MOTHER OF FT AND TFL1 regulates seed germination through a negative feedback loop modulating ABA signaling in Arabidopsis

The release of dormancy, a wake-up call for seeds to germinate

Seed dormancy determines the timing of germination, thereby contributing to successful seedling establishment and plant fitness. The induction and release of dormancy are controlled by various regulators like plant hormones and dormancy proteins. The relative strengths of these regulators are influenced by environmental factors during seed maturation and storage. In the last few years additional processes have been identified to be involved in the release of dormancy during seed storage with an important role for non-enzymatic oxidative reactions. However, the relations between the different dormancy regulators are not fully understood yet. Finally, all accumulated information will be processed in the seed during early seed imbibition and lead to the decision to germinate or not.

Karrikins: Regulators Involved in Phytohormone Signaling Networks during Seed Germination and Seedling Development

Seed germination and early seedling establishment are critical stages during a plant's life cycle. These stages are precisely regulated by multiple internal factors, including phytohormones and environmental cues such as light. As a family of small molecules discovered in wildfire smoke, karrikins (KARs) play a key role in various biological processes, including seed dormancy release, germination regulation, and seedling establishment. KARs show a high similarity with strigolactone (SL) in both chemical structure and signaling transduction pathways. Current evidence shows that KARs may regulate seed germination by mediating the biosynthesis and/or signaling transduction of abscisic acid (ABA), gibberellin (GA) and auxin [indoleacetic acid (IAA)]. Interestingly, KARs regulate seed germination differently in different species. Furthermore, the promotion effect on seedling establishment implies that KARs have a great potential application in alleviating shade avoidance response, which attracts more and more attention in plant molecular biology. In these processes, KARs may have complicated interactions with phytohormones, especially with IAA. In this updated review, we summarize the current understanding of the relationship between KARs and SL in the chemical structure, signaling pathway and the regulation of plant growth and development. Further, the crosstalk between KARs and phytohormones in regulating seed germination and seedling development and that between KARs and IAA during shade responses are discussed. Finally, future challenges and research directions for the KAR research field are suggested.

Whole genome-wide transcript profiling to identify differentially expressed genes associated with seed field emergence in two soybean low phytate mutants

BACKGROUND

Seed germination is important to soybean (Glycine max) growth and development, ultimately affecting soybean yield. A lower seed field emergence has been the main hindrance for breeding soybeans low in phytate. Although this reduction could be overcome by additional breeding and selection, the mechanisms of seed germination in different low phytate mutants remain unknown. In this study, we performed a comparative transcript analysis of two low phytate soybean mutants (TW-1 and TW-1-M), which have the same mutation, a 2 bp deletion in GmMIPS1, but show a significant difference in seed field emergence, TW-1-M was higher than that of TW-1 .

RESULTS

Numerous genes analyzed by RNA-Seq showed markedly different expression levels between TW-1-M and TW-1 mutants. Approximately 30,000-35,000 read-mapped genes and ~21000-25000 expressed genes were identified for each library. There were ~3900-9200 differentially expressed genes (DEGs) in each contrast library, the number of up-regulated genes was similar with down-regulated genes in the mutant TW-1and TW-1-M. Gene ontology functional categories of DEGs indicated that the ethylene-mediated signaling pathway, the abscisic acid-mediated signaling pathway, response to hormone, ethylene biosynthetic process, ethylene metabolic process, regulation of hormone levels, and oxidation-reduction process, regulation of flavonoid biosynthetic process and regulation of abscisic acid-activated signaling pathway had high correlations with seed germination. In total, 2457 DEGs involved in the above functional categories were identified. Twenty-two genes with 20 biological functions were the most highly up/down- regulated (absolute value Log2FC >5) in the high field emergence mutant TW-1-M and were related to metabolic or signaling pathways. Fifty-seven genes with 36 biological functions had the greatest expression abundance (FRPM >100) in germination-related pathways.

CONCLUSIONS

Seed germination in the soybean low phytate mutants is a very complex process, which involves a series of physiological, morphological and transcriptional changes. Compared with TW-1, TW-1-M had a very different gene expression profile, which included genes related to plant hormones, antioxidation, anti-stress and energy metabolism processes. Our research provides a molecular basis for understanding germination mechanisms, and is also an important resource for the genetic analysis of germination in low phytate crops. Plant hormone- and antioxidation-related genes might strongly contribute to the high germination rate in the TW-1-M mutant.

Proteome changes associated with dormancy release of Dongxiang wild rice seeds

Seed dormancy provides optimum timing for seed germination and subsequent seedling growth, but the mechanism of seed dormancy is still poorly understood. Here, we used Dongxiang wild rice (DXWR) seeds to investigate the dormancy behavior and the differentially changed proteome in embryo and endosperm during dormancy release. DXWR seed dormancy was caused by interaction of embryo and its surrounding structure, and was an intermediate physiological dormancy. During seed dormancy release, a total of 109 and 97 protein spots showed significant change in abundance and were successfully identified in embryo and endosperm, respectively. As a result of dormancy release, the abundance of nine proteins involved in storage protein, cell defense and rescue and energy changed in the same way in both embryo and endosperm, while 67 and 49 protein spots changed differentially in embryo and endosperm, respectively. Dormancy release of DXWR seeds was closely associated with degradation of storage proteins in both embryo and endosperm. At the same time, the abundance of proteins involved in metabolism, glycolysis and TCA cycle, cell growth and division, protein synthesis and destination and signal transduction increased in embryos while staying constant or decreasing in endosperms.

Lipidomic profiling analysis reveals the dynamics of phospholipid molecules in Arabidopsis thaliana seedling growth

High-throughput lipidomic profiling provides a sensitive approach for discovering minor lipid species. By using an advance in electrospray ionization tandem mass spectrometry, a large set of phospholipid molecular species (126 species) with high resolution were identified from Arabidopsis seedling; of them 31 species are newly identified (16 are unique in plants), including 13 species of phosphatidic acid (PA), nine phosphatidylcholine, six phosphatidylinositol and three phosphatidylserine. Further analysis of the lipidomic profile reveals dynamics of phospholipids and distinct species alterations during seedling development. PA molecules are found at the lowest levels in imbibition and follow an increasing trend during seedling growth, while phosphatidylethanolamine (PE) molecules show the opposite pattern with highest levels at imbibition and a general decreasing trend at later stages. Of PA molecular species, 34:2-, 34:3-, 36:4-, 36:5-, 38:3- and 38:4-PA increase during radicle emergence, and 34:2- and 34:3-PA reach highest levels during hypocotyl and cotyledon emergence from the seed coat. Conversely, molecular species of PE show higher levels in imbibition and decrease in later stages. These results suggest the crucial roles of specific molecular species and homeostasis of phospholipid molecules in seedling growth and provide insights into the mechanisms of how phospholipid molecules are involved in regulating plant development.

Revisiting the phosphatidylethanolamine-binding protein (PEBP) gene family reveals cryptic FLOWERING LOCUS T gene homologs in gymnosperms and sheds new light on functional evolution

Angiosperms and gymnosperms are two major groups of extant seed plants. It has been suggested that gymnosperms lack FLOWERING LOCUS T (FT), a key integrator at the core of flowering pathways in angiosperms. Taking advantage of newly released gymnosperm genomes, we revisited the evolutionary history of the plant phosphatidylethanolamine-binding protein (PEBP) gene family through phylogenetic reconstruction. Expression patterns in three gymnosperm taxa and heterologous expression in Arabidopsis were studied to investigate the functions of gymnosperm FT-like and TERMINAL FLOWER 1 (TFL1)-like genes. Phylogenetic reconstruction suggests that an ancient gene duplication predating the divergence of seed plants gave rise to the FT and TFL1 genes. Expression patterns indicate that gymnosperm TFL1-like genes play a role in the reproductive development process, while GymFT1 and GymFT2, the FT-like genes resulting from a duplication event in the common ancestor of gymnosperms, function in both growth rhythm and sexual development pathways. When expressed in Arabidopsis, both spruce FT-like and TFL1-like genes repressed flowering. Our study demonstrates that gymnosperms do have FT-like and TFL1-like genes. Frequent gene and genome duplications contributed significantly to the expansion of the plant PEBP gene family. The expression patterns of gymnosperm PEBP genes provide novel insight into the functional evolution of this gene family.

