ABA-insensitive3, ABA-insensitive5, and DELLAs Interact to activate the expression of SOMNUS and other high-temperature-inducible genes in imbibed seeds in Arabidopsis

Nitrate attenuates abscisic acid signaling via NIN-LIKE PROTEIN8 in Arabidopsis seed germination

Abscisic acid (ABA) suppresses Arabidopsis (Arabidopsis thaliana) seed germination and post-germinative growth. Nitrate stimulates seed germination, but whether it directly regulates ABA signaling and the associated underlying molecular mechanisms remain unknown. Here, we showed that nitrate alleviates the repressive effects of ABA on seed germination independently of the nitric oxide (NO) pathway. Moreover, nitrate attenuates ABA signaling activated by ABSCISIC ACID INSENSITIVE3 (ABI3) and ABI5, two critical transcriptional regulators of the ABA pathway. Mechanistic analyses demonstrated that ABI3 and ABI5 physically interact with the nitrate signaling-related core transcription factor NIN-LIKE PROTEIN 8 (NLP8). After ABA treatment, NLP8 suppresses ABA responses during seed germination without affecting ABA content. Notably, nitrate represses ABA signaling mainly through NLP8. Genetic analyses showed that NLP8 acts upstream of ABI3 and ABI5. Specifically, NLP8 inhibits the transcriptional functions of ABI3 and ABI5, as well as their ABA-induced accumulation. Additionally, NLP8 overexpression largely suppresses the ABA hypersensitivity of mutant plants exhibiting impaired NO biosynthesis or signaling. Collectively, our study reveals that nitrate counteracts the inhibitory effects of ABA signaling on seed germination and provides mechanistic insights into the NLP8-ABI3/ABI5 interactions and their antagonistic relationships in ABA signaling.

The transcription factor CCT30 promotes rice preharvest sprouting by regulating sugar signalling to inhibit the ABA-mediated pathway

Seed dormancy is an important adaptive trait in plants. Proper seed dormancy enables the avoidance of preharvest sprouting in the undesirable conditions like rainfall frequently. In this study, qPSR8, a major QTL for preharvest sprouting, was isolated, and a previously reported heading-date gene, CCT30, was verified as the candidate gene. The CCT30 knockout mutants (CCT30-CR) enhanced seed dormancy and ABA sensitivity as compared with the wild-type ZH11. Conversely, CCT30 overexpressing plants had opposite phenotype changes and had a decreased ABA content. The expression of ABA synthesis genes such as OsNCEDs and ABA signalling genes such as ABI3 and ABI5 were upregulated and sugar metabolism-related genes such as amylase genes were downregulated in CCT30-CR. Correspondingly, fewer free sugars, such as monosaccharides and oligosaccharides, accumulated in CCT30-CR. The freshly harvested seeds from CCT30-CR had no ability to transmit sugar signals when treated with 1% exogenous glucose. In addition, CCT30 interacted with the transcription factor OsbZIP37, which negatively regulates seed dormancy. Overall, CCT30 promotes preharvest sprouting by enhancing sugar signals that inhibit the ABA-mediated pathway, and CCT30 is a good gene for breeding rice varieties resistant to preharvest sprouting.

Transcriptional engineering for value enhancement of oilseed crops: a forward perspective

Plant-derived oils provide 20%-35% of dietary calories and are a primary source of essential omega-6 (linoleic) and omega-3 (α-linolenic) fatty acids. While traditional breeding has significantly increased yields in key oilseed crops like soybean, sunflower, canola, peanut, and cottonseed, overall gains have plateaued over the past few decades. Oilseed crops also experience substantial yield losses in both prime and marginal agricultural areas due to biotic and abiotic stresses and shifting agro-climates. Recent genomic, transcriptomic, and metabolomics research has expanded our understanding of the genetic and physiological control of fatty acid biosynthesis and composition. Many oilseed species have inherent stress-combating mechanisms, including transcription factor regulation. Advances in genome editing tools like CRISPR/Cas9 offer precise genetic modifications, targeting transcription factors and binding sites to enhance desirable traits, such as the nutritional profile and chemical composition of fatty acids. This review explores the application of genome editing in oilseed improvement, covering recent progress, challenges, and future potential to boost yield and oil content. These advancements could play a transformative role in developing resilient, nutritious crop varieties essential for sustainable food security in a changing climate.

Exploring the Role of Carbon Monoxide in Seed Physiology: Implications for Stress Tolerance and Practical Uses

Carbon monoxide (CO) is recognized as a signaling molecule in plants, inducing various physiological responses. This article briefly examines the physiological functions of CO in seed biology and seedlings' responses to environmental stresses. The activity of heme oxygenase (HO), the main enzyme responsible for CO synthesis, is a key factor controlling CO levels in plant cells. CO can influence seed germination by regulating seed dormancy through interactions with genes and hormones. Additionally, CO positively affects seedling growth by enhancing the antioxidant system, thereby increasing resistance to oxidative damage caused by stress. CO has beneficial effects on root development, root length, stomatal closure, and regulation of the photosynthetic system. Its interaction with reactive oxygen species (ROS) mediates hormone- and light-dependent growth processes during the early stages of plant development under stress. Furthermore, CO interacts with other signaling molecules, such as nitric oxide (NO), molecular hydrogen (H2), and hydrogen sulfide (H2S). By gaining a better understanding of the molecular mechanisms underlying these processes, CO can be more effectively utilized to improve seed germination and seedling growth in agricultural practices.

Unveiling the secrets of abiotic stress tolerance in plants through molecular and hormonal insights

Phytohormones are signaling substances that control essential elements of growth, development, and reactions to environmental stress. Drought, salt, heat, cold, and floods are a few examples of abiotic factors that have a significant impact on plant development and survival. Complex sensing, signaling, and stress response systems are needed for adaptation and tolerance to such pressures. Abscisic acid (ABA) is a key phytohormone that regulates stress responses. It interacts with the jasmonic acid (JA) and salicylic acid (SA) signaling pathways to direct resources toward reducing the impacts of abiotic stressors rather than fighting against pathogens. Under exposure to nanoparticles, the plant growth hormones also function as molecules that regulate stress and are known to be involved in a variety of signaling cascades. Reactive oxygen species (ROS) are detected in excess while under stress, and nanoparticles can control their formation. Understanding the way these many signaling pathways interact in plants will tremendously help breeders create food crops that can survive in deteriorating environmental circumstances brought on by climate change and that can sustain or even improve crop production. Recent studies have demonstrated that phytohormones, such as the traditional auxins, cytokinins, ethylene, and gibberellins, as well as more recent members like brassinosteroids, jasmonates, and strigolactones, may prove to be significant metabolic engineering targets for creating crop plants that are resistant to abiotic stress. In this review, we address recent developments in current understanding regarding the way various plant hormones regulate plant responses to abiotic stress and highlight instances of hormonal communication between plants during abiotic stress signaling. We also discuss new insights into plant gene and growth regulation mechanisms during stress, phytohormone engineering, nanotechnological crosstalk of phytohormones, and Plant Growth-Promoting Rhizobacteria's Regulatory Powers (PGPR) via the involvement of phytohormones.

