Seed dormancy and ABA metabolism in Arabidopsis and barley: the role of ABA 8'-hydroxylase

Mechanism of delayed seed germination caused by high temperature during grain filling in rice (Oryza sativa L.)

High temperature during grain filling considerably reduces yield and quality in rice (Oryza sativa L.); however, how high temperature affects seed germination of the next generation is not yet well understood. Here, we report that seeds from plants exposed to high temperature during the grain filling stage germinated significantly later than seeds from unstressed plants. This delay remained even after dormancy release treatments, suggesting that it was not due to primary seed dormancy determined during grain filling. In imbibed embryos of heat-stressed seeds, expression of abscisic acid (ABA) biosynthesis genes (OsNCEDs) was higher than in those of control seeds, whereas that of ABA catabolism genes (OsABA8′OHs) was lower. In the aleurone layer, despite no change in GA signaling as evidenced by no effect of heat stress on OsGAMYB gene expression, the transcripts of α-amylase genes OsAmy1C, OsAmy3B, and OsAmy3E were significantly down-regulated in heat-stressed seeds in comparison with controls. Changes in promoter methylation levels were consistent with transcriptional changes of ABA catabolism-related and α-amylase genes. These data suggest that high temperature during grain filling results in DNA methylation of ABA catabolism-related and α-amylase gene promoters, delaying germination of heat-stressed seeds.

Arabidopsis MADS-box factor AGL16 negatively regulates drought resistance via stomatal density and stomatal movement

Drought is one of the most important environmental factors limiting plant growth and productivity. The molecular mechanisms underlying plant drought resistance are complex and not yet fully understood. Here, we show that the Arabidopsis MADS-box transcription factor AGL16 acts as a negative regulator in drought resistance by regulating stomatal density and movement. Loss-of-AGL16 mutants were more resistant to drought stress and had higher relative water content, which was attributed to lower leaf stomatal density and more sensitive stomatal closure due to higher leaf ABA levels compared with the wild type. AGL16-overexpressing lines displayed the opposite phenotypes. AGL16 is preferentially expressed in guard cells and down-regulated in response to drought stress. The expression of CYP707A3 and AAO3 in ABA metabolism and SDD1 in stomatal development was altered in agl16 and overexpression lines, making them potential targets of AGL16. Using chromatin immunoprecipitation, transient transactivation, yeast one-hybrid, and electrophoretic mobility shift assays, we demonstrated that AGL16 was able to bind the CArG motifs in the promoters of the CYP707A3, AAO3, and SDD1 and regulate their transcription, leading to altered leaf stomatal density and ABA levels. Taking our findings together, AGL16 acts as a negative regulator of drought resistance by modulating leaf stomatal density and ABA accumulation.

Heterotrimeric G-proteins mediated hormonal responses in plants

Phytohormones not only orchestrate intrinsic developmental programs from germination to senescence but also regulate environmental inputs through complex signalling pathways. Despite building an own signalling network, hormones mutually contribute several signalling systems, which are also essential for plant growth and development, defense, and responses to abiotic stresses. One of such important signalling cascades is G-proteins, which act as critical regulators of a wide range of fundamental cellular processes by transducing receptor signals to the intracellular environment. G proteins are composed of α, β, and γ subunits, and the molecular switching between active and inactive conformation of Gα controls the signalling cycle. The active GTP bound Gα and freed Gβγ have both independent and tightly coordinated roles in the regulation of effector molecules, thereby modulating multiple responses, including hormonal responses. Therefore, an interplay of hormones with G-proteins fine-tunes multiple biological processes of plants; however, their molecular mechanisms are largely unknown. Functional characterization of hormone biosynthesis, perception, and signalling components, as well as identification of few effector molecules of G-proteins and their interaction networks, reduces the complexity of the hormonal signalling networks related to G-proteins. In this review, we highlight a valuable insight into the mechanisms of how the G-protein signalling cascades connect with hormonal responses to regulate increased developmental flexibility as well as remarkable plasticity of plants.

Chemical Manipulation of Abscisic Acid Signaling: A New Approach to Abiotic and Biotic Stress Management in Agriculture

The phytohormone abscisic acid (ABA) is the best-known stress signaling molecule in plants. ABA protects sessile land plants from biotic and abiotic stresses. The conserved pyrabactin resistance/pyrabactin resistance-like/regulatory component of ABA receptors (PYR/PYL/RCAR) perceives ABA and triggers a cascade of signaling events. A thorough knowledge of the sequential steps of ABA signaling will be necessary for the development of chemicals that control plant stress responses. The core components of the ABA signaling pathway have been identified with adequate characterization. The information available concerning ABA biosynthesis, transport, perception, and metabolism has enabled detailed functional studies on how the protective ability of ABA in plants might be modified to increase plant resistance to stress. Some of the significant contributions to chemical manipulation include ABA biosynthesis inhibitors, and ABA receptor agonists and antagonists. Chemical manipulation of key control points in ABA signaling is important for abiotic and biotic stress management in agriculture. However, a comprehensive review of the current knowledge of chemical manipulation of ABA signaling is lacking. Here, a thorough analysis of recent reports on small-molecule modulation of ABA signaling is provided. The challenges and prospects in the chemical manipulation of ABA signaling for the development of ABA-based agrochemicals are also discussed.

Transcription profiles reveal sugar and hormone signaling pathways mediating tree branch architecture in apple (Malus domestica Borkh.) grafted on different rootstocks

Apple trees grafted on different rootstock types, including vigorous rootstock (VR), dwarfing interstock (DIR), and dwarfing self-rootstock (DSR), are widely planted in production, but the molecular determinants of tree branch architecture growth regulation induced by rootstocks are still not well known. In this study, the branch growth phenotypes of three combinations of ‘Fuji’ apple trees grafted on different rootstocks (VR: Malus baccata; DIR: Malus baccata/T337; DSR: T337) were investigated. The VR trees presented the biggest branch architecture. The results showed that the sugar content, sugar metabolism-related enzyme activities, and hormone content all presented obvious differences in the tender leaves and buds of apple trees grafted on these rootstocks. Transcriptomic profiles of the tender leaves adjacent to the top buds allowed us to identify genes that were potentially involved in signaling pathways that mediate the regulatory mechanisms underlying growth differences. In total, 3610 differentially expressed genes (DEGs) were identified through pairwise comparisons. The screened data suggested that sugar metabolism-related genes and complex hormone regulatory networks involved the auxin (IAA), cytokinin (CK), abscisic acid (ABA) and gibberellic acid (GA) pathways, as well as several transcription factors, participated in the complicated growth induction process. Overall, this study provides a framework for analysis of the molecular mechanisms underlying differential tree branch growth of apple trees grafted on different rootstocks.

Production and roles of IAA and ABA during development of superior and inferior rice grains

Current understanding of the role of plant hormones during cereal grain filling is confounded by contradictory reports on hormone production that is based on poor methodology. We report here on the accurate measurement of indole-3-acetic acid (IAA) and abscisic acid (ABA) by combined liquid chromatography-tandem mass spectrometry in multiple reaction-monitoring mode with heavy isotope labelled internal standards. ABA and IAA contents of superior versus inferior rice grains (ABA maxima 159 ng g-1 FW and 109 ng g-1 FW, IAA maxima 2 µg g-1 FW and 1.7 µg g-1 FW respectively) correlated with the expression of biosynthetic genes and with grain fill. Results confirm that grain ABA is produced primarily by OsNCED2(5), but suggest that ABA import and metabolism also play important roles in ABA regulation. The IAA content of grains is primarily influenced by OsYUC9 and OsYUC11. However, the distinct expression profile of OsYUC12 suggests a specific role for IAA produced by this enzyme. Co-expression of OsYUC12 with OsIAA29 indicates their involvement in a common signalling pathway. Co-expression and cis-element analysis identified several aleurone-specific transcriptional regulators as well as glutelin as strong candidates for detailed investigation for direct regulation by the auxin-signalling pathway.

A Perspective on Secondary Seed Dormancy in Arabidopsis thaliana

Primary seed dormancy is the phenomenon whereby seeds newly shed by the mother plant are unable to germinate under otherwise favorable conditions for germination. Primary dormancy is released during dry seed storage (after-ripening), and the seeds acquire the capacity to germinate upon imbibition under favorable conditions, i.e., they become non-dormant. Primary dormancy can also be released from the seed by various treatments, for example, by cold imbibition (stratification). Non-dormant seeds can temporarily block their germination if exposed to unfavorable conditions upon seed imbibition until favorable conditions are available. Nevertheless, prolonged unfavorable conditions will re-induce dormancy, i.e., germination will be blocked upon exposure to favorable conditions. This phenomenon is referred to as secondary dormancy. Relative to primary dormancy, the mechanisms underlying secondary dormancy remain understudied in Arabidopsis thaliana and largely unknown. This is partly due to the experimental difficulty in observing secondary dormancy in the laboratory and the absence of established experimental protocols. Here, an overview is provided of the current knowledge on secondary dormancy focusing on A. thaliana, and a working model describing secondary dormancy is proposed, focusing on the interaction of primary and secondary dormancy.

