Hormone and RNA-seq analyses reveal the mechanisms underlying differences in seed vigour at different maize ear positions

ABA/GA₄ ratio, stress resistance, carbon and nitrogen metabolism, and chromatin structure play important roles in vigour differences of seeds located at different maize ear positions. Seed vigour, which ensures rapid and uniform field emergence across diverse environments, differs at different maize ear positions. However, little is known regarding the associated mechanisms. In this study, we determined that seed vigour, stress resistance, and carbon and nitrogen metabolism were higher in seeds from middle and bottom section of the ear, while the ABA/GA₄ ratio in the embryos was significantly lower. Compared with the seeds subjected to repeated pollination during silking, less variation in seed vigour and the ABA/GA₄ ratio in the embryos was observed in seeds at different ear positions subjected to single pollination after complete silking. This indicated that single pollination can reduce, but not eliminate, the differences in seed vigour at different ear positions. RNA-seq analysis indicated that the seed vigour differences at the different locations of the maize ears of the single pollinated treatment were related to carbon and nitrogen metabolism. In contrast, the differences in seed vigour under repeated pollination were related to chromatin structure. The present study contributes to our understanding of the mechanisms underlying differences in seed vigour at different positions on the maize ear.

The regulatory mechanism of chilling-induced dormancy transition from endo-dormancy to non-dormancy in Polygonatum kingianum Coll.et Hemsl rhizome bud

We identified three dormant stages of Polygonatum kingianum and changes that occurred during dormancy transition in the following aspects including cell wall and hormones, as well as interaction among them. Polygonatum kingianum Coll.et Hemsl (P. kingianum) is an important traditional Chinese medicine, but the mechanism of its rhizome bud dormancy has not yet been studied systematically. In this study, three dormancy phases were induced under controlled conditions, and changes occurring during the transition were examined, focusing on phytohormones and the cell wall. As revealed by HPLC-MS (High Performance Liquid Chromatography-Mass Spectrometry) analysis, the endo- to non-dormancy transition was association with a reduced abscisic acid (ABA)/gibberellin (GA₃) ratio, a decreased level of auxin (IAA) and an increased level of trans-zeatin (tZR). Transmission electron microscopy showed that plasmodesmata (PDs) and the cell wall of the bud underwent significant changes between endo- and eco-dormancy. A total of 95,462 differentially expressed genes (DEGs) were identified based on transcriptomics, and clustering and principal component analysis confirmed the different physiological statuses of the three types of bud samples. Changes in the abundance of transcripts associated with IAA, cytokinins (CTKs), GA, ABA, brassinolide (BR), jasmonic acid (JA), ethylene, salicylic acid (SA), PDs and cell wall-loosening factors were analysed during the bud dormancy transition in P. kingianum. Furthermore, nitrilase 4 (NIT4) and tryptophan synthase alpha chain (TSA1), which are related to IAA synthesis, were identified as hub genes of the co-expression network, and strong interactions between hormones and cell wall-related factors were observed. This research will provide a good model for chilling-treated rhizome bud dormancy in P. kingianum and cultivation of this plant.

Identification and Expression Analyses of SBP-Box Genes Reveal Their Involvement in Abiotic Stress and Hormone Response in Tea Plant (Camellia sinensis)

The SQUAMOSA promoter binding protein (SBP)-box gene family is a plant-specific transcription factor family. This family plays a crucial role in plant growth and development. In this study, 20 SBP-box genes were identified in the tea plant genome and classified into six groups. The genes in each group shared similar exon-intron structures and motif positions. Expression pattern analyses in five different tissues demonstrated that expression in the buds and leaves was higher than that in other tissues. The cis-elements and expression patterns of the CsSBP genes suggested that the CsSBP genes play active roles in abiotic stress responses; these responses may depend on the abscisic acid (ABA), gibberellic acid (GA), and methyl jasmonate (MeJA) signaling pathways. Our work provides a comprehensive understanding of the CsSBP family and will aid in genetically improving tea plants.

Expression of cotton PLATZ1 in transgenic Arabidopsis reduces sensitivity to osmotic and salt stress for germination and seedling establishment associated with modification of the abscisic acid, gibberellin, and ethylene signalling pathways

BACKGROUND

Zinc-finger transcription factors play central roles in plant growth, development and abiotic stress responses. PLATZ encodes a class of plant-specific zinc-finger transcription factor. However, biological functions or physiological mechanism controlled by PLATZ are currently limited.

RESULTS

GhPLATZ1 transcripts were considerably up-regulated by NaCl, mannitol, abscisic acid (ABA) and gibberellin (GA) treatments. Transgenic Arabidopsis by ectopic expression of GhPLATZ1 exhibited faster seed germination and higher seedling establishment under salt and mannitol stresses than those of wild type (WT), indicating enhanced osmotic insensitivity in GhPLATZ1 transgenic Arabidopsis. The ABA content in dry seeds of GhPLATZ1 transgenic Arabidopsis was lower than that of WT whereas the ABA content was not changed in germinating seeds under salt stress. Seed germination was faster than but the seedling establishment of transgenic Arabidopsis was similar to WT. Besides, GhPLATZ1 transgenic and WT Arabidopsis exhibited insensitivity to paclobutrazol (PAC), a GA biosynthesis inhibitor, whereas exogenous GA could eliminate the growth difference between GhPLATZ1 transgenic and WT Arabidopsis under salt stress. Moreover, exogenous 1-aminocyclopropane-1-carboxylic acid (ACC), an ethylene precursor, exerted similar effects to GA. Furthermore, ABI4 and ETO1 transcripts were significantly down-regulated, whereas ACS8 was up-regulated in GhPLATZ1 transgenic Arabidopsis under salt stress.

CONCLUSIONS

In conclusion, GhPLATZ1 had broad influence in responses to salt and mannitol stresses in transgenic Arabidopsis during seed germination and seedling establishment. The effect of GhPLATZ1 expression in transgenic Arabidopsis might be mediated by the ABA, GA, and ethylene pathways. Thus, this study provided new insights into the regulatory network in response to abiotic stresses in plants.

Transcriptomic insights into the blue light-induced female floral sex expression in cucumber (Cucumis sativus L.)

In cucurbitaceous crops, sex differentiation of flower buds is a crucial developmental process that directly affects fruit yield. Here we showed that the induction of female flower was the highest in the blue light-treated monoecious cucumber plants compared with that in other light qualities (white, green and red). High-throughput RNA-Seq analysis of the shoot apexes identified a total of 74 differently-expressed genes (DEGs), in which 52 up-regulated and 22 down-regulated under the blue light compared with that in white light. The DEGs were mainly involved in metabolic pathways, biosynthesis of secondary metabolites, plant hormone signal transduction, starch and sucrose metabolism and phenylpropanoid biosynthesis. While the  ethylene and gibberellins synthesis and signaling related genes were down-regulated, the abscisic acid and auxin signal transduction pathways were up-regulated by the blue light treatment. Furthermore, the blue light treatment up-regulated the transcription of genes relating to photosynthesis, starch and sucrose metabolism. Meanwhile, the blue light suppressed the GA₃ concentration but promoted the concentrations of auxin and photosynthetic pigments. Taken together, the results suggest that the blue light-induced female floral sex expression is closely associated with the blue light-induced changes in abscisic acid, auxin, gibberellins, photosynthesis, starch and sucrose metabolism pathways, which is potentially different from the traditional ethylene-dependent pathway.

Identification and functional study of a mild allele of SlDELLA gene conferring the potential for improved yield in tomato

Parthenocarpy, or pollination-independent fruit set, is an attractive trait for fruit production and can be induced by increased responses to the phytohormone gibberellin (GA), which regulates diverse aspects of plant development. GA signaling in plants is negatively regulated by DELLA proteins. A loss-of-function mutant of tomato DELLA (SlDELLA), procera (pro) thus exhibits enhanced GA-response phenotypes including parthenocarpy, although the pro mutation also confers some disadvantages for practical breeding. This study identified a new milder hypomorphic allele of SlDELLA, procera-2 (pro-2), which showed weaker GA-response phenotypes than pro. The pro-2 mutant contains a single nucleotide substitution, corresponding to a single amino acid substitution in the SAW subdomain of the SlDELLA. Accumulation of the mutated SlDELLA transcripts in wild-type (WT) resulted in parthenocarpy, while introduction of intact SlDELLA into pro-2 rescued mutant phenotypes. Yeast two-hybrid assays revealed that SlDELLA interacted with three tomato homologues of GID1 GA receptors with increasing affinity upon GA treatment, while their interactions were reduced by the pro and pro-2 mutations. Both pro and pro-2 mutants produced higher fruit yields under high temperature conditions, which were resulted from higher fruit set efficiency, demonstrating the potential for genetic parthenocarpy to improve yield under adverse environmental conditions.