Allelic variation of TaABI5-A4 significantly affects seed dormancy in bread wheat

KEY MESSAGE

We identified a pivotal transcription factor TaABI5-A4 that is significantly associated with pre-harvest sprouting in wheat; its function in regulating seed dormancy was confirmed in transgenic rice. ABI5 is a critical transcription factor in regulation of crop seed maturation, dormancy, germination, and post-germination. Sixteen copies of homologous sequences of ABI5 were identified in Chinese wheat line Zhou 8425B. Cultivars of two haplotypes TaABI5-A4a and TaABI5-A4b showed significantly different seed dormancies. Based on two SNPs between the sequences of TaABI5-A4a and TaABI5-A4b, two complementary dominant sequence-tagged site (STS) markers were developed and validated in a natural population of 103 Chinese wheat cultivars and advanced lines and 200 recombinant inbred lines (RILs) derived from the Yangxiaomai/Zhongyou 9507 cross; the STS markers can be used efficiently and reliably to evaluate the dormancy of wheat seeds. The transcription level of TaABI5-A4b was significantly increased in TaABI5-A4a-GFP transgenic rice lines compared with that in TaABI5-A4b-GFP. The average seed germination index of TaABI5-A4a-GFP transgenic rice lines was significantly lower than those of TaABI5-A4b-GFP. In addition, seeds of TaABI5-A4a-GFP transgenic lines had higher ABA sensitivity and endogenous ABA content, lower endogenous GA content and plant height, and thicker stem internodes than those of TaABI5-A4b-GFP. Allelic variation of TaABI5-A4-affected wheat seed dormancy and the gene function was confirmed in transgenic rice. The transgenic rice lines of TaABI5-A4a and TaABI5-A4b had significantly different sensitivities to ABA and contents of endogenous ABA and GA in mature seeds, thereby influencing the seed dormancy, plant height, and stem internode length and diameter.

Advance in the Thermoinhibition of Lettuce (Lactuca sativa L.) Seed Germination

Thermoinhibition refers to the inability of seeds to germinate when inhibited by high temperatures, but when environmental conditions return to normal, the seeds are able to germinate rapidly again, which is different from thermodormancy. Meanwhile, with global warming, the effect of the thermoinhibition phenomenon on the yield and quality of crops in agricultural production is becoming common. Lettuce, as a horticultural crop sensitive to high temperature, is particularly susceptible to the effects of thermoinhibition, resulting in yield reduction. Therefore, it is crucial to elucidate the intrinsic mechanism of action of thermoinhibition in lettuce seeds. This review mainly outlines several factors affecting thermoinhibition of lettuce seed germination, including endosperm hardening, alteration of endogenous or exogenous phytohormone concentrations, action of photosensitizing pigments, production and inhibition of metabolites, maternal effects, genetic expression, and other physical and chemical factors. Finally, we also discuss the challenges and potential of lettuce seed germination thermoinhibition research. The purpose of this study is to provide theoretical support for future research on lettuce seed germination thermoinhibition, and with the aim of revealing the mechanisms and effects behind lettuce seed thermoinhibition. This will enable the identification of more methods to alleviate seed thermoinhibition or the development of superior heat-tolerant lettuce seeds.

The MKK3 MAPK cascade integrates temperature and after-ripening signals to modulate seed germination

The timing of seed germination is controlled by the combination of internal dormancy and external factors. Temperature is a major environmental factor for seed germination. The permissive temperature range for germination is narrow in dormant seeds and expands during after-ripening (AR) (dormancy release). Quantitative trait loci analyses of preharvest sprouting in cereals have revealed that MKK3, a mitogen-activated protein kinase (MAPK) cascade protein, is a negative regulator of grain dormancy. Here, we show that the MAPKKK19/20-MKK3-MPK1/2/7/14 cascade modulates the germination temperature range in Arabidopsis seeds by elevating the germinability of the seeds at sub- and supraoptimal temperatures. The expression of MAPKKK19 and MAPKKK20 is induced around optimal temperature for germination in after-ripened seeds but repressed in dormant seeds. MPK7 activation depends on the expression levels of MAPKKK19/20, with expression occurring under conditions permissive for germination. Abscisic acid (ABA) and gibberellin (GA) are two major phytohormones which are involved in germination control. Activation of the MKK3 cascade represses ABA biosynthesis enzyme gene expression and induces expression of ABA catabolic enzyme and GA biosynthesis enzyme genes, resulting in expansion of the germinable temperature range. Our data demonstrate that the MKK3 cascade integrates temperature and AR signals to phytohormone metabolism and seed germination.

HFR1 antagonizes ABI4 to coordinate cytosolic redox status for seed germination under high-temperature stress

Seed germination and dormancy represent critical phases in the life cycle of plants, tightly regulated by endogenous phytochrome levels and environment signals. High temperatures (HT) induce the overaccumulation of reactive oxygen species (ROS) and increase abscisic acid (ABA), thereby inhibiting seed germination. Our previous findings showed that HT induced the burst of reactive nitrogen species (RNS), increasing the S-nitrosylation modification of HFR1, which effectively blocks seed germination. Importantly, stabilizing HFR1 has been shown to significantly mitigate the inhibitory effect of HT on seed germination. In this study, we reported that HT increased the protein abundance of ABI4, a crucial component in ABA signaling, which in turn activates the expression of RbohD while suppressing the expression of VTC2. This leads to the rapid generation of ROS, thereby inhibiting seed germination. Consistently, the seed germination of abi4 mutant showed insensitivity to HT with lower ROS level during seed germination, whereas transgenic lines overexpressing ABI4 showed reduced germination rates accompanied by elevated ROS levels. Furthermore, we noted that HFR1 interacts with ABI4 to sequester its activity under normal conditions. However, HT-induced ROS triggered the degradation of HFR1, consequently releasing ABI4 activity. This activation of ABI4 promotes RbohD expression, culminating in a ROS burst that suppresses seed germination. Thus, our study unveils a novel function for ABI4 in regulating ROS level and seed germination under HT stress. Throughout this process, HFR1 plays a critical role in restraining ABI4 activity to maintain an optimal endogenous ROS level, thereby ensuring seed germination under favorable environmental conditions.

The GA and ABA signaling is required for hydrogen-mediated seed germination in wax gourd

BACKGROUND

Hydrogen gas (H2), a novel and beneficial gaseous molecule, plays a significant role in plant growth and development processes. Hydrogen-rich water (HRW) is regarded as a safe and easily available way to study the physiological effects of H2 on plants. Several recent research has shown that HRW attenuates stress-induced seed germination inhibition; however, the underlying modes of HRW on seed germination remain obscure under non-stress condition.

RESULTS

In this current study, we investigated the possible roles of gibberellin (GA) and abscisic acid (ABA) in HRW-regulated seed germination in wax gourd (Benincasa hispida) through pharmacological, physiological, and transcriptome approaches. The results showed that HRW application at an optimal dose (50% HRW) significantly promoted seed germination and shortened the average germination time (AGT). Subsequent results suggested that 50% HRW treatment stimulated GA production by regulating GA biosynthesis genes (BhiGA3ox, BhiGA2ox, and BhiKAO), whereas it had no effect on the content of ABA and the expression of its biosynthesis (BhiNCED6) and catabolism genes (BhiCYP707A2) but decreased the expression of ABA receptor gene (BhiPYL). In addition, inhibition of GA production by paclobutrazol (PAC) could block the HRW-mediated germination. Treatment with ABA could hinder HRW-mediated seed germination and the ABA biosynthesis inhibitor sodium tungstate (ST) could recover the function of HRW. Furthermore, RNA-seq analysis revealed that, in the presence of GA or ABA, an abundance of genes involved in GA, ABA, and ethylene signal sensing and transduction might involve in HRW-regulated germination.

CONCLUSIONS

This study portrays insights into the mechanism of HRW-mediated seed germination, suggesting that HRW can regulate the balance between GA and ABA to mediate seed germination through ethylene signals in wax gourd.

Complex control of seed germination timing by ERF50 involves RGL2 antagonism and negative feedback regulation of DOG1

Seed dormancy governs germination timing, with both evolutionary and applied consequences. Despite extensive studies on the hormonal and genetic control of these processes, molecular mechanisms directly linking dormancy and germination remain poorly understood. By screening a collection of lines overexpressing Arabidopsis transcription factors, we identified ERF50 as a key gene to control dormancy and germination. To study its regulation, we measured seed-related physiological parameters in loss-of-function mutants and carried out transactivation, protein interaction and ChIP-PCR analyses. We found direct ERF50-mediated repression of DOG1 and activation of EXPA2 transcription, which results in enhanced seed germination. Although ERF50 expression is increased by DOG1 in dormant seeds, ERF50 germination-promoting activity is blocked by RGL2. The physiological, genetic and molecular evidence gathered here supports that ERF50 controls germination timing by regulating DOG1 levels to leverage its role as enhancer of seed germination, via RGL2 antagonism on EXPA2 expression. Our results highlight the central role of ERF50 as a feedback regulator to couple and fine-tune seed dormancy and germination.

