Cysteine-rich receptor-like kinase CRK5 as a regulator of growth, development, and ultraviolet radiation responses in Arabidopsis thaliana

Identification and characterization of the CRK gene family in the wheat genome and analysis of their expression profile in response to high temperature-induced male sterility

Cysteine-rich receptor-like kinases (CRKs) play many important roles during plant development, including defense responses under both biotic and abiotic stress, reactive oxygen species (ROS) homeostasis, callose deposition and programmed cell death (PCD). However, there are few studies on the involvement of the CRK family in male sterility due to heat stress in wheat (Triticum aestivum L.). In this study, a genome-wide characterization of the CRK family was performed to investigate the structural and functional attributes of the wheat CRKs in anther sterility caused by heat stress. A total of 95 CRK genes were unevenly distributed on 18 chromosomes, with the most genes distributed on chromosome 2B. Paralogous homologous genes with Ka/Ks ratios less than 1 may have undergone strong purifying selection during evolution and are more functionally conserved. The collinearity analysis results of CRK genes showed that wheat and Arabidopsis (A. thaliana), foxtail millet, Brachypodium distachyon (B. distachyon), and rice have three, 12, 15, and 11 pairs of orthologous genes, respectively. In addition, the results of the network interactions of genes and miRNAs showed that five miRNAs were in the hub of the interactions map, namely tae-miR9657b-5p, tae-miR9780, tae-miR9676-5p, tae-miR164, and tae-miR531. Furthermore, qRT-PCR validation of the six TaCRK genes showed that they play key roles in the development of the mononuclear stage anthers, as all six genes were expressed at highly significant levels in heat-stressed male sterile mononuclear stage anthers compared to normal anthers. We hypothesized that the TaCRK gene is significant in the process of high-temperature-induced sterility in wheat based on the combination of anther phenotypes, paraffin sections, and qRT-PCR data. These results improve our understanding of their relationship.

Identification of cysteine-rich receptor-like kinase gene family in potato: revealed StCRLK9 in response to heat, salt and drought stresses

The investigation into cysteine-rich receptor-like kinases (CRLKs) holds pivotal significance as these conserved, upstream signalling molecules intricately regulate fundamental biological processes such as plant growth, development and stress adaptation. This study undertakes a comprehensive characterisation of CRLKs in Solanum tuberosum (potato), a staple food crop of immense economic importance. Employing comparative genomics and evolutionary analyses, we identified 10 distinct CRLK genes in potato. Further categorisation into three major groups based on sequence similarity was performed. Each CRLK member in potato was systematically named according to its chromosomal position. Multiple sequence alignment and phylogenetic analyses unveiled conserved gene structures and motifs within the same groups. The genomic distribution of CRLKs was observed across Chromosomes 2-5, 8 and 12. Gene duplication analysis highlighted a noteworthy trend, with most gene pairs exhibiting a Ka/Ks ratio greater than one, indicating positive selection of StCRLKs in potato. Salt and drought stresses significantly impacted peroxidase and catalase activities in potato seedlings. The presence of diverse cis -regulatory elements, including hormone-responsive elements, underscored their involvement in myriad biotic and abiotic stress responses. Interestingly, interactions between the phytohormone auxin and CRLK proteins unveiled a potential auxin-mediated regulatory mechanism. A holistic approach combining transcriptomics and quantitative PCR validation identified StCRLK9 as a potential candidate involved in plant response to heat, salt and drought stresses. This study lays a robust foundation for future research on the functional roles of the CRLK gene family in potatoes, offering valuable insights into their diverse regulatory mechanisms and potential applications in stress management.

An update on evolutionary, structural, and functional studies of receptor-like kinases in plants

All living organisms must develop mechanisms to cope with and adapt to new environments. The transition of plants from aquatic to terrestrial environment provided new opportunities for them to exploit additional resources but made them vulnerable to harsh and ever-changing conditions. As such, the transmembrane receptor-like kinases (RLKs) have been extensively duplicated and expanded in land plants, increasing the number of RLKs in the advanced angiosperms, thus becoming one of the largest protein families in eukaryotes. The basic structure of the RLKs consists of a variable extracellular domain (ECD), a transmembrane domain (TM), and a conserved kinase domain (KD). Their variable ECDs can perceive various kinds of ligands that activate the conserved KD through a series of auto- and trans-phosphorylation events, allowing the KDs to keep the conserved kinase activities as a molecular switch that stabilizes their intracellular signaling cascades, possibly maintaining cellular homeostasis as their advantages in different environmental conditions. The RLK signaling mechanisms may require a coreceptor and other interactors, which ultimately leads to the control of various functions of growth and development, fertilization, and immunity. Therefore, the identification of new signaling mechanisms might offer a unique insight into the regulatory mechanism of RLKs in plant development and adaptations. Here, we give an overview update of recent advances in RLKs and their signaling mechanisms.

The Mining of Genetic Loci and the Analysis of Candidate Genes to Identify the Physical and Chemical Markers of Anti-Senescence in Rice

Premature senescence is a common occurrence in rice production, and seriously affects rice plants' nutrient utilization and growth. A total of 120 recombinant inbred lines (RILs) were obtained from successive self-crossing of F12 generations derived from Huazhan and Nekken2. The superoxide dismutase (SOD) activity, malondialdehyde (MDA), content and catalase (CAT) activity related to the anti-senescence traits and enzyme activity index of rice were measured for QTL mapping using 4858 SNPs. Thirteen QTLs related to anti-senescence were found, among which the highest LOD score was 5.70. Eighteen anti-senescence-related genes were found in these regions, and ten of them differed significantly between the parents. It was inferred that LOC_Os01g61500, LOC_Os01g61810, and LOC_Os04g40130 became involved in the regulation of the anti-senescence molecular network upon upregulation of their expression levels. The identified anti-senescence-related QTLs and candidate genes provide a genetic basis for further research on the mechanism of the molecular network that regulates premature senescence.

Emerging Roles of Receptor-like Protein Kinases in Plant Response to Abiotic Stresses

The productivity of plants is hindered by unfavorable conditions. To perceive stress signals and to transduce these signals to intracellular responses, plants rely on membrane-bound receptor-like kinases (RLKs). These play a pivotal role in signaling events governing growth, reproduction, hormone perception, and defense responses against biotic stresses; however, their involvement in abiotic stress responses is poorly documented. Plant RLKs harbor an N-terminal extracellular domain, a transmembrane domain, and a C-terminal intracellular kinase domain. The ectodomains of these RLKs are quite diverse, aiding their responses to various stimuli. We summarize here the sub-classes of RLKs based on their domain structure and discuss the available information on their specific role in abiotic stress adaptation. Furthermore, the current state of knowledge on RLKs and their significance in abiotic stress responses is highlighted in this review, shedding light on their role in influencing plant-environment interactions and opening up possibilities for novel approaches to engineer stress-tolerant crop varieties.

CYSTEINE-RICH RECEPTOR-LIKE PROTEIN KINASES: their evolution, structure, and roles in stress response and development

Plant-specific receptor-like protein kinases (RLKs) are central components for sensing the extracellular microenvironment. CYSTEINE-RICH RLKs (CRKs) are members of one of the biggest RLK subgroups. Their physiological and molecular roles have only begun to be elucidated, but recent studies highlight the diverse types of proteins interacting with CRKs, as well as the localization of CRKs and their lateral organization within the plasma membrane. Originally the DOMAIN OF UNKNOWN FUNCTION 26 (DUF26)-containing extracellular region of the CRKs was proposed to act as a redox sensor, but the potential activating post-translational modification or ligands perceived remain elusive. Here, we summarize recent progress in the analysis of CRK evolution, molecular function, and role in plant development, abiotic stress responses, plant immunity, and symbiosis. The currently available information on CRKs and related proteins suggests that the CRKs are central regulators of plant signaling pathways. However, more research using classical methods and interdisciplinary approaches in various plant model species, as well as structural analyses, will not only enhance our understanding of the molecular function of CRKs, but also elucidate the contribution of other cellular components in CRK-mediated signaling pathways.

Potential candidate genes and pathways related to cytoplasmic male sterility in Dianthus spiculifolius as revealed by transcriptome analysis

KEY MESSAGE

We introduced the candidate gene DsHSP70 into Arabidopsis thaliana, resulting in male gametophyte sterility and abnormal degeneration of sepals and petals. Cytoplasmic male sterility (CMS) is a useful tool for hybrid production. However, the regulatory mechanism of CMS in Dianthus spiculifolius remains unclear. In this study, we investigated whether male-sterile line of D. spiculifolius has a malformed tapetum and fails to produce normal fertile pollen. RNA sequencing technology was used to compare the gene expression patterns of the D. spiculifolius male-sterile line and its male fertility maintainer line during anther development. A total of 12,365 differentially expressed genes (DEGs) were identified, among which 1765 were commonly expressed in the S1, S2 and S3 stages. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated that these DEGs were mainly involved in oxidation-reduction processes, signal transduction and programmed cell death. Additionally, weighted correlation network analysis (WGCNA) showed that three modules may be related to male sterility. A putative regulatory pathway for the male sterility traits was constructed based on the reproductive development network. After introducing the candidate DsHSP70 gene into Arabidopsis thaliana, we found that overexpressing plants showed anther abortion and shorter filaments, and accompanied by abnormal degeneration of sepals and petals. In summary, our results identified potential candidate genes and pathways related to CMS in D. spiculifolius, providing new insights for further research on the mechanism of male sterility.

