Dormant and after-Ripened Arabidopsis thaliana Seeds are Distinguished by Early Transcriptional Differences in the Imbibed State

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.

Regulation of primary seed dormancy by MAJOR LATEX PROTEIN-LIKE PROTEIN329 in Arabidopsis is dependent on DNA-BINDING ONE ZINC FINGER6

Seeds exhibit primary dormancy to prevent germination under unfavourable conditions. Previous studies have shown that the gibberellin signalling intermediate RGA-LIKE2 (RGL2) forms a transcription factor complex with DNA-BINDING ONE ZINC FINGER6 (DOF6) in regulating seed dormancy in Arabidopsis. Using an RNA-sequencing approach, we identified MAJOR LATEX PROTEIN-LIKE PROTEIN329 (MLP329) as a downstream target of DOF6. MLP329 was found to be a positive regulator of primary seed dormancy, because freshly harvested unstratified mlp329 mutant seeds showed early germination, while unstratified transgenic seeds overexpressing MLP329 showed poor germination. MLP329 expression level was reduced in wild-type seeds upon dry storage and cold stratification. MLP329 expression level was enhanced by DOF6; however, DOF6-dependent MLP329 expression was suppressed in the presence of RGL2. MLP329 expression was enhanced in seeds treated with ABA and auxin IAA. Moreover, the mlp329 mutant seeds exhibited enhanced expression of the GA biosynthetic gene GA1 and suppression of the ABA biosynthetic gene ZEP compared to the overexpression lines. The observed suppression of DOF6-dependent MLP329 expression by RGL2 reveals a possible negative feedback mechanism to modulate seed dormancy. MLP329 also probably enhances the endogenous ABA/GA ratio to positively regulate primary seed dormancy.

Single seeds exhibit transcriptional heterogeneity during secondary dormancy induction

Seeds are highly resilient to the external environment, which allows plants to persist in unpredictable and unfavorable conditions. Some plant species have adopted a bet-hedging strategy to germinate a variable fraction of seeds in any given condition, and this could be explained by population-based threshold models. Here, in the model plant Arabidopsis (Arabidopsis thaliana), we induced secondary dormancy (SD) to address the transcriptional heterogeneity among seeds that leads to binary germination/nongermination outcomes. We developed a single-seed RNA-seq strategy that allowed us to observe a reduction in seed transcriptional heterogeneity as seeds enter stress conditions, followed by an increase during recovery. We identified groups of genes whose expression showed a specific pattern through a time course and used these groups to position the individual seeds along the transcriptional gradient of germination competence. In agreement, transcriptomes of dormancy-deficient seeds (mutant of DELAY OF GERMINATION 1) showed a shift toward higher values of the germination competence index. Interestingly, a significant fraction of genes with variable expression encoded translation-related factors. In summary, interrogating hundreds of single-seed transcriptomes during SD-inducing treatment revealed variability among the transcriptomes that could result from the distribution of population-based sensitivity thresholds. Our results also showed that single-seed RNA-seq is the method of choice for analyzing seed bet-hedging-related phenomena.

Coleorhiza-enforced seed dormancy: a novel mechanism to control germination in grasses

How the biophysical properties of overlaying tissues control growth, such as the embryonic root (radicle) during seed germination, is a fundamental question. In eudicot seeds the endosperm surrounding the radicle confers coat dormancy and controls germination responses through modulation of its cell wall mechanical properties. Far less is known for grass caryopses that differ in tissue morphology. Here we report that the coleorhiza, a sheath-like organ that surrounds the radicle in grass embryos, performs the same role in the grass weed Avena fatua (common wild oat). We combined innovative biomechanical techniques, tissue ablation, microscopy, tissue-specific gene and enzyme activity expression with the analysis of hormones and oligosaccharides. The combined experimental work demonstrates that in grass caryopses the coleorhiza indeed controls germination for which we provide direct biomechanical evidence. We show that the coleorhiza becomes reinforced during dormancy maintenance and weakened during germination. Xyloglucan endotransglycosylases/hydrolases may have a role in coleorhiza reinforcement through cell wall remodelling to confer coat dormancy. The control of germination by coleorhiza-enforced dormancy in grasses is an example of the convergent evolution of mechanical restraint by overlaying tissues.

