The Arabidopsis floral repressor BFT delays flowering by competing with FT for FD binding under high salinity

A florigen-expressing subpopulation of companion cells expresses other small proteins and reveals a nitrogen-sensitive FT repressor

The precise onset of flowering is crucial to ensure successful plant reproduction. The gene FLOWERING LOCUS T (FT) encodes florigen, a mobile signal produced in leaves that initiates flowering at the shoot apical meristem. In response to seasonal changes, FT is induced in phloem companion cells located in distal leaf regions. Thus far, a detailed molecular characterization of the FT-expressing cells has been lacking. Here, we used bulk nuclei RNA-seq and single nuclei RNA (snRNA)-seq to investigate gene expression in FT-expressing cells and other phloem companion cells. Our bulk nuclei RNA-seq demonstrated that FT-expressing cells in cotyledons and in true leaves differed transcriptionally. Within the true leaves, our snRNA-seq analysis revealed that companion cells with high FT expression form a unique cluster in which many genes involved in ATP biosynthesis are highly upregulated. The cluster also expresses other genes encoding small proteins, including the flowering and stem growth inducer FPF1-LIKE PROTEIN 1 (FLP1) and the anti-florigen BROTHER OF FT AND TFL1 (BFT). In addition, we found that the promoters of FT and the genes co-expressed with FT in the cluster were enriched for the consensus binding motifs of NITRATE-INDUCIBLE GARP-TYPE TRANSCRIPTIONAL REPRESSOR 1 (NIGT1). Overexpression of the paralogous NIGT1.2 and NIGT1.4 repressed FT expression and significantly delayed flowering under nitrogen-rich conditions, consistent with NIGT1s acting as nitrogen-dependent FT repressors. Taken together, our results demonstrate that major FT-expressing cells show a distinct expression profile that suggests that these cells may produce multiple systemic signals to regulate plant growth and development.

BdRCN4, a Brachypodium distachyon TFL1 homologue, is involved in regulation of apical meristem fate

In higher plants, the shift from vegetative to reproductive development is governed by complex interplay of internal and external signals. TERMINALFLOWER1 (TFL1) plays a crucial role in the regulation of flowering time and inflorescence architecture in Arabidopsis thaliana. This study aimed to explore the function of BdRCN4, a homolog of TFL1 in Brachypodium distachyon, through functional analyses in mutant and transgenic plants. The results revealed that overexpression of BdRCN4 in B. distachyon leads to an extended vegetative phase and reduced production of spikelets. Similar results were found in A. thaliana, where constitutive expression of BdRCN4 promoted a delay in flowering time, followed by the development of hypervegetative shoots, with no flowers or siliques produced. Our results suggest that BdRCN4 acts as a flowering repressor analogous to TFL1, negatively regulating AP1, but no LFY expression. To further validate this hypothesis, a 35S::LFY-GR co-transformation approach on 35::BdRCN4 lines was performed. Remarkably, AP1 expression levels and flower formation were restored to normal in co-transformed plants when treated with dexamethasone. Although further molecular studies will be necessary, the evidence in B. distachyon support the idea that a balance between LFY and BdRCN4/TFL1 seems to be essential for activating AP1 expression and initiating floral organ identity gene expression. This study also demonstrates interesting conservation through the molecular pathways that regulate flowering meristem transition and identity across the evolution of monocot and dicot plants.

The evolution and functional divergence of FT-related genes in controlling flowering time in Brassica rapa ssp. rapa

KEY MESSAGE

The BrrFT paralogues exhibit distinct expression patterns and play different roles in regulating flowering time, and BrrFT4 competes with BrrFT1 and BrrFT2 to interact with BrrFD proteins. Flowering time is an important agricultural trait for Brassica crops, and early bolting strongly affects the yield and quality of Brassica rapa ssp. rapa. Flowering Locus T paralogues play an important role in regulating flowering time. In this study, we identified FT-related genes in turnip by phylogenetic classification, and four BrrFT homoeologs that shared with high identities with BraFT genes were isolated. The different gene structures, promoter binding sites, and expression patterns observed indicated that these genes may play different roles in flowering time regulation. Further genetic and biochemical experiments showed that as for FT-like paralogues, BrrFT2 acted as the key floral inducer, and BrrFT1 seems to act as a mild 'florigen' protein. However, BrrFT4 acts as a floral repressor and antagonistically regulates flowering time by competing with BrrFT1 and BrrFT2 to bind BrrFD proteins. BrrFT3 may have experienced loss of function via base shift mutation. Our results revealed the potential roles of FT-related genes in flowering time regulation in turnip.

Designing salt stress-resilient crops: Current progress and future challenges

Excess soil salinity affects large regions of land and is a major hindrance to crop production worldwide. Therefore, understanding the molecular mechanisms of plant salt tolerance has scientific importance and practical significance. In recent decades, studies have characterized hundreds of genes associated with plant responses to salt stress in different plant species. These studies have substantially advanced our molecular and genetic understanding of salt tolerance in plants and have introduced an era of molecular design breeding of salt-tolerant crops. This review summarizes our current knowledge of plant salt tolerance, emphasizing advances in elucidating the molecular mechanisms of osmotic stress tolerance, salt-ion transport and compartmentalization, oxidative stress tolerance, alkaline stress tolerance, and the trade-off between growth and salt tolerance. We also examine recent advances in understanding natural variation in the salt tolerance of crops and discuss possible strategies and challenges for designing salt stress-resilient crops. We focus on the model plant Arabidopsis (Arabidopsis thaliana) and the four most-studied crops: rice (Oryza sativa), wheat (Triticum aestivum), maize (Zea mays), and soybean (Glycine max).

Flavin-containing monooxygenases FMOGS-OXs integrate flowering transition and salt tolerance in Arabidopsis thaliana

Salt stress substantially leads to flowering delay. The regulation of salt-induced late flowering has been studied at the transcriptional and protein levels; however, the involvement of secondary metabolites has rarely been investigated. Here, we report that FMOGS-OXs (EC 1.14.13.237), the enzymes that catalyze the biosynthesis of glucosinolates (GSLs), promote flowering transition in Arabidopsis thaliana. It has been reported that WRKY75 is a positive regulator, and MAF4 is a negative regulator of flowering transition. The products of FMOGS-OXs, methylsulfinylalkyl GSLs (MS GSLs), facilitate flowering by inducing WRKY75 and repressing the MAS-MAF4 module. We further show that the degradation of MS GSLs is involved in salt-induced late flowering and salt tolerance. Salt stress induces the expression of myrosinase genes, resulting in the degradation of MS GSLs, thereby relieving the promotion of WRKY75 and inhibition of MAF4, leading to delayed flowering. In addition, the degradation products derived from MS GSLs enhance salt tolerance. Previous studies have revealed that FMOGS-OXs exhibit alternative catalytic activity to form trimethylamine N-oxide (TMAO) under salt stress, which activates multiple stress-related genes to promote salt tolerance. Therefore, FMOGS-OXs integrate flowering transition and salt tolerance in various ways. Our study shed light on the functional diversity of GSLs and established a connection between flowering transition, salt resistance, and GSL metabolism.

Analysis of temperature effects on the protein accumulation of the FT-FD module using newly generated Arabidopsis transgenic plants

Arabidopsis flowering is dependent on interactions between a component of the florigens FLOWERING LOCUS T (FT) and the basic leucine zipper (bZIP) transcription factor FD. These proteins form a complex that activates the genes required for flowering competence and integrates environmental cues, such as photoperiod and temperature. However, it remains largely unknown how FT and FD are regulated at the protein level. To address this, we created FT transgenic plants that express the N-terminal FLAG-tagged FT fusion protein under the control of its own promoter in ft mutant backgrounds. FT transgenic plants complemented the delayed flowering of the ft mutant and exhibited similar FT expression patterns to wild-type Col-0 plants in response to changes in photoperiod and temperature. Similarly, we generated FD transgenic plants in fd mutant backgrounds that express the N-terminal MYC-tagged FD fusion protein under the FD promoter, rescuing the late flowering phenotypes in the fd mutant. Using these transgenic plants, we investigated how temperature regulates the expression of FT and FD proteins. Temperature-dependent changes in FT and FD protein levels are primarily regulated at the transcript level, but protein-level temperature effects have also been observed to some extent. In addition, our examination of the expression patterns of FT and FD in different tissues revealed that similar to the spatial expression pattern of FT, FD mRNA was expressed in both the leaf and shoot apex, but FD protein was only detected in the apex, suggesting a regulatory mechanism that restricts FD protein expression in the leaf during the vegetative growth phase. These transgenic plants provided a valuable platform for investigating the role of the FT-FD module in flowering time regulation.