SnRK2.10 kinase differentially modulates expression of hub WRKY transcription factors genes under salinity and oxidative stress in Arabidopsis thaliana

In nature, all living organisms must continuously sense their surroundings and react to the occurring changes. In the cell, the information about these changes is transmitted to all cellular compartments, including the nucleus, by multiple phosphorylation cascades. Sucrose Non-Fermenting 1 Related Protein Kinases (SnRK2s) are plant-specific enzymes widely distributed across the plant kingdom and key players controlling abscisic acid (ABA)-dependent and ABA-independent signaling pathways in the plant response to osmotic stress and salinity. The main deleterious effects of salinity comprise water deficiency stress, disturbances in ion balance, and the accompanying appearance of oxidative stress. The reactive oxygen species (ROS) generated at the early stages of salt stress are involved in triggering intracellular signaling required for the fast stress response and modulation of gene expression. Here we established in Arabidopsis thaliana that salt stress or induction of ROS accumulation by treatment of plants with H2O2 or methyl viologen (MV) induces the expression of several genes encoding transcription factors (TFs) from the WRKY DNA-Binding Protein (WRKY) family. Their induction by salinity was dependent on SnRK2.10, an ABA non-activated kinase, as it was strongly reduced in snrk2.10 mutants. The effect of ROS was clearly dependent on their source. Following the H2O2 treatment, SnRK2.10 was activated in wild-type (wt) plants and the induction of the WRKY TFs expression was only moderate and was enhanced in snrk2.10 lines. In contrast, MV did not activate SnRK2.10 and the WRKY induction was very strong and was similar in wt and snrk2.10 plants. A bioinformatic analysis indicated that the WRKY33, WRKY40, WRKY46, and WRKY75 transcription factors have a similar target range comprising numerous stress-responsive protein kinases. Our results indicate that the stress-related functioning of SnRK2.10 is fine-tuned by the source and intracellular distribution of ROS and the co-occurrence of other stress factors.

CRK12: A Key Player in Regulating the Phaseolus vulgaris-Rhizobium tropici Symbiotic Interaction

Cysteine-rich receptor-like kinases (CRKs) are a type of receptor-like kinases (RLKs) that are important for pathogen resistance, extracellular reactive oxygen species (ROS) signaling, and programmed cell death in plants. In a previous study, we identified 46 CRK family members in the Phaseolus vulgaris genome and found that CRK12 was highly upregulated under root nodule symbiotic conditions. To better understand the role of CRK12 in the Phaseolus-Rhizobia symbiotic interaction, we functionally characterized this gene by overexpressing (CRK12-OE) and silencing (CRK12-RNAi) it in a P. vulgaris hairy root system. We found that the constitutive expression of CRK12 led to an increase in root hair length and the expression of root hair regulatory genes, while silencing the gene had the opposite effect. During symbiosis, CRK12-RNAi resulted in a significant reduction in nodule numbers, while CRK12-OE roots showed a dramatic increase in rhizobial infection threads and the number of nodules. Nodule cross sections revealed that silenced nodules had very few infected cells, while CRK12-OE nodules had enlarged infected cells, whose numbers had increased compared to controls. As expected, CRK12-RNAi negatively affected nitrogen fixation, while CRK12-OE nodules fixed 1.5 times more nitrogen than controls. Expression levels of genes involved in symbiosis and ROS signaling, as well as nitrogen export genes, supported the nodule phenotypes. Moreover, nodule senescence was prolonged in CRK12-overexpressing roots. Subcellular localization assays showed that the PvCRK12 protein localized to the plasma membrane, and the spatiotemporal expression patterns of the CRK12-promoter::GUS-GFP analysis revealed a symbiosis-specific expression of CRK12 during the early stages of rhizobial infection and in the development of nodules. Our findings suggest that CRK12, a membrane RLK, is a novel regulator of Phaseolus vulgaris-Rhizobium tropici symbiosis.

Exogenous Methyl Jasmonate Mediated MiRNA-mRNA Network Improves Heat Tolerance of Perennial Ryegrass

Heat stress can hinder the growth of perennial ryegrass (Lolium perenne L.). Methyl jasmonate (MeJA) applied exogenously can increase heat stress tolerance in plants; however, the regulatory mechanisms involved in heat tolerance mediated by MeJA are poorly understood in perennial ryegrass. Here, the microRNA (miRNA) expression profiles of perennial ryegrass were assessed to elucidate the regulatory pathways associated with heat tolerance induced by MeJA. Plants were subjected to four treatments, namely, control (CK), MeJA pre-treatment (T), heat stress treatment (H), and MeJA pre-treatment + heat stress (TH). According to the results, 102 miRNAs were up-regulated in all treatments, with 20, 27, and 33 miRNAs being up-regulated in the T, H, and TH treatment groups, respectively. The co-expression network analysis between the deferentially expressed miRNAs and their corresponding target genes showed that 20 miRNAs modulated 51 potential target genes. Notably, the miRNAs that targeted genes related to with regards to heat tolerance were driven by MeJA, and they were involved in four pathways: novel-m0258-5p mediated signal transduction, novel-m0350-5p mediated protein homeostasis, miR397-z, miR5658-z, and novel-m0008-5p involved in cell wall component, and miR1144-z and miR5185-z dominated chlorophyll degradation. Overall, the findings of this research paved the way for more research into the heat tolerance mechanism in perennial ryegrass and provided a theoretical foundation for developing cultivars with enhanced heat tolerance.

Cysteine-rich receptor-like protein kinases: emerging regulators of plant stress responses

Cysteine-rich receptor-like kinases (CRKs) belong to a large DUF26-containing receptor-like kinase (RLK) family. They play key roles in immunity, abiotic stress response, and growth and development. How CRKs regulate diverse processes is a long-standing question. Recent studies have advanced our understanding of the molecular mechanisms underlying CRK functions in Ca2+ influx, reactive oxygen species (ROS) production, mitogen-activated protein kinase (MAPK) cascade activation, callose deposition, stomatal immunity, and programmed cell death (PCD). We review the CRK structure-function relationship with a focus on the roles of CRKs in immunity, the abiotic stress response, and the growth-stress tolerance tradeoff. We provide a critical analysis and synthesis of how CRKs control sophisticated regulatory networks that determine diverse plant phenotypic outputs.

Genetic architecture of leaf morphology revealed by integrated trait module in Catalpa bungei

Leaves are crucial for maintaining plant growth and development via photosynthesis, and their function is simultaneously regulated by a suite of phenotypic traits. Although much is known about the genetic architecture of individual leaf traits, unraveling the genetic basis of complex leaf morphology remains a challenge. Based on the functional correlation and coordination of multi-traits, we divided 15 leaf morphological traits into three modules, comprising size (area, length, width, and perimeter), shape (leaf lobes, aspect ratio, circularity, rectangularity, and the relevant ratios), and color (red, green, and blue) for an ornamental tree species, Catalpa bungei. A total of 189 significant single-nucleotide polymorphisms were identified in the leaves of C. bungei: 35, 82, and 76 in the size, shape, and color modules, respectively. Four quantitative trait loci were common between the size and shape modules, which were closely related according to phenotype correlation, genetic mapping, and mRNA analysis. The color module was independent of them. Synergistic changes in the aspect ratio, leaf lobe, and circularity suggest that these traits could be the core indicators of the leaf shape module. The LAS and SRK genes, associated with leaf lobe and circularity, were found to function in plant defense mechanisms and the growth of leaves. The associations between the SRK and CRK2 genes and the leaf lobe and circularity traits were further verified by RT-qPCR. Our findings demonstrate the importance of integrating multi-trait modules to characterize leaf morphology and facilitate a holistic understanding of the genetic architecture of intraspecific leaf morphology diversity.

CRK41 Modulates Microtubule Depolymerization in Response to Salt Stress in Arabidopsis

The pivotal role of cysteine-rich receptor-like kinases (CRKs) in modulating growth, development, and responses to stress has been widely acknowledged in Arabidopsis. However, the function and regulation of CRK41 has remained unclear. In this study, we demonstrate that CRK41 is critical for modulating microtubule depolymerization in response to salt stress. The crk41 mutant exhibited increased tolerance, while overexpression of CRK41 led to hypersensitivity to salt. Further analysis revealed that CRK41 interacts directly with the MAP kinase3 (MPK3), but not with MPK6. Inactivation of either MPK3 or MPK6 could abrogate the salt tolerance of the crk41 mutant. Upon NaCl treatment, microtubule depolymerization was heightened in the crk41 mutant, yet alleviated in the crk41mpk3 and crk41mpk6 double mutants, indicating that CRK41 suppresses MAPK-mediated microtubule depolymerizations. Collectively, these results reveal that CRK41 plays a crucial role in regulating microtubule depolymerization triggered by salt stress through coordination with MPK3/MPK6 signalling pathways, which are key factors in maintaining microtubule stability and conferring salt stress resistance in plants.

