsAnn1, 5 and 7, in roots and EsAnn1, 2 and 5 in leaves of E. salsugineum. Our comparative analysis implies that both halophytes have different regulatory mechanisms compared to A. thaliana and suggest SpAnn2 gene play important roles in mediating salt stress.

A critical review on plant annexin: Structure, function, and mechanism

Plant annexins are evolutionary conserved protein family widely exist in almost all plant species, characterized by a shorter N-terminal region and four conservative annexin repeats. Plant annexins have Ca²⁺ channel-regulating activity and peroxidase as well as ATPase/GTPase activities, which give annexins functional specificity. They are widely involved in regulating diverse aspects of biochemical and cellular processes, plant growth and development, and responses to biotic and abiotic environmental stresses. Though many studies have reviewed the function of annexins, great progress have been made in the study of plant annexins recently. In this review, we outline the current understanding of basic properties of plant annexins and summarize the emerging advances in understanding the functional roles of annexins in plants and highlight the regulation mechanisms of annexin protein in response to stress especially to salt and cold stress. The interesting questions related to plant annexin that remain to be further elucidated are also discussed.

Genome-wide identification and expression analysis of the annexin gene family in rye (Secale cereale L.)

Rye (Secale cereale L.) is one of the major cereal crops belonging to the family Triticeae and is known to be most tolerant to diverse abiotic stresses, such as cold, heat, osmotic, and salt stress. With the advancements in sequencing and bioinformatics technologies, the sequence information for the large and repetitive rye genome has become available. Plant annexins are components of the calcium signaling network that regulate signaling in abiotic stress tolerance via Ca²⁺ transport. In this study, we identified 12 novel rye annexin gene families by investigating the recently published rye genome. The annexin gene families were classified into five groups according to phylogenetic conserved motif analyses. Cis-element analysis revealed that these genes may be regulated by light, ABA, MeJA, and MYB transcription factors. Chromosome localization of the genes revealed that the gene family was conserved in many species, and high synteny was observed between the rye and wheat annexin genes. Plant tissue-specific gene expression revealed that rye annexin genes are mostly expressed in the roots, and gene expression analysis under cold, heat, PEG, and NaCl treatments showed that the genes were differentially expressed in response to different types of stresses, suggesting that each gene has a distinct role in stress signaling. The findings of this study provide a basis for further research on the role of rye annexin genes in abiotic stress signaling.

Systematic Analysis and Identification of Drought-Responsive Genes of the CAMTA Gene Family in Wheat (Triticum aestivum L.)

The calmodulin-binding transcription activator (CAMTA) is a Ca²⁺/CaM-mediated transcription factor (TF) that modulates plant stress responses and development. Although the investigations of CAMTAs in various organisms revealed a broad range of functions from sensory mechanisms to physiological activities in crops, little is known about the CAMTA family in wheat (Triticum aestivum L.). Here, we systematically analyzed phylogeny, gene expansion, conserved motifs, gene structure, cis-elements, chromosomal localization, and expression patterns of CAMTA genes in wheat. We described and confirmed, via molecular evolution and functional verification analyses, two new members of the family, TaCAMTA5-B.1 and TaCAMTA5-B.2. In addition, we determined that the expression of most TaCAMTA genes responded to several abiotic stresses (drought, salt, heat, and cold) and ABA during the seedling stage, but it was mainly induced by drought stress. Our study provides considerable information about the changes in gene expression in wheat under stress, notably that drought stress-related gene expression in TaCAMTA1b-B.1 transgenic lines was significantly upregulated under drought stress. In addition to providing a comprehensive view of CAMTA genes in wheat, our results indicate that TaCAMTA1b-B.1 has a potential role in the drought stress response induced by a water deficit at the seedling stage.

Genome-Wide Characterization and Abiotic Stresses Expression Analysis of Annexin Family Genes in Poplar

Poplar is an illustrious industrial woody plant with rapid growth, providing a range of materials, and having simple post-treatment. Various kinds of environmental stresses limit its output. Plant annexin (ANN) is a calcium-dependent phospholipid-binding protein involved in plant metabolism, growth and development, and cooperatively regulating drought resistance, salt tolerance, and various stress responses. However, the features of the PtANN gene family and different stress responses remain unknown in poplar. This study identified 12 PtANN genes in the P. trichocarpa whole-genome and PtANNs divided into three subfamilies based on the phylogenetic tree. The PtANNs clustered into the same clade shared similar gene structures and conserved motifs. The 12 PtANN genes were located in ten chromosomes, and segmental duplication events were illustrated as the main duplication method. Additionally, the PtANN4 homogenous with AtANN1 was detected localized in the cytoplasm and plasma membrane. In addition, expression levels of PtANNs were induced by multiple abiotic stresses, which indicated that PtANNs could widely participate in response to abiotic stress. These results revealed the molecular evolution of PtANNs and their profiles in response to abiotic stress.