Involvement of CONSTANS-like Proteins in Plant Flowering and Abiotic Stress Response

The process of flowering in plants is a pivotal stage in their life cycle, and the CONSTANS-like (COL) protein family, known for its photoperiod sensing ability, plays a crucial role in regulating plant flowering. Over the past two decades, homologous genes of COL have been identified in various plant species, leading to significant advancements in comprehending their involvement in the flowering pathway and response to abiotic stress. This article presents novel research progress on the structural aspects of COL proteins and their regulatory patterns within transcription complexes. Additionally, we reviewed recent information about their participation in flowering and abiotic stress response, aiming to provide a more comprehensive understanding of the functions of COL proteins.

Balancing growth amidst salt stress - lifestyle perspectives from the extremophyte model Schrenkiella parvula

Schrenkiella parvula, a leading extremophyte model in Brassicaceae, can grow and complete its lifecycle under multiple environmental stresses, including high salinity. Yet, the key physiological and structural traits underlying its stress-adapted lifestyle are unknown along with trade-offs when surviving salt stress at the expense of growth and reproduction. We aimed to identify the influential adaptive trait responses that lead to stress-resilient and uncompromised growth across developmental stages when treated with salt at levels known to inhibit growth in Arabidopsis and most crops. Its resilient growth was promoted by traits that synergistically allowed primary root growth in seedlings, the expansion of xylem vessels across the root-shoot continuum, and a high capacity to maintain tissue water levels by developing thicker succulent leaves while enabling photosynthesis during salt stress. A successful transition from vegetative to reproductive phase was initiated by salt-induced early flowering, resulting in viable seeds. Self-fertilization in salt-induced early flowering was dependent upon filament elongation in flowers otherwise aborted in the absence of salt during comparable plant ages. The maintenance of leaf water status promoting growth, and early flowering to ensure reproductive success in a changing environment, were among the most influential traits that contributed to the extremophytic lifestyle of S. parvula.

Functional Modules in the Meristems: "Tinkering" in Action

BACKGROUND

A feature of higher plants is the modular principle of body organisation. One of these conservative morphological modules that regulate plant growth, histogenesis and organogenesis is meristems-structures that contain pools of stem cells and are generally organised according to a common principle. Basic content: The development of meristems is under the regulation of molecular modules that contain conservative interacting components and modulate the expression of target genes depending on the developmental context. In this review, we focus on two molecular modules that act in different types of meristems. The WOX-CLAVATA module, which includes the peptide ligand, its receptor and the target transcription factor, is responsible for the formation and control of the activity of all meristem types studied, but it has its own peculiarities in different meristems. Another regulatory module is the so-called florigen-activated complex, which is responsible for the phase transition in the shoot vegetative meristem (e.g., from the vegetative shoot apical meristem to the inflorescence meristem).

CONCLUSIONS

The review considers the composition and functions of these two functional modules in different developmental programmes, as well as their appearance, evolution and use in plant breeding.

Comparative genomics of flowering behavior in Cannabis sativa

Cannabis sativa L. is a phenotypically diverse and multi-use plant used in the production of fiber, seed, oils, and a class of specialized metabolites known as phytocannabinoids. The last decade has seen a rapid increase in the licit cultivation and processing of C. sativa for medical end-use. Medical morphotypes produce highly branched compact inflorescences which support a high density of glandular trichomes, specialized epidermal hair-like structures that are the site of phytocannabinoid biosynthesis and accumulation. While there is a focus on the regulation of phytocannabinoid pathways, the genetic determinants that govern flowering time and inflorescence structure in C. sativa are less well-defined but equally important. Understanding the molecular mechanisms that underly flowering behavior is key to maximizing phytocannabinoid production. The genetic basis of flowering regulation in C. sativa has been examined using genome-wide association studies, quantitative trait loci mapping and selection analysis, although the lack of a consistent reference genome has confounded attempts to directly compare candidate loci. Here we review the existing knowledge of flowering time control in C. sativa, and, using a common reference genome, we generate an integrated map. The co-location of known and putative flowering time loci within this resource will be essential to improve the understanding of C. sativa phenology.

Identification, evolution and expression analyses of the whole genome-wide PEBP gene family in Brassica napus L

BACKGROUND

With the release of genomic data for B.rapa, B.oleracea, and B.napus, research on the genetic and molecular functions of Brassica spp. has entered a new stage. PEBP genes in plants play an important role in the transition to flowering as well as seed development and germination. Molecular evolutionary and functional analyses of the PEBP gene family in B.napus based on molecular biology methods can provide a theoretical basis for subsequent investigations of related regulators.

RESULTS

In this paper, we identified a total of 29 PEBP genes from B.napus that were located on 14 chromosomes and 3 random locations. Most members contained 4 exons and 3 introns; motif 1 and motif 2 were the characteristic motifs of PEBP members. On the basis of intraspecific and interspecific collinearity analyses, it is speculated that fragment replication and genomic replication are the main drivers of for the amplification and evolution of the PEBP gene in the B.napus genome. The results of promoter cis-elements prediction suggest that BnPEBP family genes are inducible promoters, which may directly or indirectly participate in multiple regulatory pathways of plant growth cycle. Furthermore, the tissue-specific expression results show that the expression levels of BnPEBP family genes in different tissues were quite different, but the gene expression organization and patterns of the same subgroup were basically the same. qRT‒PCR revealed certain spatiotemporal patterns in the expression of the PEBP subgroups in roots, stems, leaves, buds, and siliques, was tissue-specific, and related to function.

CONCLUSIONS

A systematic comparative analysis of the B.napus PEBP gene family was carried out at here. The results of gene identification, phylogenetic tree construction, structural analysis, gene duplication analysis, prediction of promoter cis-elements and interacting proteins, and expression analysis provide a reference for exploring the molecular mechanisms of BnPEBP family genes in future research.

Their C-termini divide Brassica rapa FT-like proteins into FD-interacting and FD-independent proteins that have different effects on the floral transition

Members of the FLOWERING LOCUS T (FT)-like clade of phosphatidylethanolamine-binding proteins (PEBPs) induce flowering by associating with the basic leucine zipper (bZIP) transcription factor FD and forming regulatory complexes in angiosperm species. However, the molecular mechanism of the FT-FD heterocomplex in Chinese cabbage (Brassica rapa ssp. pekinensis) is unknown. In this study, we identified 12 BrPEBP genes and focused our functional analysis on four BrFT-like genes by overexpressing them individually in an FT loss-of-function mutant in Arabidopsis thaliana. We determined that BrFT1 and BrFT2 promote flowering by upregulating the expression of floral meristem identity genes, whereas BrTSF and BrBFT, although close in sequence to their Arabidopsis counterparts, had no clear effect on flowering in either long- or short-day photoperiods. We also simultaneously genetically inactivated BrFT1 and BrFT2 in Chinese cabbage using CRISPR/Cas9-mediated genome editing, which revealed that BrFT1 and BrFT2 may play key roles in inflorescence organogenesis as well as in the transition to flowering. We show that BrFT-like proteins, except for BrTSF, are functionally divided into FD interactors and non-interactors based on the presence of three specific amino acids in their C termini, as evidenced by the observed interconversion when these amino acids are mutated. Overall, this study reveals that although BrFT-like homologs are conserved, they may have evolved to exert functionally diverse functions in flowering via their potential to be associated with FD or independently from FD in Brassica rapa.

PEBP Signaling Network in Tubers and Tuberous Root Crops

Tubers and tuberous root crops are essential carbohydrate sources and staple foods for humans, second only to cereals. The developmental phase transition, including floral initiation and underground storage organ formation, is controlled by complex signaling processes involving the integration of environmental and endogenous cues. FLOWERING LOCUS T (FT) and TERMINAL FLOWER 1/CENTRORADIALIS (TFL1/CEN), members of the phosphatidylethanolamine-binding protein (PEBP) gene family, play a central role in this developmental phase transition process. FT and FT-like proteins have a function to promote developmental phase transition, while TFL1/CEN act oppositely. The balance between FT and TFL1/CEN is critical to ensure a successful plant life cycle. Here, we present a summarized review of the role and signaling network of PEBP in floral initiation and underground storage organ formation, specifically in tubers and tuberous root crops. Lastly, we point out several questions that need to be answered in order to have a more complete understanding of the PEBP signaling network, which is crucial for the agronomical improvement of tubers and tuberous crops.