Factors Influencing Seed Dormancy and Germination and Advances in Seed Priming Technology

Seed dormancy and germination play pivotal roles in the agronomic traits of plants, and the degree of dormancy intuitively affects the yield and quality of crops in agricultural production. Seed priming is a pre-sowing seed treatment that enhances and accelerates germination, leading to improved seedling establishment. Seed priming technologies, which are designed to partially activate germination, while preventing full seed germination, have exerted a profound impact on agricultural production. Conventional seed priming relies on external priming agents, which often yield unstable results. What works for one variety might not be effective for another. Therefore, it is necessary to explore the internal factors within the metabolic pathways that influence seed physiology and germination. This review unveils the underlying mechanisms of seed metabolism and germination, the factors affecting seed dormancy and germination, as well as the current seed priming technologies that can result in stable and better germination.

DELLA proteins recruit the Mediator complex subunit MED15 to coactivate transcription in land plants

DELLA proteins are negative regulators of the gibberellin response pathway in angiosperms, acting as central hubs that interact with hundreds of transcription factors (TFs) and regulators to modulate their activities. While the mechanism of TF sequestration by DELLAs to prevent DNA binding to downstream targets has been extensively documented, the mechanism that allows them to act as coactivators remains to be understood. Here, we demonstrate that DELLAs directly recruit the Mediator complex to specific loci in Arabidopsis, facilitating transcription. This recruitment involves DELLA amino-terminal domain and the conserved MED15 KIX domain. Accordingly, partial loss of MED15 function mainly disrupted processes known to rely on DELLA coactivation capacity, including cytokinin-dependent regulation of meristem function and skotomorphogenic response, gibberellin metabolism feedback, and flavonol production. We have also found that the single DELLA protein in the liverwort Marchantia polymorpha is capable of recruiting MpMED15 subunits, contributing to transcriptional coactivation. The conservation of Mediator-dependent transcriptional coactivation by DELLA between Arabidopsis and Marchantia implies that this mechanism is intrinsic to the emergence of DELLA in the last common ancestor of land plants.

Environmentally adaptive reshaping of plant photomorphogenesis by karrikin and strigolactone signaling

Coordinated morphogenic adaptation of growing plants is critical for their survival and propagation under fluctuating environments. Plant morphogenic responses to light and warm temperatures, termed photomorphogenesis and thermomorphogenesis, respectively, have been extensively studied in recent decades. During photomorphogenesis, plants actively reshape their growth and developmental patterns to cope with changes in light regimes. Accordingly, photomorphogenesis is closely associated with diverse growth hormonal cues. Notably, accumulating evidence indicates that light-directed morphogenesis is profoundly affected by two recently identified phytochemicals, karrikins (KARs) and strigolactones (SLs). KARs and SLs are structurally related butenolides acting as signaling molecules during a variety of developmental steps, including seed germination. Their receptors and signaling mediators have been identified, and associated working mechanisms have been explored using gene-deficient mutants in various plant species. Of particular interest is that the KAR and SL signaling pathways play important roles in environmental responses, among which their linkages with photomorphogenesis are most comprehensively studied during seedling establishment. In this review, we focus on how the phytochemical and light signals converge on the optimization of morphogenic fitness. We also discuss molecular mechanisms underlying the signaling crosstalks with an aim of developing potential ways to improve crop productivity under climate changes.

A commitment for life: Decades of unraveling the molecular mechanisms behind seed dormancy and germination

Seeds are unique time capsules that can switch between 2 complex and highly interlinked stages: seed dormancy and germination. Dormancy contributes to the survival of plants because it allows to delay germination to optimal conditions. The switch between dormancy and germination occurs in response to developmental and environmental cues. In this review we provide a comprehensive overview of studies that have helped to unravel the molecular mechanisms underlying dormancy and germination over the last decades. Genetic and physiological studies provided a strong foundation for this field of research and revealed the critical role of the plant hormones abscisic acid and gibberellins in the regulation of dormancy and germination, and later natural variation studies together with quantitative genetics identified previously unknown genetic components that control these processes. Omics technologies like transcriptome, proteome, and translatomics analysis allowed us to mechanistically dissect these processes and identify new components in the regulation of seed dormancy and germination.

Highlights in gibberellin research: A tale of the dwarf and the slender

It has been almost a century since biologically active gibberellin (GA) was isolated. Here, we give a historical overview of the early efforts in establishing the GA biosynthesis and catabolism pathway, characterizing the enzymes for GA metabolism, and elucidating their corresponding genes. We then highlight more recent studies that have identified the GA receptors and early GA signaling components (DELLA repressors and F-box activators), determined the molecular mechanism of DELLA-mediated transcription reprograming, and revealed how DELLAs integrate multiple signaling pathways to regulate plant vegetative and reproductive development in response to internal and external cues. Finally, we discuss the GA transporters and their roles in GA-mediated plant development.

Light Supplementation in Pitaya Orchards Induces Pitaya Flowering in Winter by Promoting Phytohormone Biosynthesis

The interaction between light and phytohormones is crucial for plant growth and development. The practice of supplementing light at night during winter to promote pitaya flowering and thereby enhance yield has been shown to be crucial and widely used. However, it remains unclear how supplemental winter light regulates phytohormone levels to promote flowering in pitaya. In this study, through analyzing the transcriptome data of pitaya at four different stages (NL, L0, L1, L2), we observed that differentially expressed genes (DEGs) were mainly enriched in the phytohormone biosynthesis pathway. We further analyzed the data and found that cytokinin (CK) content first increased at the L0 stage and then decreased at the L1 and L2 stages after supplemental light treatment compared to the control (NL). Gibberellin (GA), auxin (IAA), salicylic acid (SA), and jasmonic acid (JA) content increased during the formation of flower buds (L1, L2 stages). In addition, the levels of GA, ethylene (ETH), IAA, and abscisic acid (ABA) increased in flower buds after one week of development (L2f). Our results suggest that winter nighttime supplemental light can interact with endogenous hormone signaling in pitaya, particularly CK, to regulate flower bud formation. These results contribute to a better understanding of the mechanism of phytohormone interactions during the induction of flowering in pitaya under supplemental light in winter.

Metabolic control of seed germination in legumes

Seed development, dormancy, and germination are connected with changes in metabolite levels. Not surprisingly, a complex regulatory network modulates biosynthesis and accumulation of storage products. Seed development has been studied profusely in Arabidopsis thaliana and has provided valuable insights into the genetic control of embryo development. However, not every inference applies to crop legumes, as these have been domesticated and selected for high seed yield and specific metabolic profiles and fluxes. Given its enormous economic relevance, considerable work has contributed to shed light on the mechanisms that control legume seed growth and germination. Here, we summarize recent progress in the understanding of regulatory networks that coordinate seed metabolism and development in legumes.