Comparative Analysis of Transcriptomes to Identify Genes Associated with Fruit Size in the Early Stage of Fruit Development in Pyrus pyrifolia

Pear (Pyrus L.) is an important commercial fruit in the world. The fruit size is one of the important characters in fruit quality. The previous research reported that the fruit size of pear was mainly caused by the number of cell in about 40 days after blossom (DAB) in nature. However, studies about the mechanisms underlying cell division in young fruit development are very limited in pear. Two pear accessions codenamed ‘GH59B’ with big fruit and ‘GH81S’ with small fruit in three stages were sampled and the RNA-seq high-throughput sequencing was used to evaluate changes of gene transcription levels in the early stage of fruit development. The difference of cell size among two samples was little in 40 DAB, implying that the difference of the fruit size was caused by the number of the cell. More than 274,517,982 high quality reads from six libraries of fruit development were sequenced. A total of 797 differentially expressed genes (DEGs) were identified. Three cytokinin dehydrogenase genes and two gibberellin 2-beta-dioxygenase gene were identified in the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to zeatin and gibberellin. Their expression was upregulated at 20 DAB in ‘GH81S’ and at 30 DAB in ‘GH59B’, suggesting that the small fruit size might be related to the early degradation of cytokinin and gibberellin inducing a short period of cell division. A total of 38 DEGs of transcription factors were found and 23 DEGs including NAC, ERF and bHLH transcription factors were highly related with cytokinin dehydrogenase and gibberellin dioxygenase genes. Altogether, the results of the present study provide information from a comprehensive gene expression analysis and insight into the molecular mechanism underlying the difference of fruit size in Pyrus pyrifolia.

Arabidopsis Aspartic Protease ASPG1 Affects Seed Dormancy, Seed Longevity and Seed Germination

Seed storage proteins (SSPs) provide free amino acids and energy for the process of seed germination. Although degradation of SSPs by the aspartic proteases isolated from seeds has been documented in vitro, there is still no genetic evidence for involvement of aspartic proteases in seed germination. Here we report that the aspartic protease ASPG1 (ASPARTIC PROTEASE IN GUARD CELL 1) plays an important role in the process of dormancy, viability and germination of Arabidopsis seeds. We show that aspg1-1 mutants have enhanced seed dormancy and reduced seed viability. A significant increase in expression of DELLA genes which act as repressors in the gibberellic acid signal transduction pathway were detected in aspg1-1 during seed germination. Seed germination of aspg1-1 mutants was more sensitive to treatment with paclobutrazol (PAC; a gibberellic acid biosynthesis inhibitor). In contrast, seed germination of ASPG1 overexpression (OE) transgenic lines showed resistant to PAC. The degradation of SSPs in germinating seeds was severely impaired in aspg1-1 mutants. Moreover, the development of aspg1-1 young seedlings was arrested when grown on the nutrient-free medium. Thus ASPG1 is important for seed dormancy, seed longevity and seed germination, and its function is associated with degradation of SSPs and regulation of gibberellic acid signaling in Arabidopsis.

Rht18 Semidwarfism in Wheat Is Due to Increased GA 2-oxidaseA9 Expression and Reduced GA Content

Semidwarfing genes have improved crop yield by reducing height, improving lodging resistance, and allowing plants to allocate more assimilates to grain growth. In wheat (Triticum aestivum), the Rht18 semidwarfing gene was identified and deployed in durum wheat before it was transferred into bread wheat, where it was shown to have agronomic potential. Rht18, a dominant and gibberellin (GA) responsive mutant, is genetically and functionally distinct from the widely used GA-insensitive semidwarfing genes Rht-B1b and Rht-D1b In this study, the Rht18 gene was identified by mutagenizing the semidwarf durum cultivar Icaro (Rht18) and generating mutants with a range of tall phenotypes. Isolating and sequencing chromosome 6A of these "overgrowth" mutants showed that they contained independent mutations in the coding region of GA2oxA9GA2oxA9 is predicted to encode a GA 2-oxidase that metabolizes GA biosynthetic intermediates into inactive products, effectively reducing the amount of bioactive GA (GA₁). Functional analysis of the GA2oxA9 protein demonstrated that GA2oxA9 converts the intermediate GA₁₂ to the inactive metabolite GA₁₁₀ Furthermore, Rht18 showed higher expression of GA2oxA9 and lower GA content compared with its tall parent. These data indicate that the increased expression of GA2oxA9 in Rht18 results in a reduction of both bioactive GA content and plant height. This study describes a height-reducing mechanism that can generate new genetic diversity for semidwarfism in wheat by combining increased expression with mutations of specific amino acid residues in GA2oxA9.

Silencing SlMED18, tomato Mediator subunit 18 gene, restricts internode elongation and leaf expansion

Mediator complex, a conserved multi-protein, is necessary for controlling RNA polymerase II (Pol II) transcription in eukaryotes. Given little is known about them in tomato, a tomato Mediator subunit 18 gene was isolated and named SlMED18. To further explore the function of SlMED18, the transgenic tomato plants targeting SlMED18 by RNAi-mediated gene silencing were generated. The SlMED18-RNAi lines exhibited multiple developmental defects, including smaller size and slower growth rate of plant and significantly smaller compound leaves. The contents of endogenous bioactive GA3 in SlMED18 silenced lines were slightly less than that in wild type. Furthermore, qRT-PCR analysis indicated that expression of gibberellins biosynthesis genes such as SlGACPS and SlGA20x2, auxin transport genes (PIN1, PIN4, LAX1 and LAX2) and several key regulators, KNOX1, KNOX2, PHAN and LANCEOLATE(LA), which involved in the leaf morphogenesis were significantly down-regulated in SlMED18-RNAi lines. These results illustrated that SlMED18 plays an essential role in regulating plant internode elongation and leaf expansion in tomato plants and it acts as a key positive regulator of gibberellins biosynthesis and signal transduction as well as auxin proper transport signalling. These findings are the basis for understanding the function of the individual Mediator subunits in tomato.

Linking hydrogen-enhanced rice aluminum tolerance with the reestablishment of GA/ABA balance and miRNA-modulated gene expression: A case study on germination

Although previous results showed that exogenous hydrogen (H₂) alleviated aluminum (Al) toxicity, the detailed mechanism remains unclear. Here, we reported that the exposure of germinating rice seeds to Al triggered H₂ production, followed by a decrease of GA/ABA ratio and seed germination inhibition. Compared to inert gas (argon), H₂ pretreatment not only strengthened H₂ production and alleviated Al-induced germination inhibition, but also partially reestablished the balance between GA and ABA. By contrast, a GA biosynthesis inhibitor paclobutrazol (PAC) could block the H₂-alleviated germination inhibition. The expression of GA biosynthesis genes (GA20ox1 and GA20ox2) and ABA catabolism genes (ABA8ox1 and ABA8ox2), was also induced by H₂. Above results indicated that GA/ABA might be partially involved in H₂ responses. Subsequent results revealed that compared with Al alone, transcripts of miR398a and miR159a were decreased by H₂, and expression levels of their target genes OsSOD2 and OsGAMYB were up-regulated. Whereas, miR528 and miR160a transcripts were increased differentially, and contrasting tendencies were observed in the changes of their target genes (OsAO and OsARF10). The transcripts of Al-tolerant gene OsSTAR1/OsSTAR2 and OsFRDL4 were up-regulated. Above results were consistent with the anti-oxidant defense, decreased Al accumulation, and enhanced citrate efflux. Together, our results provided insight into the mechanism underlying H₂-triggered Al tolerance in plants.

Exogenous auxin represses soybean seed germination through decreasing the gibberellin/abscisic acid (GA/ABA) ratio

Auxin is an important phytohormone which mediates diverse development processes in plants. Published research has demonstrated that auxin induces seed dormancy. However, the precise mechanisms underlying the effect of auxin on seed germination need further investigation, especially the relationship between auxins and both abscisic acid (ABA) and gibberellins (GAs), the latter two phytohormones being the key regulators of seed germination. Here we report that exogenous auxin treatment represses soybean seed germination by enhancing ABA biosynthesis, while impairing GA biogenesis, and finally decreasing GA1/ABA and GA4/ABA ratios. Microscope observation showed that auxin treatment delayed rupture of the soybean seed coat and radicle protrusion. qPCR assay revealed that transcription of the genes involved in ABA biosynthetic pathway was up-regulated by application of auxin, while expression of genes involved in GA biosynthetic pathway was down-regulated. Accordingly, further phytohormone quantification shows that auxin significantly increased ABA content, whereas the active GA1 and GA4 levels were decreased, resulting insignificant decreases in the ratiosGA1/ABA and GA4/ABA.Consistent with this, ABA biosynthesis inhibitor fluridone reversed the delayed-germination phenotype associated with auxin treatment, while paclobutrazol, a GA biosynthesis inhibitor, inhibited soybean seed germination. Altogether, exogenous auxin represses soybean seed germination by mediating ABA and GA biosynthesis.