ScreenSeed as a novel high throughput seed germination phenotyping method

A high throughput phenotyping tool for seed germination, the ScreenSeed technology, was developed with the aim of screening genotype responsiveness and chemical drugs. This technology was presently used with Arabidopsis thaliana seeds to allow characterizing seed samples germination behavior by incubating seeds in 96-well microplates under defined conditions and detecting radicle protrusion through the seed coat by automated image analysis. This study shows that this technology provides a fast procedure allowing to handle thousands of seeds without compromising repeatability or accuracy of the germination measurements. Potential biases of the experimental protocol were assessed through statistical analyses of germination kinetics. Comparison of the ScreenSeed procedure with commonly used germination tests based upon visual scoring displayed very similar germination kinetics.

Seed Dormancy: Molecular Control of Its Induction and Alleviation

A set of seed dormancy traits is included in this Special Issue. Thus, DELAY OF GERMINATION1 (DOG1) is reviewed in depth. Binding of DOG1 to Protein Phosphatase 2C ABSCISIC ACID (PP2C ABA) Hypersensitive Germination (AHG1) and heme are independent processes, but both are essential for DOG1’s function in vivo. AHG1 and DOG1 constitute a regulatory system for dormancy and germination. DOG1 affects the ABA INSENSITIVE5 (ABI5) expression level. Moreover, reactive oxygen species (ROS) homeostasis is linked with seed after-ripening (AR) process and the oxidation of a portion of seed long-lived (SLL) mRNAs seems to be related to dormancy release. The association of SLL mRNAs to monosomes is required for their transcriptional upregulation at the beginning of germination. Global DNA methylation levels remain stable during dormancy, decreasing when germination occurs. The remarkable intervention of auxin in the life of the seed is increasingly evident year after year. Here, its synergistic cooperation with ABA to promote the dormancy process is extensively reviewed. ABI3 participation in this process is critical. New data on the effect of alternating temperatures (ATs) on dormancy release are contained in this Special Issue. On the one hand, the transcriptome patterns stimulated at ATs comprised ethylene and ROS signaling and metabolism together with ABA degradation. On the other hand, a higher physical dormancy release was observed in Medicago truncatula under 35/15 °C than under 25/15 °C, and genome-wide association analysis identified 136 candidate genes related to secondary metabolite synthesis, hormone regulation, and modification of the cell wall. Finally, it is suggested that changes in endogenous γ-aminobutyric acid (GABA) may prevent chestnut germination, and a possible relation with H₂O₂ production is considered.

Dormancy cycling is accompanied by changes in ABA sensitivity in Polygonum aviculare seeds

Polygonum aviculare seeds show high levels of primary dormancy (PD). Low winter temperatures alleviate dormancy and high spring temperatures induce seeds into secondary dormancy (SD), naturally establishing stable seedbanks cycling through years. The objective of this work was to elucidate the mechanism(s) involved in PD expression and release, and in SD induction in these seeds, and the extent to which abscisic acid (ABA) and gibberellins (GAs) are part of these mechanisms. Quantification of endogenous ABA both prior to and during incubation, and sensitivity to ABA and GAs, were assessed in seeds with contrasting dormancy. Expression analysis was performed for candidate genes involved in hormone metabolism and signaling. It was found that endogenous ABA content does not explain either dormancy release or dormancy induction; moreover, it does not seem to play a role in dormancy maintenance. However, dormancy modifications were commonly accompanied by changes in ABA sensitivity. Concomitantly, induction into SD, but not PD, was characterized by a increased PaABI-5 and PaPYL transcription, and a rise in GA sensitivity as a possible counterbalance effect. These results suggest that dormancy cycling in this species is related to changes in embryo sensitivity to ABA; however, this sensitivity appears to be controlled by different molecular mechanisms in primary and secondary dormant seeds.