Homozygosity mapping identified loci and candidate genes responsible for freezing tolerance in Camelina sativa

Homozygosity mapping is an effective tool for detecting genomic regions responsible for a given trait when the phenotype is controlled by a limited number of dominant or co-dominant loci. Freezing tolerance is a major attribute in agricultural crops such as camelina. Previous studies indicated that freezing tolerance differences between a tolerant (Joelle) and susceptible (CO46) variety of camelina were controlled by a small number of dominant or co-dominant genes. We performed whole genome homozygosity mapping to identify markers and candidate genes responsible for freezing tolerance difference between these two genotypes. A total of 28 F3 RILs were sequenced to ∼30× coverage, and parental lines were sequenced to >30-40× coverage with Pacific Biosciences high fidelity technology and 60× coverage using Illumina whole genome sequencing. Overall, about 126k homozygous single nucleotide polymorphism markers were identified that differentiate both parents. Moreover, 617 markers were also homozygous in F3 families fixed for freezing tolerance/susceptibility. All these markers mapped to two contigs forming a contiguous stretch of chromosome 11. The homozygosity mapping detected 9 homozygous blocks among the selected markers and 22 candidate genes with strong similarity to regions in or near the homozygous blocks. Two such genes were differentially expressed during cold acclimation in camelina. The largest block contained a cold-regulated plant thionin and a putative rotamase cyclophilin 2 gene previously associated with freezing resistance in arabidopsis (Arabidopsis thaliana). The second largest block contains several cysteine-rich RLK genes and a cold-regulated receptor serine/threonine kinase gene. We hypothesize that one or more of these genes may be primarily responsible for freezing tolerance differences in camelina varieties.

The CRK5 and WRKY53 Are Conditional Regulators of Senescence and Stomatal Conductance in Arabidopsis

In Arabidopsis thaliana, cysteine-rich receptor-like kinases (CRKs) constitute a large group of membrane-localized proteins which perceive external stimuli and transduce the signal into the cell. Previous reports based on their loss-of-function phenotypes and expression profile support their role in many developmental and stress-responsive pathways. Our study revealed that one member of this family, CRK5, acts as a negative regulator of leaf aging. Enrichment of the CRK5 promoter region in W-box cis-elements demonstrated that WRKY transcription factors control it. We observed significantly enhanced WRKY53 expression in crk5 and reversion of its early-senescence phenotype in the crk5 wrky53 line, suggesting a negative feedback loop between these proteins antagonistically regulating chlorophyll a and b contents. Yeast-two hybrid assay showed further that CRK5 interacts with several proteins involved in response to water deprivation or calcium signaling, while gas exchange analysis revealed a positive effect of CRK5 on water use efficiency. Consistent with that, the crk5 plants showed disturbed foliar temperature, stomatal conductance, transpiration, and increased susceptibility to osmotic stress. These traits were fully or partially reverted to wild-type phenotype in crk5 wrky53 double mutant. Obtained results suggest that WRKY53 and CRK5 are antagonistic regulators of chlorophyll synthesis/degradation, senescence, and stomatal conductance.

Aux/IAA11 Is Required for UV-AB Tolerance and Auxin Sensing in Arabidopsis thaliana

In order to survive, plants have, over the course of their evolution, developed sophisticated acclimation and defense strategies governed by complex molecular and physiological, and cellular and extracellular, signaling pathways. They are also able to respond to various stimuli in the form of tropisms; for example, phototropism or gravitropism. All of these retrograde and anterograde signaling pathways are controlled and regulated by waves of reactive oxygen species (ROS), electrical signals, calcium, and hormones, e.g., auxins. Auxins are key phytohormones involved in the regulation of plant growth and development. Acclimation responses, which include programmed cell death induction, require precise auxin perception. However, our knowledge of these pathways is limited. The Aux/IAA family of transcriptional corepressors inhibits the growth of the plant under stress conditions, in order to maintain the balance between development and acclimation responses. In this work, we demonstrate the Aux/IAA11 involvement in auxin sensing, survival, and acclimation to UV-AB, and in carrying out photosynthesis under inhibitory conditions. The tested iaa11 mutants were more susceptible to UV-AB, photosynthetic electron transport (PET) inhibitor, and synthetic endogenous auxin. Among the tested conditions, Aux/IAA11 was not repressed by excess light stress, exclusively among its phylogenetic clade. Repression of transcription by Aux/IAA11 could be important for the inhibition of ROS formation or efficiency of ROS scavenging. We also hypothesize that the demonstrated differences in the subcellular localization of the two Aux/IAA11 protein variants might indicate their regulation by alternative splicing. Our results suggest that Aux/IAA11 plays a specific role in chloroplast retrograde signaling, since it is not repressed by high (excess) light stress, exclusively among its phylogenetic clade.

Genome-wide identification of cysteine-rich receptor-like kinases in sweet cherry reveals that PaCRK1 enhances sweet cherry resistance to salt stress

Forty PaCRKs have been identified from sweet cherry and overexpression PaCRK1 in sweet cherry enhances its resistance to salt stress. Cysteine-rich receptor-like kinases (CRKs), a large subgroup of the receptor-like kinases, play an important role in plant development and stress response. However, knowledge about CRKs and its function against adverse environmental stresses in sweet cherry were lacking. In this study, 40 PaCRKs were identified from sweet cherry (Prunus avium) genome database. Phylogenetic analysis indicated that PaCRKs could be classified into six subgroups. Transcriptome analysis showed that the expression levels of most PaCRKs were changed under external environmental stresses. Functional study showed that PaCRK1 overexpression could enhance Arabidopsis and sweet cherry tolerance to salt stress. Moreover, biochemical analysis showed that PaCRK1 increased salt tolerance of sweet cherry by regulating the expression of antioxidation-related genes and their enzyme activities. This study provides a comprehensive understanding of PaCRKs in sweet cherry and elucidates the potential role of PaCRKs in response to various environmental stimuli.

Genome-wide association, RNA-seq and iTRAQ analyses identify candidate genes controlling radicle length of wheat

The radicle, present in the embryo of a seed, is the first root to emerge at germination, and its rapid growth is essential for establishment and survival of the seedling. However, there are few studies on the critical mechanisms underlying radicle and then radicle length in wheat seedlings, despite its importance as a food crop throughout the world. In the present study, 196 wheat accessions from the Huanghuai Wheat Region were screened to measure radicle length under 4 hydroponic culture environments over 3 years. Different expression genes and proteins (DEGs/DEPs) between accessions with extremely long [Yunong 949 (WRL1), Zhongyu 9,302 (WRL2)] and short roots [Yunong 201 (WRS1), Beijing 841 (WRS2)] were identified in 12 sets of root tissue samples by RNA-seq and iTRAQ (Isobaric tags for relative and absolute quantification). Phenotypic results showed that the elongation zone was significantly longer in root accessions with long roots compared to the short-rooted accessions. A genome-wide association study (GWAS) identified four stable chromosomal regions significantly associated with radicle length, among which 1A, 4A, and 7A chromosomes regions explained 7.17% to12.93% of the phenotypic variation. The omics studies identified the expression patterns of 24 DEGs/DEPs changed at both the transcriptional and protein levels. These DEGs/DEPs were mainly involved in carbon fixation in photosynthetic organisms, photosynthesis and phenylpropanoid biosynthesis pathways. TraesCS1A02G104100 and TraesCS2B02G519100 were involved in the biosynthesis of tricin-lignins in cell walls and may affect the extension of cell walls in the radicle elongation zone. A combination of GWAS and RNA-seq analyses revealed 19 DEGs with expression changes in the four accessions, among which, TraesCS1A02G422700 (a cysteine-rich receptor-like protein kinase 6, CRK6) also showed upregulation in the comparison group by RNA-seq, iTRAQ, and qRT-PCR. BSMV-mediated gene silencing also showed that TaCRK6 improves root development in wheat. Our data suggest that TaCRK6 is a candidate gene regulating radicle length in wheat.

Systemic effects of Tuber melanosporum inoculation in two Corylus avellana genotypes

Roots of the European hazelnut (Corylus avellana L.), i.e., one of the most economically important nut species, form symbiosis with ectomycorrhizal (ECM) fungi, including truffles. Although physical interactions only occur in roots, the presence of mycorrhizal fungi can lead to metabolic changes at a systemic level, i.e., in leaves. However, how root colonization by ECM fungi modifies these processes in the host plant has so far not been widely studied. This work aimed to investigate the response in two C. avellana genotypes, focusing on leaves from plants inoculated with the black truffle Tuber melanosporum Vittad. Transcriptomic profiles of leaves of colonized plants were compared with those of non-colonized plants, as well as sugar and polyphenolic content. Results suggested that T. melanosporum has the potential to support plants in stressed conditions, leading to the systemic regulation of several genes involved in signaling and defense responses. Although further confirmation is needed, our results open new perspectives for future research aimed to highlight novel aspects in ECM symbiosis.