An Updated Overview on the Regulation of Seed Germination

The ability of a seed to germinate and establish a plant at the right time of year is of vital importance from an ecological and economical point of view. Due to the fragility of these early growth stages, their swiftness and robustness will impact later developmental stages and crop yield. These traits are modulated by a continuous interaction between the genetic makeup of the plant and the environment from seed production to germination stages. In this review, we have summarized the established knowledge on the control of seed germination from a molecular and a genetic perspective. This serves as a “backbone” to integrate the latest developments in the field. These include the link of germination to events occurring in the mother plant influenced by the environment, the impact of changes in the chromatin landscape, the discovery of new players and new insights related to well-known master regulators. Finally, results from recent studies on hormone transport, signaling, and biophysical and mechanical tissue properties are underscoring the relevance of tissue-specific regulation and the interplay of signals in this crucial developmental process.

Evidence for the Involvement of Vernalization-related Genes in the Regulation of Cold-induced Ripening in 'D'Anjou' and 'Bartlett' Pear Fruit

European pear (Pyrus communis L.) cultivars require a genetically pre-determined duration of cold-temperature exposure to induce autocatalytic system 2 ethylene biosynthesis and subsequent fruit ripening. The physiological responses of pear to cold-temperature-induced ripening have been well characterized, but the molecular mechanisms underlying this phenomenon continue to be elucidated. This study employed previously established cold temperature conditioning treatments for ripening of two pear cultivars, 'D'Anjou' and 'Bartlett'. Using a time-course transcriptomics approach, global gene expression responses of each cultivar were assessed at four stages of developmental during the cold conditioning process. Differential expression, functional annotation, and gene ontology enrichment analyses were performed. Interestingly, evidence for the involvement of cold-induced, vernalization-related genes and repressors of endodormancy release was found. These genes have not previously been described to play a role in fruit during the ripening transition. The resulting data provide insight into cultivar-specific mechanisms of cold-induced transcriptional regulation of ripening in European pear, as well as a unique comparative analysis of the two cultivars with very different cold conditioning requirements.

ABA-Dependent and ABA-Independent Functions of RCAR5/PYL11 in Response to Cold Stress

Arabidopsis thaliana has 14 abscisic acid (ABA) receptors-PYR1/PYLs/RCARs-which have diverse and redundant functions in ABA signaling; however, the precise role of these ABA receptors remains to be elucidated. Here, we report the functional characterization of RCAR5/PYL11 in response to cold stress. Expression of RCAR5 gene in dry seeds and leaves was ABA-dependent and ABA-independent, respectively. Under cold stress conditions, seed germination was negatively affected by the level of RCAR5 expression, which was dependent on ABA and was regulated by HAB1, OST1, and ABI5-downstream components of RCAR5 in ABA signaling. Leaves of RCAR5-overexpressing plants showed enhanced stomatal closure-independent of ABA-and high expression levels of cold, dehydration, and/or ABA-responsive genes compared to those of wild-type; these traits conferred enhanced freezing tolerance. Our data suggest that RCAR5 functions in response to cold stress by delaying seed germination and inducing rapid stomatal closure via ABA-dependent and ABA-independent pathways, respectively.

The expression pattern of OsDim1 in rice and its proposed function

Development of plant tissues is dependent on numerous factors, including hormone activity, signaling, cell division, and elongation. In plants, Defective Entry into Mitosis 1 (Dim1) homologs are recognized as pivotal in leaf senescence and progress of normal growth, but their role in rice has not been functionally characterized. The findings presented in this paper suggest that OsDim1 is important in early seedling development, pollen tube elongation, and impacts rice yield components. The gene is expressed in the scutellum, endosperm, embryonic root, shoot, pollen grains and tubes, as well as in several organs of the rice flower. According to the present study findings, RNAi mediated knockdown of OsDim1 resulted in phytohormonal imbalance, reduced amylase activity, affected differentiation of embryonic root elongation zone tissues, suppressed embryonic root and shoot growth, and impaired pollen tube elongation. In contrast, overexpression of OsDim1 showed significant growth in embryonic roots and shoots, while it increased culm length, total number of tillers per plant, seed setting rate, and total number of grains per panicle compared to its wild type line. In summary, we propose OsDim1 plays an important role in seedling growth and pollen tube elongation, and has pleiotropic effects on reproductive tissues.

Control of rice pre-harvest sprouting by glutaredoxin-mediated abscisic acid signaling

Pre-harvest sprouting (PHS) is one of the major problems in cereal production worldwide, which causes significant losses of both yield and quality; however, the molecular mechanism underlying PHS remains largely unknown. Here, we identified a dominant PHS mutant phs9-D. The corresponding gene PHS9 encodes a higher plant unique CC-type glutaredoxin and is specifically expressed in the embryo at the late embryogenesis stage, implying that PHS9 plays some roles in the late stage of seed development. Yeast two-hybrid screening showed that PHS9 could interact with OsGAP, which is an interaction partner of the abscicic acid (ABA) receptor OsRCAR1. PHS9- or OsGAP overexpression plants showed reduced ABA sensitivity in seed germination, whereas PHS9 or OsGAP knock-out mutant plants showed increased ABA sensitivity in seed germination, suggesting that PHS9 and OsGAP acted as negative regulators in ABA signaling during seed germination. Interestingly, the germination of PHS9 and OsGAP overexpression or knock-out plant seeds was weakly promoted by H₂ O₂ , implying that PHS9 and OsGAP could affect reactive oxygen species (ROS) signaling during seed germination. These results indicate that PHS9 plays an important role in the regulation of rice PHS through the integration of ROS signaling and ABA signaling.

Comparative Phosphoproteomic Analysis Reveals a Decay of ABA Signaling in Barley Embryos during After-Ripening

Abscisic acid (ABA) is a phytohormone and a major determinant of seed dormancy in plants. Seed dormancy is gradually lost during dry storage, a process known as 'after-ripening', and this dormancy decay is related to a decline in ABA content and sensitivity in seeds after imbibition. In this study, we aimed at investigating the effect of after-ripening on ABA signaling in barley, our cereal model species. Phosphosignaling networks in barley grains were investigated by a large-scale analysis of phosphopeptides to examine potential changes in response pathways to after-ripening. We used freshly harvested (FH) and after-ripened (AR) barley grains which showed different ABA sensitivity. A total of 1,730 phosphopeptides were identified in barley embryos isolated from half-cut grains. A comparative analysis showed that 329 and 235 phosphopeptides were upregulated or downregulated, respectively after ABA treatment, and phosphopeptides profiles were quite different between FH and AR embryos. These results were supported by peptide motif analysis which suggested that different sets of protein kinases are active in FH and AR grains. Furthermore, in vitro phosphorylation assays confirmed that some phosphopeptides were phosphorylated by SnRK2s, which are major protein kinases involved in ABA signaling. Taken together, our results revealed very distinctive phosphosignaling networks in FH and AR embryos of barley, and suggested that the after-ripening of barley grains is associated with differential regulation of phosphosignaling pathways leading to a decay of ABA signaling.

Inhibitors of Brassinosteroid Biosynthesis and Signal Transduction

Chemical inhibitors are invaluable tools for investigating protein function in reverse genetic approaches. Their application bears many advantages over mutant generation and characterization. Inhibitors can overcome functional redundancy, their application is not limited to species for which tools of molecular genetics are available and they can be applied to specific tissues or developmental stages, making them highly convenient for addressing biological questions. The use of inhibitors has helped to elucidate hormone biosynthesis and signaling pathways and here we review compounds that were developed for the plant hormones brassinosteroids (BRs). BRs are steroids that have strong growth-promoting capacities, are crucial for all stages of plant development and participate in adaptive growth processes and stress response reactions. In the last two decades, impressive progress has been made in BR inhibitor development and application, which has been instrumental for studying BR modes of activity and identifying and characterizing key players. Both, inhibitors that target biosynthesis, such as brassinazole, and inhibitors that target signaling, such as bikinin, exist and in a comprehensive overview we summarize knowledge and methodology that enabled their design and key findings of their use. In addition, the potential of BR inhibitors for commercial application in plant production is discussed.