The seed water content as a time-independent physiological trait during germination in wild tree species such as Ceiba aesculifolia

Seeds constitute a key physiological stage in plants life cycle. During seed germination, there is a spatial-temporal imbibition pattern that correlates with described physiological processes. However, only the moment of testa rupture has been described as a critical, discrete stage. Could a specific relative water content (RWC) value reflect a physiological stage useful for comparisons between seed batches? We tracked seed-by-seed imbibition during germination to homogenize sampling and selected a transcriptomic approach to analyse the physiological transitions that occur in seed batches collected in different years and with contrasting phenotypic responses to a priming treatment. The seed RWC reflected the transcriptional transitions that occur during germination, regardless of imbibition time or collection year, and revealed a set of biological processes that occur in the dry seed and during early germination are associated with the phenotypic response to priming. As climate shifts, so do the timing of developmental events important for determining organismal fitness, and poses another challenge to the comprehension of molecular and physiological processes driving the interaction between organisms and environment. In this study, we demonstrate that the use of physiological traits, specific to a particular developmental stage, is a reliable time-independent approach.

Arabidopsis chloroplast J protein DJC75/CRRJ mediates nitrate-promoted seed germination in the dark

BACKGROUND AND AIMS

Nitrate can stimulate seed germination of many plant species in the absence of light; however, the molecular mechanism of nitrate-promoted seed germination in the dark remains largely unclear and no component of this pathway has been identified yet. Here, we show that a plastid J-domain protein, DJC75/CRRJ, in arabidopsis (Arabidopsis thaliana) is important for nitrate-promoted seed germination in the dark.

METHODS

The expression of DJC75 during imbibition in the dark was investigated. The seed germination rate of mutants defective in DJC75 was determined in the presence of nitrate when light cues for seed germination were eliminated by the treatment of imbibed seeds with a pulse of far-red light to inactivate phytochrome B (phyB), or by assaying germination in the dark with seeds harbouring the phyB mutation. The germination rates of mutants defective in CRRL, a J-like protein related to DJC75, and in two chloroplast Hsp70s were also measured in the presence of nitrate in darkness.

KEY RESULTS

DJC75 was expressed during seed imbibition in the absence of light. Mutants defective in DJC75 showed seed germination defects in the presence of nitrate when light cues for seed germination were eliminated. Mutants defective in CRRL and in two chloroplast Hsp70s also exhibited similar seed germination defects. Upregulation of gibberellin biosynthetic gene GA3ox1 expression by nitrate in imbibed phyB mutant seeds was diminished when DJC75 was knocked out.

CONCLUSIONS

Our data suggest that plastid J-domain protein DJC75 regulates nitrate-promoted seed germination in the dark by upregulation of expression of the gibberellin biosynthetic gene GA3ox1 through an unknown mechanism and that DJC75 may work in concert with chloroplast Hsp70s to regulate nitrate-promoted seed germination. DJC75 is the first pathway component identified for nitrate-promoted seed germination in the dark.

Reactive Oxygen Species (ROS) and Nucleic Acid Modifications During Seed Dormancy

The seed is the propagule of higher plants and allows its dissemination and the survival of the species. Seed dormancy prevents premature germination under favourable conditions. Dormant seeds are only able to germinate in a narrow range of conditions. During after-ripening (AR), a mechanism of dormancy release, seeds gradually lose dormancy through a period of dry storage. This review is mainly focused on how chemical modifications of mRNA and genomic DNA, such as oxidation and methylation, affect gene expression during late stages of seed development, especially during dormancy. The oxidation of specific nucleotides produced by reactive oxygen species (ROS) alters the stability of the seed stored mRNAs, being finally degraded or translated into non-functional proteins. DNA methylation is a well-known epigenetic mechanism of controlling gene expression. In Arabidopsis thaliana, while there is a global increase in CHH-context methylation through embryogenesis, global DNA methylation levels remain stable during seed dormancy, decreasing when germination occurs. The biological significance of nucleic acid oxidation and methylation upon seed development is discussed.

Breaking Seed Dormancy during Dry Storage: A Useful Tool or Major Problem for Successful Restoration via Direct Seeding?