S-acylated and nucleus-localized SALT OVERLY SENSITIVE3/CALCINEURIN B-LIKE4 stabilizes GIGANTEA to regulate Arabidopsis flowering time under salt stress

The precise timing of flowering in adverse environments is critical for plants to secure reproductive success. We report a mechanism in Arabidopsis (Arabidopsis thaliana) controlling the time of flowering by which the S-acylation-dependent nuclear import of the protein SALT OVERLY SENSITIVE3/CALCINEURIN B-LIKE4 (SOS3/CBL4), a Ca2+-signaling intermediary in the plant response to salinity, results in the selective stabilization of the flowering time regulator GIGANTEA inside the nucleus under salt stress, while degradation of GIGANTEA in the cytosol releases the protein kinase SOS2 to achieve salt tolerance. S-acylation of SOS3 was critical for its nuclear localization and the promotion of flowering, but partly dispensable for salt tolerance. SOS3 interacted with the photoperiodic flowering components GIGANTEA and FLAVIN-BINDING, KELCH REPEAT, F-BOX1 and participated in the transcriptional complex that regulates CONSTANS to sustain the transcription of CO and FLOWERING LOCUS T under salinity. Thus, the SOS3 protein acts as a Ca2+- and S-acylation-dependent versatile regulator that fine-tunes flowering time in a saline environment through the shared spatial separation and selective stabilization of GIGANTEA, thereby connecting two signaling networks to co-regulate the stress response and the time of flowering.

Allele mining, amplicon sequencing and computational prediction of Solanum melongena L. FT/TFL1 gene homologs uncovers putative variants associated to seed dormancy and germination

The FT/TFL1 gene homolog family plays a crucial role in the regulation of floral induction, seed dormancy and germination in angiosperms. Despite its importance, the FT/TFL1 gene homologs in eggplant (Solanum melongena L.) have not been characterized to date. In this study, we performed a genome-wide identification of FT/TFL1 genes in eggplant using in silico genome mining. The presence of these genes was validated in four economically important eggplant cultivars (Surya, EP-47 Annamalai, Pant Samrat and Arka Nidhi) through Pacbio RSII amplicon sequencing. Our results revealed the presence of 12 FT/TFL1 gene homologs in eggplant, with evidence of diversification among FT-like genes suggesting their possible adaptations towards various environmental stimuli. The amplicon sequencing also revealed the presence of two alleles for certain genes (SmCEN-1, SmCEN-2, SmMFT-1 and SmMFT-2) of which SmMFT-2 was associated with seed dormancy and germination. This association was further supported by the observation that seed dormancy is rarely reported in domesticated eggplant cultivars, but is commonly observed in wild species. A survey of the genetic regions in domesticated cultivars and a related wild species, S. incanum, showed that the alternative allele of S. incanum was present in some members of the Pant Samrat cultivar, but was absent in most other cultivars. This difference could contribute to the differences in seed traits between wild and domesticated eggplants.

Non-photoperiodic transition of female cannabis seedlings from juvenile to adult reproductive stage

Vegetative-to-reproductive phase transition in female cannabis seedlings occurs autonomously with the de novo development of single flowers. To ensure successful sexual reproduction, many plant species originating from seedlings undergo juvenile-to-adult transition. This phase transition precedes and enables the vegetative-to-reproductive shift in plants, upon perception of internal and/or external signals such as temperature, photoperiod, metabolite levels, and phytohormones. This study demonstrates that the juvenile seedlings of cannabis gradually shift to the adult vegetative stage, as confirmed by the formation of lobed leaves, and upregulation of the phase-transition genes. In the tested cultivar, the switch to the reproductive stage occurs with the development of a pair of single flowers in the 7th node. Histological analysis indicated that transition to the reproductive stage is accomplished by the de novo establishment of new flower meristems which are not present in a vegetative stage, or as dormant meristems at nodes 4 and 6. Moreover, there were dramatic changes in the transcriptomic profile of flowering-related genes among nodes 4, 6, and 7. Downregulation of flowering repressors and an intense increase in the transcription of phase transition-related genes occur in parallel with an increase in the transcription of flowering integrators and meristem identity genes. These results support and provide molecular evidence for previous findings that cannabis possesses an autonomous flowering mechanism and the transition to reproductive phase is controlled in this plant mainly by internal signals.

Genome-wide identification and characterization profile of phosphatidy ethanolamine-binding protein family genes in carrot

Members of the family of Phosphatidy Ethanolamine-Binding Protein (PEBP) have been shown to be key regulators of the transition of plants from vegetative to reproductive phases. Here, a total of 12 PEBP proteins were identified in the carrot (Daucus carota L.) genome and classified into FT-like (4), TFL1-like (6), and MFT-like 2) subfamilies, that had different lengths (110-267 aa) and were distributed unevenly across seven chromosomes. Moreover, 13 and 31 PEBP proteins were identified in other two Apiaceae species, celery (Apium graveolens L.) and coriander (Coriandrum sativum L.). The phylogenetic and evolutionary results of these PEBP family proteins were obtained based on the protein sequences. In the three Apiaceae species, purifying selection was the main evolutionary force, and WGD, segmental duplication, and dispersed duplication have played key roles in the PEBP family expansion. The expression analysis showed that carrot PEBP genes exhibited relatively broad expression patterns across various tissues. In the period of bolting to flowering, the carrot FT-like subfamily genes were upregulated as positive regulators, and TFL1-like subfamily genes remained at lower expression levels as inhibitors. More interestingly, the members of carrot FT-like genes had different temporal-spatial expression characteristics, suggesting that they have different regulatory functions in the carrot reproductive phase. In summary, this study contributes to our understanding of the PEBP family proteins and provides a foundation for exploring the mechanism of carrot bolting and flowering for the breeding of cultivars with bolting resistance.

Genetic studies on continuous flowering in woody plant Osmanthus fragrans

Continuous flowering is a key horticultural trait in ornamental plants, whereas the specific molecular regulation mechanism remains largely unknown. In sweet osmanthus (Osmanthus fragrans Lour.), plants based on their flowering characteristics are divided into once-flowering (OF) habit and continuous flowering (CF) habit. Here, we first described the flowering phenology shifts of OF and CF habits in sweet osmanthus through paraffin section and microscope assay. Phenotypic characterization showed that CF plants had constant new shoot growth, floral transition, and blooming for 1 year, which might lead to a continuous flowering trait. We performed the transcriptome sequencing of OF and CF sweet osmanthus and analyzed the transcriptional activity of flowering-related genes. Among the genes, three floral integrators, OfFT, OfTFL1, and OfBFT, had a differential expression during the floral transition process in OF and CF habits. The expression patterns of the three genes in 1 year were revealed. The results suggested that their accumulations corresponded to the new shoots occurring and the floral transition process. Function studies suggested that OfFT acted as a flowering activator, whereas OfBFT was a flowering inhibitor. Yeast one-hybrid assay indicated that OfSPL8 was a common upstream transcription factor of OfFT and OfBFT, suggesting the vital role of OfSPL8 in continuous flowering regulation. These results provide a novel insight into the molecular mechanism of continuous flowering.

CRISPR-Cas9-mediated mutagenesis of kiwifruit BFT genes results in an evergrowing but not early flowering phenotype

Phosphatidylethanolamine-binding protein (PEBP) genes regulate flowering and architecture in many plant species. Here, we study kiwifruit (Actinidia chinensis, Ac) PEBP genes with homology to BROTHER OF FT AND TFL1 (BFT). CRISPR-Cas9 was used to target AcBFT genes in wild-type and fast-flowering kiwifruit backgrounds. The editing construct was designed to preferentially target AcBFT2, whose expression is elevated in dormant buds. Acbft lines displayed an evergrowing phenotype and increased branching, while control plants established winter dormancy. The evergrowing phenotype, encompassing delayed budset and advanced budbreak after defoliation, was identified in multiple independent lines with edits in both alleles of AcBFT2. RNA-seq analyses conducted using buds from gene-edited and control lines indicated that Acbft evergrowing plants had a transcriptome similar to that of actively growing wild-type plants, rather than dormant controls. Mutations in both alleles of AcBFT2 did not promote flowering in wild-type or affect flowering time, morphology and fertility in fast-flowering transgenic kiwifruit. In summary, editing of AcBFT2 has the potential to reduce plant dormancy with no adverse effect on flowering, giving rise to cultivars better suited for a changing climate.