Function of Protein Kinases in Leaf Senescence of Plants

Leaf senescence is an evolutionarily acquired process and it is critical for plant fitness. During senescence, macromolecules and nutrients are disassembled and relocated to actively growing organs. Plant leaf senescence process can be triggered by developmental cues and environmental factors, proper regulation of this process is essential to improve crop yield. Protein kinases are enzymes that modify their substrates activities by changing the conformation, stability, and localization of those proteins, to play a crucial role in the leaf senescence process. Impressive progress has been made in understanding the role of different protein kinases in leaf senescence recently. This review focuses on the recent progresses in plant leaf senescence-related kinases. We summarize the current understanding of the function of kinases on senescence signal perception and transduction, to help us better understand how the orderly senescence degeneration process is regulated by kinases, and how the kinase functions in the intricate integration of environmental signals and leaf age information.

Quantitative proteome analysis reveals changes of membrane transport proteins in Sedum plumbizincicola under cadmium stress

Sedum plumbizincicola is an herbaceous species tolerant of excessive cadmium accumulation in above-ground tissues. The implications of membrane proteins, especially integrative membrane proteins, in Cd detoxification of plants have received attention in recent years, but a comprehensive profiling of Cd-responsive membrane proteins from Cd hyperaccumulator plants is lacking. In this study, the membrane proteins of root, stem, and leaf tissues of S. plumbizincicola seedlings treated with Cd solution for 0, 1 or 4 days were analyzed by Tandem Mass Tag (TMT) labeling-based proteome quantification (Data are available via ProteomeXchange with identifier PXD025302). Total 3353 proteins with predicted transmembrane helices were identified and quantified in at least one tissue group. 1667 proteins were defined as DAPs (differentially abundant proteins) using fold change >1.5 with p-values <0.05. The number of DAPs involved in metabolism, transport protein, and signal transduction was significantly increased after exposure to Cd, suggesting that the synthesis and decomposition of organic compounds and the transport of ions were actively involved in the Cd tolerance process. The number of up-regulated transport proteins increased significantly from 1-day exposure to 4-day exposure, from 5 to 112, 16 to 42, 18 to 44, in root, stem, and leaf, respectively. Total 352 Cd-regulated transport proteins were identified, including ABC transporters, ion transport proteins, aquaporins, proton pumps, and organic transport proteins. Heterologous expression of SpABCB28, SpMTP5, SpNRAMP5, and SpHMA2 in yeast and subcellular localization showed the Cd-specific transport activity. The results will enhance our understanding of the molecular mechanism of Cd hypertolerance and hyperaccumulation in S. plumbizincicola and will be benefit for future genetic engineering in phytoremediation.

Silencing of ATG2 and ATG7 promotes programmed cell death in wheat via inhibition of autophagy under salt stress

Salt stress, as an abiotic stress, limits crops production worldwide. Autophagy and programmed cell death (PCD) have been functionally linked to plant adaptation to abiotic stress. However, the relation of autophagy and PCD is still under debate and the mechanism behind remains not fully understood. In this study, salt-tolerant wheat cultivar Jimai22 was used as the experimental material, and 150 mM NaCl was added to the hydroponic culture to test the effect of salt treatment. The results showed that NaCl stress enhances autophagic activity and induced occurrence of PCD in roots and leaves of wheat seedlings. Then, the barley stripe mosaic virus-induced silencing (BSMV-VIGS) method was used to inhibit autophagy by silencing the expression of ATG2 or ATG7. The results showed that silencing of ATG2 or ATG7 significantly inhibited autophagy and impaired the tolerance of wheat to NaCl stress. Moreover, silencing of ATG2 or ATG7 disrupted the absorption of Na, Cl, K and Ca elements and led to subsequent disequilibrium of Na⁺, Cl^-, K⁺ and Ca²⁺, induced generation of excess reactive oxygen species (ROS), decreased the antioxidant activity, damaged photosynthesis apparatus, increased the level of PCD and led to differential expression of the genes, two metacaspase genes, cysteine-rich receptor-like kinase (CRK) 10, and CRK26 in leaves of wheat seedlings under NaCl stress. The effect of the inhibitor 3-methyladenine (3-MA) on roots and leaves of wheat seedlings was in accordance with that of ATG2 and ATG7 silencing. Our results suggest that autophagy negatively regulates salt-induced PCD, or limits the scale of salt-induced PCD to avoid severe tissue death in wheat seedlings.

In silico analysis and expression profiling of S-domain receptor-like kinases (SD-RLKs) under different abiotic stresses in Arabidopsis thaliana

BACKGROUND

S-domain receptor-like kinases (SD-RLKs) are an important and multi-gene subfamily of plant receptor-like/pelle kinases (RLKs), which are known to play a significant role in the development and immune responses of Arabidopsis thaliana. The conserved cysteine residues in the extracellular domain of SD-RLKs make them interesting candidates for sensing reactive oxygen species (ROS), assisting oxidative stress mitigation and associated signaling pathways during abiotic stresses. However, how closely SD-RLKs are interrelated to abiotic stress mitigation and signaling remains unknown in A. thaliana.

RESULTS

This study was initiated by examining the chromosomal localization, phylogeny, sequence and differential expression analyses of 37 SD-RLK genes using publicly accessible microarray datasets under cold, osmotic stress, genotoxic stress, drought, salt, UV-B, heat and wounding. Out of 37 SD-RLKs, 12 genes displayed differential expression patterns in both the root and the shoot tissues. Promoter structure analysis suggested that these 12 SD-RLK genes harbour several potential cis-regulatory elements (CREs), which are involved in regulating multiple abiotic stress responses. Based on these observations, we investigated the expression patterns of 12 selected SD-RLKs under ozone, wounding, oxidative (methyl viologen), UV-B, cold, and light stress at different time points using semi-qRT-PCR. Of these 12 SD-SRKs, the genes At1g61360, At1g61460, At1g61380, and At4g27300 emerged as potential candidates that maintain their expression in most of the stress treatments till exposure for 12 h. Expression patterns of these four genes were further verified under similar stress treatments using qRT-PCR. The expression analysis indicated that the gene At1g61360, At1g61380, and At1g61460 were mostly up-regulated, whereas the expression of At4g27300 either up- or down-regulated in these conditions.

CONCLUSIONS

To summarize, the computational analysis and differential transcript accumulation of SD-RLKs under various abiotic stresses suggested their association with abiotic stress tolerance and related signaling in A. thaliana. We believe that a further detailed study will decipher the specific role of these representative SD-RLKs in abiotic stress mitigation vis-a-vis signaling pathways in A. thaliana.

Genome-Wide Identification and Characterization of Cysteine-Rich Receptor-Like Protein Kinase Genes in Tomato and Their Expression Profile in Response to Heat Stress

During plant growth, development and stress adaption, receptor-like protein kinases (RLKs) are essential components in perceiving and integrating extracellular stimuli and transmitting the signals to activate the downstream signaling pathways. Cysteine-rich receptor-like protein kinases (CRKs) are a large subfamily of RLKs and their roles in modulating plant disease resistance are well elucidated. However, the roles of CRKs in plant abiotic stress responses, especially heat stress, are largely unknown. In this study, 35 SlCRK genes were identified in tomato (Solanum lycopersicum) based on the multiple sequence alignment and phylogenetic relationships. SlCRK genes are tandemly distributed on seven chromosomes and have similar exon–intron organization and common conserved motifs. Various phytohormone responsive, stress responsive cis-regulatory elements and heat shock elements are predicted in the promoter regions of SlCRK genes. Transcriptome analysis of tomato fruits under heat stress revealed that most SlCRK genes were downregulated upon heat treatment. GO enrichment analyses of genes that were co-expressed with SlCRK members have identified various stress responses related and proteasomal protein catabolic process related genes, which may be involved in heat stress signaling. Overall, our results provide valuable information for further research on the roles of SlCRKs in response to abiotic stress, especially heat stress.

CIA2 and CIA2-LIKE are required for optimal photosynthesis and stress responses in Arabidopsis thaliana

Chloroplast-to-nucleus retrograde signaling is essential for cell function, acclimation to fluctuating environmental conditions, plant growth and development. The vast majority of chloroplast proteins are nuclear-encoded, and must be imported into the organelle after synthesis in the cytoplasm. This import is essential for the development of fully functional chloroplasts. On the other hand, functional chloroplasts act as sensors of environmental changes and can trigger acclimatory responses that influence nuclear gene expression. Signaling via mobile transcription factors (TFs) has been recently recognized as a way of communication between organelles and the nucleus. In this study, we performed a targeted reverse genetic screen to identify dual-localized TFs involved in chloroplast retrograde signaling during stress responses. We found that CHLOROPLAST IMPORT APPARATUS 2 (CIA2) has a functional plastid transit peptide, and can be located both in chloroplasts and the nucleus. Further, we found that CIA2, along with its homolog CIA2-like (CIL) are involved in the regulation of Arabidopsis responses to UV-AB, high light and heat shock. Finally, our results suggest that both CIA2 and CIL are crucial for chloroplast translation. Our results contribute to a deeper understanding of signaling events in the chloroplast-nucleus cross-talk.