Major genes determining yield-related traits in wheat and barley

Current development of advanced biotechnology tools allows us to characterize the role of key genes in plant productivity. The implementation of this knowledge in breeding strategies might accelerate the progress in obtaining high-yielding cultivars. The achievements of the Green Revolution were based on a specific plant ideotype, determined by a single gene involved in gibberellin signaling or metabolism. Compared with the 1950s, an enormous increase in our knowledge about the biological basis of plant productivity has opened new avenues for novel breeding strategies. The large and complex genomes of diploid barley and hexaploid wheat represent a great challenge, but they also offer a large reservoir of genes that can be targeted for breeding. We summarize examples of productivity-related genes/mutants in wheat and barley, identified or characterized by means of modern biology. The genes are classified functionally into several groups, including the following: (1) transcription factors, regulating spike development, which mainly affect grain number; (2) genes involved in metabolism or signaling of growth regulators-cytokinins, gibberellins, and brassinosteroids-which control plant architecture and in consequence stem hardiness and grain yield; (3) genes determining cell division and proliferation mainly impacting grain size; (4) floral regulators influencing inflorescence architecture and in consequence seed number; and (5) genes involved in carbohydrate metabolism having an impact on plant architecture and grain yield. The implementation of selected genes in breeding programs is discussed, considering specific genotypes, agronomic and climate conditions, and taking into account that many of the genes are members of multigene families.

Analysis of nodule senescence in pea (Pisum sativum L.) using laser microdissection, real-time PCR, and ACC immunolocalization

A delay in the senescence of symbiotic nodules could prolong active nitrogen fixation, resulting in improved crop yield and a reduced need for chemical fertilizers. The molecular genetic mechanisms underlying nodule senescence have not been extensively studied with a view to breeding varieties with delayed nodule senescence. In such studies, plant mutants with the phenotype of premature degradation of symbiotic structures are useful models to elucidate the genetic basis of nodule senescence. Using a dataset from transcriptome analysis of Medicago truncatula Gaertn. nodules and previous studies on pea (Pisum sativum L.) nodules, we developed a set of molecular markers based on genes that are known to be activated during nodule senescence. These genes encode cysteine proteases, a thiol protease, a bZIP transcription factor, enzymes involved in the biosynthesis of ethylene (ACS2 for ACC synthase and ACO1 for ACC oxidase) and ABA (AO3 for aldehyde oxidase), and an enzyme involved in catabolism of gibberellins (GA 2-oxidase). We analyzed the transcript levels of these genes in the nodules of two pea wild-types (cv. Sparkle and line Sprint-2) and two mutant lines, one showing premature nodule senescence (E135F (sym13)) and one showing no morphological signs of symbiotic structure degradation (Sprint-2Fix- (sym31)). Real-time PCR analyses revealed that all of the selected genes showed increased transcript levels during nodule aging in all phenotypes. Remarkably, at 4 weeks after inoculation (WAI), the transcript levels of all analyzed genes were significantly higher in the early senescent nodules of the mutant line E135F (sym13) and in nodules of the mutant Sprint-2Fix- (sym31) than in the active nitrogen-fixing nodules of wild-types. In contrast, the transcript levels of the same genes of both wild-types were significantly increased only at 6 WAI. We evaluated the expression of selected markers in the different histological nodule zones of pea cv. Sparkle and its mutant line E135F (sym13) by laser capture microdissection analysis. Finally, we analyzed ACC by immunolocalization in the nodules of both wild-type pea and their mutants. Together, the results indicate that nodule senescence is a general plant response to nodule ineffectiveness.

AtGIS, a C2H2 zinc-finger transcription factor from Arabidopsis regulates glandular trichome development through GA signaling in tobacco

Glandular trichome is specialized multicellular structures that have capability to synthesize and secrete secondary metabolites and protect plants from biotic and abiotic stresses. Our previous results revealed that the C2H2 zinc-finger transcription factors (GIS) acts upstream of GL3/EGL3-GL1-TTG1transcriptional activator complex to regulate trichome initiation through GA signal in Arabidopsis. In the present study, we are reporting that ectopic expression of AtGIS could regulate glandular trichome development through GA signaling in tobacco. X-gluc staining of various organs from transgenic plants showed that AtGIS expressed mainly in the glandular trichomes. Statistical analysis demonstrated that over expression of GIS increased significantly glandular trichome production on the leaf, stem, branch, and sepal in tobacco. After PAC treatment, reduction of glandular trichome production in transgenic plants was more severe with compared to wild type plants. Furthermore, GA treatment could induce expression of AtGIS. More importantly, our results also demonstrated that overexpressed AtGIS significantly affect the main components of trichome exudates, such as significantly increase the content of nicotine, Cembratriene-4, 6-diol. Taken together, these results suggest that ectopic expression of AtGIS regulates glandular trichome development and may play a key role in compounds secretion in tobacco.

Salicylic-Acid-Induced Chilling- and Oxidative-Stress Tolerance in Relation to Gibberellin Homeostasis, C-Repeat/Dehydration-Responsive Element Binding Factor Pathway, and Antioxidant Enzyme Systems in Cold-Stored Tomato Fruit

Effects of salicylic acid (SA) on gibberellin (GA) homeostasis, C-repeat/dehydration-responsive element binding factor (CBF) pathway, and antioxidant enzyme systems linked to chilling- and oxidative-stress tolerance in tomato fruit were investigated. Mature green tomatoes (Solanum lycopersicum L. cv. Moneymaker) were treated with 0, 0.5, and 1 mM SA solution for 15 min before storage at 4 °C for 28 days. In comparison to 0 or 0.5 mM SA, 1 mM SA significantly decreased the chilling injury (CI) index in tomato fruit. In the SA-treated fruit, the upregulation of GA biosynthetic gene (GA3ox1) expression was followed by gibberellic acid (GA₃) surge and DELLA protein degradation. CBF1 participated in the SA-modulated tolerance and stimulated the expression of GA catabolic gene (GA2ox1). Furthermore, 1 mM SA enhanced activities of antioxidant enzymes and, thus, reduced reactive oxygen species accumulation. Our findings suggest that SA might protect tomato fruit from CI and oxidative damage through regulating GA metabolism, CBF1 gene expression, and antioxidant enzyme activities.

The QTL GNP1 Encodes GA20ox1, Which Increases Grain Number and Yield by Increasing Cytokinin Activity in Rice Panicle Meristems

Cytokinins and gibberellins (GAs) play antagonistic roles in regulating reproductive meristem activity. Cytokinins have positive effects on meristem activity and maintenance. During inflorescence meristem development, cytokinin biosynthesis is activated via a KNOX-mediated pathway. Increased cytokinin activity leads to higher grain number, whereas GAs negatively affect meristem activity. The GA biosynthesis genes GA20oxs are negatively regulated by KNOX proteins. KNOX proteins function as modulators, balancing cytokinin and GA activity in the meristem. However, little is known about the crosstalk among cytokinin and GA regulators together with KNOX proteins and how KNOX-mediated dynamic balancing of hormonal activity functions. Through map-based cloning of QTLs, we cloned a GA biosynthesis gene, Grain Number per Panicle1 (GNP1), which encodes rice GA20ox1. The grain number and yield of NIL-GNP1^TQ were significantly higher than those of isogenic control (Lemont). Sequence variations in its promoter region increased the levels of GNP1 transcripts, which were enriched in the apical regions of inflorescence meristems in NIL-GNP1^TQ. We propose that cytokinin activity increased due to a KNOX-mediated transcriptional feedback loop resulting from the higher GNP1 transcript levels, in turn leading to increased expression of the GA catabolism genes GA2oxs and reduced GA₁ and GA₃ accumulation. This rebalancing process increased cytokinin activity, thereby increasing grain number and grain yield in rice. These findings uncover important, novel roles of GAs in rice florescence meristem development and provide new insights into the crosstalk between cytokinin and GA underlying development process.

Grain number per panicle, a valuable agronomic trait for rice yield improvement, is profoundly affected by reproductive meristem activity. This activity, in turn, is controlled by transcriptional and plant hormone regulators, especially KNOX proteins and cytokinins. However, little is known about the roles of GAs in these processes in rice and how the regulatory network functions due to the complexity of crosstalk between plant hormone regulators. In this study, we identify a novel GA biosynthesis gene in rice and demonstrate its role in improving grain number and grain yield. We also propose that the KNOX-mediated cytokinin-GA activity rebalancing mechanisms regulate inflorescence meristem development and maintenance processes, providing a possible tool for high-yield rice breeding.