Methylation in DNA, histone, and RNA during flowering under stress condition: A review

Flowering is the most critical transition period in the whole lifecycle of plants, and it is a highly sensitive period to stress. New combinations of temperature, drought stress, carbon dioxide and other abiotic/biotic conditions resulting from contemporary climate change affect the flowering process. Plants have evolved several strategies to deal with environmental stresses, including epigenetic modifications. Numerous studies show that environmental stresses trigger methylation/demethylation during flowering to preserve/accelerate plant lifecycle. What's more, histone and DNA methylation can be induced to respond to stresses, resulting in changes of flowering gene expression and enhancing stress tolerance in plants. Furthermore, RNA methylation may influence stress-regulated flowering by regulating mRNA stability and antioxidant mechanism. Our review presents the involvement of methylation in stress-repressed and stress-induced flowering. The crosstalk between methylation and small RNAs, phytohormones and exogenous substances (such as salicylic acid, nitric oxide) during flowering under different stresses were discussed. The latest regulatory evidence of RNA methylation in stress-regulated flowering was collected for the first time. Meanwhile, the limited evidences of methylation in biotic stress-induced flowering were summarized. Thus, the review provides insights into understanding of methylation mechanism in stress-regulated flowering and makes use for the development of regulating plant flowering at epigenetic level in the future.

SELF PRUNING 3C is a flowering repressor that modulates seed germination, root architecture, and drought responses

Allelic variation in the CETS (CENTRORADIALIS, TERMINAL FLOWER 1, SELF PRUNING) gene family controls agronomically important traits in many crops. CETS genes encode phosphatidylethanolamine-binding proteins that have a central role in the timing of flowering as florigenic and anti-florigenic signals. The great expansion of CETS genes in many species suggests that the functions of this family go beyond flowering induction and repression. Here, we characterized the tomato SELF PRUNING 3C (SP3C) gene, and show that besides acting as a flowering repressor it also regulates seed germination and modulates root architecture. We show that loss of SP3C function in CRISPR/Cas9-generated mutant lines increases root length and reduces root side branching relative to the wild type. Higher SP3C expression in transgenic lines promotes the opposite effects in roots, represses seed germination, and also improves tolerance to water stress in seedlings. These discoveries provide new insights into the role of SP paralogs in agronomically relevant traits, and support future exploration of the involvement of CETS genes in abiotic stress responses.

Comparative Genomic and Expression Analysis Insight into Evolutionary Characteristics of PEBP Genes in Cultivated Peanuts and Their Roles in Floral Induction

Phosphatidyl ethanolamine-binding proteins (PEBPs) are involved in regulating flowering time and various developmental processes. Functions and expression patterns in cultivated peanuts (Arachis hypogaea L.) remain unknown. In this study, 33 PEBP genes in cultivated peanuts were identified and divided into four subgroups: FT, TFL, MFT and FT-like. Gene structure analysis showed that orthologs from A and B genomes in cultivated peanuts had highly similar structures, but some orthologous genes have subgenomic dominance. Gene collinearity and phylogenetic analysis explain that some PEBP genes play key roles in evolution. Cis-element analysis revealed that PEBP genes are mainly regulated by hormones, light signals and stress-related pathways. Multiple PEPB genes had different expression patterns between early and late-flowering genotypes. Further detection of its response to temperature and photoperiod revealed that PEBPs ArahyM2THPA, ArahyEM6VH3, Arahy4GAQ4U, ArahyIZ8FG5, ArahyG6F3P2, ArahyLUT2QN, ArahyDYRS20 and ArahyBBG51B were the key genes controlling the flowering response to different flowering time genotypes, photoperiods and temperature. This study laid the foundation for the functional study of the PEBP gene in cultivated peanuts and the adaptation of peanuts to different environments.

Plant mitochondrial FMT and its mammalian homolog CLUH controls development and behavior in Arabidopsis and locomotion in mice

Mitochondria in animals are associated with development, as well as physiological and pathological behaviors. Several conserved mitochondrial genes exist between plants and higher eukaryotes. Yet, the similarities in mitochondrial function between plant and animal species is poorly understood. Here, we show that FMT (FRIENDLY MITOCHONDRIA) from Arabidopsis thaliana, a highly conserved homolog of the mammalian CLUH (CLUSTERED MITOCHONDRIA) gene family encoding mitochondrial proteins associated with developmental alterations and adult physiological and pathological behaviors, affects whole plant morphology and development under both stressed and normal growth conditions. FMT was found to regulate mitochondrial morphology and dynamics, germination, and flowering time. It also affects leaf expansion growth, salt stress responses and hyponastic behavior, including changes in speed of hyponastic movements. Strikingly, Cluh± heterozygous knockout mice also displayed altered locomotive movements, traveling for shorter distances and had slower average and maximum speeds in the open field test. These observations indicate that homologous mitochondrial genes may play similar roles and affect homologous functions in both plants and animals.

Passiflora organensis FT/TFL1 gene family and their putative roles in phase transition and floral initiation

Comprehensive analysis of the FT/TFL1 gene family in Passiflora organensis results in understanding how these genes might be involved in the regulation of the typical plant architecture presented by Passiflora species. Passion fruit (Passiflora spp) is an economic tropical fruit crop, but there is hardly any knowledge available about the molecular control of phase transition and flower initiation in this species. The florigen agent FLOWERING LOCUS T (FT) interacts with the bZIP protein FLOWERING LOCUS D (FD) to induce flowering in the model species Arabidopsis thaliana. Current models based on research in rice suggest that this interaction is bridged by 14-3-3 proteins. We identified eight FT/TFL1 family members in Passiflora organensis and characterized them by analyzing their phylogeny, gene structure, expression patterns, protein interactions and putative biological roles by heterologous expression in Arabidopsis. PoFT was highest expressed during the adult vegetative phase and it is supposed to have an important role in flowering induction. In contrast, its paralogs PoTSFs were highest expressed in the reproductive phase. While ectopic expression of PoFT in transgenic Arabidopsis plants induced early flowering and inflorescence determinacy, the ectopic expression of PoTSFa caused a delay in flowering. PoTFL1-like genes were highest expressed during the juvenile phase and their ectopic expression caused delayed flowering in Arabidopsis. Our protein-protein interaction studies indicate that the flowering activation complexes in Passiflora might deviate from the hexameric complex found in the model system rice. Our results provide insights into the potential functions of FT/TFL1 gene family members during floral initiation and their implications in the special plant architecture of Passiflora species, contributing to more detailed studies on the regulation of passion fruit reproduction.

Sulfanilamide Regulates Flowering Time through Expression of the Circadian Clock Gene LUX

Flowering time is an agriculturally important trait that can be manipulated by various approaches such as breeding, growth control and genetic modifications. Despite its potential advantages, including fine-tuning the regulation of flowering time, few reports have explored the use of chemical compounds to manipulate flowering. Here, we report that sulfanilamide, an inhibitor of folate biosynthesis, delays flowering by repressing the expression of florigen FLOWERING LOCUS T (FT) in Arabidopsis thaliana. Transcriptome deep sequencing and quantitative polymerase chain reaction analyses showed that the expression of the circadian clock gene LUX ARRYTHMO/PHYTOCLOCK1 (LUX/PCL1) is altered by sulfanilamide treatment. Furthermore, in the lux nox mutant harboring loss of function in both LUX and its homolog BROTHER OF LUX ARRHYTHMO (BOA, also named NOX), the inhibitory effect of sulfanilamide treatment on FT expression was weak and the flowering time was similar to that of the wild type, suggesting that the circadian clock may contribute to the FT-mediated regulation of flowering by sulfanilamide. Sulfanilamide also delayed flowering time in arugula (Eruca sativa), suggesting that it is involved in the regulation of flowering across Brassicaceae. We propose that sulfanilamide is a novel modulator of flowering.