The durum wheat annexin, TdAnn6, improves salt and osmotic stress tolerance in Arabidopsis via modulation of antioxidant machinery

TdAnn6 is a gene encoding an annexin protein in durum wheat (Triticum durum). The function of TdAnn6 in plant response to stress is not yet clearly understood. Here, we isolated TdAnn6 and characterized it in genetically modified Arabidopsis thaliana. Expressing TdAnn6 in Arabidopsis coincided with an improvement in stress tolerance at germination and seedling stages. In addition, TdAnn6-expressing seedling antioxidant activities were improved with lower level of malondialdehyde, and enhanced transcript levels of six stress-related genes during salt/osmotic stresses. Under greenhouse conditions, the TdAnn6 plants exhibited increased tolerance to salt or drought stress. To deepen our understanding of TdAnn6 function, we isolated a 1515-bp genomic fragment upstream of its coding sequence, designated as PrTdAnn6. The PrTdAnn6 promoter was fused to the β-glucuronidase reporter gene and transferred to Arabidopsis. By histochemical GUS staining, GUS activity was detected in the roots, leaves, and floral organs, but no activity was detected in the seeds. Furthermore, we noticed a high stimulation of promoter activity when A. thaliana seedlings were exposed to NaCl, mannitol, ABA, GA, and cold conditions. This cross-talk between tissue-specific expression and exogenous stress stimulation may provide additional layers of regulation for salt and osmotic stress responses in crops.

Characterization of Annexin gene family and functional analysis of RsANN1a involved in heat tolerance in radish (Raphanus sativus L.)

Plant annexins are a kind of conserved Ca²⁺-dependent phospholipid-binding proteins which are involved in plant growth, development and stress tolerance. Radish is an economically important annual or biennial root vegetable crop worldwide. However, the genome-wide characterization of annexin (RsANN) gene family remain largely unexplored in radish. In this study, a comprehensive identification of annexin gene family was performed at the whole genome level in radish. In total, ten RsANN genes were identified, and these putative RsANN proteins shared typical characteristics of the annexin family proteins. Phylogenetic analysis showed that the RsANNs together with annexin from Arabidopsis and rice were clustered into five groups with shared similar motif patterns. Chromosomal localization showed that these ten RsANN genes were distributed on six chromosomes (R3-R8) of radish. Several cis-elements involved in abiotic stress response were identified in the promoter regions of RsANN genes. Expression profile analysis indicated that the RsANN genes exhibited tissue-specific patterns at different growth stages and tissues. The Real-time quantitative PCR (RT-qPCR) revealed that the expression of most RsANN genes was induced under various abiotic stresses including heat, drought, salinity, oxidization and ABA stress. In addition, stress assays showed that overexpression of RsANN1a improved plant's growth and heat tolerance, while artificial microRNAs (amiRNA)-mediated knockdown of RsANN1a caused dramatically decreased survival ratio of Arabidopsis plants. These findings not only demonstrate that RsANN1a might play a critical role in the heat stress response of radish, but also facilitate clarifying the molecular mechanism of RsANN genes in regulating the biological process governing plant growth and development.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01056-5.

Genome-Wide Identification and Transcriptional Expression Analysis of Annexin Genes in Capsicum annuum and Characterization of CaAnn9 in Salt Tolerance

Annexin (Ann) is a polygenic, evolutionarily conserved, calcium-dependent and phospholipid-binding protein family, which plays key roles in plant growth, development, and stress response. However, a comprehensive understanding of CaAnn genes of pepper (Capsicum annuum) at the genome-wide level is limited. Based on the available pepper genomic information, we identified 15 members of the CaAnn gene family. Phylogenetic analysis showed that CaAnn proteins could be categorized into four different orthologous groups. Real time quantitative RT-PCR analysis showed that the CaAnn genes were tissue-specific and were widely expressed in pepper leaves after treatments with cold, salt, and drought, as well as exogenously applied MeJA and ABA. In addition, the function of CaAnn9 was further explored using the virus-induced gene silencing (VIGS) technique. CaAnn9-silenced pepper seedlings were more sensitive to salt stress, reflected by the degradation of chlorophyll, the accumulation of reactive oxygen species (ROS), and the decrease of antioxidant defense capacity. This study provides important information for further study of the role of pepper CaAnn genes and their coding proteins in growth, development, and environmental responses.