OsNAC120 balances plant growth and drought tolerance by integrating GA and ABA signaling in rice

The crosstalk between gibberellin (GA) and abscisic acid (ABA) signaling is crucial for balancing plant growth and adaption to environmental stress. Nevertheless, the molecular mechanism of their mutual antagonism still remains to be fully clarified. In this study, we found that knockout of the rice NAC (NAM, ATAF1/2, CUC2) transcription factor gene OsNAC120 inhibits plant growth but enhances drought tolerance, whereas OsNAC120 overexpression produces the opposite results. Exogenous GA can rescue the semi-dwarf phenotype of osnac120 mutants, and further study showed that OsNAC120 promotes GA biosynthesis by transcriptionally activating the GA biosynthetic genes OsGA20ox1 and OsGA20ox3. The DELLA protein SLENDER RICE1 (SLR1) interacts with OsNAC120 and impedes its transactivation ability, and GA treatment can remove the inhibition of transactivation activity caused by SLR1. On the other hand, OsNAC120 negatively regulates rice drought tolerance by repressing ABA-induced stomatal closure. Mechanistic investigation revealed that OsNAC120 inhibits ABA biosynthesis via transcriptional repression of the ABA biosynthetic genes OsNCED3 and OsNCED4. Rice OSMOTIC STRESS/ABA-ACTIVATED PROTEIN KINASE 9 (OsSAPK9) physically interacts with OsNAC120 and mediates its phosphorylation, which results in OsNAC120 degradation. ABA treatment accelerates OsNAC120 degradation and reduces its transactivation activity. Together, our findings provide evidence that OsNAC120 plays critical roles in balancing GA-mediated growth and ABA-induced drought tolerance in rice. This research will help us to understand the mechanisms underlying the trade-off between plant growth and stress tolerance and to engineer stress-resistant, high-yielding crops.

The ABI4-RGL2 module serves as a double agent to mediate the antagonistic crosstalk between ABA and GA signals

Abscisic acid (ABA) and gibberellins (GA) antagonistically mediate several biological processes, including seed germination, but the molecular mechanisms underlying ABA/GA antagonism need further investigation, particularly any role mediated by a transcription factors module. Here, we report that the DELLA protein RGL2, a repressor of GA signaling, specifically interacts with ABI4, an ABA signaling enhancer, to act as a transcription factor complex to mediate ABA/GA antagonism. The rgl2, abi3, abi4 and abi5 mutants rescue the non-germination phenotype of the ga1-t. Further, we demonstrate that RGL2 specifically interacts with ABI4 to form a heterodimer. RGL2 and ABI4 stabilize one another, and GA increases the ABI4-RGL2 module turnover, whereas ABA decreases it. At the transcriptional level, ABI4 enhances the RGL2 expression by directly binding to its promoter via the CCAC cis-element, and RGL2 significantly upregulates the transcriptional activation ability of ABI4 toward its target genes, including ABI5 and RGL2. Abscisic acid promotes whereas GA inhibits the ability of ABI4-RGL2 module to activate transcription, and ultimately ABA and GA antagonize each other. Genetic analysis demonstrated that both ABI4 and RGL2 are essential for the activity of this transcription factor module. These results suggest that the ABI4-RGL2 module mediates ABA/GA antagonism by functioning as a double agent.

A DELAY OF GERMINATION 1 (DOG1)-like protein regulates spore germination in the moss Physcomitrium patens

DELAY OF GERMINATION 1 is a key regulator of dormancy in flowering plants before seed germination. Bryophytes develop haploid spores with an analogous function to seeds. Here, we investigate whether DOG1 function during germination is conserved between bryophytes and flowering plants and analyse the underlying mechanism of DOG1 action in the moss Physcomitrium patens. Phylogenetic and in silico expression analyses were performed to identify and characterise DOG1 domain-containing genes in P. patens. Germination assays were performed to characterise a Ppdog1-like1 mutant, and replacement with AtDOG1 was carried out. Yeast two-hybrid assays were used to test the interaction of the PpDOG1-like protein with DELLA proteins from P. patens and A. thaliana. P. patens possesses nine DOG1 domain-containing genes. The DOG1-like protein PpDOG1-L1 (Pp3c3_9650) interacts with PpDELLAa and PpDELLAb and the A. thaliana DELLA protein AtRGA in yeast. Protein truncations revealed the DOG1 domain as necessary and sufficient for interaction with PpDELLA proteins. Spores of Ppdog1-l1 mutant germinate faster than wild type, but replacement with AtDOG1 reverses this effect. Our data demonstrate a role for the PpDOG1-LIKE1 protein in moss spore germination, possibly alongside PpDELLAs. This suggests a conserved DOG1 domain function in germination, albeit with differential adaptation of regulatory networks in seed and spore germination.

Genetic, Epigenetic, and Environmental Control of Seed Dormancy and Germination

Seed germination is controlled by a combination of the seed dormancy level and environmental conditions such as light, temperature, moisture, and nitrate levels. Seed dormancy is programed genetically, but it is also sensitive to maternal environmental conditions before and after anthesis. Recent developments in molecular genetics and bioinformatics have greatly enhanced our understanding of the molecular mechanisms of seed dormancy and germination in model plants and economically important crop species. This chapter focuses on temperature as an environmental factor and discusses the genetic and epigenetic mechanisms of dormancy and germination.

Gibberellin signaling regulates lignin biosynthesis to modulate rice seed shattering

The elimination of seed shattering was a key step in rice (Oryza sativa) domestication. In this paper, we show that increasing the gibberellic acid (GA) content or response in the abscission region enhanced seed shattering in rice. We demonstrate that SLENDER RICE1 (SLR1), the key repressor of GA signaling, could physically interact with the rice seed shattering-related transcription factors quantitative trait locus of seed shattering on chromosome 1 (qSH1), O. sativa HOMEOBOX 15 (OSH15), and SUPERNUMERARY BRACT (SNB). Importantly, these physical interactions interfered with the direct binding of these three regulators to the lignin biosynthesis gene 4-COUMARATE: COENZYME A LIGASE 3 (4CL3), thereby derepressing its expression. Derepression of 4CL3 led to increased lignin deposition in the abscission region, causing reduced rice seed shattering. Importantly, we also show that modulating GA content could alter the degree of seed shattering to increase harvest efficiency. Our results reveal that the "Green Revolution" phytohormone GA is important for regulating rice seed shattering, and we provide an applicable breeding strategy for high-efficiency rice harvesting.

ABI5-FLZ13 module transcriptionally represses growth-related genes to delay seed germination in response to ABA

The bZIP transcription factor ABSCISIC ACID INSENSITIVE5 (ABI5) is a master regulator of seed germination and post-germinative growth in response to abscisic acid (ABA), but the detailed molecular mechanism by which it represses plant growth remains unclear. In this study, we used proximity labeling to map the neighboring proteome of ABI5 and identified FCS-LIKE ZINC FINGER PROTEIN 13 (FLZ13) as a novel ABI5 interaction partner. Phenotypic analysis of flz13 mutants and FLZ13-overexpressing lines demonstrated that FLZ13 acts as a positive regulator of ABA signaling. Transcriptomic analysis revealed that both FLZ13 and ABI5 downregulate the expression of ABA-repressed and growth-related genes involved in chlorophyll biosynthesis, photosynthesis, and cell wall organization, thereby repressing seed germination and seedling establishment in response to ABA. Further genetic analysis showed that FLZ13 and ABI5 function together to regulate seed germination. Collectively, our findings reveal a previously uncharacterized transcriptional regulatory mechanism by which ABA mediates inhibition of seed germination and seedling establishment.

Coordination of growth and drought responses by GA-ABA signaling in rice

The drought caused by global warming seriously affects the crop growth and agricultural production. Plants have evolved distinct strategies to cope with the drought environment. Under drought stress, energy and resources should be diverted from growth toward stress management. However, the molecular mechanism underlying coordination of growth and drought response remains largely elusive. Here, we discovered that most of the gibberellin (GA) metabolic genes were regulated by water scarcity in rice, leading to the lower GA contents and hence inhibited plant growth. Low GA contents resulted in the accumulation of more GA signaling negative regulator SLENDER RICE 1, which inhibited the degradation of abscisic acid (ABA) receptor PYL10 by competitively binding to the co-activator of anaphase-promoting complex TAD1, resulting in the enhanced ABA response and drought tolerance. These results elucidate the synergistic regulation of crop growth inhibition and promotion of drought tolerance and survival, and provide useful genetic resource in breeding improvement of crop drought resistance.