Melatonin mediates the stabilization of DELLA proteins to repress the floral transition in Arabidopsis

Precise floral transition from vegetative growth phase to reproductive growth phase is very important in plant life cycle. In flowering genetic pathways, DELLA proteins are master transcriptional regulators of gibberelic acid (GA) pathway, and FLOWERING LOCUS C (FLC) is a core repressor of vernalization pathway as well as downstream of DELLAs. As a crucial messenger in plants, the possible involvement of melatonin (N-acetyl-5-methoxytryptamine) in flowering and underlying molecular mechanism are unknown in Arabidopsis. In this study, we found that exogenous melatonin treatment delayed floral transition in Arabidopsis. Exogenous melatonin treatment conferred protein stabilizations of DELLAs [REPRESSOR of ga1-3 (RGA) and RGA-LIKE3 (RGL3)], without regulating the transcripts of DELLAs and endogenous GA level. Notably, exogenous melatonin delayed plant flowering and DELLA-activated transcripts of FLC were alleviated in della mutants, and those were exacerbated in DELLA overexpressing plants. Taken together, this study provides direct link between melatonin and floral transition, and indicates the novel involvement of DELLAs-activated FLC in melatonin-mediated flowering in Arabidopsis.

Hormonal control of cold stress responses in plants

Cold stress responses in plants are highly sophisticated events that alter the biochemical composition of cells for protection from damage caused by low temperatures. In addition, cold stress has a profound impact on plant morphologies, causing growth repression and reduced yields. Complex signalling cascades are utilised to induce changes in cold-responsive gene expression that enable plants to withstand chilling or even freezing temperatures. These cascades are governed by the activity of plant hormones, and recent research has provided a better understanding of how cold stress responses are integrated with developmental pathways that modulate growth and initiate other events that increase cold tolerance. Information on the hormonal control of cold stress signalling is summarised to highlight the significant progress that has been made and indicate gaps that still exist in our understanding.

An Endosperm-Associated Cuticle Is Required for Arabidopsis Seed Viability, Dormancy and Early Control of Germination

Cuticular layers and seeds are prominent plant adaptations to terrestrial life that appeared early and late during plant evolution, respectively. The cuticle is a waterproof film covering plant aerial organs preventing excessive water loss and protecting against biotic and abiotic stresses. Cutin, consisting of crosslinked fatty acid monomers, is the most abundant and studied cuticular component. Seeds are dry, metabolically inert structures promoting plant dispersal by keeping the plant embryo in an arrested protected state. In Arabidopsis thaliana seeds, the embryo is surrounded by a single cell endosperm layer itself surrounded by a seed coat layer, the testa. Whole genome analyses lead us to identify cutin biosynthesis genes as regulatory targets of the phytohormones gibberellins (GA) and abscisic acid (ABA) signaling pathways that control seed germination. Cutin-containing layers are present in seed coats of numerous species, including Arabidopsis, where they regulate permeability to outer compounds. However, the role of cutin in mature seed physiology and germination remains poorly understood. Here we identify in mature seeds a thick cuticular film covering the entire outer surface of the endosperm. This seed cuticle is defective in cutin-deficient bodyguard1 seeds, which is associated with alterations in endospermic permeability. Furthermore, mutants affected in cutin biosynthesis display low seed dormancy and viability levels, which correlates with higher levels of seed lipid oxidative stress. Upon seed imbibition cutin biosynthesis genes are essential to prevent endosperm cellular expansion and testa rupture in response to low GA synthesis. Taken together, our findings suggest that in the course of land plant evolution cuticular structures were co-opted to achieve key physiological seed properties.

Seeds are remarkable plant structures that appeared late during land plant evolution. Indeed, within seeds plant embryos lie in a metabolic inert and highly resistant state. Seeds allow plants to disperse and find a favorable living environment. Remarkably as well, the “near-dead” embryo is able to germinate and turn into a fragile young seedling. The fragility of this transition is betrayed by the existence of control mechanisms that block germination in response to harmful environmental conditions. Seeds therefore transform plants into time and space travellers and largely explain land plant colonization by flowering plants.

The key to this success lies in the seed’s physiological feats, a major yet unresolved question in plant biology. We show that mature seeds of the model plant Arabidopsis contain an earlier land plant evolutionary innovation: the cuticle, a waxy film covering the aerial parts of the plant preventing excessive transpiration. The seed cuticle, which contains cutin, a major lipid polymer component of the leaf cuticle, encloses all the living tissues within the seed. Seeds with cutin defects are highly oxidized and have low seed viability and dormancy. They are also unable to control their germination. Thus, land plants co-opted an ancient innovation to achieve the remarkable physiology of seeds.

Loss of function mutations in the rice chromomethylase OsCMT3a cause a burst of transposition

Methylation patterns of plants are unique as, in addition to the methylation at CG dinucleotides that occurs in mammals, methylation also occurs at non-CG sites. Genes are methylated at CG sites, but transposable elements (TEs) are methylated at both CG and non-CG sites. The role of non-CG methylation in transcriptional silencing of TEs is being extensively studied at this time, but only very rare transpositions have been reported when non-CG methylation machineries have been compromised. To understand the role of non-CG methylation in TE suppression and in plant development, we characterized rice mutants with changes in the chromomethylase gene, OsCMT3a. oscmt3a mutants exhibited a dramatic decrease in CHG methylation, changes in the expression of some genes and TEs, and pleiotropic developmental abnormalities. Genome resequencing identified eight TE families mobilized in oscmt3a during normal propagation. These TEs included tissue culture-activated copia retrotransposons Tos17 and Tos19 (Lullaby), a pericentromeric clustered high-copy-number non-autonomous gypsy retrotransposon Dasheng, two copia retrotransposons Osr4 and Osr13, a hAT-tip100 transposon DaiZ, a MITE transposon mPing, and a LINE element LINE1-6_OS. We confirmed the transposition of these TEs by polymerase chain reaction (PCR) and/or Southern blot analysis, and showed that transposition was dependent on the oscmt3a mutation. These results demonstrated that OsCMT3a-mediated non-CG DNA methylation plays a critical role in development and in the suppression of a wide spectrum of TEs. These in planta mobile TEs are important for studying the interaction between TEs and the host genome, and for rice functional genomics.

Genetic analyses of the interaction between abscisic acid and gibberellins in the control of leaf development in Arabidopsis thaliana

Although abscisic acid (ABA) and gibberellins (GAs) play pivotal roles in many physiological processes in plants, their interaction in the control of leaf growth remains elusive. In this study, genetic analyses of ABA and GA interplay in leaf growth were performed in Arabidopsis thaliana. The results indicate that for the ABA and GA interaction, leaf growth of both the aba2/ga20ox1 and aba2/GA20ox1 plants, which were derived from the crosses of aba2×ga20ox1 and aba2×GA20ox1 overexpressor, respectively, exhibits partially additive effects but is similar to the aba2 mutant. Consistently, the transcriptome analysis suggests that a substantial proportion (45-65%) of the gene expression profile of aba2/ga20ox1 and aba2/GA20ox1 plants overlap and share a pattern similar to the aba2 mutant. Thus, these data suggest that ABA deficiency dominates leaf growth regardless of GA levels. Moreover, the gene ontology (GO) analysis indicates gene enrichment in the categories of hormone response, developmental and metabolic processes, and cell wall organization in these three genotypes. Leaf developmental genes are also involved in the ABA-GA interaction. Collectively, these data support that the genetic relationship of ABA and GA interaction involves multiple coordinated pathways rather than a simple linear pathway for the regulation of leaf growth.

Analyzing serial cDNA libraries revealed reactive oxygen species and gibberellins signaling pathways in the salt response of Upland cotton (Gossypium hirsutum L.)

By comparing series full-length cDNA libraries stressed and control, the dynamic process of salt stress response in Upland cotton was studied, and reactive oxygen species and gibberellins signaling pathways were proposed. The Upland cotton is the most important fiber plant with highly salt tolerance. However, the molecular mechanism underlying salt tolerance in domesticated cotton was unclear. Here, seven full-length cDNA libraries were constructed for seedling roots of Upland cotton 'Zhong G 5' at 0, 3, 12 and 48 h after the treatment of control or 150 mM NaCl stress. About 3300 colonies in each library were selected robotically for 5'-end pyrosequencing, resulting in 20,358 expressed sequence tags (ESTs) totally. And 8516 uniESTs were then assembled, including 2914 contigs and 5602 singletons, and explored for Gene Ontology (GO) function. GO comparison between serial stress libraries and control reflected the growth regulation, stimulus response, signal transduction and biology regulation processes were conducted dynamically in response to salt stress. MYB, MYB-related, WRKY, bHLH, GRAS and ERF families of transcription factors were significantly enriched in the early response. 65 differentially expressed genes (DEGs), mainly associated with reactive oxygen species (ROS) scavenging, gibberellins (GAs) metabolism, signal transduction, transcription regulation, stress response and transmembrane transport, were identified and confirmed by quantitative real-time PCR. Overexpression of selected DEGs increased tolerance against salt stress in transgenic yeast. Results in this study supported that a ROS-GAs interacting signaling pathway of salt stress response was activated in Upland cotton. Our results provided valuable gene resources for further investigation of the molecular mechanism of salinity tolerance.