To facilitate the restoration of disturbed vegetation, seeds of wild species are collected and held in dry storage, but often there is a shortage of seeds for this purpose. Thus, much research effort is expended to maximize the use of the available seeds and to ensure that they are nondormant when sown. Sowing nondormant (versus dormant) seeds in the field should increase the success of the restoration. Of the various treatments available to break seed dormancy, afterripening, that is, dormancy break during dry storage, is the most cost-effective. Seeds that can undergo afterripening have nondeep physiological dormancy, and this includes members of common families such as Asteraceae and Poaceae. In this review, we consider differences between species in terms of seed moisture content, temperature and time required for afterripening and discuss the conditions in which afterripening is rapid but could lead to seed aging and death if storage is too long. Attention is given to the induction of secondary dormancy in seeds that have become nondormant via afterripening and to the biochemical and molecular changes occurring in seeds during dry storage. Some recommendations are made for managing afterripening so that seeds are nondormant at the time for sowing. The most important recommendation probably is that germination responses of the seeds need to be monitored for germinability/viability during the storage period.

Delay of Germination-1 (DOG1): A Key to Understanding Seed Dormancy

DELAY OF GERMINATION-1 (DOG1), is a master regulator of primary dormancy (PD) that acts in concert with ABA to delay germination. The ABA and DOG1 signaling pathways converge since DOG1 requires protein phosphatase 2C (PP2C) to control PD. DOG1 enhances ABA signaling through its binding to PP2C ABA HYPERSENSITIVE GERMINATION (AHG1/AHG3). DOG1 suppresses the AHG1 action to enhance ABA sensitivity and impose PD. To carry out this suppression, the formation of DOG1-heme complex is essential. The binding of DOG1-AHG1 to DOG1-Heme is an independent processes but essential for DOG1 function. The quantity of active DOG1 in mature and viable seeds is correlated with the extent of PD. Thus, dog1 mutant seeds, which have scarce endogenous ABA and high gibberellin (GAs) content, exhibit a non-dormancy phenotype. Despite being studied extensively in recent years, little is known about the molecular mechanism underlying the transcriptional regulation of DOG1. However, it is well-known that the physiological function of DOG1 is tightly regulated by a complex array of transformations that include alternative splicing, alternative polyadenylation, histone modifications, and a cis-acting antisense non-coding transcript (asDOG1). The DOG1 becomes modified (i.e., inactivated) during seed after-ripening (AR), and its levels in viable seeds do not correlate with germination potential. Interestingly, it was recently found that the transcription factor (TF) bZIP67 binds to the DOG1 promoter. This is required to activate DOG1 expression leading to enhanced seed dormancy. On the other hand, seed development under low-temperature conditions triggers DOG1 expression by increasing the expression and abundance of bZIP67. Together, current data indicate that DOG1 function is not strictly limited to PD process, but that it is also required for other facets of seed maturation, in part by also interfering with the ethylene signaling components. Otherwise, since DOG1 also affects other processes such us flowering and drought tolerance, the approaches to understanding its mechanism of action and control are, at this time, still inconclusive.

Peptide transporter2 (PTR2) enhances water uptake during early seed germination in Arabidopsis thaliana

PTR2 in Arabidopsis thaliana is negatively regulated by ABI4 and plays a key role in water uptake by seeds, ensuring that imbibed seeds proceed to germination. Peptide transporters (PTRs) transport nitrogen-containing substrates in a proton-dependent manner. Among the six PTRs in Arabidopsis thaliana, the physiological role of the tonoplast-localized, seed embryo abundant PTR2 is unknown. In the present study, a molecular physiological analysis of PTR2 was conducted using ptr2 mutants and PTR2CO complementation lines. Compared with the wild type, the ptr2 mutant showed ca. 6 h delay in testa rupture and consequently endosperm rupture because of 17% lower water content and 10% higher free abscisic acid (ABA) content. Constitutive overexpression of the PTR2 gene under the control of the Cauliflower mosaic virus (CaMV) 35S promoter in ptr2 mutants rescued the mutant phenotypes. After cold stratification, a transient increase in ABA INSENSITIVE4 (ABI4) transcript levels during induction of testa rupture was followed by a similar increase in PTR2 transcript levels, which peaked prior to endosperm rupture. The PTR2 promoter region containing multiple CCAC motifs was recognized by ABI4 in electrophoretic mobility shift assays, and PTR2 expression was repressed by 67% in ABI4 overexpression lines compared with the wild type, suggesting that PTR2 is an immediate downstream target of ABI4. Taken together, the results suggest that ABI4-dependent temporal regulation of PTR2 expression may influence water status during seed germination to promote the post-germinative growth of imbibed seeds.