Interaction of VvDELLA2 and VvCEB1 Mediates Expression of Expansion-Related Gene during GA-Induced Enlargement of Grape Fruit

Exogenous gibberellin treatment can promote early growth of grape fruit, but the underlying regulatory mechanisms are not well understood. Here, we show that VvDELLA2 directly regulates the activity of the VvCEB1 transcription factor, a key regulator in the control of cell expansion in grape fruit. Our results show that VvCEB1 binds directly to the promoters of cell expansion-related genes in grape fruit and acts as a transcriptional activator, while VvDELLA2 blocks VvCEB1 function by binding to its activating structural domain. The exogenous gibberellin treatment relieved this inhibition by promoting the degradation of VvDELLA2 protein, thus, allowing VvCEB1 to transcriptionally activate the expression of cell expansion-related genes. In conclusion, we conclude that exogenous GA3 treatment regulates early fruit expansion by affecting the VvDELLA-VvCEB1 interaction in grape fruit development.

The master growth regulator DELLA binding to histone H2A is essential for DELLA-mediated global transcription regulation

The DELLA genes, also known as 'Green Revolution' genes, encode conserved master growth regulators that control plant development in response to internal and environmental cues. Functioning as nuclear-localized transcription regulators, DELLAs modulate expression of target genes via direct protein-protein interaction of their carboxy-terminal GRAS domain with hundreds of transcription factors (TFs) and epigenetic regulators. However, the molecular mechanism of DELLA-mediated transcription reprogramming remains unclear. Here by characterizing new missense alleles of an Arabidopsis DELLA, repressor of ga1-3 (RGA), and co-immunoprecipitation assays, we show that RGA binds histone H2A via the PFYRE subdomain within its GRAS domain to form a TF-RGA-H2A complex at the target chromatin. Chromatin immunoprecipitation followed by sequencing analysis further shows that this activity is essential for RGA association with its target chromatin globally. Our results indicate that, although DELLAs are recruited to target promoters by binding to TFs via the LHR1 subdomain, DELLA-H2A interaction via the PFYRE subdomain is necessary to stabilize the TF-DELLA-H2A complex at the target chromatin. This study provides insights into the two distinct key modular functions in DELLA for its genome-wide transcription regulation in plants.

ABI5 promotes heat stress-induced chlorophyll degradation by modulating the stability of MYB44 in cucumber

The yellowing of leaves caused by the decomposition of chlorophyll (Chl) is a characteristic event during senescence, which can be induced by various environmental stresses. However, the molecular mechanisms of high temperature-induced Chl degradation in horticultural plants remain poorly understood. Here, we found that heat stress induced Chl degradation and the expression of ABI5 and MYB44 in cucumber. Silencing of ABI5 compromised heat stress-induced Chl degradation, and the transcription of pheophytinase (PPH) and pheophorbide a oxygenase (PAO), two key genes in Chl catabolic pathway, but silencing of MYB44 exhibited the opposite results. Furthermore, ABI5 interacted with MYB44 in vitro and in vivo. ABI5 positively regulated heat stress-induced Chl degradation through two pathways. ABI5 directly bound to PPH and PAO promoters to promote their expression, leading to accelerating Chl degradation. On the other hand, the interaction between ABI5 and MYB44 reduced the binding of MYB44 to PPH and PAO promoters and led to the ubiquitination-depended protein degradation of MYB44, thereby alleviating the transcription inhibitory effect of MYB44 on PPH and PAO. Taken together, our findings propose a new regulatory network for ABI5 in regulating heat stress-induced Chl degradation.

The E3 ubiquitin ligases SINA1 and SINA2 integrate with the protein kinase CIPK20 to regulate the stability of RGL2a, a positive regulator of anthocyanin biosynthesis

Although DELLA protein destabilization mediated by post-translational modifications is essential for gibberellin (GA) signal transduction and GA-regulated anthocyanin biosynthesis, the related mechanisms remain largely unknown. In this study, we report the ubiquitination and phosphorylation of an apple DELLA protein MdRGL2a in response to GA signaling and its regulatory role in anthocyanin biosynthesis. MdRGL2a could interact with MdWRKY75 to enhance the MdWRKY75-activated transcription of anthocyanin activator MdMYB1 and interfere with the interaction between anthocyanin repressor MdMYB308 and MdbHLH3 or MdbHLH33, thereby promoting anthocyanin accumulation. A protein kinase MdCIPK20 was found to phosphorylate and protect MdRGL2a from degradation, and it was essential for MdRGL2a-promoting anthocyanin accumulation. However, MdRGL2a and MdCIPK20 were ubiquitinated and degraded by E3 ubiquitin ligases MdSINA1 and MdSINA2, respectively, both of which were activated in the presence of GA. Our results display the integration of SINA1/2 with CIPK20 to dynamically regulate GA signaling and will be helpful toward understanding the mechanism of GA signal transduction and GA-inhibited anthocyanin biosynthesis. The discovery of extensive interactions between DELLA and SINA and CIPK proteins in apple will provide reference for the study of ubiquitination and phosphorylation of DELLA proteins in other species.

OsNF-YA3 regulates plant growth and osmotic stress tolerance by interacting with SLR1 and SAPK9 in rice

The antagonism between gibberellin (GA) and abscisic acid (ABA) signaling pathways is vital to balance plant growth and stress response. Nevertheless, the mechanism by which plants determine the balance remains to be elucidated. Here, we report that rice NUCLEAR FACTOR-Y A3 (OsNF-YA3) modulates GA- and ABA-mediated balance between plant growth and osmotic stress tolerance. OsNF-YA3 loss-of-function mutants exhibit stunted growth, compromised GA biosynthetic gene expression, and decreased GA levels, while its overexpression lines have promoted growth and enhanced GA content. Chromatin immunoprecipitation-quantitative polymerase chain reaction analysis and transient transcriptional regulation assays demonstrate that OsNF-YA3 activates GA biosynthetic gene OsGA20ox1 expression. Furthermore, the DELLA protein SLENDER RICE1 (SLR1) physically interacts with OsNF-YA3 and thus inhibits its transcriptional activity. On the other side, OsNF-YA3 negatively regulates plant osmotic stress tolerance by repressing ABA response. OsNF-YA3 reduces ABA levels by transcriptionally regulating ABA catabolic genes OsABA8ox1 and OsABA8ox3 by binding to their promoters. Furthermore, OSMOTIC STRESS/ABA-ACTIVATED PROTEIN KINASE 9 (SAPK9), the positive component in ABA signaling, interacts with OsNF-YA3 and mediates OsNF-YA3 phosphorylation, resulting in its degradation in plants. Collectively, our findings establish OsNF-YA3 as an important transcription factor that positively modulates GA-regulated plant growth and negatively controls ABA-mediated water-deficit and salt tolerance. These findings shed light on the molecular mechanism underlying the balance between the growth and stress response of the plant.

DELLA proteins regulate spore germination and reproductive development in Physcomitrium patens

Proteins of the DELLA family integrate environmental signals to regulate growth and development throughout the plant kingdom. Plants expressing non-degradable DELLA proteins underpinned the development of high-yielding 'Green Revolution' dwarf crop varieties in the 1960s. In vascular plants, DELLAs are regulated by gibberellins, diterpenoid plant hormones. How DELLA protein function has changed during land plant evolution is not fully understood. We have examined the function and interactions of DELLA proteins in the moss Physcomitrium (Physcomitrella) patens, in the sister group of vascular plants (Bryophytes). PpDELLAs do not undergo the same regulation as flowering plant DELLAs. PpDELLAs are not degraded by diterpenes, do not interact with GID1 gibberellin receptor proteins and do not participate in responses to abiotic stress. PpDELLAs do share a function with vascular plant DELLAs during reproductive development. PpDELLAs also regulate spore germination. PpDELLAs interact with moss-specific photoreceptors although a function for PpDELLAs in light responses was not detected. PpDELLAs likely act as 'hubs' for transcriptional regulation similarly to their homologues across the plant kingdom. Taken together, these data demonstrate that PpDELLA proteins share some biological functions with DELLAs in flowering plants, but other DELLA functions and regulation evolved independently in both plant lineages.