ANNEXIN1 mediates calcium-dependent systemic defense in Arabidopsis plants upon herbivory and wounding

Cellular calcium (Ca) transients are endogenous signals involved in local and systemic signaling and defense activation upon environmental stress, including wounding and herbivory. Still, not all Ca²⁺ channels contributing to the signaling have been identified, nor are their modes of action fully known. Plant annexins are proteins capable of binding to anionic phospholipids and can exhibit Ca channel-like activity. Arabidopsis ANNEXIN1 (ANN1) is suggested to contribute to Ca transport. Here, we report that wounding and simulated-herbivory-induced cytosolic free Ca elevation was impaired in systemic leaves in ann1 loss-of-function plants. We provide evidence for a role of ANN1 in local and systemic defense of plants attacked by herbivorous Spodoptera littoralis larvae. Bioassays identified ANN1 as a positive defense regulator. Spodoptera littoralis feeding on ann1 gained significantly more weight than larvae feeding on wild-type, whereas those feeding on ANN1-overexpressing lines gained less weight. Herbivory and wounding both induced defense-related responses on treated leaves, such as jasmonate accumulation and defense gene expression. These responses remained local and were strongly reduced in systemic leaves in ann1 plants. Our results indicate that ANN1 plays an important role in activation of systemic rather than local defense in plants attacked by herbivorous insects.

Overexpression of Cassava MeAnn2 Enhances the Salt and IAA Tolerance of Transgenic Arabidopsis

Annexins are a superfamily of soluble calcium-dependent phospholipid-binding proteins that have considerable regulatory effects in plants, especially in response to adversity and stress. The Arabidopsis thaliana AtAnn1 gene has been reported to play a significant role in various abiotic stress responses. In our study, the cDNA of an annexin gene highly similar to AtAnn1 was isolated from the cassava genome and named MeAnn2. It contains domains specific to annexins, including four annexin repeat sequences (I–IV), a Ca²⁺-binding sequence, Ca²⁺-independent membrane-binding-related tryptophan residues, and a salt bridge-related domain. MeAnn2 is localized in the cell membrane and cytoplasm, and it was found to be preferentially expressed in the storage roots of cassava. The overexpression of MeAnn2 reduced the sensitivity of transgenic Arabidopsis to various Ca²⁺, NaCl, and indole-3-acetic acid (IAA) concentrations. The expression of the stress resistance-related gene AtRD29B and auxin signaling pathway-related genes AtIAA4 and AtLBD18 in transgenic Arabidopsis was significantly increased under salt stress, while the Malondialdehyde (MDA) content was significantly lower than that of the control. These results indicate that the MeAnn2 gene may increase the salt tolerance of transgenic Arabidopsis via the IAA signaling pathway.

Genome-wide association study and gene network analyses reveal potential candidate genes for high night temperature tolerance in rice

High night temperatures (HNT) are shown to significantly reduce rice (Oryza sativa L.) yield and quality. A better understanding of the genetic architecture of HNT tolerance will help rice breeders to develop varieties adapted to future warmer climates. In this study, a diverse indica rice panel displayed a wide range of phenotypic variability in yield and quality traits under control night (24 °C) and higher night (29 °C) temperatures. Genome-wide association analysis revealed 38 genetic loci associated across treatments (18 for control and 20 for HNT). Nineteen loci were detected with the relative changes in the traits between control and HNT. Positive phenotypic correlations and co-located genetic loci with previously cloned grain size genes revealed common genetic regulation between control and HNT, particularly grain size. Network-based predictive models prioritized 20 causal genes at the genetic loci based on known gene/s expression under HNT in rice. Our study provides important insights for future candidate gene validation and molecular marker development to enhance HNT tolerance in rice. Integrated physiological, genomic, and gene network-informed approaches indicate that the candidate genes for stay-green trait may be relevant to minimizing HNT-induced yield and quality losses during grain filling in rice by optimizing source-sink relationships.

Heat Sensing and Lipid Reprograming as a Signaling Switch for Heat Stress Responses in Wheat

Temperature is an essential physical factor that affects the plant life cycle. Almost all plant species have evolved a robust signal transduction system that enables them to sense changes in the surrounding temperature, relay this message and accordingly adjust their metabolism and cellular functions to avoid heat stress-related damage. Wheat (Triticum aestivum), being a cool-season crop, is very sensitive to heat stress. Any increase in the ambient temperature, especially at the reproductive and grain-filling stages, can cause a drastic loss in wheat yield. Heat stress causes lipid peroxidation due to oxidative stress, resulting in the damage of thylakoid membranes and the disruption of their function, which ultimately decreases photosynthesis and crop yield. The cell membrane/plasma membrane plays prominent roles as an interface system that perceives and translates the changes in environmental signals into intracellular responses. Thus, membrane lipid composition is a critical factor in heat stress tolerance or susceptibility in wheat. In this review, we elucidate the possible involvement of calcium influx as an early heat stress-responsive mechanism in wheat plants. In addition, the physiological implications underlying the changes in lipid metabolism under high-temperature stress in wheat and other plant species will be discussed. In-depth knowledge about wheat lipid reprograming can help develop heat-tolerant wheat varieties and provide approaches to solve the impact of global climate change.