Two FD homologs from London plane (Platanus acerifolia) are associated with floral initiation and flower morphology

The flowering-time gene FD encodes a bZIP transcription factor that interacts with FLOWERING LOCUS T (FT) to induce flowering in Arabidopsis. Previous research has identified two FT homologs of Platanus acerifolia, PaFT and PaFTL, which each have different expression patterns and are involved in diverse developmental processes. However, it is not known whether such FT/FD complexes participate in the flowering processes in P. acerifolia. Therefore, we isolated two closely related FD homologs, PaFDL1 and PaFDL2, and investigated their functions through the analysis of expression profiles, transgenic phenotypes, their interactions with different FT proteins, and potential cis-regulatory elements in their promoters. The PaFDL genes were found to display their maximal expression levels during the stage of floral transition, and subsequent expression patterns were also seen to be related to inflorescence developmental stage. In addition, both PaFDL1 and PaFDL2 were found to be subject to post-transcriptional alternative splicing, each gene producing two transcript forms. Transgenic tobacco overexpressing each of the four resulting transcript types displayed accelerated floral initiation and produced abnormal flowers. The results suggested that the complete PaFDL proteins may interact with different PaFT/PaFTL proteins in order to fulfill both conservative and diverse functions in floral initiation and floral development.

Asymmetric expansions of FT and TFL1 lineages characterize differential evolution of the EuPEBP family in the major angiosperm lineages

Background

In flowering plants, precise timing of the floral transition is crucial to maximize chances of reproductive success, and as such, this process has been intensively studied. FLOWERING LOCUS T (FT) and TERMINAL FLOWER1 (TFL1) have been identified as closely related eukaryotic phosphatidylethanolamine-binding proteins (‘EuPEBPs’) that integrate multiple environmental stimuli, and act antagonistically to determine the optimal timing of the floral transition. Extensive research has demonstrated that FT acts similar to hormonal signals, being transported in the phloem from its primary site of expression in leaves to its primary site of action in the shoot meristem; TFL1 also appears to act as a mobile signal. Recent work implicates FT, TFL1, and the other members of the EuPEBP family, in the control of other important processes, suggesting that the EuPEBP family may be key general regulators of developmental transitions in flowering plants. In eudicots, there are a small number of EuPEBP proteins, but in monocots, and particularly grasses, there has been a large, but uncharacterized expansion of EuPEBP copy number, with unknown consequences for the EuPEBP function.

Results

To systematically characterize the evolution of EuPEBP proteins in flowering plants, and in land plants more generally, we performed a high-resolution phylogenetic analysis of 701 PEBP sequences from 208 species. We refine previous models of EuPEBP evolution in early land plants, demonstrating the algal origin of the family, and pin-pointing the origin of the FT/TFL1 clade at the base of monilophytes. We demonstrate how a core set of genes (MFT1, MFT2, FT, and TCB) at the base of flowering plants has undergone differential evolution in the major angiosperm lineages. This includes the radical expansion of the FT family in monocots into 5 core lineages, further re-duplicated in the grass family to 12 conserved clades.

Conclusions

We show that many grass FT proteins are strongly divergent from other FTs and are likely neo-functional regulators of development. Our analysis shows that monocots and eudicots have strongly divergent patterns of EuPEBP evolution.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-021-01128-8.

Comparative Transcriptomic Analysis of Differentially Expressed Transcripts Associated with Flowering Time of Loquat (Eriobotya japonica Lindl.)

Flowering is an important phenophase of plant species, however, knowledge about the regulatory mechanism controlling flowering cues in loquat is limited. To identify candidate genes regulating flowering time in loquat, we used RNA-Seq technology to conduct a comparative transcriptome analysis of differentiating apical buds collected from the early-flowering variety ‘Baiyu’ and the late-flowering variety ‘Huoju’. A total of 28,842 differentially expressed transcripts (DETs) were identified. Of these, 42 DETs controlled flowering time while 17 other DETs were associated with the ABA signaling pathway. Compared with those in ‘Huoju’, EjFT, EjFY, EjFLK, and EjCAL1-like were significantly upregulated in ‘Baiyu’. Moreover, transcripts of the ABA 8′-hydroxylases (EjABH2, EjABH4, and EjABH4-like2), the ABA receptors (EjPYL4/8), and the bZIP transcription factor EjABI5-like were upregulated in ‘Baiyu’ compared with ‘Huoju’. Hence, they might regulate loquat flowering time. There was no significant difference between ‘Baiyu’ and ‘Huoju’ in terms of IAA content. However, the ABA content was about ten-fold higher in the apical buds of ‘Baiyu’ than in those of ‘Huoju’. The ABA:IAA ratio sharply rose and attained a peak during bud differentiation. Thus, ABA is vital in regulating floral bud formation in loquat. The results of the present study help clarify gene transcription during loquat flowering.

FT5a interferes with the Dt1-AP1 feedback loop to control flowering time and shoot determinacy in soybean

Flowering time and stem growth habit determine inflorescence architecture in soybean, which in turn influences seed yield. Dt1, a homolog of Arabidopsis TERMINAL FLOWER 1 (TFL1), is a major controller of stem growth habit, but its underlying molecular mechanisms remain unclear. Here, we demonstrate that Dt1 affects node number and plant height, as well as flowering time, in soybean under long-day conditions. The bZIP transcription factor FDc1 physically interacts with Dt1, and the FDc1-Dt1 complex directly represses the expression of APETALA1 (AP1). We propose that FT5a inhibits Dt1 activity via a competitive interaction with FDc1 and directly upregulates AP1. Moreover, AP1 represses Dt1 expression by directly binding to the Dt1 promoter, suggesting that AP1 and Dt1 form a suppressive regulatory feedback loop to determine the fate of the shoot apical meristem. These findings provide novel insights into the roles of Dt1 and FT5a in controlling the stem growth habit and flowering time in soybean, which determine the adaptability and grain yield of this important crop.

Reassessing the role of ion homeostasis for improving salinity tolerance in crop plants

Soil salinity is a constraint for major agricultural crops leading to severe yield loss, which may increase with the changing climatic conditions. Disruption in the cellular ionic homeostasis is one of the primary responses induced by elevated sodium ions (Na⁺ ). Therefore, unraveling the mechanism of Na⁺ uptake and transport in plants along with the characterization of the candidate genes facilitating ion homeostasis is obligatory for enhancing salinity tolerance in crops. This review summarizes the current advances in understanding the ion homeostasis mechanism in crop plants, emphasizing the role of transporters involved in the regulation of cytosolic Na⁺ level along with the conservation of K⁺ /Na⁺ ratio. Furthermore, expression profiles of the candidate genes for ion homeostasis were also explored under various developmental stages and tissues of Oryza sativa based on the publicly available microarray data. The review also gives an up-to-date summary on the efforts to increase salinity tolerance in crops by manipulating selected stress-associated genes. Overall, this review gives a combined view on both the ionomic and molecular background of salt stress tolerance in plants.

Genome-wide characterization of PEBP family genes in nine Rosaceae tree species and their expression analysis in P. mume

BACKGROUND

Phosphatidylethanolamine-binding proteins (PEBPs) constitute a common gene family found among animals, plants and microbes. Plant PEBP proteins play an important role in regulating flowering time, plant architecture as well as seed dormancy. Though PEBP family genes have been well studied in Arabidopsis and other model species, less is known about these genes in perennial trees.

RESULTS

To understand the evolution of PEBP genes and their functional roles in flowering control, we identified 56 PEBP members belonging to three gene clades (MFT-like, FT-like, and TFL1-like) and five lineages (FT, BFT, CEN, TFL1, and MFT) across nine Rosaceae perennial species. Structural analysis revealed highly conserved gene structure and protein motifs among Rosaceae PEBP proteins. Codon usage analysis showed slightly biased codon usage across five gene lineages. With selection pressure analysis, we detected strong purifying selection constraining divergence within most lineages, while positive selection driving the divergence of FT-like and TFL1-like genes from the MFT-like gene clade. Spatial and temporal expression analyses revealed the essential role of FT in regulating floral bud breaking and blooming in P. mume. By employing a weighted gene co-expression network approach, we inferred a putative FT regulatory module required for dormancy release and blooming in P. mume.

CONCLUSIONS

We have characterized the PEBP family genes in nine Rosaceae species and examined their phylogeny, genomic syntenic relationship, duplication pattern, and expression profiles during flowering process. These results revealed the evolutionary history of PEBP genes and their functions in regulating floral bud development and blooming among Rosaceae tree species.