CYP707As are effectors of karrikin and strigolactone signalling pathways in Arabidopsis thaliana and parasitic plants

Karrikins stimulate Arabidopsis thaliana germination, whereas parasitic weeds of the Orobanchaceae family have evolved to respond to host-exuded compounds such as strigolactones, dehydrocostus lactone, and 2-phenylethyl isothiocyanate. In Phelipanche ramosa, strigolactone-induced germination was shown to require one of the CYP707A proteins involved in abscisic acid catabolism. Here, germination and gene expression were analysed to investigate the role of CYP707As in germination of both parasitic plants and Arabidopsis upon perception of germination stimulants, after using pharmacological inhibitors and Arabidopsis mutants disrupting germination signals. CYP707A genes were up-regulated upon treatment with effective germination stimulants in both parasitic plants and Arabidopsis. Obligate parasitic plants exhibited both intensified up-regulation of CYP707A genes and increased sensitivity to the CYP707A inhibitor abscinazole-E2B, whereas Arabidopsis cyp707a mutants still positively responded to germination stimulation. In Arabidopsis, CYP707A regulation required the canonical karrikin signalling pathway KAI2/MAX2/SMAX1 and the transcription factor WRKY33. Finally, CYP707As and WRKY33 also modulated Arabidopsis root architecture in response to the synthetic strigolactone rac-GR24, and wrky33-1 exhibited a shoot hyperbranched phenotype. This study suggests that the lack of host-independent germination in obligate parasites is associated with an exacerbated CYP707A induction and that CYP707As and WRKY33 are new players involved in a variety of strigolactone/karrikin responses.

Transcriptome Analysis of Low-Temperature-Induced Breaking of Garlic Aerial Bulb Dormancy

The long history of asexual reproduction of garlic using garlic cloves has resulted in virus accumulation and genetic depression. Propagation of garlic seedlings by tissue culture can both eliminate viruses and improve breeding efficiency. Aerial bulbs are the first-choice materials for breeding virus-free garlic seedlings under external conditions, but they show dormancy just like garlic bulbs. However, low temperatures can quickly break dormancy. In this research, we used a high-throughput sequencing method to sequence aerial bulbs during dormancy and after low-temperature-induced breaking of dormancy to screen out the key differentially expressed genes (DEGs) associated with low temperature and to provide a theoretical basis for exploring the molecular mechanism of low-temperature-induced breaking of aerial bulb dormancy. The high-throughput transcriptome sequencing results showed that 6,675 DEGs were upregulated and 36,596 DEGs were downregulated in the aerial bulbs given low-temperature treatment. Then, 19,507 DEGs were assigned KEGG annotations, among which most DEGs were annotated to the metabolism pathway (11,817 genes, accounting for 60.58%), followed by the genetic information processing pathway (4,521 genes, accounting for 23.18%). The DEGs were mostly concentrated in pathways such as protein processing in the endoplasmic reticulum, plant-pathogen interaction, plant hormone signal transduction, and ribosome biogenesis in eukaryotes, with significant enrichment. The key DEGs related to calcium signaling, hormonal signaling, and transcription factors were screened out, including CaM, CDPK, and CML in accessory pathways of calcium signaling; GA20ox, GAI1, and GA2ox in accessory pathways of hormonal signaling; and transcription factor genes such as MYB, AP2/ERF, bHLH, MADS, and bZIP. qRT-PCR verification results were consistent with the sequencing results, indicating that the transcriptome sequencing data were accurate and reliable. Our results provide a theoretical basis for breaking the dormancy of aerial bulbs with low-temperature treatment to produce virus-free seedlings and increase the output and quality of garlic.

The interplay of PsABAUGT1 with other abscisic acid metabolic genes in the regulation of ABA homeostasis during the development of pea seeds and germination in the presence of H2O2

Inactivation of abscisic acid (ABA) in vitro may be catalyzed either by ABA 8'-hydroxylase (ABA8'OH) or by ABA uridine diphosphate glucosyltransferase (ABAUGT), which conjugates ABA with glucose. However, the involvement of these enzymes in the control of ABA content in vivo, especially ABAUGT, has not been fully elucidated. In pea seeds, both PsABAUGT1 and PsABA8'OH1 contribute to the reduction of ABA content during seed maturation and imbibition; however, during the first hours of imbibition, a high expression of only PsABAUGT1 was observed. Imbibition of seeds with H2O2 increased the ABA content despite the oxygen availability and altered the expression of metabolic genes. The expression of the biosynthetic gene 9-cis-epoxycarotene dioxygenase (PsNCED2) was increased, while that of PsABAUGT1 was decreased in each H2O2 experiment despite O2 availability. Under hypoxia, only seeds imbibed with H2O2 germinated, while under nonlimiting oxygen conditions, the germination rate was not altered by H2O2. Under hypoxia, the germination rate of H2O2-imbibed seeds seemed to not depend on the absolute ABA content and rather on the balance between ABA and gibberellins (GA), as H2O2 increased the expression of GA synthesis genes. Overexpression of PsABAUGT1 in Arabidopsis decreases seed ABA content, accelerates germination and reduces seed sensitivity to exogenously applied ABA, confirming the ability of PsABAUGT1 to inactivate ABA. Thus, PsABAUGT1 is a new player in the regulation of ABA content in maturating and imbibed pea seeds, both under standard conditions and in response to H2O2.

Coumarin-Induced Delay of Rice Seed Germination Is Mediated by Suppression of Abscisic Acid Catabolism and Reactive Oxygen Species Production

Abscisic acid (ABA) is a crucial phytohormone for the regulation of seed germination. The ABA content of seeds is regulated by synthesis and catabolic pathways. Coumarin, an important plant allelochemical, can inhibit seed germination effectively, although whether it is involved in the regulation of ABA content during seed germination has not been elucidated. For the study reported herein, we show that coumarin effectively inhibits rice seed germination and vivipary. We found that the ABA content gradually decreased in water-imbibed rice seeds and that the content and activity of the Oryza sativa 9-cis epoxycarotenoid dioxygenases (OsNCEDs), which are ABA synthases, decreased during seed germination. At the transcription level, the expression of OsNCED1-3 appeared to decrease, whereas the expression of the ABA 8'-hydroxylase 2 and 3 genes (OsABA8'ox2/3) first appeared to increase and then decrease. Samples of rice seeds were also imbibed in water containing coumarin, which increased their ABA content but did not significantly increase the activity or content of their OsNCEDs or OsNCED1-3 transcription. Interestingly, coumarin imbibition remarkably reduced OsABA8'ox2/3 expression in rice embryos, which partially explained how coumarin increased the ABA content of germinating rice embryos. Coumarin also inhibited the accumulation of reactive oxygen species (ROS) in rice embryos and increased the activity of superoxide dismutase and catalase, which are indispensable for seed germination. These results indicate that coumarin delays seed germination by inhibiting ABA catabolism, particularly by decreasing the expression of OsABA8'ox2/3 rather than by increasing ABA synthesis. Moreover, coumarin increases the ABA content while decreasing the ROS content in rice embryos. Our results enhance our understanding of the regulation of ABA and ROS during seed germination and provide theoretical support for application of coumarin to prevent sprouting before crop harvesting.

Pollen Developmental Arrest: Maintaining Pollen Fertility in a World With a Changing Climate

During evolution of land plants, the haploid gametophytic stage has been strongly reduced in size and the diploid sporophytic phase has become the dominant growth form. Both male and female gametophytes are parasitic to the sporophyte and reside in separate parts of the flower located either on the same plant or on different plants. For fertilization to occur, bi-cellular or tri-cellular male gametophytes (pollen grains) have to travel to the immobile female gametophyte in the ovary. To survive exposure to a hostile atmosphere, pollen grains are thought to enter a state of complete or partial developmental arrest (DA). DA in pollen is strongly associated with acquisition of desiccation tolerance (DT) to extend pollen viability during air travel, but occurrence of DA in pollen is both species-dependent and at the same time strongly dependent on the reigning environmental conditions at the time of dispersal. Several environmental stresses (heat, drought, cold, humidity) are known to affect pollen production and viability. Climate change is also posing a serious threat to plant reproductive behavior and crop productivity. It is therefore timely to gain a better understanding of how DA and pollen viability are controlled in plants and how pollen viability can be protected to secure crop yields in a changing environment. Here, we provide an overview of how DA and pollen viability are controlled and how the environment affects them. We make emphasis on what is known and areas where a deeper understanding is needed.