The Evolution of the FT/TFL1 Genes in Amaranthaceae and Their Expression Patterns in the Course of Vegetative Growth and Flowering in Chenopodium rubrum

The FT/TFL1 gene family controls important aspects of plant development: MFT-like genes affect germination, TFL1-like genes act as floral inhibitors, and FT-like genes are floral activators. Gene duplications produced paralogs with modified functions required by the specific lifestyles of various angiosperm species. We constructed the transcriptome of the weedy annual plant Chenopodium rubrum and used it for the comprehensive search for the FT/TFL1 genes. We analyzed their phylogenetic relationships across Amaranthaceae and all angiosperms. We discovered a very ancient phylogenetic clade of FT genes represented by the CrFTL3 gene of C. rubrum Another paralog CrFTL2 showed an unusual structural rearrangement which might have contributed to the functional shift. We examined the transcription patterns of the FT/TFL1 genes during the vegetative growth and floral transition in C. rubrum to get clues about their possible functions. All the genes except for the constitutively expressed CrFTL2 gene, and the CrFTL3 gene, which was transcribed only in seeds, exhibited organ-specific expression influenced by the specific light regime. The CrFTL1 gene was confirmed as a single floral activator from the FT/TFL1 family in C. rubrum Its floral promoting activity may be counteracted by CrTFL1 C. rubrum emerges as an easily manipulated model for the study of floral induction in weedy fast-cycling plants lacking a juvenile phase.

The NF-YC-RGL2 module integrates GA and ABA signalling to regulate seed germination in Arabidopsis

The antagonistic crosstalk between gibberellic acid (GA) and abscisic acid (ABA) plays a pivotal role in the modulation of seed germination. However, the molecular mechanism of such phytohormone interaction remains largely elusive. Here we show that three Arabidopsis NUCLEAR FACTOR-Y C (NF-YC) homologues NF-YC3, NF-YC4 and NF-YC9 redundantly modulate GA- and ABA-mediated seed germination. These NF-YCs interact with the DELLA protein RGL2, a key repressor of GA signalling. The NF-YC–RGL2 module targets ABI5, a gene encoding a core component of ABA signalling, via specific CCAAT elements and collectively regulates a set of GA- and ABA-responsive genes, thus controlling germination. These results suggest that the NF-YC–RGL2–ABI5 module integrates GA and ABA signalling pathways during seed germination.

Crosstalk between gibberellic acid (GA) and abscisic acid (ABA) regulates seed germination. Here the authors show that NF-YC transcription factors can interact with the RGL2 DELLA protein to regulate expression of ABI5 and therefore modulate ABA- and GA-responsive gene expression.

Characterization and Functional Analysis of PEBP Family Genes in Upland Cotton (Gossypium hirsutum L.)

Upland cotton (Gossypium hirsutum L.) is a naturally occurring photoperiod-sensitive perennial plant species. However, sensitivity to the day length was lost during domestication. The phosphatidylethanolamine-binding protein (PEBP) gene family, of which three subclades have been identified in angiosperms, functions to promote and suppress flowering in photoperiod pathway. Recent evidence indicates that PEBP family genes play an important role in generating mobile flowering signals. We isolated homologues of the PEBP gene family in upland cotton and examined their regulation and function. Nine PEBP-like genes were cloned and phylogenetic analysis indicated the genes belonged to four subclades (FT, MFT, TFL1 and PEBP). Cotton PEBP-like genes showed distinct expression patterns in relation to different cotton genotypes, photoperiod responsive and cultivar maturity. The GhFT gene expression of a semi-wild race of upland cotton were strongly induced under short day condition, whereas the GhPEBP2 gene expression was induced under long days. We also elucidated that GhFT but not GhPEBP2 interacted with FD-like bZIP transcription factor GhFD and promote flowering under both long- and short-day conditions. The present result indicated that GhPEBP-like genes may perform different functions. This work corroborates the involvement of PEBP-like genes in photoperiod response and regulation of flowering time in different cotton genotypes, and contributes to an improved understanding of the function of PEBP-like genes in cotton.

Comparative analysis of the pteridophyte Adiantum MFT ortholog reveals the specificity of combined FT/MFT C and N terminal interaction with FD for the regulation of the downstream gene AP1

To study the evolution of phosphatidylethanolamine-binding protein (PEBP) gene families in non-flowering plants, we performed a functional analysis of the PEBP gene AcMFT of the MFT clade in the pteridophyte Adiantum capillus-veneris. The expression of AcMFT was regulated by photoperiod similar to that for FT under both long day and short day conditions. Ectopic expression of AcMFT in Arabidopsis promotes the floral transition and partially complements the late flowering defect in transgenic Arabidopsis ft-1 mutants, suggesting that AcMFT functions similarly to FT in flowering plants. Interestingly, a similar partial compensation of the ft-1 late flowering phenotype was observed in Arabidopsis ectopically expressing only exon 4 of the C terminus of AcMFT and FT. This result indicated that the fourth exon of AcMFT and FT plays a similar and important role in promoting flowering. Further analysis indicated that exons 1-3 in the N terminus specifically enhanced the function of FT exon 4 in controlling flowering in Arabidopsis. Protein pull-down assays indicated that Arabidopsis FD proteins interact with full-length FT and AcMFT, as well as peptides encoded by 1-3 exon fragments or the 4th exon alone. Furthermore, similar FRET efficiencies for FT-FD and AcMFT-FD heterodimer in nucleus were observed. These results indicated that FD could form the similar complex with FT and AcMFT. Further analysis indicated that the expression of AP1, a gene downstream of FT, was up-regulated more strongly by FT than AcMFT in transgenic Arabidopsis. Our results revealed that AcMFT from a non-flowering plant could interact with FD to regulate the floral transition and that this function was reduced due to the weakened ability of AcMFT-FD to activate the downstream gene AP1.

Proteomics analysis reveals distinct involvement of embryo and endosperm proteins during seed germination in dormant and non-dormant rice seeds

Seed germination is a complex trait which is influenced by many genetic, endogenous and environmental factors, but the key event(s) associated with seed germination are still poorly understood. In present study, the non-dormant cultivated rice Yannong S and the dormant Dongxiang wild rice seeds were used as experimental materials, we comparatively investigated the water uptake, germination time course, and the differential proteome of the effect of embryo and endosperm on germination of these two types of seeds. A total of 231 and 180 protein spots in embryo and endosperm, respectively, showed a significant change in abundance during germination. We observed that the important proteins associated with seed germination included those involved in metabolism, energy production, protein synthesis and destination, storage protein, cell growth and division, signal transduction, cell defense and rescue. The contribution of embryo and endosperm to seed germination is different. In embryo, the proteins involved in amino acid activation, sucrose cleavage, glycolysis, fermentation and protein synthesis increased; in endosperm, the proteins involved in sucrose cleavage and glycolysis decreased, and those with ATP and CoQ synthesis and proteolysis increased. Our results provide some new knowledge to understand further the mechanism of seed germination.

Plant hormone-mediated regulation of stress responses

BACKGROUND

Being sessile organisms, plants are often exposed to a wide array of abiotic and biotic stresses. Abiotic stress conditions include drought, heat, cold and salinity, whereas biotic stress arises mainly from bacteria, fungi, viruses, nematodes and insects. To adapt to such adverse situations, plants have evolved well-developed mechanisms that help to perceive the stress signal and enable optimal growth response. Phytohormones play critical roles in helping the plants to adapt to adverse environmental conditions. The elaborate hormone signaling networks and their ability to crosstalk make them ideal candidates for mediating defense responses.

RESULTS

Recent research findings have helped to clarify the elaborate signaling networks and the sophisticated crosstalk occurring among the different hormone signaling pathways. In this review, we summarize the roles of the major plant hormones in regulating abiotic and biotic stress responses with special focus on the significance of crosstalk between different hormones in generating a sophisticated and efficient stress response. We divided the discussion into the roles of ABA, salicylic acid, jasmonates and ethylene separately at the start of the review. Subsequently, we have discussed the crosstalk among them, followed by crosstalk with growth promoting hormones (gibberellins, auxins and cytokinins). These have been illustrated with examples drawn from selected abiotic and biotic stress responses. The discussion on seed dormancy and germination serves to illustrate the fine balance that can be enforced by the two key hormones ABA and GA in regulating plant responses to environmental signals.

CONCLUSIONS

The intricate web of crosstalk among the often redundant multitudes of signaling intermediates is just beginning to be understood. Future research employing genome-scale systems biology approaches to solve problems of such magnitude will undoubtedly lead to a better understanding of plant development. Therefore, discovering additional crosstalk mechanisms among various hormones in coordinating growth under stress will be an important theme in the field of abiotic stress research. Such efforts will help to reveal important points of genetic control that can be useful to engineer stress tolerant crops.