Calcium-hydrogen sulfide crosstalk during K+-deficient NaCl stress operates through regulation of Na+/H+ antiport and antioxidative defense system in mung bean roots

Present investigation reports the role of calcium (Ca²⁺) and hydrogen sulfide (H₂S) crosstalk associated with Vigna radiata seedlings subjected to K⁺ deficient conditions under short-term (24 h) and long-term (72 h) NaCl stress. Perusal of the data reveals that under short-term NaCl stress an initial decline in K⁺ level led to the elevation in Ca²⁺ and H₂S levels along with improvement in antioxidant system and reduction in reactive oxygen species (ROS) production. Under long-term NaCl stress a further decline in K⁺ content was deleterious that led to a lower K⁺/Na⁺ ratio. This was followed by reduction in antioxidant system along with excessive accumulation of ROS and methylglyoxal content, and increased membrane damage. However, supplementation of the seedling roots with Ca²⁺ enhanced biosynthesis of H₂S through enhancing cysteine pool. The present findings suggest that synergistic action of Ca²⁺ and H₂S induced the activity of H⁺-ATPase that created H⁺ gradient which in turn induced Na⁺/H⁺ antiport system that accelerated K⁺ influx and Na⁺ efflux. All of these together contributed to a higher K⁺/Na⁺ ratio, activation of antioxidative defense system, and maintenance of redox homeostasis and membrane integrity in Ca²⁺-supplemented stressed seedlings. Role of Ca²⁺ and H₂S in the regulation of Na⁺/H⁺ antiport system was validated by the use of sodium orthovanadate (plasma membrane H⁺-ATPase inhibitor), tetraethylammonium chloride (K⁺ channel blocker), and amiloride (Na⁺/H⁺ antiporter inhibitor). Application of Ca²⁺-chelator EGTA (ethylene glycol-bis(b-aminoethylether)-N,N,N',N'-tetraacetic acid) and H₂S scavenger hypotaurine abolished the effect of Ca²⁺, suggesting the involvement of Ca²⁺ and H₂S in the alleviation of NaCl stress. Moreover, use of EGTA and HT also substantiates the downstream functioning of H₂S during Ca²⁺-mediated regulation of plant adaptive responses to NaCl stress. To sum up, present findings reveal the association of Ca²⁺ and H₂S signaling in the regulation of ion homeostasis and antioxidant defense during K⁺-deficient NaCl stress.

Morphological, Physiological and Molecular Markers for Salt-Stressed Plants

Plant growth and development is adversely affected by different kind of stresses. One of the major abiotic stresses, salinity, causes complex changes in plants by influencing the interactions of genes. The modulated genetic regulation perturbs metabolic balance, which may alter plant's physiology and eventually causing yield losses. To improve agricultural output, researchers have concentrated on identification, characterization and selection of salt tolerant varieties and genotypes, although, most of these varieties are less adopted for commercial production. Nowadays, phenotyping plants through Machine learning (deep learning) approaches that analyze the images of plant leaves to predict biotic and abiotic damage on plant leaves have increased. Here, we review salinity stress related markers on molecular, physiological and morphological levels for crops such as maize, rice, ryegrass, tomato, salicornia, wheat and model plant, Arabidopsis. The combined analysis of data from stress markers on different levels together with image data are important for understanding the impact of salt stress on plants.

Genome-wide member identification, phylogeny and expression analysis of PEBP gene family in wheat and its progenitors

The phosphatidylethanolamine binding protein (PEBP) family comprises ancient proteins found throughout the biosphere that play an important role in plant growth and development, flowering, seed development and dormancy. However, not all PEBP genes have been identified or analyzed in common wheat (Triticum aestivum L.) and its progenitors. In this study, we identified the PEBP genes in common wheat, Triticum dicoccoides, Triticum urartu and Aegilops tauschii by searching whole genome sequences, and characterized these genes by phylogenetic and transcriptome analyses. A total of 76, 38, 16 and 22 PEBP genes were identified in common wheat, T. dicoccoides, T. urartu and Ae. tauschii, respectively. Phylogenetic analysis classified the PEBP genes into four subfamilies (PEBP-like, MFT-like, TFL-like and FT-like); the PEBP-like subfamily was identified as a new subfamily with genes in this subfamily were conserved in plants. Group 2, 3 and 5 chromosomes of common wheat and its progenitors contained more PEBP genes than other chromosomes. The PEBP genes were conserved in wheat during evolution, and tandem duplication played a more important role in the amplification of PEBP genes than segmental duplication. Furthermore, transcriptome analysis revealed that PEBP genes showed tissue/organ-specific expression profiles and some PEBP genes were induced to express by biotic stresses. Quantitative real-time PCR (qRT-PCR) analysis revealed that seven randomly selected PEBP genes expressed differently during seed germination under cold, drought, flood, heat and salt stress treatments, and five of these genes (TaPEBP1, TaPEBP5, TaPEBP9, TaPEBP66 and TaPEBP69) showed significantly higher expression under different stress treatments, indicating that these genes play important roles during seed germination under stress conditions.

Gene expression changes occurring at bolting time are associated with leaf senescence in Arabidopsis

In plants, the vegetative to reproductive phase transition (termed bolting in Arabidopsis) generally precedes age-dependent leaf senescence (LS). Many studies describe a temporal link between bolting time and LS, as plants that bolt early, senesce early, and plants that bolt late, senesce late. The molecular mechanisms underlying this relationship are unknown and are potentially agriculturally important, as they may allow for the development of crops that can overcome early LS caused by stress-related early-phase transition. We hypothesized that leaf gene expression changes occurring in synchrony with bolting were regulating LS. ARABIDOPSIS TRITHORAX (ATX) enzymes are general methyltransferases that regulate the adult vegetative to reproductive phase transition. We generated an atx1, atx3, and atx4 (atx1,3,4) triple T-DNA insertion mutant that displays both early bolting and early LS. This mutant was used in an RNA-seq time-series experiment to identify gene expression changes in rosette leaves that are likely associated with bolting. By comparing the early bolting mutant to vegetative WT plants of the same age, we were able to generate a list of differentially expressed genes (DEGs) that change expression with bolting as the plants age. We trimmed the list by intersection with publicly available WT datasets, which removed genes from our DEG list that were atx1,3,4 specific. The resulting 398 bolting-associated genes (BAGs) are differentially expressed in a mature rosette leaf at bolting. The BAG list contains many well-characterized LS regulators (ORE1, WRKY45, NAP, WRKY28), and GO analysis revealed enrichment for LS and LS-related processes. These bolting-associated LS regulators may contribute to the temporal coupling of bolting time to LS.

Evolution and functional diversification of FLOWERING LOCUS T/TERMINAL FLOWER 1 family genes in plants

Plant growth and development, particularly the induction of flowering, are tightly controlled by key regulators in response to endogenous and environmental cues. The FLOWERING LOCUS T (FT)/TERMINAL FLOWER 1 (TFL1) family of phosphatidylethanolamine-binding protein (PEBP) genes is central to plant development, especially the regulation of flowering time and plant architecture. FT, the long-sought florigen, promotes flowering and TFL1 represses flowering. The balance between FT and TFL1 modulates plant architecture by switching the meristem from indeterminate to determinate growth, or vice versa. Recent studies in a broad range of plant species demonstrated that, in addition to their roles in flowering time and plant architecture, FT/TFL1 family genes participate in diverse aspects of plant development, such as bamboo seed germination and potato tuber formation. In this review, we briefly summarize the evolution of the FT/TFL1 family and highlight recent findings on their conserved and divergent functions in different species.

Molecular genetic analyses of abiotic stress responses during plant reproductive development

Plant responses to abiotic stresses during vegetative growth have been extensively studied for many years. Daily environmental fluctuations can have dramatic effects on plant vegetative growth at multiple levels, resulting in molecular, cellular, physiological, and morphological changes. Plants are even more sensitive to environmental changes during reproductive stages. However, much less is known about how plants respond to abiotic stresses during reproduction. Fortunately, recent advances in this field have begun to provide clues about these important processes, which promise further understanding and a potential contribution to maximize crop yield under adverse environments. Here we summarize information from several plants, focusing on the possible mechanisms that plants use to cope with different types of abiotic stresses during reproductive development, and present a tentative molecular portrait of plant acclimation during reproductive stages. Additionally, we discuss strategies that plants use to balance between survival and productivity, with some comparison among different plants that have adapted to distinct environments.