Auxin contributes to jasmonate-mediated regulation of abscisic acid signaling during seed germination in Arabidopsis

Abscisic acid (ABA) represses seed germination and postgerminative growth in Arabidopsis thaliana. Auxin and jasmonic acid (JA) stimulate ABA function; however, the possible synergistic effects of auxin and JA on ABA signaling and the underlying molecular mechanisms remain elusive. Here, we show that exogenous auxin works synergistically with JA to enhance the ABA-induced delay of seed germination. Auxin biosynthesis, perception, and signaling are crucial for JA-promoted ABA responses. The auxin-dependent transcription factors AUXIN RESPONSE FACTOR10 (ARF10) and ARF16 interact with JASMONATE ZIM-DOMAIN (JAZ) repressors of JA signaling. ARF10 and ARF16 positively mediate JA-increased ABA responses, and overaccumulation of ARF16 partially restores the hyposensitive phenotype of JAZ-accumulating plants defective in JA signaling in response to combined ABA and JA treatment. Furthermore, ARF10 and ARF16 physically associate with ABSCISIC ACID INSENSITIVE5 (ABI5), a critical regulator of ABA signaling, and the ability of ARF16 to stimulate JA-mediated ABA responses is mainly dependent on ABI5. ARF10 and ARF16 activate the transcriptional function of ABI5, whereas JAZ repressors antagonize their effects. Collectively, our results demonstrate that auxin contributes to the synergetic modulation of JA on ABA signaling, and explain the mechanism by which ARF10/16 coordinate with JAZ and ABI5 to integrate the auxin, JA, and ABA signaling pathways.

Genome-wide characterization and expression of DELLA genes in Cucurbita moschata reveal their potential roles under development and abiotic stress

DELLA gene family plays a key role in regulating plant development and responding to stress. Currently, many DELLA family members have been identified in plants, however, information on DELLA genes in pumpkin (Cucurbita moschata) is scarce. In this study, physical and chemical properties, gene structure cis-regulatory elements and expression of CmoDELLA genes were examined in pumpkin. We found that seven CmoDELLA genes were identified in pumpkin, and they were unevenly classified into five chromosomes. CmoDELLA proteins were relatively unstable and their secondary structures were mainly made up α-helix and random coil. All seven CmoDELLA proteins contained typical DELLA domain and GRAS domain, however, motif numbers between CmoDELLA proteins were unevenly distributed, implying the complex evolution and functional diversification of CmoDELLA proteins. Cis-regulatory elements analysis revealed that CmoDELLA genes might play an essential role in regulating plant growth and development, and response to stress in pumpkin. Transcriptome data in the roots, stems, leaves and fruits demonstrated that CmoDELLA2, CmoDELLA3 and CmoDELLA7 were related to the stems development, CmoDELLA1, CmoDELLA4, CmoDELLA5 and CmoDELLA6 were associated with the fruits development. Furthermore, we found that CmoDELLA1 and CmoDELLA5 were up-regulated under NaCl stress. CmoDELLA1, CmoDELLA2, CmoDELLA3, CmoDELLA5, CmoDELLA6 and CmoDELLA7 were remarkably induced under waterlogging stress. While, all of the 7 CmoDELLA genes showed significantly induced expression under cold stress. The expression patterns under abiotic stress suggested that CmoDELLA genes might mediate the stress response of pumpkin to NaCl, waterlogging and cold, however, the functions of different CmoDELLA genes varied under different stress. Overall, our study provides valuable information for further research about the potential functions and regulatory networks of CmoDELLA genes in pumpkin.

Recent progress in molecular genetics and omics-driven research in seed biology

Elucidating the mechanisms that control seed development, metabolism, and physiology is a fundamental issue in biology. Michel Caboche had long been a catalyst for seed biology research in France up until his untimely passing away last year. To honour his memory, we have updated a review written under his coordination in 2010 entitled "Arabidopsis seed secrets unravelled after a decade of genetic and omics-driven research". This review encompassed different molecular aspects of seed development, reserve accumulation, dormancy and germination, that are studied in the lab created by M. Caboche. We have extended the scope of this review to highlight original experimental approaches implemented in the field over the past decade such as omics approaches aimed at investigating the control of gene expression, protein modifications, primary and specialized metabolites at the tissue or even cellular level, as well as seed biodiversity and the impact of the environment on seed quality.

Transcriptomic insights into the effects of abscisic acid on the germination of Magnolia sieboldii K. Koch seed

Magnolia sieboldii K. Koch is a deciduous tree species. However, the wild resource of M. sieboldii has been declining due to excessive utilization and seed dormancy. In our previous research, M. sieboldii seeds have morphophysiological dormancy and low germination rates under natural conditions. The aim of the present study was to identify the genes involved in dormancy maintenance. In this study, the germination percentage of M. sieboldii seeds negatively correlated with the content of endogenous abscisic acid (ABA). The hydration of seeds for germination showed three distinct phases. Five key time points were identified: 0 h imbibition (dry seed, GZ), 0 day after imbibition (DAI), 16 DAI, 40 DAI, and 56 DAI. The comprehensive transcript profiles of M. sieboldii seeds treated with ABA and water at the five key germinating stages were obtained. A total of 9641 differentially expressed genes (DEGs) were identified, and 208 and 197 common DEGs were found throughout the ABA and water treatments, respectively. Compared with that in the GZ, 518, 696, 2133, and 1535 DEGs were identified in the SH group at 0, 16, 40 and 56 DAI, respectively. 666, 1725, 1560 and 1415 DEGs were identified in the ABA group at 0, 16, 40, and 56 DAI, respectively. Among the identified DEGs, 12 722 were annotated with GO terms, the top three enriched GO terms were different among the DEGs at 56 DAI in the ABA vs. SH treatments. KEGG pathway enrichment analysis for DEGs indicated that oxidative phosphorylation, protein processing in endoplasmic reticulum, starch and sucrose metabolism play an important role in seed response to ABA. 1926 TFs are obtained and classified into 72 families from the M. sieboldii transcriptome. Results of differential gene expression analysis together with qRT-PCR indicated that phase II is crucial for rapid and successful seed germination. This study is the first to present the global expression patterns of ABA-regulated transcripts in M. sieboldii seeds at different germinating phases.

Impact of climate perturbations on seeds and seed quality for global agriculture

In agriculture, seeds are the most basic and vital input on which croplands productivity depends. These implies a good starting material, good production lines and good storage options. High-quality seed lots must be free of pests and pathogens and contain a required degree of genetic purity. Seeds need also to be stored in good condition between harvest and later sowing, to insure later on the field a good plant density and higher crop yield. In general, these parameters are already widely accepted and considered in many countries where advanced technologies evaluate them. However, the more and more frequently devastating climate changes observed around the world has put seed quality under threat, and current seeds may not be adapted to hazardous and unpredictable conditions. Climate-related factors such as temperature and water availability directly affect seed development and later germination. For these reasons, investigating seed quality in response to climate changes is a step to propose new crop varieties and practices that will bring solutions for our future.

Uncovering the involvement of DoDELLA1-interacting proteins in development by characterizing the DoDELLA gene family in Dendrobium officinale

BACKGROUND

Gibberellins (GAs) are widely involved in plant growth and development. DELLA proteins are key regulators of plant development and a negative regulatory factor of GA. Dendrobium officinale is a valuable traditional Chinese medicine, but little is known about D. officinale DELLA proteins. Assessing the function of D. officinale DELLA proteins would provide an understanding of their roles in this orchid's development.

RESULTS

In this study, the D. officinale DELLA gene family was identified. The function of DoDELLA1 was analyzed in detail. qRT-PCR analysis showed that the expression levels of all DoDELLA genes were significantly up-regulated in multiple shoots and GA3-treated leaves. DoDELLA1 and DoDELLA3 were significantly up-regulated in response to salt stress but were significantly down-regulated under drought stress. DoDELLA1 was localized in the nucleus. A strong interaction was observed between DoDELLA1 and DoMYB39 or DoMYB308, but a weak interaction with DoWAT1.