Regulation of Arabidopsis thaliana seed dormancy and germination by 12-oxo-phytodienoic acid

We previously demonstrated that the oxylipin 12-oxo-phytodienoic acid (OPDA) acts along with abscisic acid to regulate seed germination in Arabidopsis thaliana, but the mechanistic details of this synergistic interaction remain to be elucidated. Here, we show that OPDA acts through the germination inhibition effects of abscisic acid, the abscisic acid-sensing ABI5 protein, and the gibberellin-sensing RGL2 DELLA protein. We further demonstrate that OPDA also acts through another dormancy-promoting factor, MOTHER-OF-FT-AND-TFL1 (MFT). Both abscisic acid and MFT positively feed back into the OPDA pathway by promoting its accumulation. These results confirm the central role of OPDA in regulating seed dormancy and germination in A. thaliana and underline the complexity of interactions between OPDA and other dormancy-promoting factors such as abscisic acid, RGL2, and MFT.

Identification, Functional Study, and Promoter Analysis of HbMFT1, a Homolog of MFT from Rubber Tree (Hevea brasiliensis)

A homolog of MOTHER OF FT AND TFL1 (MFT) was isolated from Heveabrasiliensis and its biological function was investigated. Protein multiple sequence alignment and phylogenetic analysis revealed that HbMFT1 conserved critical amino acid residues to distinguish MFT, FLOWERING LOCUS T (FT) and TERMINAL FLOWER1 (TFL1)-like proteins and showed a closer genetic relationship to the MFT-like group. The accumulation of HbMFT1 was generally detected in various tissues except pericarps, with the highest expression in embryos and relatively higher expression in roots and stems of seedlings, flowering inflorescences, and male and female flowers. HbMFT1 putative promoter analysis showed that tissue-specific, environmental change responsive and hormone-signaling responsive elements were generally present. HbMFT1 was strongly induced under a short-day condition at 28 °C, with the highest expression after the onset of a day. Overexpression of HbMFT1 inhibited seed germination, seedling growth, and flowering in transgenic Arabidopsis. The qRT-PCR further confirmed that APETALA1 (AP1) and FRUITFULL (FUL) were drastically down-regulated in 35S::HbMFT1 plants. A histochemical β-glucuronidase (GUS) assay showed that HbMFT1::GUS activity was mainly detected in stamens and mature seeds coinciding with its original expression and notably induced in rosette leaves and seedlings of transgenic Arabidopsis by exogenous abscisic acid (ABA) due to the presence of ABA cis-elements in HbMFT1 promoter. These results suggested that HbMFT1 was mainly involved in maintenance of seed maturation and stamen development, but negatively controlled germination, growth and development of seedlings and flowering. In addition, the HbMFT1 promoter can be utilized in controlling transgene expression in stamens and seeds of rubber tree or other plant species.

Effects of Parental Temperature and Nitrate on Seed Performance are Reflected by Partly Overlapping Genetic and Metabolic Pathways

Seed performance is affected by the seed maturation environment, and previously we have shown that temperature, nitrate and light intensity were the most influential environmental factors affecting seed performance. Seeds developed in these environments were selected to assess the underlying metabolic pathways, using a combination of transcriptomics and metabolomics. These analyses revealed that the effects of the parental temperature and nitrate environments were reflected by partly overlapping genetic and metabolic networks, as indicated by similar changes in the expression levels of metabolites and transcripts. Nitrogen metabolism-related metabolites (asparagine, γ-aminobutyric acid and allantoin) were significantly decreased in both low temperature (15 °C) and low nitrate (N0) maturation environments. Correspondingly, nitrogen metabolism genes (ALLANTOINASE, NITRATE REDUCTASE 1, NITRITE REDUCTASE 1 and NITRILASE 4) were differentially regulated in the low temperature and nitrate maturation environments, as compared with control conditions. High light intensity during seed maturation increased galactinol content, and displayed a high correlation with seed longevity. Low light had a genotype-specific effect on cell surface-encoding genes in the DELAY OF GERMINATION 6-near isogenic line (NILDOG6). Overall, the integration of phenotypes, metabolites and transcripts led to new insights into the regulation of seed performance.

Karrikins delay soybean seed germination by mediating abscisic acid and gibberellin biogenesis under shaded conditions

Karrikins (KAR) are a class of signal compounds, discovered in wildfire smoke, which affect seed germination. Currently, numerous studies have focused on the model plant Arabidopsis in the KAR research field, rather than on crops. Thus the regulatory mechanisms underlying KAR regulation of crop seed germination are largely unknown. Here, we report that KAR delayed soybean seed germination through enhancing abscisic acid (ABA) biosynthesis, while impairing gibberellin (GA) biogenesis. Interestingly, KAR only retarded soybean seed germination under shaded conditions, rather than under dark and white light conditions, which differs from in Arabidopsis. Phytohormone quantification showed that KAR enhanced ABA biogenesis while impairing GA biosynthesis during the seed imbibition process, and subsequently, the ratio of active GA4 to ABA was significantly reduced. Further qRT-PCR analysis showed that the transcription pattern of genes involved in ABA and GA metabolic pathways are consistent with the hormonal measurements. Finally, fluridone, an ABA biogenesis inhibitor, remarkably rescued the delayed-germination phenotype of KAR-treatment; and paclobutrazol, a GA biosynthesis inhibitor, inhibited soybean seed germination. Taken together, these evidences suggest that KAR inhibit soybean seed germination by mediating the ratio between GA and ABA biogenesis.

Comparative transcriptome analysis of wheat embryo and endosperm responses to ABA and H2O2 stresses during seed germination

BACKGROUND

Wheat embryo and endosperm play important roles in seed germination, seedling survival, and subsequent vegetative growth. ABA can positively regulate dormancy induction and negatively regulates seed germination at low concentrations, while low H2O2 concentrations promote seed germination of cereal plants. In this report, we performed the first integrative transcriptome analysis of wheat embryo and endosperm responses to ABA and H2O2 stresses.

RESULTS

We used the GeneChip® Wheat Genome Array to conduct a comparative transcriptome microarray analysis of the embryo and endosperm of elite Chinese bread wheat cultivar Zhengmai 9023 in response to ABA and H2O2 treatments during seed germination. Transcriptome profiling showed that after H2O2 and ABA treatments, the 64 differentially expressed genes in the embryo were closely related to DNA synthesis, CHO metabolism, hormone metabolism, and protein degradation, while 121 in the endosperm were involved mainly in storage reserves, transport, biotic and abiotic stresses, hormone metabolism, cell wall metabolism, signaling, and development. Scatter plot analysis showed that ABA treatment increased the similarity of regulated patterns between the two tissues, whereas H2O2 treatment decreased the global expression similarity. MapMan analysis provided a global view of changes in several important metabolism pathways (e.g., energy reserves mobilization, cell wall metabolism, and photosynthesis), as well as related functional groups (e.g., cellular processes, hormones, and signaling and transport) in the embryo and endosperm following exposure of seeds to ABA and H2O2 treatments during germination. Quantitative RT-PCR analysis was used to validate the expression patterns of nine differentially expressed genes.

CONCLUSIONS

Wheat seed germination involves regulation of a large number of genes involved in many functional groups. ABA/H2O2 can repress/promote seed germination by coordinately regulating related gene expression. Our results provide novel insights into the transcriptional regulation mechanisms of embryo and endosperm in response to ABA and H2O2 treatments during seed germination.

ABA-HYPERSENSITIVE BTB/POZ PROTEIN 1 functions as a negative regulator in ABA-mediated inhibition of germination in Arabidopsis

To elucidate the contribution of CRL3-ABA-mediated responses, we attempted to find CRL3 substrate receptors involved in ABA signaling. One gene named ABA-HYPERSENSITIVE BTB/POZ PROTEIN 1 (AHT1) was upregulated more than 2.5 times by ABA, and its coding region possessed a BTB/POZ domain, which is the common feature of CRL3 substrate receptors. Loss of AHT1 led to retardation of the germination process, not inhibition of root growth. AHT1 transcripts also increased in response to mannitol, NaCl and drought treatments at the seedling stage and in dry seeds. High expression of AHT1 in dry seeds was inhibited by the defect of ABA signaling components such as ABI1, ABI3 and SRKs indicating that the expression of AHT1 is dependent on ABA signaling. Among bZIP transcription factors participating in ABA signaling, the losses of ABI5/DPBF1, AREB1/ABF2, EEL/DPBF4 and DPBF2/bZIP67 resulted in reduced AHT1 expression, showing that these transcription factors play a positive role in ABA-induced AHT1 expression. While loss of AHT1 did not affect the expression pattern of NCED3, ABI2, SRKs and AREB/ABF genes, it led to hyperinduction of ABI5/DPBF genes such as ABI5/DPBF1, EEL/DPBF4 and AREB3/DPBF3, which are mainly involved in seed development and germination, as well as ABA-inducible genes transactivated by ABI5. Overall, these findings indicate that AHT1 negatively regulates ABA-mediated inhibition of germination, possibly by repressing the expression of a subset of ABI5/DPBF subfamily genes, and that AHT1 may be regulated by a negative feedback process through its linkage with a part of ABI5/DPBF proteins.