Comprehensive analyses of the annexin (ANN) gene family in Brassica rapa, Brassica oleracea and Brassica napus reveals their roles in stress response

Annexins (ANN) are a multigene, evolutionarily conserved family of calcium-dependent and phospholipid-binding proteins that play important roles in plant development and stress resistance. However, a systematic comprehensive analysis of ANN genes of Brassicaceae species (Brassica rapa, Brassica oleracea, and Brassica napus) has not yet been reported. In this study, we identified 13, 12, and 26 ANN genes in B. rapa, B. oleracea, and B. napus, respectively. About half of these genes were clustered on various chromosomes. Molecular evolutionary analysis showed that the ANN genes were highly conserved in Brassicaceae species. Transcriptome analysis showed that different group ANN members exhibited varied expression patterns in different tissues and under different (abiotic stress and hormones) treatments. Meanwhile, same group members from Arabidopsis thaliana, B. rapa, B. oleracea, and B. napus demonstrated conserved expression patterns in different tissues. The weighted gene coexpression network analysis (WGCNA) showed that BnaANN genes were induced by methyl jasmonate (MeJA) treatment and played important roles in jasmonate (JA) signaling and multiple stress response in B. napus.

Comprehensive Atlas of Wheat (Triticum aestivum L.) AUXIN RESPONSE FACTOR Expression During Male Reproductive Development and Abiotic Stress

AUXIN RESPONSE FACTOR (ARF) proteins regulate a wide range of signaling pathways, from general plant growth to abiotic stress responses. Here, we performed a genome-wide survey in wheat (Triticum aestivum) and identified 69 TaARF members that formed 24 homoeologous groups. Phylogenetic analysis clustered TaARF genes into three clades, similar to ARF genes in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa). Structural characterization suggested that ARF gene structure and domain composition are well conserved between plant species. Expression profiling revealed diverse patterns of TaARF transcript levels across a range of developmental stages, tissues, and abiotic stresses. A number of TaARF genes shared similar expression patterns and were preferentially expressed in anthers. Moreover, our systematic analysis identified three anther-specific TaARF genes (TaARF8, TaARF9, and TaARF21) whose expression was significantly altered by low temperature in thermosensitive genic male-sterile (TGMS) wheat; these TaARF genes are candidates to participate in the cold-induced male sterility pathway, and offer potential applications in TGMS wheat breeding and hybrid seed production. Moreover, we identified putative functions for a set of TaARFs involved in responses to abscisic acid and abiotic stress. Overall, this study characterized the wheat ARF gene family and generated several hypotheses for future investigation of ARF function during anther development and abiotic stress.

Insights into plant annexins function in abiotic and biotic stress tolerance

Crop productivity depends heavily on several biotic and abiotic factors. Plant annexins are a multigene family of calcium-dependent phospholipid-binding proteins that function in response to environmental stresses and signaling during growth and development of plants. We recently isolated and characterized a Triticum durum annexin, called TdANN12, which is upregulated by different abiotic stresses. Overexpression of TdANN12 in transgenic tobacco improves stress tolerance through ROS removal. This mini-review outlines the functional characterization of plant annexin genes and suggests how these features could be exploitated to improve stress tolerance in plants. Furthermore, transgenic overexpression of plant annexin genes in crops (tobacco, tomato, rice, alfalfa, cotton, and potato) will be discussed as a promising approach to acquire abiotic and biotic stress tolerance.

Genome-Wide Identification and Expression Profiles of Late Embryogenesis-Abundant (LEA) Genes during Grain Maturation in Wheat (Triticum aestivum L.)

Late embryogenesis-abundant (LEA) genes play important roles in plant growth and development, especially the cellular dehydration tolerance during seed maturation. In order to comprehensively understand the roles of LEA family members in wheat, we carried out a series of analyses based on the latest genome sequence of the bread wheat Chinese Spring. 121 Triticum aestivum L. LEA (TaLEA) genes, classified as 8 groups, were identified and characterized. TaLEA genes are distributed in all chromosomes, most of them with a low number of introns (≤3). Expression profiles showed that most TaLEA genes expressed specifically in grains. By qRT-PCR analysis, we confirmed that 12 genes among them showed high expression levels during late stage grain maturation in two spring wheat cultivars, Yangmai16 and Yangmai15. For most genes, the peak of expression appeared earlier in Yangmai16. Statistical analysis indicated that expression level of 8 genes in Yangmai 16 were significantly higher than Yangmai 15 at 25 days after anthesis. Taken together, our results provide more knowledge for future functional analysis and potential utilization of TaLEA genes in wheat breeding.