Shedding light on integrative GA signaling

Gibberellic acid (GA) regulates a diversity of processes associated with plant growth and development. The DELLA proteins act as repressors of GA signaling, and are destabilized by GA. Although it is known that GA signaling integrates various endogenous and environmental signals, the molecular basis of their modulation of plant growth and development is only now beginning to be understood. The current suggestion is that the DELLA proteins act as one possible quantitative modulator of plant growth, achieved by integrating multiple environmental and hormonal signals via protein-protein interactions. This review discusses recent elaborations of the de-repression model proposed to describe the GA response, and focuses on integrative networks thought to regulate plant growth, development and the adaptation to a fluctuating environment.

Hormones, polyamines, and cell wall metabolism during oil palm fruit mesocarp development and ripening

Oil palm is one of the most productive oil-producing crops and can store up to 90% oil in its fruit mesocarp. Oil palm fruit is a sessile drupe consisting of a fleshy mesocarp from which palm oil is extracted. Biochemical changes in the mesocarp cell walls, polyamines, and hormones at different ripening stages of oil palm fruits were studied, and the relationship between the structural and the biochemical metabolism of oil palm fruits during ripening is discussed. Time-course analysis of the changes in expression of polyamines, hormones, and cell-wall-related genes and metabolites provided insights into the complex processes and interactions involved in fruit development. Overall, a strong reduction in auxin-responsive gene expression was observed from 18 to 22 weeks after pollination. High polyamine concentrations coincided with fruit enlargement during lipid accumulation and latter stages of maturation. The trend of abscisic acid (ABA) concentration was concordant with GA₄ but opposite to the GA₃ profile such that as ABA levels increase the resulting elevated ABA/GA₃ ratio clearly coincides with maturation. Polygalacturonase, expansin, and actin gene expressions were also observed to increase during fruit maturation. The identification of the master regulators of these coordinated processes may allow screening for oil palm variants with altered ripening profiles.

The effect of mepiquat chloride on elongation of cotton (Gossypium hirsutum L.) internode is associated with low concentration of gibberellic acid

The growth regulator mepiquat chloride (MC) is globally used in cotton (Gossypium hirsutum L.) canopy manipulation to avoid excess growth and yield loss. However, little information is available as to whether the modification of plant architecture by MC is related to alterations in gibberellic acid (GA) metabolism and signaling. Here, the role of GA metabolism and signaling was investigated in cotton seedlings treated with MC. The MC significantly decreased endogenous GA3 and GA4 levels in the elongating internode, which inhibited cell elongation by downregulating GhEXP and GhXTH2, and then reducing plant height. Biosynthetic and metabolic genes of GA were markedly suppressed within 2-10d of MC treatment, which also downregulated the expression of DELLA-like genes. A remarkable feedback regulation was observed at the early stage of MC treatment when GA biosynthetic and metabolic genes expression was evidently upregulated. Mepiquat chloride action was controlled by temporal translocation and spatial accumulation which regulated GA biosynthesis and signal expression for maintaining GA homeostasis. The results suggested that MC application could reduce endogenous GA levels in cotton through controlled GA biosynthetic and metabolic genes expression, which might inhibit cell elongation, thereby shortening the internode and reducing plant height.

Biochemical and Molecular Analyses of Gibberellin Biosynthesis in Fungi

The plant hormone, gibberellin (GA), regulates plant growth and development. It was first isolated as a superelongation-promoting diterpenoid from the fungus, Gibberella fujikuroi. G. fujikuroi uses different GA biosynthetic intermediates from those in plants to produce GA3. Another class of GA-producing fungus, Phaeosphaeria sp. L487, synthesizes GA1 by using the same intermediates as those in plants. A molecular analysis of GA biosynthesis in Phaeosphaeria sp. has revealed that diterpene cyclase and cytochrome P450 monooxygenases were involved in the plant-like biosynthesis of GA1. Fungal ent-kaurene synthase is a bifunctional cyclase. Subsequent oxidation steps are catalyzed by P450s, leading to biologically active GA1. GA biosynthesis in plants is divided into three steps involving soluble enzymes and membrane-bound cytochrome P450. The activation of plant GAs is catalyzed by soluble 2-oxoglutarate-dependent dioxygenases, which is in contrast to the catalysis of fungal GA biosynthesis. This difference suggests that the origin of fungal GA biosynthesis is evolutionally independent of that in plants.

A novel lily anther-specific gene encodes adhesin-like proteins associated with exine formation during anther development

The anther-specific gene LLA1271 isolated from lily (Lilium longiflorum Thunb.) anthers is novel and exists in two forms. The protein encoded by LLA1271 may represent an adhesin-like protein first found in higher plants. The protein contains a typical N-terminal signal peptide followed by a highly conserved repeat domain. The LLA1271 gene is temporally expressed at the phase of microspore development. RNA blot and RNA in situ hybridization analyses demonstrated that the gene was expressed both in the tapetum and in the microspore. The gene is endo- and exogenously induced by gibberellin. Studies with the gibberellin biosynthesis inhibitor uniconazole and an inhibitor of ethylene activity, 2,5-norbornadien (NBD), revealed that LLA1271 is negatively regulated by ethylene, and a cross-talk of regulation between gibberellin and ethylene occurs in young anthers. The treatment with NBD caused the tapetum to become densely cytoplasmic and highly polarized, whereas uniconazole arrested tapetal development in a state close to that of a tapetum without treatment. The LLA1271 protein is heat stable and heterogeneous. An immunoblot of separated protein fractions of the anther revealed that the LLA1271 protein was detected in protein fraction of the microspore released from the cell wall by treatment with either 0.5% or 2% Triton X-100. Ectopic expression of LLA1271 resulted in impaired stamen and low pollen germination. Scanning electron microscopy of TAP::LLA1271 pollen showed distorted exine formation and patterning. The LLA1271 protein once synthesized in both the tapetum and microspore is secreted and deposited on the surface of microspores, moderately affecting exine formation and patterning.

Isolation and characterisation of a dwarf rice mutant exhibiting defective gibberellins biosynthesis

We have isolated a severe dwarf mutant derived from a Ds (Dissociation) insertion mutant rice (Oryza sativa var. japonica c.v. Dongjin). This severe dwarf phenotype, has short and dark green leaves, reduced shoot growth early in the seedling stage, and later severe dwarfism with failure to initiate flowering. When treated with bioactive GA3 , mutants are restored to the normal wild-type phenotype. Reverse transcription PCR analyses of 22 candidate genes related to the gibberellin (GA) biosynthesis pathway revealed that among 22 candidate genes tested, a dwarf mutant transcript was not expressed only in one OsKS2 gene. Genetic analysis revealed that the severe dwarf phenotype was controlled by recessive mutation of a single nuclear gene. The putative OsKS2 gene was a chromosome 4-located ent-kaurene synthase (KS), encoding the enzyme that catalyses an early step of the GA biosynthesis pathway. Sequence analysis revealed that osks2 carried a 1-bp deletion in the ORF region of OsKS2, which led to a loss-of-function mutation. The expression pattern of OsKS2 in wild-type cv Dongjin, showed that it is expressed in all organs, most prominently in the stem and floral organs. Morphological characteristics of the dwarf mutant showed dramatic modifications in internal structure and external morphology. We propose that dwarfism in this mutant is caused by a point mutation in OsKS2, which plays a significant role in growth and development of higher plants. Further investigation on OsKS2 and other OsKS-like proteins is underway and may yield better understanding of the putative role of OsKS in severe dwarf mutants.