Two Faces of One Seed: Hormonal Regulation of Dormancy and Germination

Seed plants have evolved to maintain the dormancy of freshly matured seeds until the appropriate time for germination. Seed dormancy and germination are distinct physiological processes, and the transition from dormancy to germination is not only a critical developmental step in the life cycle of plants but is also important for agricultural production. These processes are precisely regulated by diverse endogenous hormones and environmental cues. Although ABA (abscisic acid) and GAs (gibberellins) are known to be the primary phytohormones that antagonistically regulate seed dormancy, recent findings demonstrate that another phytohormone, auxin, is also critical for inducing and maintaining seed dormancy, and therefore might act as a key protector of seed dormancy. In this review, we summarize our current understanding of the sophisticated molecular networks involving the critical roles of phytohormones in regulating seed dormancy and germination, in which AP2-domain-containing transcription factors play key roles. We also discuss the interactions (crosstalk) of diverse hormonal signals in seed dormancy and germination, focusing on the ABA/GA balance that constitutes the central node.

The Role and Regulation of ABI5 (ABA-Insensitive 5) in Plant Development, Abiotic Stress Responses and Phytohormone Crosstalk

ABA Insensitive 5 (ABI5) is a basic leucine zipper transcription factor that plays a key role in the regulation of seed germination and early seedling growth in the presence of ABA and abiotic stresses. ABI5 functions in the core ABA signaling, which is composed of PYR/PYL/RCAR receptors, PP2C phosphatases and SnRK2 kinases, through the regulation of the expression of genes that contain the ABSCISIC ACID RESPONSE ELEMENT (ABRE) motif within their promoter region. The regulated targets include stress adaptation genes, e.g., LEA proteins. However, the expression and activation of ABI5 is not only dependent on the core ABA signaling. Many transcription factors such as ABI3, ABI4, MYB7 and WRKYs play either a positive or a negative role in the regulation of ABI5 expression. Additionally, the stability and activity of ABI5 are also regulated by other proteins through post-translational modifications such as phosphorylation, ubiquitination, sumoylation and S-nitrosylation. Moreover, ABI5 also acts as an ABA and other phytohormone signaling integrator. Components of auxin, cytokinin, gibberellic acid, jasmonate and brassinosteroid signaling and metabolism pathways were shown to take part in ABI5 regulation and/or to be regulated by ABI5. Monocot orthologs of AtABI5 have been identified. Although their roles in the molecular and physiological adaptations during abiotic stress have been elucidated, knowledge about their detailed action still remains elusive. Here, we describe the recent advances in understanding the action of ABI5 in early developmental processes and the adaptation of plants to unfavorable environmental conditions. We also focus on ABI5 relation to other phytohormones in the abiotic stress response of plants.

Dormancy and germination: How does the crop seed decide?

Whether seeds germinate or maintain dormancy is decided upon through very intricate physiological processes. Correct timing of these processes is most important for the plants life cycle. If moist conditions are encountered, a low dormancy level causes pre-harvest sprouting in various crop species, such as wheat, corn and rice, this decreases crop yield and negatively impacts downstream industrial processing. In contrast, a deep level of seed dormancy prevents normal germination even under favourable conditions, resulting in a low emergence rate during agricultural production. Therefore, an optimal seed dormancy level is valuable for modern mechanised agricultural systems. Over the past several years, numerous studies have demonstrated that diverse endogenous and environmental factors regulate the balance between dormancy and germination, such as light, temperature, water status and bacteria in soil, and phytohormones such as ABA (abscisic acid) and GA (gibberellic acid). In this updated review, we highlight recent advances regarding the molecular mechanisms underlying regulation of seed dormancy and germination processes, including the external environmental and internal hormonal cues, and primarily focusing on the staple crop species. Furthermore, future challenges and research directions for developing a full understanding of crop seed dormancy and germination are also discussed.

Factorial combinations of protein interactions generate a multiplicity of florigen activation complexes in wheat and barley

The FLOWERING LOCUS T (FT) protein is a central component of a mobile flowering signal (florigen) that is transported from leaves to the shoot apical meristem (SAM). Two FT monomers and two DNA-binding bZIP transcription factors interact with a dimeric 14-3-3 protein bridge to form a hexameric protein complex. This complex, designated as the 'florigen activation complex' (FAC), plays a critical role in flowering. The wheat homologue of FT, designated FT1 (= VRN3), activates expression of VRN1 in the leaves and the SAM, promoting flowering under inductive long days. In this study, we show that FT1, other FT-like proteins, and different FD-like proteins, can interact with multiple wheat and barley 14-3-3 proteins. We also identify the critical amino acid residues in FT1 and FD-like proteins required for their interactions, and demonstrate that 14-3-3 proteins are necessary bridges to mediate the FT1-TaFDL2 interaction. Using in vivo bimolecular fluorescent complementation (BiFC) assays, we demonstrate that the interaction between FT1 and 14-3-3 occurs in the cytoplasm, and that this complex is then translocated to the nucleus, where it interacts with TaFDL2 to form a FAC. We also demonstrate that a FAC including FT1, TaFDL2 and Ta14-3-3C can bind to the VRN1 promoter in vitro. Finally, we show that relative transcript levels of FD-like and 14-3-3 genes vary among tissues and developmental stages. Since FD-like proteins determine the DNA specificity of the FACs, variation in FD-like gene expression can result in spatial and temporal modulation of the effects of mobile FT-like signals.

The FLOWERING LOCUS T/TERMINAL FLOWER 1 Gene Family: Functional Evolution and Molecular Mechanisms

In plant development, the flowering transition and inflorescence architecture are modulated by two homologous proteins, FLOWERING LOCUS T (FT) and TERMINAL FLOWER 1 (TFL1). The florigen FT promotes the transition to reproductive development and flowering, while TFL1 represses this transition. Despite their importance to plant adaptation and crop improvement and their extensive study by the plant community, the molecular mechanisms controlling the opposing actions of FT and TFL1 have remained mysterious. Recent studies in multiple species have unveiled diverse roles of the FT/TFL1 gene family in developmental processes other than flowering regulation. In addition, the striking evolution of FT homologs into flowering repressors has occurred independently in several species during the evolution of flowering plants. These reports indicate that the FT/TFL1 gene family is a major target of evolution in nature. Here, we comprehensively survey the conserved and diverse functions of the FT/TFL1 gene family throughout the plant kingdom, summarize new findings regarding the unique evolution of FT in multiple species, and highlight recent work elucidating the molecular mechanisms of these proteins.

Accumulation of long-lived mRNAs associated with germination in embryos during seed development of rice

Mature dry seeds contain translatable mRNAs called long-lived mRNAs. Early studies have shown that protein synthesis during the initial phase of seed germination occurs from long-lived mRNAs, without de novo transcription. However, the gene expression systems that generate long-lived mRNAs in seeds are not well understood. To examine the accumulation of long-lived mRNAs in developing rice embryos, germination tests using the transcriptional inhibitor actinomycin D (Act D) were performed with the Japonica rice cultivar Nipponbare. Although over 70% of embryos at 10 days after flowering (DAF) germinated in the absence of the inhibitor, germination was remarkably impaired in embryos treated with Act D. In contrast, more than 70% of embryos at 20, 25, 30 and 40 DAF germinated in the presence of Act D. The same results were obtained when another cultivar, Koshihikari, was used, indicating that the long-lived mRNAs required for germination predominantly accumulate in embryos between 10 and 20 DAF during seed development. RNA-Seq identified 529 long-lived mRNA candidates, encoding proteins such as ABA, calcium ion and phospholipid signalling-related proteins, and HSP DNA J, increased from 10 to 20 DAF and were highly abundant in 40 DAF embryos of Nipponbare and Koshihikari. We also revealed that these long-lived mRNA candidates are clearly up-regulated in 10 DAF germinating embryos after imbibition, suggesting that the accumulation of these mRNAs in embryos is indispensable for the induction of germination. The findings presented here may facilitate in overcoming irregular seed germination or producing more vigorous seedlings.