Overexpression of Triticum durum TdAnn12 gene confers stress tolerance through scavenging reactive oxygen species in transgenic tobacco

Plant annexins are proteins with multiple functions and roles in plant development and responses to abiotic stresses. We report here the functional analysis of the TdAnn12 annexin protein isolated from Triticum durum Desf. We have previously shown that TdAnn12 expression is highly induced by different abiotic stresses. In the present study, to investigate the physiological and biochemical stress-induced responses, we overexpressed TdAnn12 in tobacco. We demonstrate that transgenic tobacco plants expressing TdAnn12 exhibited enhanced tolerance to salt, osmotic stress and H2O2 at the seedling stage. Under greenhouse conditions, these plants showed tolerance to drought and salt stresses. Moreover, scavenging reactive oxygen species (ROS), higher chlorophyll content, lower lipid peroxidation levels and increased antioxidant activities (peroxidase, catalase and superoxide dismutase) were observed. Finally, accumulation of TdAnn12 in tobacco positively affects the regulation of some stress-related genes (MnSOD, APX1, CAT1, P5CS, NHX1, SOS1 and DREB1A). TdAnn12 interacts directly or indirectly with stress-related genes that could stimulate an adaptive potential to gain tolerance which is not present in non-transgenic (NT) plants. Our results clearly show that overexpression of TdAnn12 in transgenic tobacco improves stress tolerance through the removal of ROS.

RNAi-Based Biocontrol of Wheat Nematodes Using Natural Poly-Component Biostimulants

With the growing global demands on sustainable food production, one of the biggest challenges to agriculture is associated with crop losses due to parasitic nematodes. While chemical pesticides have been quite successful in crop protection and mitigation of damage from parasites, their potential harm to humans and environment, as well as the emergence of nematode resistance, have necessitated the development of viable alternatives to chemical pesticides. One of the most promising and targeted approaches to biocontrol of parasitic nematodes in crops is that of RNA interference (RNAi). In this study we explore the possibility of using biostimulants obtained from metabolites of soil streptomycetes to protect wheat (Triticum aestivum L.) against the cereal cyst nematode Heterodera avenae by means of inducing RNAi in wheat plants. Theoretical models of uptake of organic compounds by plants, and within-plant RNAi dynamics, have provided us with useful insights regarding the choice of routes for delivery of RNAi-inducing biostimulants into plants. We then conducted in planta experiments with several streptomycete-derived biostimulants, which have demonstrated the efficiency of these biostimulants at improving plant growth and development, as well as in providing resistance against the cereal cyst nematode. Using dot blot hybridization we demonstrate that biostimulants trigger a significant increase of the production in plant cells of si/miRNA complementary with plant and nematode mRNA. Wheat germ cell-free experiments show that these si/miRNAs are indeed very effective at silencing the translation of nematode mRNA having complementary sequences, thus reducing the level of nematode infestation and improving plant resistance to nematodes. Thus, we conclude that natural biostimulants produced from metabolites of soil streptomycetes provide an effective tool for biocontrol of wheat nematode.

Organization and evolution of the chalcone synthase gene family in bread wheat and relative species

Background

Flavonoid compounds are secondary plant metabolites, having a functional importance in plant development, protection from pathogens and unfavorable environmental factors. Chalcone synthase (CHS) is a key enzyme in the biosynthesis of flavonoids; it is involved in biosynthesis of all classes of flavonoid compounds. Nevertheless, the Chs gene family in bread wheat (Triticum aestivum L.) has been not characterized yet. The aim of the current study was to investigate structural and functional organization of the Chs genes and evolution of this gene family in bread wheat and relative species.

Results

The nucleotide sequences of the eight Chs copies in T. aestivum were identified. Among them, two homoeologous sets of the Chs genes were located on the short (Chs-A1, −B1, −D1) and the long (Chs-A4, −B4, −D4) arms of homoeologous group 2 chromosomes. Two paralogous gene copies in the B-genome (Chs-B2, −B3) were located in the distal regions of 2BS chromosome. To clarify the origin of Chs duplications in the B-genome the phylogenetic analysis with the Chs sequences of Triticum and Aegilops species carrying ancestral genomes was conducted. It was estimated that the first duplication event occurred in the genome of the common ancestor of Triticum and Aegilops genera about 10–12 million years ago (MYA), then another copy was formed in the ancestor of the B-genome about 6–7 MYA. A homology modeling revealed high sequence similarity of bread wheat CHS enzymes. A number of short deletions in coding regions of some Chs sequences are not expected to have any significant functional effects. Estimation of transcriptional activity of the Chs copies along with a comparative analysis of their promoters structure suggested their functional specialization, which likely contributed to the maintaining of the duplicated Chs genes in wheat genome.

Conclusions

From possible ten Chs copies in bread wheat genome, eight members of this family retained their intact structure and activity, while two copies appear to be lost at the level of diploid and tetraploid ancestors. Transcriptional assay along with a comparative analysis of the cis-regulatory elements revealed their functional diversification. The multiple functions supported by the Chs family are assumed to be a driving force for duplications of the Chs gene and their retention in plant genome.

Electronic supplementary material

The online version of this article (10.1186/s12863-019-0727-y) contains supplementary material, which is available to authorized users.