CONCLUSIONS

In D. officinale, a developmental regulatory network involves a close link between DELLA and other key proteins in this orchid's life cycle. DELLA plays a crucial role in D. officinale development.

Insights on the stem elongation of spur-type bud sport mutant of 'Red Delicious' apple

The decreased capacity of auxin-, CTK-, and BR-mediated cell division and cell enlargement pathways, combined with the enhanced capacity of GA and ETH-, JA-, ABA-, SA-mediated stress-resistant pathways were presumed to be the crucial reasons for the formation of spur-type 'Red Delicious' mutants. Vallee Spur', which exhibit short internodes and compact tree shape, is the fourth generation of the spur-type bud sport mutant of 'Red Delicious'. However, the underlying molecular mechanism of these properties remains unclear. Here, comparative phenotypic, full-length transcriptome and phytohormone analyses were performed between 'Red Delicious' (NSP) and 'Vallee Spur' (SP). The new shoot internode length of NSP was ˃ 1.53-fold higher than that of the SP mutant. Cytological analysis showed that the stem cells of the SP mutant were smaller and more tightly arranged relative to the NSP. By Iso-Seq, a total of 1426 differentially expressed genes (DEGs) were detected, including 808 upregulated and 618 downregulated genes in new shoot apex with 2 leaves of the SP mutant. Gene expressions involved in auxin, cytokinin (CTK), and brassinosteroid (BR) signal transduction were mostly downregulated in the SP mutant, whereas those involved in gibberellin (GA), ethylene (ETH), jasmonate (JA), ABA, and salicylic acid (SA) signal transduction were mostly upregulated. The overall thermogram analysis of hormone levels in the shoot apex carrying two leaves detected by LC-MS/MS absolute quantification showed that the levels of IAA-Asp, IAA, iP7G, OPDA, and 6-deoxyCS were significantly upregulated in the SP mutant, while the remaining 28 hormones were significantly downregulated. It is speculated that the decreased capacity of auxin, CTK, and BR-mediated cell division and cell enlargement pathways is crucial for the formation of the SP mutant. GA and stress-resistant pathways of ETH, JA, ABA, and SA also play vital roles in stem elongation. These results highlight the involvement of phytohormones in the formation of stem elongation occurring in 'Red Delicious' spur-type bud sport mutants and provide information for exploring its biological mechanism.

The eINTACT system dissects bacterial exploitation of plant osmosignalling to enhance virulence

Bacteria inject effector proteins into host cells to manipulate cellular processes that promote disease. Since bacteria deliver minuscule amounts of effectors only into targeted host cells, it is technically challenging to capture effector-dependent cellular changes from bulk-infected host tissues. Here, we report a new technique called effector-inducible isolation of nuclei tagged in specific cell types (eINTACT), which facilitates affinity-based purification of nuclei from Arabidopsis plant cells that have received Xanthomonas bacterial effectors. Analysis of purified nuclei reveals that the Xanthomonas effector XopD manipulates the expression of Arabidopsis abscisic acid signalling-related genes and activates OSCA1.1, a gene encoding a calcium-permeable channel required for stomatal closure in response to osmotic stress. The loss of OSCA1.1 causes leaf wilting and reduced bacterial growth in infected leaves, suggesting that OSCA1.1 promotes host susceptibility. eINTACT allows us to uncover that XopD exploits host OSCA1.1/abscisic acid osmosignalling-mediated stomatal closure to create a humid habitat that favours bacterial growth and opens up a new avenue for accurately elucidating functions of effectors from numerous gram-negative plant bacteria in native infection contexts.

Chromatin dynamics associated with seed desiccation tolerance/sensitivity at early germination in Medicago truncatula

Desiccation tolerance (DT) has contributed greatly to the adaptation of land plants to severe water-deficient conditions. DT is mostly observed in reproductive parts in flowering plants such as seeds. The seed DT is lost at early post germination stage but is temporally re-inducible in 1 mm radicles during the so-called DT window following a PEG treatment before being permanently silenced in 5 mm radicles of germinating seeds. The molecular mechanisms that activate/reactivate/silence DT in developing and germinating seeds have not yet been elucidated. Here, we analyzed chromatin dynamics related to re-inducibility of DT before and after the DT window at early germination in Medicago truncatula radicles to determine if DT-associated genes were transcriptionally regulated at the chromatin levels. Comparative transcriptome analysis of these radicles identified 948 genes as DT re-induction-related genes, positively correlated with DT re-induction. ATAC-Seq analyses revealed that the chromatin state of genomic regions containing these genes was clearly modulated by PEG treatment and affected by growth stages with opened chromatin in 1 mm radicles with PEG (R1P); intermediate openness in 1 mm radicles without PEG (R1); and condensed chromatin in 5 mm radicles without PEG (R5). In contrast, we also showed that the 103 genes negatively correlated with the re-induction of DT did not show any transcriptional regulation at the chromatin level. Additionally, ChIP-Seq analyses for repressive marks H2AK119ub and H3K27me3 detected a prominent signal of H3K27me3 on the DT re-induction-related gene sequences at R5 but not in R1 and R1P. Moreover, no clear H2AK119ub marks was observed on the DT re-induction-related gene sequences at both developmental radicle stages, suggesting that silencing of DT process after germination will be mainly due to H3K27me3 marks by the action of the PRC2 complex, without involvement of PRC1 complex. The dynamic of chromatin changes associated with H3K27me3 were also confirmed on seed-specific genes encoding potential DT-related proteins such as LEAs, oleosins and transcriptional factors. However, several transcriptional factors did not show a clear link between their decrease of chromatin openness and H3K27me3 levels, suggesting that their accessibility may also be regulated by additional factors, such as other histone modifications. Finally, in order to make these comprehensive genome-wide analyses of transcript and chromatin dynamics useful to the scientific community working on early germination and DT, we generated a dedicated genome browser containing all these data and publicly available at https://iris.angers.inrae.fr/mtseedepiatlas/jbrowse/?data=Mtruncatula.

Manipulating GA-Related Genes for Cereal Crop Improvement

The global population is projected to experience a rapid increase in the future, which poses a challenge to global food sustainability. The "Green Revolution" beginning in the 1960s allowed grain yield to reach two billion tons in 2000 due to the introduction of semi-dwarfing genes in cereal crops. Semi-dwarfing genes reduce the gibberellin (GA) signal, leading to short plant stature, which improves the lodging resistance and harvest index under modern fertilization practices. Here, we reviewed the literature on the function of GA in plant growth and development, and the role of GA-related genes in controlling key agronomic traits that contribute to grain yield in cereal crops. We showed that: (1) GA is a significant phytohormone in regulating plant development and reproduction; (2) GA metabolism and GA signalling pathways are two key components in GA-regulated plant growth; (3) GA interacts with other phytohormones manipulating plant development and reproduction; and (4) targeting GA signalling pathways is an effective genetic solution to improve agronomic traits in cereal crops. We suggest that the modification of GA-related genes and the identification of novel alleles without a negative impact on yield and adaptation are significant in cereal crop breeding for plant architecture improvement. We observed that an increasing number of GA-related genes and their mutants have been functionally validated, but only a limited number of GA-related genes have been genetically modified through conventional breeding tools and are widely used in crop breeding successfully. New genome editing technologies, such as the CRISPR/Cas9 system, hold the promise of validating the effectiveness of GA-related genes in crop development and opening a new venue for efficient and accelerated crop breeding.