Genomic, Transcriptomic, and Phenomic Variation Reveals the Complex Adaptation of Modern Maize Breeding

The temperate-tropical division of early maize germplasms to different agricultural environments was arguably the greatest adaptation process associated with the success and near ubiquitous importance of global maize production. Deciphering this history is challenging, but new insight has been gained from examining 558 529 single nucleotide polymorphisms, expression data of 28 769 genes, and 662 traits collected from 368 diverse temperate and tropical maize inbred lines in this study. This is a new attempt to systematically exploit the mechanisms of the adaptation process in maize. Our results indicate that divergence between tropical and temperate lines apparently occurred 3400-6700 years ago. Seven hundred and one genomic selection signals and transcriptomic variants including 2700 differentially expressed individual genes and 389 rewired co-expression network genes were identified. These candidate signals were found to be functionally related to stress responses, and most were associated with directionally selected traits, which may have been an advantage under widely varying environmental conditions faced by maize as it was migrated away from its domestication center. Our study also clearly indicates that such stress adaptation could involve evolution of protein-coding sequences as well as transcriptome-level regulatory changes. The latter process may be a more flexible and dynamic way for maize to adapt to environmental changes along its short evolutionary history.

The Arabidopsis MYB96 transcription factor plays a role in seed dormancy

Seed dormancy facilitates to endure environmental disadvantages by confining embryonic growth until the seeds encounter favorable environmental conditions for germination. Abscisic acid (ABA) and gibberellic acid (GA) play a pivotal role in the determination of the seed dormancy state. ABA establishes seed dormancy, while GA triggers seed germination. Here, we demonstrate that MYB96 contributes to the fine-tuning of seed dormancy regulation through the coordination of ABA and GA metabolism. The MYB96-deficient myb96-1 seeds germinated earlier than wild-type seeds, whereas delayed germination was observed in the activation-tagging myb96-1D seeds. The differences in germination rate disappeared after stratification or after-ripening. The MYB96 transcription factor positively regulates ABA biosynthesis genes 9-CIS-EPOXYCAROTENOID DIOXYGENASE 2 (NCED2), NCED5, NCED6, and NCED9, and also affects GA biosynthetic genes GA3ox1 and GA20ox1. Notably, MYB96 directly binds to the promoters of NCED2 and NCED6, primarily modulating ABA biosynthesis, which subsequently influences GA metabolism. In agreement with this, hyperdormancy of myb96-1D seeds was recovered by an ABA biosynthesis inhibitor fluridone, while hypodormancy of myb96-1 seeds was suppressed by a GA biosynthesis inhibitor paclobutrazol (PAC). Taken together, the metabolic balance of ABA and GA underlies MYB96 control of primary seed dormancy.

Epigallocatechin-3-gallate functions as a physiological regulator by modulating the jasmonic acid pathway

Flavonoids, a class of plant polyphenols derived from plant secondary metabolism, play important roles in plant development and have beneficial effects on human health. Epigallocatechin-3-gallate (EGCG) is the most abundant polyphenol, and its molecular and biochemical mechanism have been followed with interest. The shared signaling heritage or convergence of organisms has allowed us to extend this research into the model plant, Arabidopsis thaliana. Here, we showed that EGCG could promote jasmonic acid (JA) signaling in A. thaliana. EGCG not only inhibited seed germination but also elevated the resistance to necrotrophic Botrytis cinerea, partly by altering the relative strength of JA signaling. Accordingly, JA marker gene induction, seed germination inhibition and the increased resistance to B. cinerea were attenuated in the JA-insensitive coi1-2 mutant. The coi1-2 mutant was partially insensitive to the treatment of EGCG, further implicating the function of EGCG in JA signaling and/or perception. Our results indicate that EGCG, a member of the flavonoid class of polyphenols, affects signal processing in seed development and disease susceptibility via modulation of JA signaling.

Functional evolution of phosphatidylethanolamine binding proteins in soybean and Arabidopsis

Gene duplication provides resources for novel gene functions. Identification of the amino acids responsible for functional conservation and divergence of duplicated genes will strengthen our understanding of their evolutionary course. Here, we conducted a systemic functional investigation of phosphatidylethanolamine binding proteins (PEBPs) in soybean (Glycine max) and Arabidopsis thaliana. Our results demonstrated that after the ancestral duplication, the lineage of the common ancestor of the FLOWERING LOCUS T (FT) and TERMINAL FLOWER1 (TFL1) subfamilies functionally diverged from the MOTHER OF FT AND TFL1 (MFT) subfamily to activate flowering and repress flowering, respectively. They also underwent further specialization after subsequent duplications. Although the functional divergence increased with duplication age, we observed rapid functional divergence for a few pairs of young duplicates in soybean. Association analysis between amino acids and functional variations identified critical amino acid residues that led to functional differences in PEBP members. Using transgenic analysis, we validated a subset of these differences. We report clear experimental evidence for the functional evolution of the PEBPs in the MFT, FT, and TFL1 subfamilies, which predate the origin of angiosperms. Our results highlight the role of amino acid divergence in driving evolutionary novelty after duplication.

A promoter analysis of MOTHER OF FT AND TFL1 1 (JcMFT1), a seed-preferential gene from the biofuel plant Jatropha curcas

MOTHER OF FT AND TFL1 (MFT)-like genes belong to the phosphatidylethanoamine-binding protein (PEBP) gene family in plants. In contrast to their homologs FLOWERING LOCUS T (FT)-like and TERMINAL FLOWER 1 (TFL1)-like genes, which are involved in the regulation of the flowering time pathway, MFT-like genes function mainly during seed development and germination. In this study, a full-length cDNA of the MFT-like gene JcMFT1 from the biodiesel plant Jatropha curcas (L.) was isolated and found to be highly expressed in seeds. The promoter of JcMFT1 was cloned and characterized in transgenic Arabidopsis. A histochemical β-glucuronidase (GUS) assay indicated that the JcMFT1 promoter was predominantly expressed in both embryos and endosperms of transgenic Arabidopsis seeds. Fluorometric GUS analysis revealed that the JcMFT1 promoter was highly active at the mid to late stages of seed development. After seed germination, the JcMFT1 promoter activity decreased gradually. In addition, both the JcMFT1 expression in germinating Jatropha embryos and its promoter activity in germinating Arabidopsis embryos were induced by abscisic acid (ABA), possibly due to two ABA-responsive elements, a G-box and an RY repeat, in the JcMFT1 promoter region. These results show that the JcMFT1 promoter is seed-preferential and can be used to control transgene expression in the seeds of Jatropha and other transgenic plants.

Identification of a soybean MOTHER OF FT AND TFL1 homolog involved in regulation of seed germination

Seed germination is an important event in the life cycle of seed plants, and is controlled by complex and coordinated genetic networks. Many genes involved in the regulation of this process have been identified in different plant species so far. Recent studies in both Arabidopsis and wheat have uncovered a new role of MOTHER OF FT AND TFL1 (MFT) in seed germination. Here, we reported a homolog of MFT in soybean (GmMFT) which strongly expressed in seeds. Detailed expression analysis showed that the mRNA level of GmMFT increased with seed development but declined during seed germination. The transcription of GmMFT also responded to exogenous application of ABA and GA3. Ectopic expression of GmMFT CDS in Arabidopsis moderately inhibited seed germination. All these evidences suggest that GmMFT may be a negative regulator of seed germination.

TRANSPARENT TESTA8 Inhibits Seed Fatty Acid Accumulation by Targeting Several Seed Development Regulators in Arabidopsis

Fatty acids (FAs) and FA-derived complex lipids play important roles in plant growth and vegetative development and are a class of prominent metabolites stored in mature seeds. The factors and regulatory networks that control FA accumulation in plant seeds remain largely unknown. The role of TRANSPARENT TESTA8 (TT8) in the regulation of flavonoid biosynthesis and the formation of seed coat color is extensively studied; however, its function in affecting seed FA biosynthesis is poorly understood. In this article, we show that Arabidopsis (Arabidopsis thaliana) TT8 acts maternally to affect seed FA biosynthesis and inhibits seed FA accumulation by down-regulating a group of genes either critical to embryonic development or important in the FA biosynthesis pathway. Moreover, the tt8 mutation resulted in reduced deposition of protein in seeds during maturation. Posttranslational activation of a TT8-GLUCOCORTICOID RECEPTOR fusion protein and chromatin immunoprecipitation assays demonstrated that TT8 represses the activities of LEAFY COTYLEDON1, LEAFY COTYLEDON2, and FUSCA3, the critical transcriptional factors important for seed development, as well as CYTIDINEDIPHOSPHATE DIACYLGLYCEROL SYNTHASE2, which mediates glycerolipid biosynthesis. These results help us to understand the entire function of TT8 and increase our knowledge of the complicated networks regulating the formation of FA-derived complex lipids in plant seeds.