Dormancy cycling: translation-related transcripts are the main difference between dormant and non-dormant seeds in the field

Primary seed dormancy is a mechanism that orchestrates the timing of seed germination in order to prevent out-of-season germination. Secondary dormancy can be induced in imbibed seeds when they encounter prolonged unfavourable conditions. Secondary dormancy is not induced during dry storage, and therefore the mechanisms underlying this process have remained largely unexplored. Here, a 2-year seed burial experiment in which dormancy cycling was studied at the physiological and transcriptional level is presented. For these analyses six different Arabidopsis thaliana genotypes were used: Landsberg erecta (Ler) and the dormancy associated DELAY OF GERMINATION (DOG) near-isogenic lines 1, 2, 3, 6 and 22 (NILDOG1, 2, 3, 6 and 22). The germination potential of seeds exhumed from the field showed that these seeds go through dormancy cycling and that the dynamics of this cycling is genotype dependent. RNA-seq analysis revealed large transcriptional changes during dormancy cycling, especially at the time points preceding shifts in dormancy status. Dormancy cycling is driven by soil temperature and the endosperm is important in the perception of the environment. Genes that are upregulated in the low- to non-dormant stages are enriched for genes involved in translation, indicating that the non-dormant seeds are prepared for rapid seed germination.

Transcriptional Differences in Peanut (Arachis hypogaea L.) Seeds at the Freshly Harvested, After-ripening and Newly Germinated Seed Stages: Insights into the Regulatory Networks of Seed Dormancy Release and Germination

Seed dormancy and germination are the two important traits related to plant survival, reproduction and crop yield. To understand the regulatory mechanisms of these traits, it is crucial to clarify which genes or pathways participate in the regulation of these processes. However, little information is available on seed dormancy and germination in peanut. In this study, seeds of the variety Luhua No.14, which undergoes nondeep dormancy, were selected, and their transcriptional changes at three different developmental stages, the freshly harvested seed (FS), the after-ripening seed (DS) and the newly germinated seed (GS) stages, were investigated by comparative transcriptomic analysis. The results showed that genes with increased transcription in the DS vs FS comparison were overrepresented for oxidative phosphorylation, the glycolysis pathway and the tricarboxylic acid (TCA) cycle, suggesting that after a period of dry storage, the intermediates stored in the dry seeds were rapidly mobilized by glycolysis, the TCA cycle, the glyoxylate cycle, etc.; the electron transport chain accompanied by respiration was reactivated to provide ATP for the mobilization of other reserves and for seed germination. In the GS vs DS pairwise comparison, dozens of the upregulated genes were related to plant hormone biosynthesis and signal transduction, including the majority of components involved in the auxin signal pathway, brassinosteroid biosynthesis and signal transduction as well as some GA and ABA signal transduction genes. During seed germination, the expression of some EXPANSIN and XYLOGLUCAN ENDOTRANSGLYCOSYLASE genes was also significantly enhanced. To investigate the effects of different hormones during seed germination, the contents and differential distribution of ABA, GAs, BRs and IAA in the cotyledons, hypocotyls and radicles, and plumules of three seed sections at different developmental stages were also investigated. Combined with previous data in other species, it was suggested that the coordination of multiple hormone signal transduction nets plays a key role in radicle protrusion and seed germination.

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.