Calcium transport across plant membranes: mechanisms and functions

Contents Summary 49 I. Introduction 49 II. Physiological and structural characteristics of plant Ca²⁺ -permeable ion channels 50 III. Ca²⁺ extrusion systems 61 IV. Concluding remarks 64 Acknowledgements 64 References 64 SUMMARY: Calcium is an essential structural, metabolic and signalling element. The physiological functions of Ca²⁺ are enabled by its orchestrated transport across cell membranes, mediated by Ca²⁺ -permeable ion channels, Ca²⁺ -ATPases and Ca²⁺ /H⁺ exchangers. Bioinformatics analysis has not determined any Ca²⁺ -selective filters in plant ion channels, but electrophysiological tests do reveal Ca²⁺ conductances in plant membranes. The biophysical characteristics of plant Ca²⁺ conductances have been studied in detail and were recently complemented by molecular genetic approaches. Plant Ca²⁺ conductances are mediated by several families of ion channels, including cyclic nucleotide-gated channels (CNGCs), ionotropic glutamate receptors, two-pore channel 1 (TPC1), annexins and several types of mechanosensitive channels. Key Ca²⁺ -mediated reactions (e.g. sensing of temperature, gravity, touch and hormones, and cell elongation and guard cell closure) have now been associated with the activities of specific subunits from these families. Structural studies have demonstrated a unique selectivity filter in TPC1, which is passable for hydrated divalent cations. The hypothesis of a ROS-Ca²⁺ hub is discussed, linking Ca²⁺ transport to ROS generation. CNGC inactivation by cytosolic Ca²⁺ , leading to the termination of Ca²⁺ signals, is now mechanistically explained. The structure-function relationships of Ca²⁺ -ATPases and Ca²⁺ /H⁺ exchangers, and their regulation and physiological roles are analysed.

Heterologous expression of Brassica juncea annexin, AnnBj2 confers salt tolerance and ABA insensitivity in transgenic tobacco seedlings

Annexins are multifunctional proteins with roles in plant development and alleviation of stress tolerance. In the present communication, we report on the effect of heterologous expression of Brassica juncea annexin, AnnBj2 in tobacco. Transgenic tobacco plants expressing AnnBj2 exhibited salt-tolerant and abscisic acid (ABA)-insensitive phenotype at the seedling stage. Biochemical analysis showed that AnnBj2 transgenic plants retained higher chlorophyll and proline content, and lower malondialdehyde (MDA) levels compared to the null line under salt stress. They exhibited better water retention capacity compared to the null segregant (NS) line. AnnBj2 overexpression altered the transcript levels of several stress-related marker genes involved in reactive oxygen species (ROS) scavenging and abiotic stress signaling. Taken together, these results suggest a positive role for AnnBj2 in salt stress response upon heterologous expression in tobacco.

Gene Expression Patterns in Roots of Camelina sativa With Enhanced Salinity Tolerance Arising From Inoculation of Soil With Plant Growth Promoting Bacteria Producing 1-Aminocyclopropane-1-Carboxylate Deaminase or Expression the Corresponding acdS Gene

Camelina sativa treated with plant growth-promoting bacteria (PGPB) producing 1-aminocyclopropane-1-carboxylate deaminase (acdS) or transgenic lines expressing acdS exhibit increased salinity tolerance. AcdS reduces the level of stress ethylene to below the point where it is inhibitory to plant growth. The study determined that several mechanisms appear to be responsible for the increased salinity tolerance and that the effect of acdS on gene expression patterns in C. sativa roots during salt stress is a function of how it is delivered. Growth in soil treated with the PGPB (Pseudomonas migulae 8R6) mostly affected ethylene- and abscisic acid-dependent signaling in a positive way, while expression of acdS in transgenic lines under the control of the broadly active CaMV 35S promoter or the root-specific rolD promoter affected auxin, jasmonic acid and brassinosteroid signaling and/biosynthesis. The expression of genes involved in minor carbohydrate metabolism were also up-regulated, mainly in roots of lines expressing acdS. Expression of acdS also affected the expression of genes involved in modulating the level of reactive oxygen species (ROS) to prevent cellular damage, while permitting ROS-dependent signal transduction. Though the root is not a photosynthetic tissue, acdS had a positive effect on the expression of genes involved in photosynthesis.

ROS-Activated Ion Channels in Plants: Biophysical Characteristics, Physiological Functions and Molecular Nature