Environment sensing in spring-dispersed seeds of a winter annual Arabidopsis influences the regulation of dormancy to align germination potential with seasonal changes

Seed dormancy cycling plays a crucial role in the lifecycle timing of many plants. Little is known of how the seeds respond to the soil seed bank environment following dispersal in spring into the short-term seed bank before seedling emergence in autumn. Seeds of the winter annual Arabidopsis ecotype Cvi were buried in field soils in spring and recovered monthly until autumn and their molecular eco-physiological responses were recorded. DOG1 expression is initially low and then increases as dormancy increases. MFT expression is negatively correlated with germination potential. Abscisic acid (ABA) and gibberellin (GA) signalling responds rapidly following burial and adjusts to the seasonal change in soil temperature. Collectively these changes align germination potential with the optimum climate space for seedling emergence. Seeds naturally dispersed to the soil in spring enter a shallow dormancy cycle dominated by spatial sensing that adjusts germination potential to the maximum when soil environment is most favourable for germination and seedling emergence upon soil disturbance. This behaviour differs subtly from that of seeds overwintered in the soil seed bank to spread the period of potential germination in the seed population (existing seed bank and newly dispersed). As soil temperature declines in autumn, deep dormancy is re-imposed as seeds become part of the persistent seed bank.

iNID: an analytical framework for identifying network models for interplays among developmental signaling in Arabidopsis

Integration of internal and external cues into developmental programs is indispensable for growth and development of plants, which involve complex interplays among signaling pathways activated by the internal and external factors (IEFs). However, decoding these complex interplays is still challenging. Here, we present a web-based platform that identifies key regulators and Network models delineating Interplays among Developmental signaling (iNID) in Arabidopsis. iNID provides a comprehensive resource of (1) transcriptomes previously collected under the conditions treated with a broad spectrum of IEFs and (2) protein and genetic interactome data in Arabidopsis. In addition, iNID provides an array of tools for identifying key regulators and network models related to interplays among IEFs using transcriptome and interactome data. To demonstrate the utility of iNID, we investigated the interplays of (1) phytohormones and light and (2) phytohormones and biotic stresses. The results revealed 34 potential regulators of the interplays, some of which have not been reported in association with the interplays, and also network models that delineate the involvement of the 34 regulators in the interplays, providing novel insights into the interplays collectively defined by phytohormones, light, and biotic stresses. We then experimentally verified that BME3 and TEM1, among the selected regulators, are involved in the auxin-brassinosteroid (BR)-blue light interplay. Therefore, iNID serves as a useful tool to provide a basis for understanding interplays among IEFs.

Cloning of seed dormancy genes (TaSdr) associated with tolerance to pre-harvest sprouting in common wheat and development of a functional marker

After cloning and mapping of wheat TaSdr genes, both the functional markers for TaSdr - B1 and TaVp - 1B were validated, and the distribution of allelic variations at TaSdr - B1 locus in the wheat cultivars from 19 countries was characterized. Seed dormancy is a major factor associated with pre-harvest sprouting (PHS) in common wheat (Triticum aestivum L.). Wheat TaSdr genes, orthologs of OsSdr4 conferring seed dormancy in rice, were cloned by a comparative genomics approach. They were located on homoeologous group 2 chromosomes, and designated as TaSdr-A1, TaSdr-B1 and TaSdr-D1, respectively. Sequence analysis of TaSdr-B1 revealed a SNP at the position -11 upstream of the initiation codon, with bases A and G in cultivars with low and high germination indices (GI), respectively. A cleaved amplified polymorphism sequence marker Sdr2B was developed based on the SNP, and subsequently functional analysis of TaSdr-B1 was conducted by association and linkage mapping. A QTL for GI co-segregating with Sdr2B explained 6.4, 7.8 and 8.7 % of the phenotypic variances in a RIL population derived from Yangxiaomai/Zhongyou 9507 grown in Shijiazhuang, Beijing and the averaged data from those environments, respectively. Two sets of Chinese wheat cultivars were used for association mapping, and results indicated that TaSdr-B1 was significantly associated with GI. Analysis of the allelic distribution at the TaSdr-B1 locus showed that the frequencies of TaSdr-B1a associated with a lower GI were high in cultivars from Japan, Australia, Argentina, and the Middle and Lower Yangtze Valley Winter Wheat Region and Southwest Winter Wheat Region in China. This study provides not only a reliable functional marker for molecular-assisted selection of PHS in wheat breeding programs, but also gives novel information for a comprehensive understanding of seed dormancy.

TRANSPARENT TESTA2 regulates embryonic fatty acid biosynthesis by targeting FUSCA3 during the early developmental stage of Arabidopsis seeds

TRANSPARENT TESTA2 (TT2) regulates the biosynthesis of proanthocyanidins in the seed coat of Arabidopsis. We recently found that TT2 also participates in inhibition of fatty acid (FA) biosynthesis in the seed embryo. However, the mechanism by which TT2 suppresses the accumulation of seed FA remains unclear. In this study, we show that TT2 is expressed in embryos at an early developmental stage. TT2 is directly bound to the regulatory region of FUSCA3 (FUS3), and mediates the expression of numerous genes in the FA biosynthesis pathway. These genes include BCCP2, CAC2, MOD1 and KASII, which encode proteins involved in the initial steps of FA chain formation, FAD2 and FAD3, which are responsible for FA desaturation, and FAE1, which catalyzes very-long-chain FA elongation. Loss of function of TT2 results in reduced expression of GLABRA2 but does not cause a significant reduction in the mucilage attached to the seed coats, which competes with FA for photosynthates. TT2 is expressed in both maternal seed coats and embryonic tissues, but proanthocyanidins are only found in wild-type seed coats and not in embryonic tissues. The amount of proanthocyanidins in the seed coat is negatively correlated with the amount of FAs in the embryo.

Identification of QTLs with additive, epistatic and QTL × development interaction effects for seed dormancy in rice

Seed dormancy (SD) is an important agronomic trait affecting crop yield and quality. In this study, one rice population of recombinant inbred lines (RILs) was used to determine the genetic characteristics of SD at the early (4 weeks after heading), middle (5 weeks after heading) and late (6 weeks after heading) development stages. The level of SD decreased with the process of seed development, and the SD was significantly affected by the heading date (HD) and temperature at the early and middle development stages. A total of eight additive quantitative trait loci (QTLs) for SD were identified at three development stages, and more QTLs were expressed at the early and late development stages. Among them, four, one and three additive QTLs were identified at the early, middle and late development stages, respectively. Epistatic QTLs and QTL-by-development interactions were detected by the joint analysis of multi-development phenotypic values, and one additive and two epistatic QTLs were identified. The phenotypic variation of SD explained by each additive, epistatic QTL and QTL × development interaction ranged from 8.0 to 13.5 %, 0.7 to 3.9 % and 1.3 to 2.8 %, respectively. One major QTL qSD7.1 for SD was tightly linked to the major QTL qHD7.4 for HD, which might be applied to reveal the relationship of SD and HD. By comparing chromosomal positions of these additive QTLs with those previously identified, five additive QTLs qSD1.1, qSD2.1, qSD2.2, qSD4.1 and qSD4.2 might represent novel genes. The best three cross combinations for the development of RIL populations were predicted to improve SD. The selected RILs and the identified QTLs might be applicable to improve the rice pre-harvest sprouting tolerance by the marker-assisted selection approach.

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

Soil salinity is one of the most serious agricultural problems that significantly reduce crop yields in the arid and semi-arid regions. It influences various phases of plant growth and developmental processes, such as seed germination, leaf and stem growth, and reproductive propagation. Salt stress delays the onset of flowering in many plant species. We have previously reported that the Arabidopsis BROTHER OF FT AND TFL1 (BFT) acts as a floral repressor under salt stress. However, the molecular mechanisms underlying the BFT function in the salt regulation of flowering induction is unknown. In this work, we found that BFT delays flowering under high salinity by competing with FLOWERING LOCUS T (FT) for binding to the FD transcription factor. The flowering time of FD-deficient fd-2 mutant was insensitive to high salinity. BFT interacts with FD in the nucleus via the C-terminal domain of FD, which is also required for the interaction of FD with FT, and interferes with the FT-FD interaction. These observations indicate that BFT constitutes a distinct salt stress signaling pathway that modulates the function of the FT-FD module and possibly provides an adaptation strategy that fine-tunes photoperiodic flowering under high salinity.