Seed germination and dormancy: The classic story, new puzzles, and evolution

This review highlights recent progresses in seed germination and dormancy research. Research on the weakening of the endosperm during germination, which is almost a classic theme in seed biology, was resumed by α-xylosidase studies. Strong genetic evidence was presented to suggest that the quality control of xyloglucan biosynthesis in the endosperm (and the embryo) plays a critical role in germination. Further analyses on the endosperm and the adjacent layers have suggested that the cutin coat in the endosperm-testa interphase negatively affects germination while the endosperm-embryo interphase produces a sheath that facilitates germination. These progresses significantly advanced our understanding of seed germination mechanisms. A breakthrough in dormancy research, on the other hand, revealed the unique abscisic acid signaling pathway that is regulated by DELAY OF GERMINATION1 (DOG1). The detailed analysis of DOG1 expression uncovered the intriguing story of reciprocal regulation of the sense-antisense pair, which generated new questions. Recent studies also suggested that the DOG1 function is not limited to dormancy but extended through general seed maturation, which provokes questions about the evolution of DOG1 family proteins. Seed biology is becoming more exciting with the classic stories being revitalized and new puzzles emerging from the frontier.

Re-localization of hormone effectors is associated with dormancy alleviation by temperature and after-ripening in sunflower seeds

Temperature is the primary factor that affects seed dormancy and germination. However, the molecular mechanism that underlies its effect on dormancy alleviation remained largely unknown. In this study, we investigate hormone involvement in temperature induced germination as compared to that caused by after-ripening. Dormant (D) sunflower seeds cannot germinate at 10 °C but fully germinate at 20 °C. After-ripened seeds become non-dormant (ND), i.e. able to germinate at 10 °C. Pharmacological experiments showed the importance of abscisic acid (ABA), gibberellins (GAs) and ethylene in temperature- and after-ripening-induced germination of sunflower seeds. Hormone quantification showed that after-ripening is mediated by a decline in both ABA content and sensitivity while ABA content is increased in D seeds treated at 10 or 20 °C, suggesting that ABA decrease is not a prerequisite for temperature induced dormancy alleviation. GAs and ethylene contents were in accordance with germination potential of the three conditions (GA₁ was higher in D 20 °C and ND 10 °C than in D 10 °C). Transcripts analysis showed that the major change concerns ABA and GAs metabolism genes, while ABA signalling gene expression was significantly unchanged. Moreover, another level of hormonal regulation at the subcellular localization has been revealed by immunocytolocalization study. Indeed, ABA, protein Abscisic acid-Insensitive 5 (ABI5), involved in ABA-regulated gene expression and DELLA protein RGL2, a repressor of the gibberellins signalling pathway, localized mainly in the nucleus in non-germinating seeds while they localized in the cytosol in germinating seeds. Furthermore, ACC-oxidase (ACO) protein, the key ethylene biosynthesis enzyme, was detected in the meristem only in germinating seeds. Our results reveal the importance of hormone actors trafficking in the cell and their regulation in specialized tissue such as the meristem in dormancy alleviation and germination.

Comparative Phosphoproteomic Analysis of Barley Embryos with Different Dormancy during Imbibition

Dormancy is the mechanism that allows seeds to become temporally quiescent in order to select the right time and place to germinate. Like in other species, in barley, grain dormancy is gradually reduced during after-ripening. Phosphosignaling networks in barley grains were investigated by a large-scale analysis of phosphoproteins to examine potential changes in response pathways to after-ripening. We used freshly harvested (FH) and after-ripened (AR) barley grains which showed different dormancy levels. The LC-MS/MS analysis identified 2346 phosphopeptides in barley embryos, with 269 and 97 of them being up- or downregulated during imbibition, respectively. A number of phosphopeptides were differentially regulated between FH and AR samples, suggesting that phosphoproteomic profiles were quite different between FH and AR grains. Motif analysis suggested multiple protein kinases including SnRK2 and MAPK could be involved in such a difference between FH and AR samples. Taken together, our results revealed phosphosignaling pathways in barley grains during the water imbibition process.

Interlinked regulatory loops of ABA catabolism and biosynthesis coordinate fruit growth and ripening in woodland strawberry

Fruit growth and ripening are controlled by multiple phytohormones. How these hormones coordinate and interact with each other to control these processes at the molecular level is unclear. We found in the early stages of Fragaria vesca (woodland strawberry) fruit development, auxin increases both widths and lengths of fruits, while gibberellin [gibberellic acid (GA)] mainly promotes their longitudinal elongation. Auxin promoted GA biosynthesis and signaling by activating GA biosynthetic and signaling genes, suggesting auxin function is partially dependent on GA function. To prevent the repressive effect of abscisic acid (ABA) on fruit growth, auxin and GA suppressed ABA accumulation during early fruit development by activating the expression of FveCYP707A4a encoding cytochrome P450 monooxygenase that catalyzes ABA catabolism. At the onset of fruit ripening, both auxin and GA levels decreased, leading to a steep increase in the endogenous level of ABA that drives fruit ripening. ABA repressed the expression of FveCYP707A4a but promoted that of FveNCED, a rate-limiting step in ABA biosynthesis. Accordingly, altering FveCYP707A4a expression changed the endogenous ABA levels and affected FveNCED expression. Hence, ABA catabolism and biosynthesis are tightly linked by feedback and feedforward loops to limit ABA contents for fruit growth and to quickly increase ABA contents for the onset of fruit ripening. These results indicate that FveCYP707A4a not only regulates ABA accumulation but also provides a hub to coordinate fruit size and ripening times by relaying auxin, GA, and ABA signals.

PHYTOCHROME INTERACTING FACTOR1 interactions leading to the completion or prolongation of seed germination

In Arabidopsis thaliana, the basic Helix Loop Helix transcription factor, PHYTOCHROME INTERACTING FACTOR1 (PIF1) is known to orchestrate the seed transcriptome such that, ultimately, proteins repressing the completion of germination are produced in darkness. While PIF1-mediated control of abscisic acid (ABA) and gibberellic acid (GA) anabolism/catabolism is indirect, PIF1 action favors ABA while discriminating against GA, firmly establishing ABA's repressive influence on the completion of germination. The result is tissue that is more sensitive to and producing more ABA; and is less responsive to and deficient in GA. Illumination of the appropriate wavelength activates phytochrome which enters the nucleus, and binds to PIF1, initiating PIF1's phosphorylation by diverse kinases, subsequent polyubiquitination, and hydrolysis. One mechanism by which phosphorylated PIF1 is eliminated from the cells of the seed upon illumination involves an F-BOX protein, COLD TEMPERATURE GERMINATING10 (CTG10). Discovered in an unbiased screen of activation tagged lines hastening the completion of seed germination at 10°C, one indirect consequence of CTG10 action in reducing PIF1 titer, should be to enhance the transcription of genes whose products work to increase bioactive GA titer, shifting the intracellular milieu from one that is repressive to, toward one conducive to, the completion of seed germination. We have tested this hypothesis using a variety of Arabidopsis lines altered in CTG10 amounts. Here we demonstrate using bimolecular fluorescence complementation that PIF1 interacts with CTG10 and show that, in light exposed seeds, PIF1 is more persistent in ctg10 relative to WT seeds while it is less stable in seeds over-expressing CTG10. These results are congruent with the relative transcript abundance from three genes whose products are involved in bioactive GA accumulation. We put forth a model of how PIF1 interactions in imbibed seeds change during germination and how a permissive light signal influences these changes, leading to the completion of germination of these positively photoblastic propagules.

Abscisic acid catabolism enhances dormancy release of grapevine buds

The molecular mechanism regulating dormancy release in grapevine buds is as yet unclear. It was formerly proposed that dormancy is maintained by abscisic acid (ABA)-mediated repression of bud-meristem activity and that removal of this repression triggers dormancy release. It was also proposed that such removal of repression may be achieved via natural or artificial up-regulation of VvA8H-CYP707A4, which encodes ABA 8'-hydroxylase, and is the most highly expressed paralog in grapevine buds. The current study further examines these assumptions, and its experiments reveal that (a) hypoxia and ethylene, stimuli of bud dormancy release, enhance expression of VvA8H-CYP707A4 within grape buds, (b) the VvA8H-CYP707A4 protein accumulates during the natural transition to the dormancy release stage, and (c) transgenic vines overexpressing VvA8H-CYP707A4 exhibit increased ABA catabolism and significant enhancement of bud break in controlled and natural environments and longer basal summer laterals. The results suggest that VvA8H-CYP707A4 functions as an ABA degrading enzyme, and are consistent with a model in which the VvA8H-CYP707A4 level in the bud is up-regulated by natural and artificial bud break stimuli, which leads to increased ABA degradation capacity, removal of endogenous ABA-mediated repression, and enhanced regrowth. Interestingly, it also hints at sharing of regulatory steps between latent and lateral bud outgrowth.