Effects of Propranolol on Growth, Lipids and Energy Metabolism and Oxidative Stress Response of Phaeodactylum tricornutum

Simple Summary

In the past two decades, increasing attention has been directed to investigate the incidence and consequences of pharmaceuticals in the aquatic environment. Propranolol is a non-selective β-adrenoceptor blocker used in large quantities worldwide to treat cardiovascular conditions. Diatoms (model organism) exposed to this compound showed evident signs of oxidative stress, a significant reduction of the autotrophic O₂ production and an increase in the heterotrophic mitochondrial respiration. Additionally, diatoms exposed to propranolol showed a consumption of its storage lipids. In ecological terms this will have cascading impacts in the marine trophic webs, where these organisms are key elements, through a reduction of the water column oxygenation and essential fatty acid availability to the heterotrophic organisms that depend on these primary producers. In ecotoxicological terms, diatoms photochemical and fatty acid traits showed to be potential good biomarkers for toxicity assessment of diatoms exposed to this widespread pharmaceutical compound.

Abstract

Present demographic trends suggest a rise in the contributions of human pharmaceuticals into coastal ecosystems, underpinning an increasing demand to evaluate the ecotoxicological effects and implications of drug residues in marine risk assessments. Propranolol, a non-selective β-adrenoceptor blocker, is used worldwide to treat high blood pressure conditions and other related cardiovascular conditions. Although diatoms lack β-adrenoceptors, this microalgal group presents receptor-like kinases and proteins with a functional analogy to the animal receptors and that can be targeted by propranolol. In the present work, the authors evaluated the effect of this non-selective β-adrenoceptor blocker in diatom cells using P. tricornutum as a model organism, to evaluate the potential effect of this compound in cell physiology (growth, lipids and energy metabolism and oxidative stress) and its potential relevance for marine ecosystems. Propranolol exposure leads to a significant reduction in diatom cell growth, more evident in the highest concentrations tested. This is likely due to the observed impairment of the main primary photochemistry processes and the enhancement of the mitochondrial respiratory activity. More specifically, propranolol decreased the energy transduction from photosystem II (PSII) to the electron transport chain, leading to an increase in oxidative stress levels. Cells exposed to propranolol also exhibited high-dissipated energy flux, indicating that this excessive energy is efficiently diverted, to some extent, from the photosystems, acting to prevent irreversible photoinhibition. As energy production is impaired at the PSII donor side, preventing energy production through the electron transport chain, diatoms appear to be consuming storage lipids as an energy backup system, to maintain essential cellular functions. This consumption will be attained by an increase in respiratory activity. Considering the primary oxygen production and consumption pathways, propranolol showed a significant reduction of the autotrophic O₂ production and an increase in the heterotrophic mitochondrial respiration. Both mechanisms can have negative effects on marine trophic webs, due to a decrease in the energetic input from marine primary producers and a simultaneous oxygen production decrease for heterotrophic species. In ecotoxicological terms, bio-optical and fatty acid data appear as highly efficient tools for ecotoxicity assessment, with an overall high degree of classification when these traits are used to build a toxicological profile, instead of individually assessed.

Reshaping of the Arabidopsis thaliana Proteome Landscape and Co-regulation of Proteins in Development and Immunity

Proteome remodeling is a fundamental adaptive response, and proteins in complexes and functionally related proteins are often co-expressed. Using a deep sampling strategy we define core proteomes of Arabidopsis thaliana tissues with around 10 000 proteins per tissue, and absolutely quantify (copy numbers per cell) nearly 16 000 proteins throughout the plant lifecycle. A proteome-wide survey of global post-translational modification revealed amino acid exchanges pointing to potential conservation of translational infidelity in eukaryotes. Correlation analysis of protein abundance uncovered potentially new tissue- and age-specific roles of entire signaling modules regulating transcription in photosynthesis, seed development, and senescence and abscission. Among others, the data suggest a potential function of RD26 and other NAC transcription factors in seed development related to desiccation tolerance as well as a possible function of cysteine-rich receptor-like kinases (CRKs) as ROS sensors in senescence. All of the components of ribosome biogenesis factor (RBF) complexes were found to be co-expressed in a tissue- and age-specific manner, indicating functional promiscuity in the assembly of these less-studied protein complexes in Arabidopsis.Furthermore, we characterized detailed proteome remodeling in basal immunity by treating Arabidopsis seeldings with flg22. Through simultaneously monitoring phytohormone and transcript changes upon flg22 treatment, we obtained strong evidence of suppression of jasmonate (JA) and JA-isoleucine (JA-Ile) levels by deconjugation and hydroxylation by IAA-ALA RESISTANT3 (IAR3) and JASMONATE-INDUCED OXYGENASE 2 (JOX2), respectively, under the control of JASMONATE INSENSITIVE 1 (MYC2), suggesting an unrecognized role of a new JA regulatory switch in pattern-triggered immunity. Taken together, the datasets generated in this study present extensive coverage of the Arabidopsis proteome in various biological scenarios, providing a rich resource available to the whole plant science community.

Genomic Dissection of a Wild Region in a Superior Solanum pennellii Introgression Sub-Line with High Ascorbic Acid Accumulation in Tomato Fruit

The Solanum pennellii introgression lines (ILs) have been exploited to map quantitative trait loci (QTLs) and identify favorable alleles that could improve fruit quality traits in tomato varieties. Over the past few years, ILs exhibiting increased content of ascorbic acid in the fruit have been selected, among which the sub-line R182. The aims of this work were to identify the genes of the wild donor S. pennellii harbored by the sub-line and to detect genes controlling ascorbic acid accumulation by using genomics tools. A Genotyping-By-Sequencing (GBS) approach confirmed that no wild introgressions were present in the sub-line besides one region on chromosome 7. By using a dense single nucleotide polymorphism (SNP) map obtained by RNA sequencing (RNA-Seq), the wild region of the sub-line was finely identified; thus, defining 39 wild genes that replaced 33 genes of the ILs genetic background (cv. M82). The differentially expressed genes mapping in the region and the variants detected among the cultivated and the wild alleles evidenced the potential role of the novel genes present in the wild region. Interestingly, one upregulated gene, annotated as a major facilitator superfamily protein, showed a novel structure in R182, with respect to the parental lines. These genes will be further investigated using gene editing strategies.

Plasma membrane proteomic analysis by TMT-PRM provides insight into mechanisms of aluminum resistance in tamba black soybean roots tips

Aluminum (Al) toxicity in acid soil is a worldwide agricultural problem that inhibits crop growth and productivity. However, the signal pathways associated with Al tolerance in plants remain largely unclear. In this study, tandem mass tag (TMT)-based quantitative proteomic methods were used to identify the differentially expressed plasma membrane (PM) proteins in Tamba black soybean (TBS) root tips under Al stress. Data are available via ProteomeXchange with identifier PXD017160. In addition, parallel reaction monitoring (PRM) was used to verify the protein quantitative data. The results showed that 907 PM proteins were identified in Al-treated plants. Among them, compared to untreated plants, 90 proteins were differentially expressed (DEPs) with 46 up-regulated and 44 down-regulated (fold change > 1.3 or < 0.77, p < 0.05). Functional enrichment based on GO, KEGG and protein domain revealed that the DEPs were associated with membrane trafficking and transporters, modifying cell wall composition, defense response and signal transduction. In conclusion, our results highlight the involvement of GmMATE13, GmMATE75, GmMATE87 and H⁺-ATPase in Al-induced citrate secretion in PM of TBS roots, and ABC transporters and Ca²⁺ have been implicated in internal detoxification and signaling of Al, respectively. Importantly, our data provides six receptor-like protein kinases (RLKs) as candidate proteins for further investigating Al signal transmembrane mechanisms.

A novel cysteine-rich receptor-like kinase gene, TaCRK2, contributes to leaf rust resistance in wheat

Leaf rust, caused by Puccinia triticina, is one of the most destructive fungal diseases in wheat production worldwide. The hypersensitive reaction (HR) is an important defence response against P. triticina infection. In this study, the physiological races 165 and 260 of P. triticina were combined with a line derived from the bread wheat cultivar Thatcher with the leaf rust resistance locus Lr26 to form compatible and incompatible combinations, respectively. Based on an RNA-Seq database of the interaction systems, a new wheat cysteine-rich receptor-like kinase gene, TaCRK2, is specifically induced and up-regulated in the incompatible combination. We identified that TaCRK2 was regulated in a Ca²⁺ -dependent manner. Knockdown of TaCRK2 by virus-induced gene silencing and RNAi leads to a dramatic increase in HR area and the number of haustorial mother cells at the single infection site. In addition, urediniospores, a P. triticina-specific pathogenic marker in compatible combinations, were observed on leaf surfaces of silenced plants at approximately 15 days after inoculation in the incompatible combination. Moreover, transcription levels of TaPR1, TaPR2, and TaPR5 were obviously reduced in TaCRK2-silenced plants. TaCRK2 overexpression in Nicotiana benthamiana induced strong HR-like cell death. Finally, transient expression of green fluorescent protein fused with TaCRK2 in N. benthamiana indicated that TaCRK2 localizes in the endoplasmic reticulum. Thus, TaCRK2 plays an important role in the resistance to P. triticina infection and has a positive regulation effect on the HR cell death process induced by P. triticina.