Conserved CO-FT regulons contribute to the photoperiod flowering control in soybean

BACKGROUND

CO and FT orthologs, belonging to the BBX and PEBP family, respectively, have important and conserved roles in the photoperiod regulation of flowering time in plants. Soybean genome experienced at least three rounds of whole genome duplications (WGDs), which resulted in multiple copies of about 75% of genes. Subsequent subfunctionalization is the main fate for paralogous gene pairs during the evolutionary process.

RESULTS

The phylogenic relationships revealed that CO orthologs were widespread in the plant kingdom while FT orthologs were present only in angiosperms. Twenty-eight CO homologous genes and twenty-four FT homologous genes were gained in the soybean genome. Based on the collinear relationship, the soybean ancestral CO ortholog experienced three WGD events, but only two paralogous gene pairs (GmCOL1/2 and GmCOL5/13) survived in the modern soybean. The paralogous gene pairs, GmCOL1/2 or GmCOL5/13, showed similar expression patterns in pair but different between pairs, indicating that they functionally diverged. GmFTL1 to 7 were derived from the same ancestor prior to the whole genome triplication (WGT) event, and after the Legume WGD event the ancestor diverged into two branches, GmFTL3/5/7 and GmFTL1/2/4/6. GmFTL7 were truncated in the N-terminus compared to other FT-lineage genes, but ubiquitously expressed. Expressions of GmFTL1 to 6 were higher in leaves at the flowering stage than that at the seedling stage. GmFTL3 was expressed at the highest level in all tissues except roots at the seedling stage, and its circadian pattern was different from the other five ones. The transcript of GmFTL6 was highly accumulated in seedling roots. The circadian rhythms of GmCOL5/13 and GmFT1/2/4/5/6 were synchronized in a day, demonstrating the complicate relationship of CO-FT regulons in soybean leaves. Over-expression of GmCOL2 did not rescue the flowering phenotype of the Arabidopsis co mutant. However, ectopic expression of GmCOL5 did rescue the co mutant phenotype. All GmFTL1 to 6 showed flower-promoting activities in Arabidopsis.

CONCLUSIONS

After three recent rounds of whole genome duplications in the soybean, the paralogous genes of CO-FT regulons showed subfunctionalization through expression divergence. Then, only GmCOL5/13 kept flowering-promoting activities, while GmFTL1 to 6 contributed to flowering control. Additionally, GmCOL5/13 and GmFT1/2/3/4/5/6 showed similar circadian expression profiles. Therefore, our results suggested that GmCOL5/13 and GmFT1/2/3/4/5/6 formed the complicate CO-FT regulons in the photoperiod regulation of flowering time in soybean.

AtEXP2 is involved in seed germination and abiotic stress response in Arabidopsis

Expansins are cell wall proteins that promote cell wall loosening by inducing pH-dependent cell wall extension and stress relaxation. Expansins are required in a series of physiological developmental processes in higher plants such as seed germination. Here we identified an Arabidopsis expansin gene AtEXPA2 that is exclusively expressed in germinating seeds and the mutant shows delayed germination, suggesting that AtEXP2 is involved in controlling seed germination. Exogenous GA application increased the expression level of AtEXP2 during seed germination, while ABA application had no effect on AtEXP2 expression. Furthermore, the analysis of DELLA mutants show that RGL1, RGL2, RGA, GAI are all involved in repressing AtEXP2 expression, and RGL1 plays the most dominant role in controlling AtEXP2 expression. In stress response, exp2 mutant shows higher sensitivity than wild type in seed germination, while overexpression lines of AtEXP2 are less sensitive to salt stress and osmotic stress, exhibiting enhanced tolerance to stress treatment. Collectively, our results suggest that AtEXP2 is involved in the GA-mediated seed germination and confers salt stress and osmotic stress tolerance in Arabidopsis.

Functional genomics of seed dormancy in wheat: advances and prospects

Seed dormancy is a mechanism underlying the inability of viable seeds to germinate under optimal environmental conditions. To achieve rapid and uniform germination, wheat and other cereal crops have been selected against dormancy. As a result, most of the modern commercial cultivars have low level of seed dormancy and are susceptible to preharvest sprouting when wet and moist conditions occur prior to harvest. As it causes substantial loss in grain yield and quality, preharvest sprouting is an ever-present major constraint to the production of wheat. The significance of the problem emphasizes the need to incorporate an intermediate level of dormancy into elite wheat cultivars, and this requires detailed dissection of the mechanisms underlying the regulation of seed dormancy and preharvest sprouting. Seed dormancy research in wheat often involves after-ripening, a period of dry storage during which seeds lose dormancy, or comparative analysis of seeds derived from dormant and non-dormant cultivars. The increasing development in wheat genomic resources along with the application of transcriptomics, proteomics, and metabolomics approaches in studying wheat seed dormancy have extended our knowledge of the mechanisms acting at transcriptional and post-transcriptional levels. Recent progresses indicate that some of the molecular mechanisms are associated with hormonal pathways, epigenetic regulations, targeted oxidative modifications of seed mRNAs and proteins, redox regulation of seed protein thiols, and modulation of translational activities. Given that preharvest sprouting is closely associated with seed dormancy, these findings will significantly contribute to the designing of efficient strategies for breeding preharvest sprouting tolerant wheat.

Environmental stress and flowering time: the photoperiodic connection

Plants maximize their chances to survive adversities by reprogramming their development according to environmental conditions. Adaptive variations in the timing to flowering reflect the need for plants to set seeds under the most favorable conditions. A complex network of genetic pathways allows plants to detect and integrate external (e.g., photoperiod and temperature) and/or internal (e.g., age) information to initiate the floral transition. Furthermore different types of environmental stresses play an important role in the floral transition. The emerging picture is that stress conditions often affect flowering through modulation of the photoperiodic pathway. In this review we will discuss different modes of cross talk between stress signaling and photoperiodic flowering, highlighting the central role of the florigen genes in this process.

Seed dormancy and germination-emerging mechanisms and new hypotheses

Seed dormancy has played a significant role in adaptation and evolution of seed plants. While its biological significance is clear, molecular mechanisms underlying seed dormancy induction, maintenance and alleviation still remain elusive. Intensive efforts have been made to investigate gibberellin and abscisic acid metabolism in seeds, which greatly contributed to the current understanding of seed dormancy mechanisms. Other mechanisms, which might be independent of hormones, or specific to the seed dormancy pathway, are also emerging from genetic analysis of "seed dormancy mutants." These studies suggest that chromatin remodeling through histone ubiquitination, methylation and acetylation, which could lead to transcription elongation or gene silencing, may play a significant role in seed dormancy regulation. Small interfering RNA and/or long non-coding RNA might be a trigger of epigenetic changes at the seed dormancy or germination loci, such as DELAY OF GERMINATION1. While new mechanisms are emerging from genetic studies of seed dormancy, novel hypotheses are also generated from seed germination studies with high throughput gene expression analysis. Recent studies on tissue-specific gene expression in tomato and Arabidopsis seeds, which suggested possible "mechanosensing" in the regulatory mechanisms, advanced our understanding of embryo-endosperm interaction and have potential to re-draw the traditional hypotheses or integrate them into a comprehensive scheme. The progress in basic seed science will enable knowledge translation, another frontier of research to be expanded for food and fuel production.

The gated induction system of a systemic floral inhibitor, antiflorigen, determines obligate short-day flowering in chrysanthemums

Photoperiodic floral induction has had a significant impact on the agricultural and horticultural industries. Changes in day length are perceived in leaves, which synthesize systemic flowering inducers (florigens) and inhibitors (antiflorigens) that determine floral initiation at the shoot apex. Recently, FLOWERING LOCUS T (FT) was found to be a florigen; however, the identity of the corresponding antiflorigen remains to be elucidated. Here, we report the identification of an antiflorigen gene, Anti-florigenic FT/TFL1 family protein (AFT), from a wild chrysanthemum (Chrysanthemum seticuspe) whose expression is mainly induced in leaves under noninductive conditions. Gain- and loss-of-function analyses demonstrated that CsAFT acts systemically to inhibit flowering and plays a predominant role in the obligate photoperiodic response. A transient gene expression assay indicated that CsAFT inhibits flowering by directly antagonizing the flower-inductive activity of CsFTL3, a C. seticuspe ortholog of FT, through interaction with CsFDL1, a basic leucine zipper (bZIP) transcription factor FD homolog of Arabidopsis. Induction of CsAFT was triggered by the coincidence of phytochrome signals with the photosensitive phase set by the dusk signal; flowering occurred only when night length exceeded the photosensitive phase for CsAFT induction. Thus, the gated antiflorigen production system, a phytochrome-mediated response to light, determines obligate photoperiodic flowering response in chrysanthemums, which enables their year-round commercial production by artificial lighting.