Plant Development and Crop Yield: The Role of Gibberellins

Gibberellins have been classically related to a few key developmental processes, thus being essential for the accurate unfolding of plant genetic programs. After more than a century of research, over one hundred different gibberellins have been described. There is a continuously increasing interest in gibberellins research because of their relevant role in the so-called "Green Revolution", as well as their current and possible applications in crop improvement. The functions attributed to gibberellins have been traditionally restricted to the regulation of plant stature, seed germination, and flowering. Nonetheless, research in the last years has shown that these functions extend to many other relevant processes. In this review, the current knowledge on gibberellins homeostasis and mode of action is briefly outlined, while specific attention is focused on the many different responses in which gibberellins take part. Thus, those genes and proteins identified as being involved in the regulation of gibberellin responses in model and non-model species are highlighted. The present review aims to provide a comprehensive picture of the state-of-the-art perception of gibberellins molecular biology and its effects on plant development. This picture might be helpful to enhance our current understanding of gibberellins biology and provide the know-how for the development of more accurate research and breeding programs.

Phytochrome B enhances seed germination tolerance to high temperature by reducing S-nitrosylation of HFR1

Light and ambient high temperature (HT) have opposite effects on seed germination. Light induces seed germination through activating the photoreceptor phytochrome B (phyB), resulting in the stabilization of the transcription factor HFR1, which in turn sequesters the suppressor PIF1. HT suppresses seed germination and triggers protein S-nitrosylation. Here, we find that HT suppresses seed germination by inducing the S-nitrosylation of HFR1 at C164, resulting in its degradation, the release of PIF1, and the activation of PIF1-targeted SOMNUS (SOM) expression to alter gibberellin (GA) and abscisic acid (ABA) metabolism. Active phyB (phyBY276H ) antagonizes HFR1 S-nitrosylation and degradation by increasing S-nitrosoglutathione reductase (GSNOR) activity. In line with this, substituting cysteine-164 of HFR1 with serine (HFR1C164S ) abolishes the S-nitrosylation of HFR1 and decreases the HT-induced degradation of HFR1. Taken together, our study suggests that HT and phyB antagonistically modulate the S-nitrosylation level of HFR1 to coordinate seed germination, and provides the possibility to enhance seed thermotolerance through gene-editing of HFR1.

Physiological and Transcriptomic Responses of Growth in Neolamarckia cadamba Stimulated by Exogenous Gibberellins

(1) The phytohormones gibberellins (GAs) play a crucial role in plant growth and development, such as seed germination, flowering, fruiting, and stem elongation. Although many biological roles of GAs have been studied intensively, the molecular mechanisms of GAs in woody plants are still unclear. (2) In this study, we investigated the effects of exogenous application of GAs on Neolamarckia cadamba. (3) The height and biomass of N. cadamba increased after 7 days of GA treatment, especially on the second internode. Transcriptome analysis showed that although the majority of genes involved in the GA signaling pathway were up-regulated, the expression of GA20 oxidase (GA20ox) and GA3 oxidase (GA3ox) was down-regulated in the 3 days GA-treated group compared to the CK group. The expression of the cell elongation-related basic helix-loop-helix genes bHLH74 and bHLH49 was up-regulated in the GA-treated group compared with the CK group. Transcriptional expression levels of transcription factors involved in hormone signaling were changed, mainly including bHLH, ethylene response factor (ERF), and WRKY families. In addition, the transcriptional expression level of the key enzymes engaged in the phenylalanine pathway was downregulated after GA treatment. (4) In brief, our findings reveal the physiological and molecular mechanisms of exogenous GA treatment stimulation in N. cadamba.

Arabidopsis thaliana E3 ligase AIRP4 is involved in GA synthesis

Arabidopsis abscisic acid ABA-Insensitive RING Proteins (AtAIRP1-4) are RING E3s that play significant roles in ABA-signaling pathways. However, it is still unclear whether they have other functions. Here, AtAIRP4 was determined to play a role in response to gibberellin A3 (GA₃) in Arabidopsis thaliana. After proAtAIRP4::GUS transgenic lines were treated with GA₃, the GUS activity decreased in hypocotyls. Increased hypocotyl elongation in response to GA₃ seen in WT was not observed in the AtAIRP4-overexpression lines, whereas AtAIRP4-overexpression lines were hypersensitive to Paclobutrazol (PAC, an inhibitor of GA biosynthesis) during the seed germination stage. Additionally, AtAIRP4-overexpressing lines showed the lowest level of primary root elongation in the presence of GA₃. The levels of endogenous GA₃ in 35S::AtAIRP4 lines were lower than those in wild-type. In addition, among the plants, the mRNA levels of the GA synthetic gene GIBBERELLIN 20-OXIDASE1 (GA20ox1) was the lowest in overexpressing line. However, the expression of the response gene DELLA RGA-LIKE3 (RGL3) was the highest in overexpressing lines after treatment with GA₃. Thus, AtAIRP4 plays a negative role in GA-mediated hypocotyl elongation and root growth, and it inhibits the synthesis of endogenous biologically active GA₃ to some extent.

Integration of ABA, GA, and light signaling in seed germination through the regulation of ABI5

Seed germination is precisely controlled by a variety of signals, among which light signals and the phytohormones abscisic acid (ABA) and gibberellin (GA) play crucial roles. New findings have greatly increased our understanding of the mechanisms by which these three signals regulate seed germination and the close connections between them. Although much work has been devoted to ABA, GA, and light signal interactions, there is still no systematic description of their combination, especially in seed germination. In this review, we integrate ABA, GA, and light signaling in seed germination through the direct and indirect regulation of ABSCISIC ACID INSENSITIVE5 (ABI5), the core transcription factor that represses seed germination in ABA signaling, into our current understanding of the regulatory mechanism of seed germination.

ABSCISIC ACID INSENSITIVE 5 mediates light-ABA/gibberellin crosstalk networks during seed germination

Appropriate timing of seed germination is crucial for plant survival and has important implications for agricultural production. Timely germination relies on harmonious interactions between endogenous developmental signals, especially abscisic acid (ABA) and gibberellins (GAs), and environmental cues such as light. Recently, a series of investigations of a three-way crosstalk between phytochromes, ABA, and GAs in the regulation of seed germination demonstrated that the transcription factor ABSCISIC ACID INSENSITIVE 5 (ABI5) is a central mediator in the light-ABA/GA cascades. Here, we review current knowledge of ABI5 as a key player in light-, ABA-, and GA-signaling pathways that precisely control seed germination. We highlight recent advances in ABI5-related studies, focusing on the regulation of seed germination, which is strictly controlled at both the transcriptional and the protein levels by numerous light-regulated factors. We further discuss the components of ABA and GA signaling pathways that could regulate ABI5 during seed germination, including transcription factors, E3 ligases, protein kinases, and phosphatases. The precise molecular mechanisms by which ABI5 mediates ABA-GA antagonistic crosstalk during seed germination are also discussed. Finally, some potential research hotspots underlying ABI5-mediated seed germination regulatory networks are proposed.

The qLTG1.1 candidate gene CsGAI regulates low temperature seed germination in cucumber

The CsGAI gene, identified by map-based, was involved in regulating seed germination in low temperature via the GA and ABA signaling pathways. Low temperature reduces the percentage of seeds germinating and delays seed germinating time, thus posing a threat to cucumber production. However, the molecular mechanism regulating low temperature germination in cucumber is unknown. We here dissected a major quantitative trait locus qLTG1.1 that controls seed germination at low temperature in cucumber. First, we fine-mapped qLTG1.1 to a 46.3-kb interval, containing three candidate genes. Sequence alignment and gene expression analysis identified Csa1G408720 as the gene of interest that was highly expressed in seeds, and encoded a highly conserved, low temperature-regulated DELLA family protein CsGAI. GUS expression analysis indicated that higher promoter activity underscored higher transcriptional expression of the CsGAI gene. Consistent with the known roles of GAI in ABA and GA signaling during germination, genes involved in the GA (CsGA2ox, CsGA3ox) and ABA biosynthetic pathways (CsABA1, CsABA2, CsAAO3 and CsNCED) were found to be differently regulated in the tolerant and sensitive genotypes under low temperatures, and this was reflected in differences in their ratio of GA-to-ABA. Based on these data, we proposed a working model explaining how CsGAI integrates the GA and ABA signaling pathways, to regulate cucumber seed germination at low temperature, thus providing new insights into this mechanism.