Arabidopsis MATE45 antagonizes local abscisic acid signaling to mediate development and abiotic stress responses

Anthocyanins provide ideal visual markers for the identification of mutations that disrupt molecular responses to abiotic stress. We screened Arabidopsis mutants of ABC (ATP-Binding Cassette) and MATE (Multidrug And Toxic compound Extrusion) transporter genes under nutritional stress and identified four genes (ABCG25,ABCG9,ABCG5, and MATE45) required for normal anthocyanin pigmentation. ABCG25 was previously demonstrated to encode a vascular-localized cellular exporter of abscisic acid (ABA). Our results show that MATE45 encodes an aerial meristem- and a vascular-localized transporter associated with the trans-Golgi, and that it plays an important role in controlling the levels and distribution of ABA in growing aerial meristems and non-meristematic tissues. MATE45 promoter-GUS reporter fusions revealed the activity localized to the leaf and influorescence meristems and the vasculature. Loss-of-function mate45 mutants exhibited accelerated rates of aerial organ initiation suggesting at least partial functional conservation with the maize ortholog bige1. The aba2-1 mutant, which is deficient in ABA biosynthesis, exhibited a number of phenotypes that were rescued in the mate45-1 aba2-1 double mutant. mate45 exhibited enhanced the seed dormancy, and germination was hypersensitive to ABA. Enhanced frequency of leaf primordia growth in mate45 seedlings grown in nutrient imbalance stress was ABA-dependent. The ABA signaling reporter construct pRD29B::GUS revealed elevated levels of ABA signaling in the true leaf primordia of mate45 seedlings grown under nutritional stress, and gradually reduced signaling in surrounding cotyledon and hypocotyl tissues concomitant with reduced expressions of ABCG25. Our results suggest a role of MATE45 in reducing meristematic ABA and in maintaining ABA distribution in adjacent non-meristematic tissues.

Differential influence of molybdenum and tungsten on the growth of barley seedlings and the activity of aldehyde oxidase under salinity

The influence of molybdenum, tungsten on germination and growth of barley Hordeum vulgare L. was studied. Results of this study revealed the differential effect of heavy metals on seedlings growth. Exogenous molybdenum treatment stimulated the growth of seedlings. The addition of the metal significantly stimulated root elongation. Contrastingly, the addition of tungsten resulted in increased seed germination and inhibits the growth of seedlings. The negative effect of tungsten on the growth of barley was more profound for roots of plants. In addition, the influence of metals on the growth of plants was also tested in saline conditions. It is shown that under salinity stress plant growth drastically decreased in presence of tungsten. Results of this study showed that activity of molybdenum-containing aldehyde oxidase (AO; EC 1.2.3.1) was also significantly affected by metals. The activity of AO in leaves and roots enhanced with increasing concentrations of molybdate, while tungstate treatment inhibited the enzyme activity. Perhaps, the differential influence of molybdenum and tungsten on the growth of barley is a direct effect of metals on aldehyde oxidase activity in plants. Moreover, the intense negative effect of tungsten treatment on barley growth under salinity conditions emphasizes an important role of aldehyde oxidase in plant resistance to stress factors.

Endosperm sugar accumulation caused by mutation of PHS8/ISA1 leads to pre-harvest sprouting in rice

Pre-harvest sprouting (PHS) is an unfavorable trait in cereal crops that could seriously decrease grain yield and quality. Although some PHS-associated quantitative trait loci or genes in cereals have been reported, the molecular mechanism underlying PHS remains largely elusive. Here, we characterized a rice mutant, phs8, which exhibits PHS phenotype accompanied by sugary endosperm. Map-based cloning revealed that PHS8 encodes a starch debranching enzyme named isoamylase1. Mutation in PHS8 resulted in the phytoglycogen breakdown and sugar accumulation in the endosperm. Intriguingly, with increase of sugar contents, decreased expression of OsABI3 and OsABI5 as well as reduced sensitivity to abscisic acid (ABA) were found in the phs8 mutant. Using rice suspension cell system, we confirmed that exogenous sugar is sufficient to suppress the expression of both OsABI3 and OsABI5. Furthermore, overexpression of OsABI3 or OsABI5 could partially rescue the PHS phenotype of phs8. Therefore, our study presents important evidence supporting that endosperm sugar not only acts as an essential energy source for seed germination but also determines seed dormancy and germination by affecting ABA signaling.

The varied ability of grains to synthesize and catabolize ABA is one of the factors affecting dormancy and its release by after-ripening in imbibed triticale grains of cultivars with different pre-harvest sprouting susceptibilities

Abscisic acid (ABA) is a phytohormone involved in the acquisition of primary dormancy during seeds maturation as well as dormancy maintenance in imbibed seeds. After imbibition, the ABA content decreased to a much lower level in embryos of freshly harvested triticale grains of the Leontino cultivar, which is more susceptible to pre-harvest sprouting (PHS) than embryos of the Fredro cultivar. Lower ABA content in the Leontino cultivar resulted from increased expression of TsABA8'OH1 and TsABA8'OH2, which encode ABA 8'-hydroxylase and are involved in ABA catabolism. Higher ABA content and maintenance of dormancy in Fredro grains were correlated with intensified ABA biosynthesis, which resulted from higher expression of TsNCED1, which encodes 9-cis-epoxycarotenoid dioxygenase. These results suggest that grains of triticale cultivars with different resistance to PHS vary in their ability to metabolize ABA after imbibition. After-ripening did not affect the ABA content in embryos of dry grains of either triticale cultivar. However, after-ripening caused dormancy release in Fredro grains and significantly affected the ABA content and the rate of its metabolism after imbibition. A more rapid decline in ABA content in imbibed Fredro grains was accompanied by decreased transcript levels of TsNCED1 as well as increased expression of TsABA8'OH1 and TsABA8'OH2. Thus, after-ripening may affect dormancy of grains through reduction of the ABA biosynthesis rate and intensified ABA catabolism. Overexpression of TsNCED1 in tobacco increases ABA content and delays germination, while overexpression of TsABA8'OH2 decreases ABA content, accelerates germination, and reduces the sensitivity to ABA of transgenic seeds compared to seeds of wild-type plants. Therefore, these genes might play an important role in the regulation of triticale grain dormancy, thus affecting susceptibility to PHS.

Overexpression of Tobacco GCN2 Stimulates Multiple Physiological Changes Associated With Stress Tolerance

General control non-derepressible-2 (GCN2) is a ubiquitous protein kinase that phosphorylates the α subunit of the eukaryotic initiation factor, eIF2, preventing the initiation of a new cycle of protein synthesis, subsequently reducing the global protein biosynthesis. GCN2 can also regulate the response of plants to biotic and abiotic stresses. In this study, two GCN2 homologs, NtGCN2-1 and NtGCN2-2, were cloned from Nicotiana tabacum, and were predicted to have been derived from their progenitors in N. tomentosiformis and N. sylvestris, respectively. The phosphorylation of NteIF2α could be activated by promoting the expression of NtGCN2 with plant hormones, including salicylic acid (SA), azelaic acid (AZA), methyl jasmonate (MeJA), and by imposition of different stresses (Bemisia tabaci infection, drought, and cold), indicating that NtGCN2 is involved in the response of plants to multiple biotic and abiotic stresses. We also observed that the overexpression of NtGCN2-1 significantly influenced different physiological processes. It promoted seed germination and root elongation. The content of total soluble sugars and reducing sugars were decreased, whereas those of chlorophyll a and b were increased in the GCN2 overexpressing plants. In addition, the overexpressing plants had lower content of reactive oxygen species and exhibited higher antioxidant activities. These physiological alterations could be attributed to the changes in the endogenous phytohormones, decrease in the SA and abscisic acid content, and accumulation of MeJA and AZA. It indicated that the overexpression of NtGCN2 in tobacco, stimulated the plant defense responses via phosphorylation of NteIF2α and regulation of plant hormones, and changes in the antioxidant ability and plant nutrient status.

Assay for abscisic acid 8'-hydroxylase activity of cloned plant cytochrome P450 oxidases in Saccharomyces cerevisiae

The plant hormone abscisic acid (ABA) regulates many processes, including response to drought, seed dormancy and abscission of leaves and fruits. For maintenance of ABA homeostasis, catabolism of ABA by 8'-hydroxylation and subsequent cyclisation to phaseic acid (PA) is crucial. However, detection of ABA 8'-hydroxylation activity is tedious. We present a simple and rapid method for detection of ABA 8'-hydroxylase activity by cloning cDNAs of interest and expressing the respective protein in yeast. Upon addition of ABA, PA is formed and subsequently quantified in the yeast cell culture supernatant by heart cutting 2D-HPLC or GC-MS.

Spatiotemporal modulation of abscisic acid and gibberellin metabolism and signalling mediates the effects of suboptimal and supraoptimal temperatures on seed germination in wheat (Triticum aestivum L.)