A MADS-box gene is specifically expressed in fibers of cotton (Gossypium hirsutum) and influences plant growth of transgenic Arabidopsis in a GA-dependent manner

In this study, a cDNA, GhMADS14, encoding a typical MADS-box protein with 223 amino acids was isolated from a cotton cDNA library. Fluorescent microscopy indicated that the GhMADS14 protein was localized in the cell nucleus. GhMADS14 was specifically expressed in the elongating fibers, and its expression was gradually enhanced at early stages of fiber elongation and reached its peak in 9-10 DPA fibers. Overexpression of GhMADS14 in Arabidopsis hindered plant growth. Measurement and statistical analysis revealed that hypocotyl length of GhMADS14 transgenic seedlings was significantly reduced, and the height of the mature transgenic plants was remarkably less than that of the wild type. Furthermore, expression of GA 20-oxidase (AtGA20ox1 and AtGA20ox2) and GA 3-oxidase (AtGA3ox1 and AtGA3ox2) genes was remarkably reduced, whereas AtGA2ox1 and AtGA2ox8 were dramatically up-regulated in the transgenic plants, compared with the wild type. These results suggested that overexpression of GhMADS14 in Arabidopsis may alter expression levels of the genes related to GA biosynthetic and metabolic pathways, resulting in the reduction of endogenous GA amounts in cells. As a result, the transgenic plants grew slowly and display a GA-deficient phenotype.

A forward genetic approach in Arabidopsis thaliana identifies a RING-type ubiquitin ligase as a novel determinant of seed longevity

Seed longevity is important to preserve crops and wild plants and it is limited by progressive cellular damage (aging) during storage. The induction of cellular stress defenses and the formation of the seed coat are crucial protecting events during seed development, a process mediated in Arabidopsis thaliana by the transcription factors LEC1, LEC2, FUS3 and the abscisic acid-activated ABI3. In order to identify novel determinants of seed longevity we have screened an activation-tagging mutant collection of Arabidopsis and isolated a dominant mutant with increased seed longevity under both natural and accelerated aging conditions. Molecular characterization indicates that the mutant phenotype is caused by over-expression of the At2g26130 gene encoding a RING-type zinc finger putative ubiquitin ligase. Loss of function of this gene in a T-DNA insertion mutant resulted in decreased seed longevity. We named this important gene for seed longevity RSL1 (from Ring finger of Seed Longevity1) and we could demonstrate ubiquitin ligase activity with the recombinant protein. Morphological alterations in shoot tissues of the RSL1 over-expressing plants and analysis of gibberellins levels suggest that RSL1 may increase gibberellins responses by some unknown mechanism. These results validate the forward genetic approach to seed longevity and anticipate the identification of many novel determinants of this important trait.

Structure and expression of GSL1 and GSL2 genes encoding gibberellin stimulated-like proteins in diploid and highly heterozygous tetraploid potato reveals their highly conserved and essential status

BACKGROUND

GSL1 and GSL2, Gibberellin Stimulated-Like proteins (also known as Snakin-1 and Snakin-2), are cysteine-rich peptides from potato (Solanum tuberosum L.) with antimicrobial properties. Similar peptides in other species have been implicated in diverse biological processes and are hypothesised to play a role in several aspects of plant development, plant responses to biotic or abiotic stress through their participation in hormone crosstalk, and redox homeostasis. To help resolve the biological roles of GSL1 and GSL2 peptides we have undertaken an in depth analysis of the structure and expression of these genes in potato.

RESULTS

We have characterised the full length genes for both GSL1 (chromosome 4) and GSL2 (chromosome 1) from diploid and tetraploid potato using the reference genome sequence of potato, coupled with further next generation sequencing of four highly heterozygous tetraploid cultivars. The frequency of SNPs in GSL1 and GSL2 were very low with only one SNP every 67 and 53 nucleotides in exon regions of GSL1 and GSL2, respectively. Analysis of comprehensive RNA-seq data substantiated the role of specific promoter motifs in transcriptional control of gene expression. Expression analysis based on the frequency of next generation sequence reads established that GSL2 was expressed at a higher level than GSL1 in 30 out of 32 tissue and treatment libraries. Furthermore, both the GSL1 and GSL2 genes exhibited constitutive expression that was not up regulated in response to biotic or abiotic stresses, hormone treatments or wounding. Potato transformation with antisense knock-down expression cassettes failed to recover viable plants.

CONCLUSIONS

The potato GSL1 and GSL2 genes are very highly conserved suggesting they contribute to an important biological function. The known antimicrobial activity of the GSL proteins, coupled with the FPKM analysis from RNA-seq data, implies that both genes contribute to the constitutive defence barriers in potatoes. The lethality of antisense knock-down expression of GSL1 and GSL2, coupled with the rare incidence of SNPs in these genes, suggests an essential role for this gene family. These features are consistent with the GSL protein family playing a role in several aspects of plant development in addition to plant defence against biotic stresses.

Overexpression of the Galega orientalis gibberellin receptor improves biomass production in transgenic tobacco

Gibberellins (GAs) are well-known phytohormones that contribute to a wide range of plant growth and development functions including stem elongation and leaf expansion. GA receptors perceive GA and transmit signals to activate GA-regulated reactions. In this study, a GA receptor gene with homology to other leguminous plants was isolated from Galega orientalis and termed GoGID. The 1732-bp full-length GoGID gene included an open reading frame of 1035 bp encoding a peptide of 344 amino acids. Sequence analysis indicated that GoGID shares conserved HGGS motif and active amino acid sites (Ser-Asp-Val/IIe) that are essential for maintaining it GA-binding activity. GoGID mRNA expression was more abundant in leaves than in roots or stems and could be up-regulated by the exogenous hormones. Overexpression of GoGID in transgenic tobacco plants promoted plant elongation and improved biomass production. These results suggested that GoGID functions as a GA receptor to alter GA-mediated signaling. GoGID may have a role in genetic engineering for the improvement of forage crops.

The Fragaria vesca homolog of suppressor of overexpression of constans1 represses flowering and promotes vegetative growth

In the annual long-day plant Arabidopsis thaliana, suppressor of overexpression of constans1 (SOC1) integrates endogenous and environmental signals to promote flowering. We analyzed the function and regulation of the SOC1 homolog (Fragaria vesca [Fv] SOC1) in the perennial short-day plant woodland strawberry (Fragaria vesca). We found that Fv SOC1 overexpression represses flower initiation under inductive short days, whereas its silencing causes continuous flowering in both short days and noninductive long days, similar to mutants in the floral repressor Fv terminal flower1 (Fv TFL1). Molecular analysis of these transgenic lines revealed that Fv SOC1 activates Fv TFL1 in the shoot apex, leading to the repression of flowering in strawberry. In parallel, Fv SOC1 regulates the differentiation of axillary buds to runners or axillary leaf rosettes, probably through the activation of gibberellin biosynthetic genes. We also demonstrated that Fv SOC1 is regulated by photoperiod and Fv flowering locus T1, suggesting that it plays a central role in the photoperiodic control of both generative and vegetative growth in strawberry. In conclusion, we propose that Fv SOC1 is a signaling hub that regulates yearly cycles of vegetative and generative development through separate genetic pathways.

Transcriptional programs related to phytochrome A function in Arabidopsis seed germination

In Arabidopsis seeds, germination is promoted only by phytochromes, principally phytochrome B (phyB) and phytochrome A (phyA). Despite the abundant information concerning the molecular basis of phyB signaling downstream of PIF1/PIL5, the signaling network inducing germination by phyA is poorly known. Here, we describe the influence of phyA on the transcriptome of Arabidopsis seeds when germination is induced by a far-red (FR) pulse. The expression of 11% of the genome was significantly regulated by phyA. Most of the genes were up-regulated and the changes noted late (i.e. 5 h after a FR pulse), whereas changes in down-regulated genes were more abundant earlier (i.e. 0.5 h after a FR pulse). Auxin- and GA-associated elements were overrepresented in the genes that were modified by phyA. A significant number of genes whose expression was affected by phyA had not been previously reported to be dependent on PIL5. Among them, homozygotic mutant seeds of MYB66, a SAUR-like protein, PIN7, and GASA4 showed an impaired promotion of germination by phyA. Natural variation at the transcriptional level was found in early signaling and GA metabolic genes, but not in ABA metabolic and expansin genes between Columbia and Landsberg erecta accessions. Although phyA and phyB/PIL5 signaling pathways share some molecular components, our data suggest that phyA signaling is partially independent of PIL5 when germination is promoted by very low fluences of light.