Ion channels activated by reactive oxygen species (ROS) have been found in the plasma membrane of charophyte Nitella flixilis, dicotyledon Arabidopsis thaliana, Pyrus pyrifolia and Pisum sativum, and the monocotyledon Lilium longiflorum. Their activities have been reported in charophyte giant internodes, root trichoblasts and atrichoblasts, pollen tubes, and guard cells. Hydrogen peroxide and hydroxyl radicals are major activating species for these channels. Plant ROS-activated ion channels include inwardly-rectifying, outwardly-rectifying, and voltage-independent groups. The inwardly-rectifying ROS-activated ion channels mediate Ca2+-influx for growth and development in roots and pollen tubes. The outwardly-rectifying group facilitates K⁺ efflux for the regulation of osmotic pressure in guard cells, induction of programmed cell death, and autophagy in roots. The voltage-independent group mediates both Ca2+ influx and K⁺ efflux. Most studies suggest that ROS-activated channels are non-selective cation channels. Single-channel studies revealed activation of 14.5-pS Ca2+ influx and 16-pS K⁺ efflux unitary conductances in response to ROS. The molecular nature of ROS-activated Ca2+ influx channels remains poorly understood, although annexins and cyclic nucleotide-gated channels have been proposed for this role. The ROS-activated K⁺ channels have recently been identified as products of Stellar K⁺ Outward Rectifier (SKOR) and Guard cell Outwardly Rectifying K⁺ channel (GORK) genes.

Structural and functional characterisation of two novel durum wheat annexin genes in response to abiotic stress

Abiotic stress results in massive loss of crop productivity throughout the world. Understanding the plant gene regulatory mechanisms involved in stress responses is very important. Annexins are a conserved multigene family of Ca-dependent, phospholipid-binding proteins with suggested functions in response to environmental stresses and signalling during plant growth and development. Annexins function to counteract oxidative stress, maintain cell redox homeostasis and enhance drought tolerance. A full-length cDNA of two genes (TdAnn6 and TdAnn12) encoding annexin proteins were isolated and characterised from Tunisian durum wheat varieties (Triticum turgidum L. subsp. durum cv. Mahmoudi). Analyses of the deduced proteins encoded by annexin cDNAs (TdAnn6 and TdAnn12) indicate the presence of the characteristic four repeats of 70-75 amino acids and the motifs proposed to be involved in Ca2+ binding. Gene expression patterns obtained by real-time PCR revealed differential temporal and spatial regulation of the two annexin genes in durum wheat under different abiotic stress conditions such as salt (NaCl 150mM), osmotic (10% polyethylene glycol 8000), ionic (LiCl 10mM), oxidative (H2O2), ABA (100µM), salicylic acid (10mM), cold (4°C) and heat (37°C) stress. The two annexin genes were not regulated by heavy metal stress (CdCl2 150µM). Moreover, heterologous expression of TdAnn6 and TdAnn12 in yeast improves its tolerance to abiotic stresses, suggesting annexin's involvement in theses stress tolerance mechanisms. Taken together, our results show that the two newly isolated wheat annexin might play an active role in modulating plant cell responses to abiotic stress responses.

Genome-Wide Identification and Expression Analysis of the HD-Zip Gene Family in Wheat (Triticum aestivum L.)

The homeodomain-leucine zipper (HD-Zip) gene family, as plant-specific transcription factors, plays an important role in plant development and growth as well as in the response to diverse stresses. Although HD-Zip genes have been extensively studied in many plants, they had not yet been studied in wheat, especially those involved in response to abiotic stresses. In this study, 46 wheat HD-Zip genes were identified using a genome-wide search method. Phylogenetic analysis classified these genes into four groups, numbered 4, 5, 17 and 20 respectively. In total, only three genes with A, B and D homoeologous copies were identified. Furthermore, the gene interaction networks found that the TaHDZ genes played a critical role in the regulatory pathway of organ development and osmotic stress. Finally, the expression profiles of the wheat HD-Zips in different tissues and under various abiotic stresses were investigated using the available RNA sequencing (RNA-Seq) data and then validated by quantitative real-time polymerase chain reaction (qRT-PCR) to obtain the tissue-specific and stress-responsive candidates. This study systematically identifies the HD-Zip gene family in wheat at the genome-wide level, providing important candidates for further functional analysis and contributing to the better understanding of the molecular basis of development and stress tolerance in wheat.

Mechanisms of cytosolic calcium elevation in plants: the role of ion channels, calcium extrusion systems and NADPH oxidase-mediated 'ROS-Ca2+ Hub'

Elevation in the cytosolic free calcium is crucial for plant growth, development and adaptation. Calcium influx into plant cells is mediated by Ca2+ depolarisation-activated, hyperpolarisation-activated and voltage-independent Ca2+-permeable channels (DACCs, HACCs and VICCs respectively). These channels are encoded by the following gene families: (1) cyclic nucleotide-gated channels (CNGCs), (2) ionotropic glutamate receptors (GLRs), (3) annexins, (4) 'mechanosensitive channels of small (MscS) conductance'-like channels (MSLs), (5) 'mid1-complementing activity' channels (MCAs), Piezo channels, and hyperosmolality-induced [Ca2+]cyt. channel 1 (OSCA1). Also, a 'tandem-pore channel1' (TPC1) catalyses Ca2+ efflux from the vacuole in response to the plasma membrane-mediated Ca2+ elevation. Recent experimental data demonstrated that Arabidopsis thaliana (L.) Heynh. CNGCs 2, 5-10, 14, 16 and 18, GLRs 1.2, 3.3, 3.4, 3.6 and 3.7, TPC1, ANNEXIN1, MSL9 and MSL10,MCA1 and MCA2, OSCA1, and some their homologues counterparts in other species, are responsible for Ca2+ currents and/or cytosolic Ca2+ elevation. Extrusion of Ca2+ from the cytosol is mediated by Ca2+-ATPases and Ca2+/H+ exchangers which were recently examined at the level of high resolution crystal structure. Calcium-activated NADPH oxidases and reactive oxygen species (ROS)-activated Ca2+ conductances form a self-amplifying 'ROS-Ca2+hub', enhancing and transducing Ca2+ and redox signals. The ROS-Ca2+ hub contributes to physiological reactions controlled by ROS and Ca2+, demonstrating synergism and unity of Ca2+ and ROS signalling mechanisms.