Seed germination is a complex process regulated by intrinsic hormonal cues such as abscisic acid (ABA) and gibberellin (GA), and environmental signals including temperature. Using pharmacological, molecular and metabolomics approaches, we show that supraoptimal temperature delays wheat seed germination through maintaining elevated embryonic ABA level via increased expression of ABA biosynthetic genes (TaNCED1 and TaNCED2), increasing embryo ABA sensitivity through upregulation of genes regulating ABA signalling positively (TaPYL5, TaSnRK2, ABI3 and ABI5) and decreasing embryo GA sensitivity via induction of TaRHT1 that regulates GA signalling negatively. Endospermic ABA and GA appeared to have minimal roles in regulating germination at supraoptimal temperature. Germination inhibition by suboptimal temperature is associated with elevated ABA level in the embryo and endosperm tissues, mediated by induction of TaNCEDs and decreased expression of endospermic ABA catabolic genes (TaCYP707As), and increased ABA sensitivity in both tissues via upregulation of TaPYL5, TaSnRK2, ABI3 and ABI5 in the embryo and TaSnRK2 and ABI5 in the endosperm. Furthermore, suboptimal temperature suppresses GA synthesis in both tissues and GA sensitivity in the embryo via repressing GA biosynthetic genes (TaGA20ox and TaGA3ox2) and inducing TaRHT1, respectively. These results highlight that spatiotemporal modulation of ABA and GA metabolism and signalling in wheat seeds underlies germination response to temperature.

Proanthocyanidins in seed coat tegmen and endospermic cap inhibit seed germination in Sapium sebiferum

Sapium sebiferum, an ornamental and bio-energetic plant, is propagated by seed. Its seed coat contains germination inhibitors and takes a long time to stratify for germination. In this study, we discovered that the S. sebiferum seed coat (especially the tegmen) and endospermic cap (ESC) contained high levels of proanthocyanidins (PAs). Seed coat and ESC removal induced seed germination, whereas exogenous application with seed coat extract (SCE) or PAs significantly inhibited this process, suggesting that PAs in the seed coat played a major role in regulating seed germination in S. sebiferum. We further investigated how SCE affected the expression of the seed-germination-related genes. The results showed that treatment with SCE upregulated the transcription level of the dormancy-related gene, gibberellins (GAs) suppressing genes, abscisic acid (ABA) biosynthesis and signalling genes. SCE decreased the transcript levels of ABA catabolic genes, GAs biosynthesis genes, reactive oxygen species genes and nitrates-signalling genes. Exogenous application of nordihydroguaiaretic acid, gibberellic acid, hydrogen peroxide and potassium nitrate recovered seed germination in seed-coat-extract supplemented medium. In this study, we highlighted the role of PAs, and their interactions with the other germination regulators, in the regulation of seed dormancy in S. sebiferum.

Seed Dormancy Involves a Transcriptional Program That Supports Early Plastid Functionality during Imbibition

Red rice fully dormant seeds do not germinate even under favorable germination conditions. In several species, including rice, seed dormancy can be removed by dry-afterripening (warm storage); thus, dormant and non-dormant seeds can be compared for the same genotype. A weedy (red) rice genotype with strong dormancy was used for mRNA expression profiling, by RNA-Seq, of dormant and non-dormant dehulled caryopses (here addressed as seeds) at two temperatures (30 °C and 10 °C) and two durations of incubation in water (8 h and 8 days). Aim of the study was to highlight the differences in the transcriptome of dormant and non-dormant imbibed seeds. Transcript data suggested important differences between these seeds (at least, as inferred by expression-based metabolism reconstruction): dry-afterripening seems to impose a respiratory impairment onto non-dormant seeds, thus glycolysis is deduced to be preferentially directed to alcoholic fermentation in non-dormant seeds but to alanine production in dormant ones; phosphoenolpyruvate carboxykinase, pyruvate phosphate dikinase and alanine aminotransferase pathways appear to have an important gluconeogenetic role associated with the restoration of plastid functions in the dormant seed following imbibition; correspondingly, co-expression analysis pointed out a commitment to guarantee plastid functionality in dormant seeds. At 8 h of imbibition, as inferred by gene expression, dormant seeds appear to preferentially use carbon and nitrogen resources for biosynthetic processes in the plastid, including starch and proanthocyanidins accumulation. Chromatin modification appears to be a possible mechanism involved in the transition from dormancy to germination. Non-dormant seeds show higher expression of genes related to cell wall modification, suggesting they prepare for acrospire/radicle elongation.

Molecular Mechanisms Underlying Abscisic Acid/Gibberellin Balance in the Control of Seed Dormancy and Germination in Cereals

Seed dormancy is an adaptive trait that does not allow the germination of an intact viable seed under favorable environmental conditions. Non-dormant seeds or seeds with low level of dormancy can germinate readily under optimal environmental conditions, and such a trait leads to preharvest sprouting, germination of seeds on the mother plant prior to harvest, which significantly reduces the yield and quality of cereal crops. High level of dormancy, on the other hand, may lead to non-uniform germination and seedling establishment. Therefore, intermediate dormancy is considered to be a desirable trait as it prevents the problems of sprouting and allows uniformity of postharvest germination of seeds. Induction, maintenance, and release of seed dormancy are complex physiological processes that are influenced by a wide range of endogenous and environmental factors. Plant hormones, mainly abscisic acid (ABA) and gibberellin (GA), are the major endogenous factors that act antagonistically in the control of seed dormancy and germination; ABA positively regulates the induction and maintenance of dormancy, while GA enhances germination. Significant progress has been made in recent years in the elucidation of molecular mechanisms regulating ABA/GA balance and thereby dormancy and germination in cereal seeds, and this review summarizes the current state of knowledge on the topic.

Screening and identification of key genes regulating fall dormancy in alfalfa leaves

Fall dormancy (FD) determines the adaptation of an alfalfa variety and affects alfalfa production and quality. However, the molecular mechanism underlying FD remains poorly understood. Here, 44 genes regulating FD were identified by comparison of the transcriptomes from leaves of Maverick (fall-dormant alfalfa) and CUF101(non-fall-dormant), during FD and non-FD and were classified them depending on their function. The transcription of IAA-amino acid hydrolase ILR1-like 1, abscisic acid receptor PYL8, and monogalactosyldiacylglycerol synthase-3 in Maverick leaves was regulated by daylength and temperature, and the transcription of the abscisic acid receptor PYL8 was mainly affected by daylength. The changes in the expression of these genes and the abundance of their messenger RNA (mRNA) in Maverick leaves differed from those in CUF101 leaves, as evidenced by the correlation analysis of their mRNA abundance profiles obtained from April to October. The present findings suggested that these genes are involved in regulating FD in alfalfa.

Antisense transcription represses Arabidopsis seed dormancy QTL DOG1 to regulate drought tolerance

Plants have developed multiple strategies to sense the external environment and to adapt growth accordingly. Delay of germination 1 (DOG1) is a major quantitative trait locus (QTL) for seed dormancy strength in Arabidopsis thaliana that is reported to be expressed exclusively in seeds. DOG1 is extensively regulated, with an antisense transcript (asDOG1) suppressing its expression in seeds. Here, we show that asDOG1 shows high levels in mature plants where it suppresses DOG1 expression under standard growth conditions. Suppression is released by shutting down antisense transcription, which is induced by the plant hormone abscisic acid (ABA) and drought. Loss of asDOG1 results in constitutive high-level DOG1 expression, conferring increased drought tolerance, while inactivation of DOG1 causes enhanced drought sensitivity. The unexpected role of DOG1 in environmental adaptation of mature plants is separate from its function in seed dormancy regulation. The requirement of asDOG1 to respond to ABA and drought demonstrates that antisense transcription is important for sensing and responding to environmental changes in plants.

microRNAs participate in gene expression regulation and phytohormone cross-talk in barley embryo during seed development and germination

BACKGROUND

Small RNA and degradome sequencing have identified a large number of miRNA-target pairs in plant seeds. However, detailed spatial and temporal studies of miRNA-mediated regulation, which can reflect links between seed development and germination are still lacking.

RESULTS

In this study, we extended our investigation on miRNAs-involved gene regulation by a combined analysis of seed maturation and germination in barley. Through bioinformatics analysis of small RNA sequencing data, a total of 1324 known miRNA families and 448 novel miRNA candidates were identified. Of those, 16 known miRNAs with 40 target genes, and three novel miRNAs with four target genes were confirmed based on degradome sequencing data. Conserved miRNA families such as miR156, miR168, miR166, miR167, and miR894 were highly expressed in embryos of developing and germinating seeds. A barley-specific miRNA, miR5071, which was predicted to target an OsMLA10-like gene, accumulated at a high level, suggesting its involvement in defence response during these two developmental stages. Based on target prediction and Kyoto Encyclopedia of Genes and Genomes analysis of putative targets, nine highly expressed miRNAs were found to be related to phytohormone signalling and hormone cross-talk. Northern blot and qRT-PCR analysis showed that these miRNAs displayed differential expression patterns during seed development and germination, indicating their different roles in hormone signalling pathways. In addition, we showed that miR393 affected seed development through targeting two genes encoding the auxin receptors TIR1/AFBs in barley, as over-expression of miR393 led to an increased length-width ratio of seeds, whereas target mimic (MIM393)-mediated inhibition of its activity decreased the 1000-grain weight of seeds. Furthermore, the expression of auxin-responsive genes, abscisic acid- and gibberellic acid-related genes was altered in miR393 misexpression lines during germination and early seedling growth.