TaMFT-A1 is associated with seed germination sensitive to temperature in winter wheat

The ability of seed to germinate under favorable environmental conditions is critical for seedling emergence, plant establishment, subsequent development and growth of adult plants, and it is controlled by internal genetic factors and external environmental factors. Winter wheat in the southern Great Plains is often planted six weeks before the optimal planting date to produce more biomass for cattle grazing during the winter season. A high seed germination rate in this higher soil temperature environment is required for this specific management system. In this study, a major QTL for temperature-sensitive germination was mapped on the short arm of chromosome 3A (QTsg.osu-3A) in a RIL population generated from two winter wheat cultivars. Furthermore, TaMFT-A1, previously reported to regulate seed dormancy and pre-harvest sprouting in spring wheat cultivars, was mapped tightly associated with the peak of QTsg.osu-3A. However, allelic variation in TaMFT-A1 between the two winter wheat cultivars differed from that was observed in spring wheat cultivars. There were 87 SNPs (single nucleotide polymorphisms) and 12 indels (insertions/deletions) in TaMFT-A1 between the Jagger allele for high germination and the 2174 allele for low germination in the after-ripened seeds, in comparison with 2 SNPs between the two alleles for differential pre-harvest sprouting in spring wheat cultivars. The Jagger TaMFT-A1 allele is a novel haplotype and appears extensively in winter wheat cultivars. TaMFT-A1 transcript levels were up-regulated by high temperature but down-regulated by low temperature or seed storage time. These findings suggest that TaMFT-A1 may invoke different mechanisms for controlling seed dormancy/germination among winter wheat cultivars.

Cloning and characterization of a critical regulator for preharvest sprouting in wheat

Sprouting of grains in mature spikes before harvest is a major problem in wheat (Triticum aestivum) production worldwide. We cloned and characterized a gene underlying a wheat quantitative trait locus (QTL) on the short arm of chromosome 3A for preharvest sprouting (PHS) resistance in white wheat using comparative mapping and map-based cloning. This gene, designated TaPHS1, is a wheat homolog of a MOTHER OF FLOWERING TIME (TaMFT)-like gene. RNA interference-mediated knockdown of the gene confirmed that TaPHS1 positively regulates PHS resistance. We discovered two causal mutations in TaPHS1 that jointly altered PHS resistance in wheat. One GT-to-AT mutation generates a mis-splicing site, and the other A-to-T mutation creates a premature stop codon that results in a truncated nonfunctional transcript. Association analysis of a set of wheat cultivars validated the role of the two mutations on PHS resistance. The molecular characterization of TaPHS1 is significant for expediting breeding for PHS resistance to protect grain yield and quality in wheat production.

ABA and the ubiquitin E3 ligase KEEP ON GOING affect proteolysis of the Arabidopsis thaliana transcription factors ABF1 and ABF3

The ABA Binding Factor/ABA-Responsive Element Binding Proteins (ABF/AREB) subfamily of bZIP-type transcription factors are positive effectors of ABA responses. Here, we examine the proteolytic regulation of two members: Arabidopsis thaliana ABF1 and ABF3. Both transcription factors are unstable in seedlings, and their degradation is sensitive to proteasome inhibition. ABA treatment of seedlings leads to their rapid accumulation, the result of slowed proteolysis. Deletion of the conserved C-terminal region required for 14-3-3 interaction destabilizes the proteins. The degradation of ABF1 and ABF3 are slower in vivo in seedlings lacking the ubiquitin E3 ligase KEEP ON GOING (KEG), and in vitro in extracts from keg seedlings, implicating KEG in their degradation. ABF1 and ABF3 are ubiquitylation substrates of KEG in vitro, and in vitro pull-down assays document their direct interaction. In contrast to ABI5, another KEG substrate, the degradation of ABFs and proteolytic regulation of ABFs by ABA still occurs in keg seedlings, suggesting that additional E3s participate in ABF1 and ABF3 proteolysis. Loss of ABF1 or ABF3 in the keg background has a phenotypic effect similar to the loss of ABI5, and there is no additional rescue of the keg phenotype in abf1 abf3 abi5 keg seedlings. This result suggests that the abundance of other substrates is altered in keg seedlings, affecting growth. In conclusion, ABF1 and ABF3 abundance is affected by ABA and KEG, and the conserved C4 region serves as a stabilizing element.

Cloning and characterization of a critical regulator for preharvest sprouting in wheat

Sprouting of grains in mature spikes before harvest is a major problem in wheat (Triticum aestivum) production worldwide. We cloned and characterized a gene underlying a wheat quantitative trait locus (QTL) on the short arm of chromosome 3A for preharvest sprouting (PHS) resistance in white wheat using comparative mapping and map-based cloning. This gene, designated TaPHS1, is a wheat homolog of a MOTHER OF FLOWERING TIME (TaMFT)-like gene. RNA interference-mediated knockdown of the gene confirmed that TaPHS1 positively regulates PHS resistance. We discovered two causal mutations in TaPHS1 that jointly altered PHS resistance in wheat. One GT-to-AT mutation generates a mis-splicing site, and the other A-to-T mutation creates a premature stop codon that results in a truncated nonfunctional transcript. Association analysis of a set of wheat cultivars validated the role of the two mutations on PHS resistance. The molecular characterization of TaPHS1 is significant for expediting breeding for PHS resistance to protect grain yield and quality in wheat production.

Mapping of QTL for seed dormancy in a winter oilseed rape doubled haploid population

Following winter oilseed rape cultivation, considerable numbers of volunteer oilseed rape plants may occur in subsequent years in following crops. The appearance of volunteer oilseed rape plants is based on the capability of the seeds to become secondary dormant and to survive in this stage for many years in the soil. Genetic reduction of secondary seed dormancy in oilseed rape could provide a means to reduce the frequency of volunteer plants and especially the dispersal of transgenic oilseed rape. The objective of the present study was to analyse the inheritance of primary and secondary seed dormancy in a winter oilseed rape doubled haploid population derived from the cross Express 617 × R53 and to study correlations to other seed traits. Field experiments were performed in Germany for 2 years at two locations with two replicates. Seeds harvested from open pollinated plants were used for all analyses, including a laboratory test for seed dormancy. A previously developed molecular marker map of the doubled haploid population was used to map QTL of the relevant traits. For primary, secondary and total seed dormancy, the results showed significant effects of the genotypes and their interactions, with years and locations. Two, four and five QTL were detected for primary, secondary and total seed dormancy which explained 19, 35 and 42 % of the phenotypic variance, respectively. Results show that secondary seed dormancy is a heritable trait and that selection for low secondary seed dormancy is possible.

Gibberellins and abscisic acid signal crosstalk: living and developing under unfavorable conditions

Plants adapt to adverse environments by integrating growth and development to environmentally activated cues. Within the adaptive signaling networks, plant hormones tightly control convergent developmental and stress adaptive processes and coordinate cellular responses to external and internal conditions. Recent studies have uncovered novel antagonizing roles of the plant hormones gibberellin (GA) and abscisic acid (ABA) in integrating growth and development in plants with environmental signaling. According to current concepts, GRAS transcription factors of the DELLA and SCARECROW-LIKE (SCL) types have a key role as major growth regulators and have pivotal functions in modulating GA signaling. Significantly, current models emphasize a function of DELLA proteins as central regulators in GA homeostasis. DELLA proteins interact with the cellular GA receptor GID1 (GA-INSENSITIVE DWARF1) and degradation of DELLAs activates the function of GA. Supplementary to the prevailing view of a pivotal role of GRAS family transcriptional factors in plant growth regulation, recent work has suggested that the DELLA and SCL proteins integrate generic GA responses into ABA-controlled abiotic stress tolerance. Here, we review and discuss how GRAS type proteins influence plant development and versatile adaptation as hubs in GA and ABA triggered signaling pathways.