GASA14 regulates leaf expansion and abiotic stress resistance by modulating reactive oxygen species accumulation

Gibberellic acid (GA) can regulate many plant developmental processes. GAST1 has been identified as a GA-stimulated transcript, and Arabidopsis GAST-like genes are known to constitute the GASA family. However, the functions of most GASA genes are not clear at present. In this study, the function of GASA14, a member of the GASA family, was investigated. GASA14 expression was upregulated by GA and downregulated by the transcriptional regulators that repress GA responses, the DELLA proteins GAI and RGA. Phenotypic analysis showed that growth of the GASA14 null mutant (gasa14-1) line was retarded, and the growth of the 35S::GASA14 lines were promoted in young plants. Furthermore, seed germination of the gasa14-1 plants showed more sensitivity to paclobutrazol (an inhibitor of GA biosynthesis) than Columbia (Col) plants, suggesting that GASA14 is required for GA-dependent responses. Analysis of the responses of the gasa14-1 and 35S::GASA14 lines to abscisic acid (ABA) and salt revealed that germination and seedling establishment of gasa14-1 were poorer than those of Col plants and that the 35S::GASA14 lines were more resistant to ABA and salt. Further analysis showed that overexpression of GASA14 could suppress reactive oxygen species (ROS) accumulation. Taken together, these results demonstrated that GASA14 regulates leaf expansion and abiotic stress resistance by modulating ROS accumulation. Because GASA14 contains both GASA (GA-stimulated in Arabidopsis) and PRP (proline-rich protein) domains, the PRP domain coding sequence was overexpressed in Col plants and it was found that the growth of the transgenic plants and the responses to ABA and salt were not altered. These results thus suggest that the GASA domain is necessary for the functions of GASA14.

Promotion of growth by elevated carbon dioxide is coordinated through a flexible transcriptional network in Arabidopsis

Although gibberellins (GAs) promote many developmental responses in plants, little is known about how the hormone interacts with environmental signals at the molecular level for regulating plant growth. Recently, we have demonstrated that inhibition of growth by the GA biosynthesis inhibitor paclobutrazol (PAC) at ambient [CO₂] (350 µmol CO₂ mol(-1)) is reverted by elevated [CO₂] (750 μmol CO₂ mol(-1)). Our finding points to an important role of elevated [CO₂] as a signal allowing higher growth rates of low-GA plants. GA promotes plant growth via a complex transcriptional network that integrates multiple signaling pathways. Herein, we discuss how elevated [CO₂] stimulates biomass accumulation in a GA-independent manner by regulating the expression of growth-related genes.

Expression of 9-cis-EPOXYCAROTENOID DIOXYGENASE4 is essential for thermoinhibition of lettuce seed germination but not for seed development or stress tolerance

Thermoinhibition, or failure of seeds to germinate at warm temperatures, is common in lettuce (Lactuca sativa) cultivars. Using a recombinant inbred line population developed from a lettuce cultivar (Salinas) and thermotolerant Lactuca serriola accession UC96US23 (UC), we previously mapped a quantitative trait locus associated with thermoinhibition of germination to a genomic region containing a gene encoding a key regulated enzyme in abscisic acid (ABA) biosynthesis, 9-cis-EPOXYCAROTENOID DIOXYGENASE4 (NCED4). NCED4 from either Salinas or UC complements seeds of the Arabidopsis thaliana nced6-1 nced9-1 double mutant by restoring germination thermosensitivity, indicating that both NCED4 genes encode functional proteins. Transgenic expression of Salinas NCED4 in UC seeds resulted in thermoinhibition, whereas silencing of NCED4 in Salinas seeds led to loss of thermoinhibition. Mutations in NCED4 also alleviated thermoinhibition. NCED4 expression was elevated during late seed development but was not required for seed maturation. Heat but not water stress elevated NCED4 expression in leaves, while NCED2 and NCED3 exhibited the opposite responses. Silencing of NCED4 altered the expression of genes involved in ABA, gibberellin, and ethylene biosynthesis and signaling pathways. Together, these data demonstrate that NCED4 expression is required for thermoinhibition of lettuce seeds and that it may play additional roles in plant responses to elevated temperature.

Differences and similarities in the photoregulation of gibberellin metabolism between rice and dicots

In rice seedlings, elongation of leaf sheaths is suppressed by light stimuli. The response is mediated by two classes of photoreceptors, phytochromes and cryptochromes. However, it remains unclear how these photoreceptors interact in the process. Our recent study using phytochrome mutants and novel cryptochrome RNAi lines revealed that cryptochromes and phytochromes function cooperatively, but independently to reduce active GA contents in seedlings in visible light. Blue light captured by cryptochrome 1 (cry1a and cry1b) induces robust expression of GA 2-oxidase genes (OsGA2ox4-7). In parallel, phytochrome B with auxiliary action of phytochrome A mediates repression of GA 20-oxidase genes (OsGA20ox2 and OsGA20ox4). The independent effects cumulatively reduce active GA contents, leading to a suppression of leaf sheath elongation. These regulatory mechanisms are distinct from phytochrome B function in dicots. We discuss reasons why the distinct system appeared in rice, and advantages of the rice system in early photomorphogenesis.

Transcript profiling of Paoenia ostii during artificial chilling induced dormancy release identifies activation of GA pathway and carbohydrate metabolism

Endo-dormant flower buds must pass through a period of chilling to reinitiate growth and subsequent flowering, which is a major obstacle to the forcing culture of tree peony in winter. Customized cDNA microarray (8×15 K element) was used to investigate gene expression profiling in tree peony 'Feng Dan Bai' buds during 24 d chilling treatment at 0-4°C. According to the morphological changes after the whole plants were transferred to green house, endo-dormancy was released after 18 d chilling treatment, and prolonged chilling treatment increased bud break rate. Pearson correlation hierarchical clustering of sample groups was highly consistent with the dormancy transitions revealed by morphological changes. Totally 3,174 significantly differentially-expressed genes (P<0.05) were observed through endo-dormancy release process, of which the number of up-regulated (1,611) and that of down-regulated (1,563) was almost the same. Functional annotation of differentially-expressed genes revealed that cellular process, metabolic process, response to stimulus, regulation of biological process and development process were well-represented. Hierarchical clustering indicated that activation of genes involved in carbohydrate metabolism (Glycolysis, Citrate cycle and Pentose phosphate pathway), energy metabolism and cell growth. Based on the results of GO analysis, totally 51 probes presented in the microarray were associated with GA response and GA signaling pathway, and 22 of them were differently expressed. The expression profiles also revealed that the genes of GA biosynthesis, signaling and response involved in endo-dormancy release. We hypothesized that activation of GA pathway played a central role in the regulation of dormancy release in tree peony.

UniVIO: a multiple omics database with hormonome and transcriptome data from rice

Plant hormones play important roles as signaling molecules in the regulation of growth and development by controlling the expression of downstream genes. Since the hormone signaling system represents a complex network involving functional cross-talk through the mutual regulation of signaling and metabolism, a comprehensive and integrative analysis of plant hormone concentrations and gene expression is important for a deeper understanding of hormone actions. We have developed a database named Uniformed Viewer for Integrated Omics (UniVIO: http://univio.psc.riken.jp/), which displays hormone-metabolome (hormonome) and transcriptome data in a single formatted (uniformed) heat map. At the present time, hormonome and transcriptome data obtained from 14 organ parts of rice plants at the reproductive stage and seedling shoots of three gibberellin signaling mutants are included in the database. The hormone concentration and gene expression data can be searched by substance name, probe ID, gene locus ID or gene description. A correlation search function has been implemented to enable users to obtain information of correlated substance accumulation and gene expression. In the correlation search, calculation method, range of correlation coefficient and plant samples can be selected freely.

Overexpression of soybean GmCBL1 enhances abiotic stress tolerance and promotes hypocotyl elongation in Arabidopsis

Although extensive studies and remarkable progress have been made with Arabidopsis calcineurin B-like proteins (CBLs), knowledge of their functions in other plant species is still limited. Here we isolated gene GmCBL1 from soybean, a homolog of AtCBL1 in Arabidopsis. GmCBL1 was differentially induced by multiple abiotic stress and plant hormones, and its transcripts were abundant in seedlings and mature roots. We over-expressed GmCBL1 in Arabidopsis and found that it enhanced tolerances to both high salt and drought stresses in the transgenic plants. Overexpression of GmCBL1 also promoted hypocotyl elongation under light conditions. GmCBL1 may regulate stress tolerance through activation of stress-related genes, and may control hypocotyl development by altering the expression of gibberellin biosynthesis-related genes. This study identifies a putative soybean CBL gene that functions in both stress tolerance and light-dependent hypocotyl development.