CONCLUSIONS

Our work indicates that miRNA-target pairs participate in gene expression regulation and hormone interaction in barley embryo and provides evidence that miR393-mediated auxin response regulation affects grain development and influences gibberellic acid and abscisic acid homeostasis during germination.

Sumoylation stabilizes RACK1B and enhance its interaction with RAP2.6 in the abscisic acid response

The highly conserved eukaryotic WD40 repeat protein, Receptor for Activated C Kinase 1 (RACK1), is involved in the abscisic acid (ABA) response in Arabidopsis. However, the regulation of RACK1 and the proteins with which it interacts are poorly understood. Here, we show that RACK1B is sumoylated at four residues, Lys50, Lys276, Lys281 and Lys291. Sumoylation increases RACK1B stability and its tolerance to ubiquitination-mediated degradation in ABA response. As a result, sumoylation leads to enhanced interaction between RACK1B and RAP2.6, an AP2/ERF family transcription factor. RACK1B binds directly to the AP2 domain of RAP2.6, which alters the affinity of RAP2.6 for CE1 and GCC cis-acting regulatory elements. Taken together, our findings illustrate that protein stability controlled by dynamic post-transcriptional modification is a critical regulatory mechanism for RACK1B, which functions as scaffold protein for RAP2.6 in ABA signaling.

The biomechanics of seed germination

From a biomechanical perspective, the completion of seed (and fruit) germination depends on the balance of two opposing forces: the growth potential of the embryonic axis (radicle-hypocotyl growth zone) and the restraint of the seed-covering layers (endosperm, testa, and pericarp). The diverse seed tissues are composite materials which differ in their dynamic properties based on their distinct cell wall composition and water uptake capacities. The biomechanics of embryo cell growth during seed germination depend on irreversible cell wall loosening followed by water uptake due to the decreasing turgor, and this leads to embryo elongation and eventually radicle emergence. Endosperm weakening as a prerequisite for radicle emergence is a widespread phenomenon among angiosperms. Research into the biochemistry and biomechanics of endosperm weakening has demonstrated that the reduction in puncture force of a seed's micropylar endosperm is environmentally and hormonally regulated and involves tissue-specific expression of cell wall remodelling proteins such as expansins, diverse hydrolases, and the production of directly acting apoplastic reactive oxygen. The endosperm-weakening biomechanics and its underlying cell wall biochemistry differ between the micropylar (ME) and chalazal (CE) endosperm domains. In the ME, they involve cell wall loosening, cell separation, and programmed cell death to provide decreased and localized ME tissue resistance, autolysis, and finally the formation of an ME hole required for radicle emergence. Future work will further unravel the molecular mechanisms, environmental regulation, and evolution of the diverse biomechanical cell wall changes underpinning the control of germination by endosperm weakening.

Reactive Oxygen Species Generated by NADPH Oxidases Promote Radicle Protrusion and Root Elongation during Rice Seed Germination

Seed germination is a complicated biological process that requires regulation through various enzymatic and non-enzymatic mechanisms. Although it has been recognized that reactive oxygen species (ROS) regulate radicle emergence and root elongation in a non-enzymatic manner during dicot seed germination, the role of ROS in monocot seed germination remains unknown. NADPH oxidases (NOXs) are the major ROS producers in plants; however, whether and how NOXs regulate rice seed germination through ROS generation remains unclear. Here, we report that diphenyleneiodinium (DPI), a specific NOX inhibitor, potently inhibited embryo and seedling growth—especially that of the radicle and of root elongation—in a dose-dependent manner. Notably, the DPI-mediated inhibition of radicle and root growth could be eliminated by transferring seedlings from DPI to water. Furthermore, ROS production/accumulation during rice seed germination was quantified via histochemistry. Superoxide radicals (O₂⁻), hydrogen peroxide (H₂O₂) and hydroxyl radicals (^•OH) accumulated steadily in the coleorhiza, radicle and seedling root of germinating rice seeds. Expression profiles of the nine typical NOX genes were also investigated. According to quantitative PCR, OsNOX5, 7 and 9 were expressed relatively higher. When seeds were incubated in water, OsNOX5 expression progressively increased in the embryo from 12 to 48 h, whereas OsNOX7 and 9 expressions increased from 12 to 24 h and decreased thereafter. As expected, DPI inhibits the expression at predetermined time points for each of these genes. Taken together, these results suggest that ROS produced by NOXs are involved in radicle and root elongation during rice seed germination, and OsNOX5, 7 and 9 could play crucial roles in rice seed germination. These findings will facilitate further studies of the roles of ROS generated by NOXs during seed germination and seedling establishment and also provide valuable information for the regulation of NOX family gene expression in germinating seeds of monocot cereals.

Transcriptome analysis of the oriental melon (Cucumis melo L. var. makuwa) during fruit development

Background

The oriental melon (Cucumis melo L. var. makuwa) is one of the most important cultivated cucurbits grown widely in Korea, Japan, and northern China. It is cultivated because its fruit has a sweet aromatic flavor and is rich in soluble sugars, organic acids, minerals, and vitamins. In order to elucidate the genetic and molecular basis of the developmental changes that determine size, color, and sugar contents of the fruit, we performed de novo transcriptome sequencing to analyze the genes expressed during fruit development.

Results

We identified a total of 47,666 of representative loci from 100,875 transcripts and functionally annotated 33,963 of the loci based on orthologs in Arabidopsis thaliana. Among those loci, we identified 5,173 differentially expressed genes, which were classified into 14 clusters base on the modulation of their expression patterns. The expression patterns suggested that the differentially expressed genes were related to fruit development and maturation through diverse metabolic pathways. Analyses based on gene set enrichment and the pathways described in the Kyoto Encyclopedia of Genes and Genomes suggested that the expression of genes involved in starch and sucrose metabolism and carotenoid biosynthesis were regulated dynamically during fruit development and subsequent maturation.

Conclusion

Our results provide the gene expression patterns related to different stages of fruit development and maturation in the oriental melon. The expression patterns give clues about important regulatory mechanisms, especially those involving starch, sugar, and carotenoid biosynthesis, in the development of the oriental melon fruit.

The Interrelationship between Abscisic Acid and Reactive Oxygen Species Plays a Key Role in Barley Seed Dormancy and Germination

Seed dormancy is one of the adaptive responses in the plant life cycle and an important agronomic trait. Reactive oxygen species (ROS) release seed dormancy and promote seed germination in several cereal crops; however, the key regulatory mechanism of ROS-mediated seed dormancy and germination remains controversial. Here, we focused on the relationship between hydrogen peroxide (a ROS) and abscisic acid (ABA) in dormant and non-dormant barley seeds. The hydrogen peroxide (H₂O₂) level produced in barley seed embryos after imbibition was higher in non-dormant seeds than in dormant seeds. H₂O₂ regulated the ABA content in the embryos through ABA-8'-hydroxylase, an ABA catabolic enzyme. Moreover, compared with non-dormant seeds, in dormant seeds the activity of NADPH oxidase, which produces ROS, was lower, whereas the activity of catalase, which is a H₂O₂ scavenging enzyme, was higher, as was the expression of HvCAT2. Furthermore, precocious germination of isolated immature embryos was suppressed by the transient introduction of HvCAT2 driven by the maize (Zea mays) ubiquitin promoter. HvCAT2 expression was regulated through an ABA-responsive transcription factor (HvABI5) induced by ABA. These results suggest that the changing of balance between ABA and ROS is active in barley seed embryos after imbibition and regulates barley seed dormancy and germination.