High Resolution Mapping of QTLs for Heat Tolerance in Rice Using a 5K SNP Array

BACKGROUND

Heat stress is one of the major abiotic threats to rice production, next to drought and salinity stress. Incidence of heat stress at reproductive phase of the crop results in abnormal pollination leading to floret sterility, low seed set and poor grain quality. Identification of QTLs and causal genes for heat stress tolerance at flowering will facilitate breeding for improved heat tolerance in rice. In the present study, we used 272 F₈ recombinant inbred lines derived from a cross between Nagina22, a well-known heat tolerant Aus cultivar and IR64, a heat sensitive popular Indica rice variety to map the QTLs for heat tolerance.

RESULTS

To enable precise phenotyping for heat stress tolerance, we used a controlled phenotyping facility available at ICAR-Indian Institute of Wheat and Barley Research, Karnal, India. Based on 'days to 50% flowering' data of the RILs, we followed staggered sowing to synchronize flowering to impose heat stress at uniform stage. Using the Illumina infinium 5K SNP array for genotyping the parents and the RILs, and stress susceptibility and stress tolerance indices (SSI and STI) of percent spikelet sterility and yield per plant (g), we identified five QTLs on chromosomes 3, 5, 9 and 12. The identified QTLs explained phenotypic variation in the range of 6.27 to 21. 29%. Of these five QTLs, two high effect QTLs, one novel (qSTIPSS9.1) and one known (qSTIY5.1/qSSIY5.2), were mapped in less than 400 Kbp genomic regions, comprising of 65 and 54 genes, respectively.

CONCLUSIONS

The present study identified two major QTLs for heat tolerance in rice in narrow physical intervals, which can be employed for crop improvement by marker assisted selection (MAS) after development of suitable scorable markers for breeding of high yielding heat tolerant rice varieties. This is the first report of a major QTL for heat tolerance on chromosome 9 of rice. Further, a known QTL for heat tolerance on chromosome 5 was narrowed down from 23 Mb to 331 Kbp in this study.

High Resolution Mapping of QTLs for Heat Tolerance in Rice Using a 5K SNP Array

BACKGROUND

Heat stress is one of the major abiotic threats to rice production, next to drought and salinity stress. Incidence of heat stress at reproductive phase of the crop results in abnormal pollination leading to floret sterility, low seed set and poor grain quality. Identification of QTLs and causal genes for heat stress tolerance at flowering will facilitate breeding for improved heat tolerance in rice. In the present study, we used 272 F₈ recombinant inbred lines derived from a cross between Nagina22, a well-known heat tolerant Aus cultivar and IR64, a heat sensitive popular Indica rice variety to map the QTLs for heat tolerance.

RESULTS

To enable precise phenotyping for heat stress tolerance, we used a controlled phenotyping facility available at ICAR-Indian Institute of Wheat and Barley Research, Karnal, India. Based on 'days to 50% flowering' data of the RILs, we followed staggered sowing to synchronize flowering to impose heat stress at uniform stage. Using the Illumina infinium 5K SNP array for genotyping the parents and the RILs, and stress susceptibility and stress tolerance indices (SSI and STI) of percent spikelet sterility and yield per plant (g), we identified five QTLs on chromosomes 3, 5, 9 and 12. The identified QTLs explained phenotypic variation in the range of 6.27 to 21. 29%. Of these five QTLs, two high effect QTLs, one novel (qSTIPSS9.1) and one known (qSTIY5.1/qSSIY5.2), were mapped in less than 400 Kbp genomic regions, comprising of 65 and 54 genes, respectively.

CONCLUSIONS

The present study identified two major QTLs for heat tolerance in rice in narrow physical intervals, which can be employed for crop improvement by marker assisted selection (MAS) after development of suitable scorable markers for breeding of high yielding heat tolerant rice varieties. This is the first report of a major QTL for heat tolerance on chromosome 9 of rice. Further, a known QTL for heat tolerance on chromosome 5 was narrowed down from 23 Mb to 331 Kbp in this study.