The cysteine-rich receptor-like protein kinase CRK28 modulates Arabidopsis growth and development and influences abscisic acid responses

CRK28, a cysteine-rich receptor-like kinase, plays a role in root organogenesis and overall growth of plants and antagonizes abscisic acid response in seed germination and primary root growth. Receptor-like kinases (RLK) orchestrate development and adaptation to environmental changes in plants. One of the largest RLK groups comprises cysteine-rich receptor-like kinases (CRKs), for which the function of most members remains unknown. In this report, we show that the loss of function of CRK28 led to the formation of roots that are longer and more branched than the parental (Col-0) plantlets, and this correlates with an enhanced domain of the mitotic reporter CycB1:uidA in primary root meristems, whereas CRK28 overexpressing lines had the opposite phenotype, including slow root growth and reduced lateral root formation. Epidermal cell analyses revealed that crk28 mutants had reduced root hair length and increased trichome number, whereas 35S::CRK28 lines present primary roots with longer root hairs but lesser trichomes in leaves. The overall growth in soil of crk28 mutant and CRK28 overexpressing lines was reduced or enhanced, respectively, when compared to the parental (Col-0) seedlings, while germination, root growth and expression analyses of ABI3 and ABI5 further showed that CRK28 modulates ABA responses, which may be important to fine-tune plant morphogenesis. Our study unravels the participation of RLK signaling in root growth and epidermal cell differentiation.

CRK2 Enhances Salt Tolerance by Regulating Callose Deposition in Connection with PLDα1

High salinity is an increasingly prevalent source of stress to which plants must adapt. The receptor-like protein kinases, including members of the Cys-rich receptor-like kinase (CRK) subfamily, are a highly expanded family of transmembrane proteins in plants that are largely responsible for communication between cells and the extracellular environment. Various CRKs have been implicated in biotic and abiotic stress responses; however, their functions on a cellular level remain largely uncharacterized. Here we have shown that CRK2 enhances salt tolerance at the germination stage in Arabidopsis (Arabidopsis thaliana) and also modulates root length. We established that functional CRK2 is required for salt-induced callose deposition. In doing so, we revealed a role for callose deposition in response to increased salinity and demonstrated its importance for salt tolerance during germination. Using fluorescently tagged proteins, we observed specific changes in the subcellular localization of CRK2 in response to various stress treatments. Many of CRK2's cellular functions were dependent on phospholipase D activity, as were the subcellular localization changes. Thus, we propose that CRK2 acts downstream of phospholipase D during salt stress, promoting callose deposition and regulating plasmodesmal permeability, and that CRK2 adopts specific stress-dependent subcellular localization patterns that allow it to carry out its functions.

Genetic and phenotypic analyses indicate that resistance to flooding stress is uncoupled from performance in cultivated sunflower

Given the rising risk of extreme weather caused by climate change, enhancement of abiotic stress resistance in crops is increasingly urgent. But will the development of stress-resistant cultivars come at the cost of yield under ideal conditions? We hypothesize that this need not be inevitable, because resistance alleles with minimal pleiotropic costs may evade artificial selection and be retained in crop germplasm. Genome-wide association (GWA) analyses for variation in plant performance and flooding response were conducted in cultivated sunflower, a globally important oilseed. We observed broad variation in flooding responses among genotypes. Flooding resistance was not strongly correlated with performance in control conditions, suggesting no inherent trade-offs. Consistent with this finding, we identified a subset of loci conferring flooding resistance, but lacking antagonistic effects on growth. Genetic diversity loss at candidate genes underlying these loci was significantly less than for other resistance genes during cultivated sunflower evolution. Despite bottlenecks associated with domestication and improvement, low-cost resistance alleles remain within the cultivated sunflower gene pool. Thus, development of cultivars that are both flooding-tolerant and highly productive should be straightforward. Results further indicate that estimates of pleiotropic costs from GWA analyses explain, in part, patterns of diversity loss in crop genomes.

Modulation of defence and iron homeostasis genes in rice roots by the diazotrophic endophyte Herbaspirillum seropedicae

Rice is staple food of nearly half the world’s population. Rice yields must therefore increase to feed ever larger populations. By colonising rice and other plants, Herbaspirillum spp. stimulate plant growth and productivity. However the molecular factors involved are largely unknown. To further explore this interaction, the transcription profiles of Nipponbare rice roots inoculated with Herbaspirillum seropedicae were determined by RNA-seq. Mapping the 104 million reads against the Oryza sativa cv. Nipponbare genome produced 65 million unique mapped reads that represented 13,840 transcripts each with at least two-times coverage. About 7.4% (1,014) genes were differentially regulated and of these 255 changed expression levels more than two times. Several of the repressed genes encoded proteins related to plant defence (e.g. a putative probenazole inducible protein), plant disease resistance as well as enzymes involved in flavonoid and isoprenoid synthesis. Genes related to the synthesis and efflux of phytosiderophores (PS) and transport of PS-iron complexes were induced by the bacteria. These data suggest that the bacterium represses the rice defence system while concomitantly activating iron uptake. Transcripts of H. seropedicae were also detected amongst which transcripts of genes involved in nitrogen fixation, cell motility and cell wall synthesis were the most expressed.

QTL mapping for micronutrients concentration and yield component traits in a hexaploid wheat mapping population

Bread wheat is a major staple cereal provides more than 20% of dietary energy and protein supply to global population. However, with increasing population growth, the problem of nutritional deficiencies is increasingly affecting the health of resource people with predominantly cereal-based diet. Therefore, the development of wheat genotypes with micronutrient-dense grains along with high-yield potential is one of the major priorities of wheat biofortification program at CIMMYT. We conducted a QTL mapping study using a recombinant inbred line (RIL) population derived from a cross between a Chinese parental line with highGZnC and a Mexican commercial bread wheat cultivar Roelfs F2007 to identify QTLs that could potentially be integrated in mineral nutrient concentrations and agronomic-related traits breeding. We evaluated 200 RIL lines for mineral nutrient concentrations and agronomic-related traits over two years. A total of 60 QTLs were detected, of which 10 QTLs for GZnC, 9 for GFeC, 5 for GPC and 36 for agronomic-related traits. Moreover, a total of 55 promising candidate genes were identified from the list of associated markers for GFeC and GZnC using the recently annotated wheat genome sequence. We identified the promising genomic regions with high mineral nutrient concentrations and acceptable yield potential, which are good resource for further use in wheat biofortification breeding programs.

Genomic dissection and transcriptional profiling of Cysteine-rich receptor-like kinases in five cereals and functional characterization of TaCRK68-A

Cysteine-rich receptor-like kinases (CRK) constitute one of the largest subfamily of receptor-like kinases, which play crucial roles in plant development and stress response. In total, 43, 37, 36, 38 and 170 CRK genes including duplicated genes were identified in the genome of Brachypodium distachyon, Hordeum vulgare, Oryza sativa, Sorghum bicolor and Triticum aestivum, respectively. These CRK proteins were tightly clustered into four phylogenetic groups and exhibited close syntenic relationship among orthologous genes. Majority of CRK proteins contain a transmembrane domain for plasma membrane localization. The organization of exon/intron, domains and motifs were variably conserved. Tissue-specific expression suggested the involvement of certain CRK genes in plant development. Modulated expression revealed their specific stress-responsive functions. Co-expression and interaction analysis indicated their role in signaling. Ks value and divergence time analysis suggested duplication of TaCRK genes before the hybridization of T. aestivum sub-genomes. Expression comparison of duplicated TaCRK genes revealed functional retention, neofunctionalization or pseudo-functionalization. Recombinant expression of a stress-responsive gene TaCRK68-A in Escherichia coli and Saccharomyces cerevisiae displayed enhanced tolerance against heat, drought, cold and salinity stresses. The study suggested vital functions of CRKs during development and stresses, and provides the basis for functional characterization of each gene in future studies.

LSD1-, EDS1- and PAD4-dependent conditional correlation among salicylic acid, hydrogen peroxide, water use efficiency and seed yield in Arabidopsis thaliana

In Arabidopsis thaliana, LESION SIMULATING DISEASE 1 (LSD1), ENHANCED DISEASE SUSCEPTIBILITY 1 (EDS1) and PHYTOALEXIN DEFICIENT 4 (PAD4) proteins are regulators of cell death (CD) in response to abiotic and biotic stresses. Hormones, such as salicylic acid (SA), and reactive oxygen species, such as hydrogen peroxide (H₂ O₂ ), are key signaling molecules involved in plant CD. The proposed mathematical models presented in this study suggest that LSD1, EDS1 and PAD4 together with SA and H₂ O₂ are involved in the control of plant water use efficiency (WUE), vegetative growth and generative development. The analysis of Arabidopsis wild-type and single mutants lsd1, eds1, and pad4, as well as double mutants eds1/lsd1 and pad4/lsd1, demonstrated the strong conditional correlation between SA/H₂ O₂ and WUE that is dependent on LSD1, EDS1 and PAD4 proteins. Moreover, we found a strong correlation between the SA/H₂ O₂ homeostasis of 4-week-old Arabidopsis leaves and a total seed yield of 9-week-old plants. Altogether, our results prove that SA and H₂ O₂ are conditionally regulated by LSD1/EDS/PAD4 to govern WUE, biomass accumulation and seed yield. Conditional correlation and the proposed models presented in this study can be used as the starting points in the creation of a plant breeding algorithm that would allow to estimate the seed yield at the initial stage of plant growth, based on WUE, SA and H₂ O₂ content.