Salt Tolerance Mechanisms of Plants

Crop loss due to soil salinization is an increasing threat to agriculture worldwide. This review provides an overview of cellular and physiological mechanisms in plant responses to salt. We place cellular responses in a time- and tissue-dependent context in order to link them to observed phases in growth rate that occur in response to stress. Recent advances in phenotyping can now functionally or genetically link cellular signaling responses, ion transport, water management, and gene expression to growth, development, and survival. Halophytes, which are naturally salt-tolerant plants, are highlighted as success stories to learn from. We emphasize that (a) filling the major knowledge gaps in salt-induced signaling pathways, (b) increasing the spatial and temporal resolution of our knowledge of salt stress responses, (c) discovering and considering crop-specific responses, and (d) including halophytes in our comparative studies are all essential in order to take our approaches to increasing crop yields in saline soils to the next level.

Salt-Tolerant Plant Growth Promoting Rhizobacteria for Enhancing Crop Productivity of Saline Soils

Soil salinity has emerged as a serious issue for global food security. It is estimated that currently about 62 million hectares or 20 percent of the world's irrigated land is affected by salinity. The deposition of an excess amount of soluble salt in cultivable land directly affects crop yields. The uptake of high amount of salt inhibits diverse physiological and metabolic processes of plants even impacting their survival. The conventional methods of reclamation of saline soil which involve scraping, flushing, leaching or adding an amendment (e.g., gypsum, CaCl2, etc.) are of limited success and also adversely affect the agro-ecosystems. In this context, developing sustainable methods which increase the productivity of saline soil without harming the environment are necessary. Since long, breeding of salt-tolerant plants and development of salt-resistant crop varieties have also been tried, but these and aforesaid conventional approaches are not able to solve the problem. Salt tolerance and dependence are the characteristics of some microbes. Salt-tolerant microbes can survive in osmotic and ionic stress. Various genera of salt-tolerant plant growth promoting rhizobacteria (ST-PGPR) have been isolated from extreme alkaline, saline, and sodic soils. Many of them are also known to mitigate various biotic and abiotic stresses in plants. In the last few years, potential PGPR enhancing the productivity of plants facing salt-stress have been researched upon suggesting that ST-PGPR can be exploited for the reclamation of saline agro-ecosystems. In this review, ST-PGPR and their potential in enhancing the productivity of saline agro-ecosystems will be discussed. Apart from this, PGPR mediated mechanisms of salt tolerance in different crop plants and future research trends of using ST-PGPR for reclamation of saline soils will also be highlighted.

Functional divergence between soybean FLOWERING LOCUS T orthologues FT2a and FT5a in post-flowering stem growth

Genes in the FLOWERING LOCUS T (FT) family integrate external and internal signals to control various aspects of plant development. In soybean (Glycine max), FT2a and FT5a play a major role in floral induction, but their roles in post-flowering reproductive development remain undetermined. Ectopic overexpression analyses revealed that FT2a and FT5a similarly induced flowering, but FT5a was markedly more effective than FT2a for the post-flowering termination of stem growth. The down-regulation of Dt1, a soybean orthologue of Arabidopsis TERMINAL FLOWER1, in shoot apices in early growing stages of FT5a-overexpressing plants was concomitant with highly up-regulated expression of APETALA1 orthologues. The Dt2 gene, a repressor of Dt1, was up-regulated similarly by the overexpression of FT2a and FT5a, suggesting that it was not involved in the control of stem termination by FT5a. In addition to the previously reported interaction with FDL19, a homologue of the Arabidopsis bZIP protein FD, both FT2a and FT5a interacted with FDL12, but only FT5a interacted with FDL06. Our results suggest that FT2a and FT5a have different functions in the control of post-flowering stem growth. A specific interaction of FT5a with FDL06 may play a key role in determining post-flowering stem growth in soybean.

CONSTANS delays Arabidopsis flowering under short days

Long days (LD) promote flowering of Arabidopsis thaliana compared with short days (SD) by activating the photoperiodic pathway. Here we show that growth under very-SD (3 h) or darkness (on sucrose) also accelerates flowering on a biological scale, indicating that SD actively repress flowering compared with very-SD. CONSTANS (CO) repressed flowering under SD, and the early flowering of co under SD required FLOWERING LOCUS T (FT). FT was expressed at a basal level in the leaves under SD, but these levels were not enhanced in co. This indicates that the action of CO in A. thaliana is not the mirror image of the action of its homologue in rice. In the apex, CO enhanced the expression of TERMINAL FLOWER 1 (TFL1) around the time when FT expression is important to promote flowering. Under SD, the tfl1 mutation was epistatic to co and in turn ft was epistatic to tfl1. These observations are consistent with the long-standing but not demonstrated model where CO can inhibit FT induction of flowering by affecting TFL1 expression.

Reproductive Physiology of Halophytes: Current Standing

Background: Halophytes possess efficient salt-tolerance mechanisms and can complete their life cycles in naturally saline soils with NaCl contents exceeding 200 mM. While a significant progress have been made in recent decades elucidating underlying salt-tolerance mechanisms, these studies have been mostly confined to the vegetative growth stage. At the same time, the capacity to generate high-quality seeds and to survive early developmental stages under saline conditions, are both critically important for plants. Halophytes perform well in both regards, whereas non-halophytes cannot normally complete their life cycles under saline conditions. Scope: Research into the effects of salinity on plant reproductive biology has gained momentum in recent years. However, it remains unclear whether the reproductive biology of halophytes differs from that of non-halophytes, and whether their reproductive processes benefit, like their vegetative growth, from the presence of salt in the rhizosphere. Here, we summarize current knowledge of the mechanisms underlying the superior reproductive biology of halophytes, focusing on critical aspects including control of flowering time, changes in plant hormonal status and their impact on anther and pollen development and viability, plant carbohydrate status and seed formation, mechanisms behind the early germination of halophyte seeds, and the role of seed polymorphism. Conclusion: Salt has beneficial effects on halophyte reproductive growth that include late flowering, increased flower numbers and pollen vitality, and high seed yield. This improved performance is due to optimal nutrition during vegetative growth, alterations in plant hormonal status, and regulation of flowering genes. In addition, the seeds of halophytes harvested under saline conditions show higher salt tolerance than those obtained under non-saline condition, largely due to increased osmolyte accumulation, more optimal hormonal composition (e.g., high gibberellic acid and low abcisic acid content) and, in some species, seed dimorphism. In the near future, identifying key genes involved in halophyte reproductive physiology and using them to transform crops could be a promising approach to developing saline agriculture.

Different divergence events for three pairs of PEBPs in Gossypium as implied by evolutionary analysis

INTRODUCTION

The phosphatidylethanolamine-binding protein (PEBP) gene family plays a crucial role in seed germination, reproductive transformation, and other important developmental processes in plants, but its distribution in Gossypium genomes or species, evolutionary properties, and the fates of multiple duplicated genes remain unclear.

OBJECTIVES

The primary objectives of this study were to elucidate the distribution and characteristics of PEBP genes in Gossypium, as well as the evolutionary pattern of duplication and deletion, and functional differentiation of PEBPs in plants.

METHODS

Using the PEBP protein sequences in Arabidopsis thaliana as queries, blast alignment was carried out for the identification of PEBP genes in four sequenced cotton species. Using the primers designed according to the PEBP genome sequences, PEBP genes were cloned from 15 representative genomes of Gossypium genus, and the gene structure, CDS sequence, protein sequence and properties were predicted and phylogenetic analysis was performed. Taking PEBP proteins of grape as reference, grouping of orthologous gene, analysis of phylogeny and divergence of PEBPs in nine species were conducted to reconstruct the evolutionary pattern of PEBP genes in plants.

RESULTS

We identified and cloned 160 PEBPs from 15 cotton species, and the phylogenetic analysis showed that the genes could be classified into the following three subfamilies: MFT-like, FT-like and TFL1-like. There were eight single orthologous group (OG) members in each diploid and 16 double OG members in each tetraploid. An analysis of the expression and selective pressure indicated that expression divergence and strong purification selection within the same OG presented in the PEBP gene family.

CONCLUSION

An evolutionary pattern of duplication and deletion of the PEBP family in the evolutionary history of Gossypium was suggested, and three pairs of genes resulted from different whole-genome duplication events.