SHB1/HY1 Alleviates Excess Boron Stress by Increasing BOR4 Expression Level and Maintaining Boron Homeostasis in Arabidopsis Roots

Boron is an essential mineral nutrient for higher plant growth and development. However, excessive amounts of boron can be toxic. Here, we report on the characterization of an Arabidopsis mutant, shb1 (sensitive to high-level of boron 1), which exhibits hypersensitivity to excessive boron in roots. Positional cloning demonstrated that the shb1 mutant bears a point mutation in a gene encoding a heme oxygenase 1 (HO1) corresponding to the HY1 gene involved in photomorphogenesis. The transcription level of the SHB1/HY1 gene in roots is up-regulated under excessive boron stimulation. Either overexpressing SHB1/HY1 or applying the HO1 inducer hematin reduces boron accumulation in roots and confers high boron tolerance. Furthermore, carbon monoxide and bilirubin, catalytic products of HO1, partially rescue the boron toxicity-induced inhibition of primary root growth in shb1. Additionally, the mRNA level of BOR4, a boron efflux transporter, is reduced in shb1 roots with high levels of boron supplementation, and hematin cannot relieve the boron toxicity-induced root inhibition in bor4 mutants. Taken together, our study reveals that HO1 acts via its catalytic by-products to promote tolerance of excessive boron by up-regulating the transcription of the BOR4 gene and therefore promoting the exclusion of excessive boron in root cells.

Promotion of Germination Using Hydroxamic Acid Inhibitors of 9-cis-Epoxycarotenoid Dioxygenase

Abscisic acid (ABA) inhibits seed germination and the regulation of ABA biosynthesis has a role in maintenance of seed dormancy. The key rate-limiting step in ABA biosynthesis is catalyzed by 9-cis-epoxycarotenoid dioxygenase (NCED). Two hydroxamic acid inhibitors of carotenoid cleavage dioxygenase (CCD), D4 and D7, previously found to inhibit CCD and NCED in vitro, are shown to have the novel property of decreasing mean germination time of tomato (Solanum lycopersicum L.) seeds constitutively overexpressing LeNCED1. Post-germination, D4 exhibited no negative effects on tomato seedling growth in terms of height, dry weight, and fresh weight. Tobacco (Nicotiana tabacum L.) seeds containing a tetracycline-inducible LeNCED1 transgene were used to show that germination could be negatively and positively controlled through the chemical induction of gene expression and the chemical inhibition of the NCED protein: application of tetracycline increased mean germination time and delayed hypocotyl emergence in a similar manner to that observed when exogenous ABA was applied and this was reversed by D4 when NCED expression was induced at intermediate levels. D4 also improved germination in lettuce (Lactuca sativa L.) seeds under thermoinhibitory temperatures and in tomato seeds imbibed in high osmolarity solutions of polyethylene glycol. D4 reduced ABA and dihydrophaseic acid accumulation in tomato seeds overexpressing LeNCED1 and reduced ABA accumulation in wild type tomato seeds imbibed on polyethylene glycol. The evidence supports a mode of action of D4 through NCED inhibition, and this molecule provides a lead compound for the design of NCED inhibitors with greater specificity and potency.

Reactive oxygen species induced by cold stratification promote germination of Hedysarum scoparium seeds

Seed germination is comprehensively regulated by multiple intrinsic and extrinsic factors, and reactive oxygen species (ROS) are relatively new among these factors. However, the role and underlying mechanisms of ROS in germination regulation remain largely unknown. In this study, we initially found that cold stratification could promote germination and respiration of Hedysarum scoparium seeds, especially at low temperature. We then noted that a ROS environment change induced by hydrogen peroxide (H₂O₂) or methylviologen (MV) could similarly promote seed germination. On the other hand, the ROS scavenger N-acetyl-L-cysteine (NAC) suppressed germination of cold-stratified H. scoparium seeds, indicating a stimulatory role of ROS upon seed germination. An increased accumulation of O₂^- was detected in embryonic axes of cold-stratified seeds, and stratification-induced ROS generation as well as progressive accumulation of ROS during germination was further confirmed at the cellular level by confocal microscopy. Moreover, protein carbonylation in cold-stratified seeds was enhanced during germination, which was reversed by NAC treatment. Finally, the relationship between ROS and abscisic acid (ABA) or gibberellin (GA) in germination regulation was investigated. ABA treatment significantly inhibited germination and reduced the H₂O₂ content in both cold-stratified and non-cold-stratified seeds. Furthermore, we found that cold stratification mediates the down-regulation of the ABA content and increase of GA, suggesting an interaction between ROS and ABA/GA. These results in H. scoparium shed new light on the positive role of ROS and their cross-talk between plant hormones in seed germination.

Abscisic acid content and the expression of genes related to its metabolism during maturation of triticale grains of cultivars differing in pre-harvest sprouting susceptibility

Abscisic acid (ABA) is a plant hormone that plays a predominant role in the onset and maintenance of primary dormancy. Peak ABA accumulation in embryos of triticale grains was observed before any significant loss of water and was higher in Fredro, a cultivar less susceptible to pre-harvest sprouting (PHS), than in Leontino, a cultivar more sensitive to PHS. At full maturity, embryonic ABA content in Fredro was twice as high as in Leontino. Two full-length cDNAs of 9-cis-epoxycarotenoid dioxygenase (TsNCED1, TsNCED2), an enzyme involved in ABA biosynthesis, and two full-length cDNAs of ABA 8'-hydroxylase (TsABA8'OH1 and TsABA8'OH2), an enzyme involved in ABA catabolism, were identified in triticale grains and characterized. The maximum transcript level of both TsNCED1 and TsNCED2 preceded the peak of ABA accumulation, suggesting that both TsNCEDs contribute to reach this peak, although the expression of TsNCED1 was significantly higher in Fredro than in Leontino. High expression of TsABA8'OH2 and TsABA8'OH1 was observed long before and at the end of the ABA accumulation peak, respectively, but no differences were observed between cultivars. The obtained results suggest that mainly TsNCED1 might be related to the higher ABA content and higher resistance of Fredro to PHS. However, Fredro embryos not only have higher ABA content, but also exhibit greater sensitivity to ABA, which may also have a significant effect on grain dormancy and lower susceptibility to PHS for grains of this cultivar.

Abscinazole-E3M, a practical inhibitor of abscisic acid 8'-hydroxylase for improving drought tolerance

Abscisic acid (ABA) is an essential phytohormone that regulates plant water use and drought tolerance. However, agricultural applications of ABA have been limited because of its rapid inactivation in plants, which involves hydroxylation of ABA by ABA 8′-hydroxylase (CYP707A). We previously developed a selective inhibitor of CYP707A, (−)-Abz-E2B, by structurally modifying S-uniconazole, which functions as an inhibitor of CYP707A and as a gibberellin biosynthetic enzyme. However, its synthetic yield is too low for practical applications. Therefore, we designed novel CYP707A inhibitors, Abz-T compounds, that have simpler structures in which the 1,2,3-triazolyl ring of (−)-Abz-E2B has been replaced with a triple bond. They were successfully synthesised in shorter steps, resulting in greater yields than that of (−)-Abz-E2B. In the enzymatic assays, one of the Abz-T compounds, (−)-Abz-E3M, acted as a strong and selective inhibitor of CYP707A, similar to (−)-Abz-E2B. Analysis of the biological effects in Arabidopsis revealed that (−)-Abz-E3M enhanced ABA’s effects more than (−)-Abz-E2B in seed germination and in the expression of ABA-responsive genes. Treatment with (−)-Abz-E3M induced stomatal closure and improved drought tolerance in Arabidopsis. Furthermore, (−)-Abz-E3M also increased the ABA response in rice and maize. Thus, (−)-Abz-E3M is a more practical and effective inhibitor of CYP707A than (−)-Abz-E2B.

Abscisic acid metabolic genes of wheat (Triticum aestivum L.): identification and insights into their functionality in seed dormancy and dehydration tolerance

The three homeologues of wheat NCED2 were identified; the wheat NCED2A and CYP707A1B affect seed ABA level and dormancy but not leaf ABA level and transpirational water loss in Arabidopsis. Biosynthesis and catabolism of abscisic acid (ABA) in plants are primarily regulated by 9-cis-epoxycarotenoid dioxygenases (NCEDs) and ABA 8'-hydroxylase (ABA8'OH), respectively. The present study identified the complete coding sequences of a second NCED gene, designated as TaNCED2, and its homeologues (TaNCED2A, TaNCED2B and TaNCED2D) in hexaploid wheat, and characterized its functionality in seed dormancy and leaf dehydration tolerance using the TaNCED2A homeologue. The study also investigated the role of the B genome copy of the cytochrome P450 monooxygenase 707A1 (CYP707A1) gene of hexaploid wheat (TaCYP707A1B), which encodes ABA8'OH, in regulating the two traits as this has not been studied before. Ectopic expression of TaNCED2A and TaCYP707A1B in Arabidopsis resulted in altered seed ABA level and dormancy with no effect on leaf ABA content and transpirational water loss. To gain insights into the physiological roles of TaNCED2 and TaCYP707A1 in wheat, the study examined their spatiotemporal expression patterns and determined the genomic contributions of transcripts to their total expression.