Limited ventilation causes stress and changes in Arabidopsis morphological, physiological and molecular phenotype during in vitro growth

A huge number of experiments in plant biology are conducted in sterile, sealed containers, providing environmental stability and full control of factors influencing the plant system. With respect to roots the in vitro growth has another benefit - the ease of conducting visual observations when grown in transparent media. Moreover, straightforward measurements of in vitro grown root systems make them a sensitive and convenient sensor of multiple stresses which may occur during experiments. In order to optimize root nematode infection tests for Arabidopsis mutants with relatively mild phenotypes, two Petri dish sealing techniques were tested (permeable medical adhesive tape and a popular non-permeable plastic film). Using standard experimental settings applied for infection tests, the root architecture, nematode infections, ion leakage, efficiency of photosynthesis, ethylene (ET) production, and CO₂ accumulation were monitored in Arabidopsis thaliana Ws-0 wild-type and lsd1 (lesion stimulating disease 1) plants, which is a conditional dependent programmed cell death mutant. All tested parameters gave statistically significant differences between the analyzed sealing tapes, indicating the importance of air exchange. This factor is quite obvious but often ignored in experiments performed in Petri dishes. The results clearly indicate that stress is greater in air-tight sealed plates. These observations were supported by the great expression variation of several marker genes associated with reactive oxygen species (ROS), ET, salicylic (SA), and jasmonic acid (JA) biosynthesis and signaling in two-week-old seedlings. These results are discussed in light of the observed changes in the ET and CO₂ concentration. Our results clearly indicate the importance of culture parameters for monitoring of abiotic and biotic stress responses in laboratory conditions, including accurate mutant phenotyping.

Cysteine-Rich Receptor-Like Kinase Gene Family Identification in the Phaseolus Genome and Comparative Analysis of Their Expression Profiles Specific to Mycorrhizal and Rhizobial Symbiosis

Receptor-like kinases (RLKs) are conserved upstream signaling molecules that regulate several biological processes, including plant development and stress adaptation. Cysteine (C)-rich receptor-like kinases (CRKs) are an important class of RLK that play vital roles in disease resistance and cell death in plants. Genome-wide analyses of CRK genes have been carried out in Arabidopsis and rice, while functional characterization of some CRKs has been carried out in wheat and tomato in addition to Arabidopsis. A comprehensive analysis of the CRK gene family in leguminous crops has not yet been conducted, and our understanding of their roles in symbiosis is rather limited. Here, we report the comprehensive analysis of the PhaseolusCRK gene family, including identification, sequence similarity, phylogeny, chromosomal localization, gene structures, transcript expression profiles, and in silico promoter analysis. Forty-six CRK homologs were identified and phylogenetically clustered into five groups. Expression analysis suggests that PvCRK genes are differentially expressed in both vegetative and reproductive tissues. Further, transcriptomic analysis revealed that shared and unique CRK genes were upregulated during arbuscular mycorrhizal and rhizobial symbiosis. Overall, the systematic analysis of the PvCRK gene family provides valuable information for further studies on the biological roles of CRKs in various Phaseolus tissues during diverse biological processes, including Phaseolus-mycorrhiza/rhizobia symbiosis.

Semi-dominant mutation in the cysteine-rich receptor-like kinase gene, ALS1, conducts constitutive defence response in rice

Plants have evolved a sophisticated two-branch defence system to prevent the growth and spread of pathogen infection. The novel Cys-rich repeat (CRR) containing receptor-like kinases, known as CRKs, were reported to mediate defence resistance in plants. For rice, there are only two reports of CRKs. A semi-dominant lesion mimic mutant als1 (apoptosis leaf and sheath 1) in rice was identified to demonstrate spontaneous lesions on the leaf blade and sheath. A map-based cloning strategy was used for fine mapping and cloning of ALS1, which was confirmed to be a typical CRK in rice. Functional studies of ALS1 were conducted, including phylogenetic analysis, expression analysis, subcellular location and blast resistance identification. Most pathogenesis-related (PR) genes and other defence-related genes were activated and up-regulated to a high degree. ALS1 was expressed mainly in the leaf blade and sheath, in which further study revealed that ALS1 was present in the vascular bundles. ALS1 was located in the cell membrane of rice protoplasts, and its mutation did not change its subcellular location. Jasmonic acid (JA) and salicylic acid (SA) accumulation were observed in als1, and enhanced blast resistance was also observed. The mutation of ALS1 caused a constitutively activated defence response in als1. The results of our study imply that ALS1 participates in a defence response resembling the common SA-, JA- and NH1-mediated defence responses in rice.

Transcriptome Profiles of Strawberry (Fragaria vesca) Fruit Interacting With Botrytis cinerea at Different Ripening Stages

Gray mold caused by Botrytis cinerea is a major cause of economic losses in strawberry fruit production, limiting fruit shelf life and commercialization. When the fungus infects Fragaria × ananassa strawberry at flowering or unripe fruit stages, symptoms develop after an extended latent phase on ripe fruits before or after harvesting. To elucidate the growth kinetics of B. cinerea on flower/fruit and the molecular responses associated with low susceptibility of unripe fruit stages, woodland strawberry Fragaria vesca flowers and fruits, at unripe white and ripe red stages, were inoculated with B. cinerea. Quantification of fungal genomic DNA within 72 h postinoculation (hpi) showed limited fungal growth on open flower and white fruit, while on red fruit, the growth was exponential starting from 24 hpi and sporulation was observed within 48 hpi. RNA sequencing applied to white and red fruit at 24 hpi showed that a total of 2,141 genes (12.5% of the total expressed genes) were differentially expressed due to B. cinerea infection. A broad transcriptional reprogramming was observed in both unripe and ripe fruits, involving in particular receptor and signaling, secondary metabolites, and defense response pathways. Membrane-localized receptor-like kinases and nucleotide-binding site leucine-rich repeat genes were predominant in the surveillance system of the fruits, most of them being downregulated in white fruits and upregulated in red fruits. In general, unripe fruits exhibited a stronger defense response than red fruits. Genes encoding for pathogenesis-related proteins and flavonoid polyphenols as well as genes involved in cell-wall strengthening were upregulated, while cell-softening genes appeared to be switched off. As a result, B. cinerea remained quiescent in white fruits, while it was able to colonize ripe red fruits.

Improving photosynthesis, plant productivity and abiotic stress tolerance - current trends and future perspectives

With unfavourable climate changes and an increasing global population, there is a great need for more productive and stress-tolerant crops. As traditional methods of crop improvement have probably reached their limits, a further increase in the productivity of crops is expected to be possible using genetic engineering. The number of potential genes and metabolic pathways, which when genetically modified could result in improved photosynthesis and biomass production, is multiple. Photosynthesis, as the only source of carbon required for the growth and development of plants, attracts much attention is this respect, especially the question concerning how to improve CO₂ fixation and limit photorespiration. The most promising direction for increasing CO₂ assimilation is implementating carbon concentrating mechanisms found in cyanobacteria and algae into crop plants, while hitherto performed experiments on improving the CO₂ fixation versus oxygenation reaction catalyzed by Rubisco are less encouraging. On the other hand, introducing the C₄ pathway into C₃ plants is a very difficult challenge. Among other points of interest for increased biomass production is engineering of metabolic regulation, certain proteins, nucleic acids or phytohormones. In this respect, enhanced sucrose synthesis, assimilate translocation to sink organs and starch synthesis is crucial, as is genetic engineering of the phytohormone metabolism. As abiotic stress tolerance is one of the key factors determining crop productivity, extensive studies are being undertaken to develop transgenic plants characterized by elevated stress resistance. This can be accomplished due to elevated synthesis of antioxidants, osmoprotectants and protective proteins. Among other promising targets for the genetic engineering of plants with elevated stress resistance are transcription factors that play a key role in abiotic stress responses of plants. In this review, most of the approaches to improving the productivity of plants that are potentially promising and have already been undertaken are described. In addition to this, the limitations faced, potential challenges and possibilities regarding future research are discussed.