Gibberellins regulate the transcription of the continuous flowering regulator, RoKSN, a rose TFL1 homologue

The role of gibberellins (GAs) during floral induction has been widely studied in the annual plant Arabidopsis thaliana. Less is known about this control in perennials. It is thought that GA is a major regulator of flowering in rose. In spring, low GA content may be necessary for floral initiation. GA inhibited flowering in once-flowering roses, whereas GA did not block blooming in continuous-flowering roses. Recently, RoKSN, a homologue of TFL1, was shown to control continuous flowering. The loss of RoKSN function led to continuous flowering behaviour. The objective of this study was to understand the molecular control of flowering by GA and the involvement of RoKSN in this inhibition. In once-flowering rose, the exogenous application of GA(3) in spring inhibited floral initiation. Application of GA(3) during a short period of 1 month, corresponding to the floral transition, was sufficient to inhibit flowering. At the molecular level, RoKSN transcripts were accumulated after GA(3) treatment. In spring, this accumulation is correlated with floral inhibition. Other floral genes such as RoFT, RoSOC1, and RoAP1 were repressed in a RoKSN-dependent pathway, whereas RoLFY and RoFD repression was RoKSN independent. The RoKSN promoter contained GA-responsive cis-elements, whose deletion suppressed the response to GA in a heterologous system. In summer, once-flowering roses did not flower even after exogenous application of a GA synthesis inhibitor that failed to repress RoKSN. A model is presented for the GA inhibition of flowering in spring mediated by the induction of RoKSN. In summer, factors other than GA may control RoKSN.

Florigenic and antiflorigenic signaling in plants

The evidence that FLOWERING LOCUS T (FT) protein, and its paralog TWIN SISTER OF FT, act as the long-distance floral stimulus, or at least that they are part of it in diverse plant species, has attracted much attention in recent years. Studies to understand the physiological and molecular apparatuses that integrate spatial and temporal signals to regulate developmental transitions in plants have occupied countless scientists and have resulted in an unmanageably large amount of research data. Analysis of these data has helped to identify multiple systemic florigenic and antiflorigenic regulators. This study gives an overview of the recent research on gene products, phytohormones and other metabolites that have been demonstrated to have florigenic or antiflorigenic functions in plants.

Green revolution trees: semidwarfism transgenes modify gibberellins, promote root growth, enhance morphological diversity, and reduce competitiveness in hybrid poplar

Semidwarfism has been used extensively in row crops and horticulture to promote yield, reduce lodging, and improve harvest index, and it might have similar benefits for trees for short-rotation forestry or energy plantations, reclamation, phytoremediation, or other applications. We studied the effects of the dominant semidwarfism transgenes GA Insensitive (GAI) and Repressor of GAI-Like, which affect gibberellin (GA) action, and the GA catabolic gene, GA 2-oxidase, in nursery beds and in 2-year-old high-density stands of hybrid poplar (Populus tremula × Populus alba). Twenty-nine traits were analyzed, including measures of growth, morphology, and physiology. Endogenous GA levels were modified in most transgenic events; GA(20) and GA(8), in particular, had strong inverse associations with tree height. Nearly all measured traits varied significantly among genotypes, and several traits interacted with planting density, including aboveground biomass, root-shoot ratio, root fraction, branch angle, and crown depth. Semidwarfism promoted biomass allocation to roots over shoots and substantially increased rooting efficiency with most genes tested. The increased root proportion and increased leaf chlorophyll levels were associated with changes in leaf carbon isotope discrimination, indicating altered water use efficiency. Semidwarf trees had dramatically reduced growth when in direct competition with wild-type trees, supporting the hypothesis that semidwarfism genes could be effective tools to mitigate the spread of exotic, hybrid, and transgenic plants in wild and feral populations.

Characterization of the fungal gibberellin desaturase as a 2-oxoglutarate-dependent dioxygenase and its utilization for enhancing plant growth

The biosynthesis of gibberellic acid (GA(3)) by the fungus Fusarium fujikuroi is catalyzed by seven enzymes encoded in a gene cluster. While four of these enzymes are characterized as cytochrome P450 monooxygenases, the nature of a fifth oxidase, GA(4) desaturase (DES), is unknown. DES converts GA(4) to GA(7) by the formation of a carbon-1,2 double bond in the penultimate step of the pathway. Here, we show by expression of the des complementary DNA in Escherichia coli that DES has the characteristics of a 2-oxoglutarate-dependent dioxygenase. Although it has low amino acid sequence homology with known 2-oxoglutarate-dependent dioxygenases, putative iron- and 2-oxoglutarate-binding residues, typical of such enzymes, are apparent in its primary sequence. A survey of sequence databases revealed that homologs of DES are widespread in the ascomycetes, although in most cases the homologs must participate in non-gibberellin (GA) pathways. Expression of des from the cauliflower mosaic virus 35S promoter in the plant species Solanum nigrum, Solanum dulcamara, and Nicotiana sylvestris resulted in substantial growth stimulation, with a 3-fold increase in height in S. dulcamara compared with controls. In S. nigrum, the height increase was accompanied by a 20-fold higher concentration of GA(3) in the growing shoots than in controls, although GA(1) content was reduced. Expression of des was also shown to partially restore growth in plants dwarfed by ectopic expression of a GA 2-oxidase (GA-deactivating) gene, consistent with GA(3) being protected from 2-oxidation. Thus, des has the potential to enable substantial growth increases, with practical implications, for example, in biomass production.

Photocontrol of bud burst involves gibberellin biosynthesis in Rosa sp

Light is a critical determinant of plant shape by controlling branching patterns and bud burst in many species. To gain insight into how light induces bud burst, we investigated whether its inductive effect in rose was related to gibberellin (GA) biosynthesis. In axillary buds of beheaded plants subject to light, the expression of two GA biosynthesis genes (RoGA20ox and RoGA3ox) was promptly and strongly induced, while that of a GA-catabolism genes (RoGA2ox) was reduced. By contrast, lower expression levels of these two GA biosynthesis genes were found in darkness, and correlated with a total inhibition of bud burst. This effect was dependent on both light intensity and quality. In in vitro cultured buds, the inductive effect of light on the growth of preformed leaves and SAM organogenic activity was inhibited by ancymidol and paclobutrazol, two effectors of GA biosynthesis. This effect was concentration-dependent, and negated by GA(3). However, GA(3) alone could not rescue bud burst in the dark. GA biosynthesis was also required for the expression and activity of a vacuolar invertase, and therefore for light-induced sugar metabolism within buds. These findings are evidence that GA biosynthesis contributes to the light effect on bud burst and lay the foundations of a better understanding of its exact role in plant branching.

Characterization of sck1, a novel Castanea mollissima mutant with the extreme short catkins and decreased gibberellin

A novel Chinese chestnut (Castanea mollissima Bl.) mutant with extreme short catkins, here was named sck1 and has been characterized in the present study. This sck1 caused 6-fold shorter than wild-type catkins. Endogenous gibberellic acids markedly decreased in the mutant, and application of exogenous GA(3) could partially restore the sck1 phenotype to the wild-type phenotype. Paclobutrazol (PP(333)), an antagonist of GAs biosynthesis, could significantly inhibit the wild-type catkins growth, and lead to a short catkins phenotype similar to the sck1. In addition, compared to the wild-type catkins, the mRNA expression level of ent-kaurenoic acid oxidase (KAO), a gibberellin biosynthesis key gene, was significantly down-regulated (P<0.01) in the sck1. Importantly, transient over-expression of a normal CmKAO gene in short catkins also could partially restore the wild-type phenotype. Real-time PCR and semi-quantitative analysis showed that the mRNA expression level of KAO was significantly up-regulated. In addition, transient RNA interference of CmKAO in wild-type catkins led the mRNA expression level of KAO decrease significantly and inhibited the wild-type catkins elongation strongly. Taken together, our results suggest that the lower gibberellic acids content that is due to decreased CmKAO expression level may contribute to the generation of the extreme short male catkins, sck1.

DELLA signaling mediates stress-induced cell differentiation in Arabidopsis leaves through modulation of anaphase-promoting complex/cyclosome activity

Drought is responsible for considerable yield losses in agriculture due to its detrimental effects on growth. Drought responses have been extensively studied, but mostly on the level of complete plants or mature tissues. However, stress responses were shown to be highly tissue and developmental stage specific, and dividing tissues have developed unique mechanisms to respond to stress. Previously, we studied the effects of osmotic stress on dividing leaf cells in Arabidopsis (Arabidopsis thaliana) and found that stress causes early mitotic exit, in which cells end their mitotic division and start endoreduplication earlier. In this study, we analyzed this phenomenon in more detail. Osmotic stress induces changes in gibberellin metabolism, resulting in the stabilization of DELLAs, which are responsible for mitotic exit and earlier onset of endoreduplication. Consequently, this response is absent in mutants with altered gibberellin levels or DELLA activity. Mitotic exit and onset of endoreduplication do not correlate with an up-regulation of known cell cycle inhibitors but are the result of reduced levels of DP-E2F-LIKE1/E2Fe and UV-B-INSENSITIVE4, both inhibitors of the developmental transition from mitosis to endoreduplication by modulating anaphase-promoting complex/cyclosome activity, which are down-regulated rapidly after DELLA stabilization. This work fits into an emerging view of DELLAs as regulators of cell division by regulating the transition to endoreduplication and differentiation.