The Arabidopsis thaliana CONSTANS-LIKE 4 (COL4) - A Modulator of Flowering Time

Appropriate control of flowering time is crucial for crop yield and the reproductive success of plants. Flowering can be induced by a number of molecular pathways that respond to internal and external signals. In Arabidopsis, expression of the key florigenic signal FLOWERING LOCUS T (FT) is positively regulated by CONSTANS (CO) a BBX protein sharing high sequence similarity with 16 CO-like proteins. Within this study, we investigated the role of the Arabidopsis CONSTANS-LIKE 4 (COL4), whose role in flowering control was unknown. We demonstrate that, unlike CO, COL4 is a flowering repressor in long days (LD) and short days (SD) and acts on the expression of FT and FT-like genes as well as on SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1). Reduction of COL4 expression level leads to an increase of FT and APETALA 1 (AP1) expression and to accelerated flowering, while the increase of COL4 expression causes a flowering delay. Further, the observed co-localization of COL4 protein and CO in nuclear speckles supports the idea that the two act as an antagonistic pair of transcription factors. This interaction may serve the fine-tuning of flowering time control and other light dependent plant developmental processes.

Novel screening protocol for precise phenotyping of salt-tolerance at reproductive stage in rice

The present study reports an unequivocal and improved protocol for efficient screening of salt tolerance at flowering stage in rice, which can aid phenotyping of population for subsequent identification of QTLs associated with salinity stress, particularly at reproductive stage. To validate the new method, the selection criteria, level and time of imposition of stress; plant growth medium were standardized using three rice genotypes. The setup was established with a piezometer placed in a perforated pot for continuous monitoring of soil EC and pH throughout the period of study. Further, fertilizer enriched soil was partially substituted by gravels for stabilization and maintaining the uniformity of soil EC in pots without hindering its buffering capacity. The protocol including modified medium (Soil:Stone, 4:1) at 8 dS m^-1 salinity level was validated using seven different genotypes possessing differential salt sensitivity. Based on the important selection traits such as high stability index for plant yield, harvest index and number of grains/panicle and also high K⁺ concentration and low Na⁺- K⁺ ratio in flag leaf at grain filling stage were validated and employed in the evaluation of a mapping population in the modified screening medium. The method was found significantly efficient for easy maintenance of desired level of soil salinity and identification of genotypes tolerant to salinity at reproductive stage.

The FT/FD-dependent initiation of flowering under long-day conditions in the day-neutral species Nicotiana tabacum originates from the facultative short-day ancestor Nicotiana tomentosiformis

Photoperiod is an important external stimulus governing the precise timing of the floral transition in plants. Members of the FLOWERING LOCUS T (FT)-like clade of phosphatidylethanolamine-binding proteins induce this developmental process in numerous species by forming regulatory protein complexes with FD-like bZIP transcription factors. We identified several thus far unknown FT-like and FD-like genes in the genus Nicotiana and found that, even in the day-neutral species Nicotiana tabacum, floral initiation requires the photoperiod-dependent expression of several FT-like genes. Furthermore, floral promotion under long-day (LD) and short-day (SD) conditions is mediated by an FT-like protein (NtFT5) that originates from the genome of the paternal, facultative SD ancestor Nicotiana tomentosiformis. In contrast, its ortholog of the maternal LD ancestor Nicotiana sylvestris is not present in the genome of N. tabacum cv. SR1. Expression profiling in N. tabacum and its ancestors confirmed the relevance of these FT and FD orthologs in the context of polyploidization. We also found that floral inhibition by tobacco FT-like proteins is not restricted to SD conditions, highlighting the coincident expression of tobacco FT-like genes encoding floral activators and floral inhibitors. Multicolor bimolecular fluorescence complementation analysis revealed the preferential formation of FT/FD complexes that promote rather than inhibit flowering, which in concert with the regulation of NtFT and NtFD expression could explain how floral promotion overcomes floral repression during the floral transition in tobacco.

North European invasion by common ragweed is associated with early flowering and dominant changes in FT/TFL1 expression

During the last two centuries, the North American common ragweed (Ambrosia artemisiifolia L.) invaded a large part of the globe. Local adaptation of this species was revealed by a common garden experiment, demonstrating that the distribution of the species in Europe could extend considerably to the North. Our study compares two populations of common ragweed (one from the native range and one from the invaded range) that differ in flowering time in the wild: the invasive population flowers earlier than the native population under non-inductive long-day photoperiods. Experiments conducted in controlled environments established that the two populations differ in their flowering time even under inductive short-day photoperiods, suggesting a change in autonomous flowering control. Genetic analysis revealed that early flowering is dominantly inherited and accompanied by the increased expression of the floral activator AaFTL1 and decreased expression of the floral repressor AaFTL2. Early flowering is also accompanied by reduced reproductive output, which is evolutionarily disadvantageous under long vegetation periods. In contrast, under short vegetation periods, only early-flowering plants can produce any viable seeds, making the higher seed set of late-flowering plants irrelevant. Thus, earlier flowering appears to be a specific adaptation to the higher latitudes of northern Europe.

TFL1-Like Proteins in Rice Antagonize Rice FT-Like Protein in Inflorescence Development by Competition for Complex Formation with 14-3-3 and FD

Hd3a, a rice homolog of FLOWERING LOCUS T (FT), is a florigen that induces flowering. Hd3a forms a ternary 'florigen activation complex' (FAC) with 14-3-3 protein and OsFD1 transcription factor, a rice homolog of FD that induces transcription of OsMADS15, a rice homolog of APETALA1 (AP1), which leads to flowering. TERMINAL FLOWER 1 (TFL1) represses flowering and controls inflorescence architecture. However, the molecular basis for floral repression by TFL1 remains poorly understood. Here we show that RICE CENTRORADIALIS (RCN), rice TFL1-like proteins, compete with Hd3a for 14-3-3 binding. All four RCN genes are predominantly expressed in the vasculature, and RCN proteins are transported to the shoot apex to antagonize florigen activity and regulate inflorescence development. The antagonistic function of RCN to Hd3a is dependent on its 14-3-3 binding activity. Our results suggest a molecular basis for regulation of the balance between florigen FT and anti-florigen TFL1.

WRKY71 Acts Antagonistically Against Salt-Delayed Flowering in Arabidopsis thaliana

Soil salinity affects various aspects of plant growth and development including flowering. Usually, plants show a delayed flowering phenotype under high salinity conditions, whereas some plants will risk their life to continue to grow, thereby escaping serious salt stress to achieve reproductive success. However, the molecular mechanisms of the escape strategies are not clear yet. In this work, we report that the transcription factor WRKY71 helps escape salt stress in Arabidopsis. The expression of the WRKY71 wild-type (WT) allele was salinity inducible. Compared with Col-0, high salt stress caused only a marginal delay in the flowering time of the activation-tagged mutant WRKY71-1D. However, flowering in the RNA interference (RNAi)-based multiple WRKY knock-out mutant (w71w8 + 28RNAi) was dramatically later than in the WT under high salinity conditions. Meanwhile, expression of FLOWERING LOCUS T (FT) and LEAFY (LFY) was greater in WRKY71-1D than in the WT, and lower in w71w8 + 28RNAi under salinity-stressed conditions. The suggestion is that WRKY71 activity hastens flowering, thereby providing a means for the plant to complete its life cycle in the presence of salt stress.

Toward a Molecular Understanding of Abscisic Acid Actions in Floral Transition

The transition from the vegetative growth phase to flowering is a crucial checkpoint for plant reproduction and survival, especially under environmental stress conditions. Numerous factors regulate flowering time, including exogenous environmental cues such as day length and temperature, as well as salt and drought stresses, and endogenous phytohormone signaling cascades. Gibberellins and ABA are one classic combination of phytohormones which antagonistically regulate several biological processes, including seed dormancy and germination, primary root growth and seedling development. As regards control of flowering time, gibberellin exhibits a positive role, and represents an important pathway in the regulation of floral transition. However, over the past decades, numerous investigations have demonstrated that the contribution of the stress hormone ABA to floral transition is still controversial, as both positive and negative effects have been documented. It is important to determine why and how ABA shows this contradictory effect on flowering time. In this up to date review, primarily based on recent publications and emerging data, we summarize the distinct and contrasting roles of ABA on floral transition, while the detailed molecular mechanisms underlying these roles are discussed. Finally, the remaining challenges and open questions in this topic are presented.