Genome-wide analysis of the soybean CRK-family and transcriptional regulation by biotic stress signals triggering plant immunity

Cysteine-rich receptor-like kinases (CRKs) are transmembrane proteins that exhibit ectodomains containing the domain of unknown function 26 (DUF26). The CRKs form a large subfamily of receptor-like kinases in plants, and their possible functions remain to be elucidated. Several lines of evidence suggest that CRKs play important roles in plant defense responses to environmental stress, including plant immunity. We performed a genome-wide analysis of CRK encoding genes in soybean (Glycine max). We found 91 GmCRKs distributed in 16 chromosomes, and identified several tandem and segmental duplications, which influenced the expansion of this gene family. According to our phylogenetic analysis, GmCRKs are grouped in four clades. Furthermore, 12% of the members exhibited GmCRKs with a duplicated bi-modular organization of the ectodomains, containing four DUF26 domains. Expression analysis of GmCRKs was performed by exploring publicly available databases, and by RT-qPCR analysis of selected genes in soybean leaves responding to biotic stress signals. GmCRKs exhibited diverse expression patterns in leaves, stems, roots, and other tissues. Some of them were highly expressed in only one type of tissue, suggesting predominant roles in specific tissues. Furthermore, several GmCRKs were induced with PAMPs, DAMPs and the pathogens Phakopsora pachyrhizi and Phytophthora sojae. Expression profiles of several GmCRKs encoding highly similar proteins exhibited antagonist modes of regulation. The results suggest a fine-tuning control of GmCRKs transcriptional regulation in response to external stimuli, including PAMPs and DAMPs. This study offers a comprehensive view of the GmCRKs family in soybean, and provides a foundation for evolutionary and functional analysis of this family of plant proteins involved in the perception of pathogens and activation of plant immunity.

Friend or foe? Reactive oxygen species production, scavenging and signaling in plant response to environmental stresses

In the natural environment, plants are exposed to a variety of biotic and abiotic stress conditions that trigger rapid changes in the production and scavenging of reactive oxygen species (ROS). The production and scavenging of ROS is compartmentalized, which means that, depending on stimuli type, they can be generated and eliminated in different cellular compartments such as the apoplast, plasma membrane, chloroplasts, mitochondria, peroxisomes, and endoplasmic reticulum. Although the accumulation of ROS is generally harmful to cells, ROS play an important role in signaling pathways that regulate acclimatory and defense responses in plants, such as systemic acquired acclimation (SAA) and systemic acquired resistance (SAR). However, high accumulations of ROS can also trigger redox homeostasis disturbance which can lead to cell death, and in consequence, to a limitation in biomass and yield production. Different ROS have various half-lifetimes and degrees of reactivity toward molecular components such as lipids, proteins, and nucleic acids. Thus, they play different roles in intra- and extra-cellular signaling. Despite their possible damaging effect, ROS should mainly be considered as signaling molecules that regulate local and systemic acclimatory and defense responses. Over the past two decades it has been proven that ROS together with non-photochemical quenching (NPQ), hormones, Ca²⁺ waves, and electrical signals are the main players in SAA and SAR, two physiological processes essential for plant survival and productivity in unfavorable conditions.

Changes in gene expression in Camelina sativa roots and vegetative tissues in response to salinity stress

The response of Camelina sativa to salt stress was examined. Salt reduced shoot, but not root length. Root and shoot weight were affected by salt, as was photosynthetic capacity. Salt did not alter micro-element concentration in shoots, but increased macro-element (Ca and Mg) levels. Gene expression patterns in shoots indicated that salt stress may have led to shuttling of Na+ from the cytoplasm to the tonoplast and to an increase in K+ and Ca+2 import into the cytoplasm. In roots, gene expression patterns indicated that Na+ was exported from the cytoplasm by the SOS pathway and that K+ was imported in response to salt. Genes involved in chelation and storage were up-regulated in shoots, while metal detoxification appeared to involve various export mechanisms in roots. In shoots, genes involved in secondary metabolism leading to lignin, anthocyanin and wax production were up-regulated. Partial genome partitioning was observed in roots and shoots based on the expression of homeologous genes from the three C. sativa sub-genomes. Sub-genome I and II were involved in the response to salinity stress to about the same degree, while about 10% more differentially-expressed genes were associated with sub-genome III.

Receptor-Like Cytoplasmic Kinases: Central Players in Plant Receptor Kinase-Mediated Signaling

Receptor kinases (RKs) are of paramount importance in transmembrane signaling that governs plant reproduction, growth, development, and adaptation to diverse environmental conditions. Receptor-like cytoplasmic kinases (RLCKs), which lack extracellular ligand-binding domains, have emerged as a major class of signaling proteins that regulate plant cellular activities in response to biotic/abiotic stresses and endogenous extracellular signaling molecules. By associating with immune RKs, RLCKs regulate multiple downstream signaling nodes to orchestrate a complex array of defense responses against microbial pathogens. RLCKs also associate with RKs that perceive brassinosteroids and signaling peptides to coordinate growth, pollen tube guidance, embryonic and stomatal patterning, floral organ abscission, and abiotic stress responses. The activity and stability of RLCKs are dynamically regulated not only by RKs but also by other RLCK-associated proteins. Analyses of RLCK-associated components and substrates have suggested phosphorylation relays as a major mechanism underlying RK-mediated signaling.

GA3 application in grapes (Vitis vinifera L.) modulates different sets of genes at cluster emergence, full bloom, and berry stage as revealed by RNA sequence-based transcriptome analysis

In grapes (Vitis vinifera L.), exogenous gibberellic acid (GA₃) is applied at different stages of bunch development to achieve desirable bunch shape and berry size in seedless grapes used for table purpose. RNA sequence-based transcriptome analysis was used to understand the mechanism of GA₃ action at cluster emergence, full bloom, and berry stage in table grape variety Thompson Seedless. At cluster emergence, rachis samples were collected at 6 and 24 h after application of GA₃, whereas flower clusters and berry samples were collected at 6, 24, and 48 h after application at full bloom and 3-4 mm berry stages. Seven hundred thirty-three genes were differentially expressed in GA₃-treated samples. At rachis and flower cluster stage respectively, 126 and 264 genes were found to be significantly differentially expressed within 6 h of GA₃ application. The number of DEG reduced considerably at 24 h. However, at berry stage, major changes occurred even at 24 h and a number of DEGs at 6 and 24 h were 174 and 191, respectively. As compared to upregulated genes, larger numbers of genes were downregulated. Stage-specific response to the GA₃ application was observed as evident from the unique set of DEGs at each stage and only a few common genes among three stages. Among the DEGs, 67 were transcription factors. Functional categorization and enrichment analysis revealed that several transcripts involved in sucrose and hexose metabolism, hormone and secondary metabolism, and abiotic and biotic stimuli were enriched in response to application of GA₃. A high correlation was recorded for real-time PCR and transcriptome data for selected DEGs, thus indicating the robustness of transcriptome data obtained in this study for understanding the GA₃ response at different stages of berry development in grape. Chromosomal localization of DEGs and identification of polymorphic microsatellite markers in selected genes have potential for their use in breeding for varieties with improved bunch architecture.

Root transcripts associated with arsenic accumulation in hyperaccumulator Pteris vittata

Hyperaccumulation of arsenic (As) by brake fern Pteris vittata has been described as an important genetic trait that provides an option for development of a sustainable phytoremediation process for As mitigation. Accumulation of very high concentration of arsenic in above-ground tissues may be the result of arsenic vacuole compartmentalization, but the mechanism(s) of arsenic uptake and transport by underground tissues are largely unknown. In this study, we made an attempt towards understanding the molecular mechanism of As hyperaccumulation in this plant. A time-dependent As accumulation study indicates an exponential accumulation of As from 7 to 30 days of arsenic exposure in fronds, and day 3-7 in roots. Root transcriptome analysis identified 554,973 transcripts. Further, subsets of 824 transcripts were differentially expressed between treated and control samples. Many of the genes of critical As-stress response, transcription factors and metal transporters, biosynthesis of chelating compounds involved in uptake and accumulation mechanisms were identified. The genes that were highly expressed such as cysteine-rich RLK, and ABC transporter G family member 26 needs further studies along with arsenite transmembrane transporter. The analysis of generated transcriptome dataset has provided valuable information and platform for further functional studies.

Deep sequencing and in silico analysis of small RNA library reveals novel miRNA from leaf Persicaria minor transcriptome

In current era, majority of microRNA (miRNA) are being discovered through computational approaches which are more confined towards model plants. Here, for the first time, we have described the identification and characterization of novel miRNA in a non-model plant, Persicaria minor (P. minor) using computational approach. Unannotated sequences from deep sequencing were analyzed based on previous well-established parameters. Around 24 putative novel miRNAs were identified from 6,417,780 reads of the unannotated sequence which represented 11 unique putative miRNA sequences. PsRobot target prediction tool was deployed to identify the target transcripts of putative novel miRNAs. Most of the predicted target transcripts (mRNAs) were known to be involved in plant development and stress responses. Gene ontology showed that majority of the putative novel miRNA targets involved in cellular component (69.07%), followed by molecular function (30.08%) and biological process (0.85%). Out of 11 unique putative miRNAs, 7 miRNAs were validated through semi-quantitative PCR. These novel miRNAs discoveries in P. minor may develop and update the current public miRNA database.