Regulatory actors and alternative routes for Arabidopsis seed germination are revealed using a pathway-based analysis of transcriptomic datasets

Regulation of seed germination by dormancy relies on a complex network of transcriptional and post-transcriptional modifications during seed imbibition that controls seed adaptive responses to environmental cues. High-throughput technologies have brought significant progress in the understanding of this phenomenon and have led to identify major regulators of seed germination, mostly by studying the behaviour of highly differentially expressed genes. However, the actual models of transcriptome analysis cannot catch additive effects of small variations of gene expression in individual signalling or metabolic pathways, which are also likely to control germination. Therefore, the comprehension of the molecular mechanism regulating germination is still incomplete and to gain knowledge about this process we have developed a pathway-based analysis of transcriptomic Arabidopsis datasets, to identify regulatory actors of seed germination. The method allowed quantifying the level of deregulation of a wide range of pathways in dormant versus non-dormant seeds. Clustering pathway deregulation scores of germinating and dormant seed samples permitted the identification of mechanisms involved in seed germination such as RNA transport or vitamin B6 metabolism, for example. Using this method, which was validated by metabolomics analysis, we also demonstrated that Col and Cvi seeds follow different metabolic routes for completing germination, demonstrating the genetic plasticity of this process. We finally provided an extensive basis of analysed transcriptomic datasets that will allow further identification of mechanisms controlling seed 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.

Integrating proteomics and enzymatic profiling to decipher seed metabolism affected by temperature in seed dormancy and germination

Temperature is an important environmental factor affecting seed dormancy and germination. The mechanism by which temperature induces germination in dormant seeds is however still unclear. Proteomic study has been performed in dormant sunflower seeds during imbibition at permissive and non-permissive temperatures for germination, 20 and 10 °C, respectively. Proteome analysis showed an increase of proteins belonging to metabolism and energy from the first hours of imbibition followed by a decrease of proteins involved in protein metabolism and seed storage in germinating compared to non-germinating seeds. Proteomic study was completed by polysome and proteasome activity assessment and enzymatic profiling on several altered proteins involved in metabolism and energy. Results showed that 20 °C treatment induced the activation of both protein synthesis and degradation processes, the latter being related to proteasome activity during the germination sensu stricto, and to other degradation processes such as proteases during the post-germination. Interestingly, enzymatic profiles showed that TCA cycle and glycolysis were more active in non-germinating seeds in the phase I of the germination sensu stricto. This result suggests the regulation of central metabolism activity in germinating seeds. The control of energy production during imbibition seems to be involved in molecular networks controlling seed dormancy and germination.

Biology in the Dry Seed: Transcriptome Changes Associated with Dry Seed Dormancy and Dormancy Loss in the Arabidopsis GA-Insensitive sleepy1-2 Mutant

Plant embryos can survive years in a desiccated, quiescent state within seeds. In many species, seeds are dormant and unable to germinate at maturity. They acquire the capacity to germinate through a period of dry storage called after-ripening (AR), a biological process that occurs at 5-15% moisture when most metabolic processes cease. Because stored transcripts are among the first proteins translated upon water uptake, they likely impact germination potential. Transcriptome changes associated with the increased seed dormancy of the GA-insensitive sly1-2 mutant, and with dormancy loss through long sly1-2 after-ripening (19 months) were characterized in dry seeds. The SLY1 gene was needed for proper down-regulation of translation-associated genes in mature dry seeds, and for AR up-regulation of these genes in germinating seeds. Thus, sly1-2 seed dormancy may result partly from failure to properly regulate protein translation, and partly from observed differences in transcription factor mRNA levels. Two positive regulators of seed dormancy, DELLA GAI (GA-INSENSITIVE) and the histone deacetylase HDA6/SIL1 (MODIFIERS OF SILENCING1) were strongly AR-down-regulated. These transcriptional changes appeared to be functionally relevant since loss of GAI function and application of a histone deacetylase inhibitor led to decreased sly1-2 seed dormancy. Thus, after-ripening may increase germination potential over time by reducing dormancy-promoting stored transcript levels. Differences in transcript accumulation with after-ripening correlated to differences in transcript stability, such that stable mRNAs appeared AR-up-regulated, and unstable transcripts AR-down-regulated. Thus, relative transcript levels may change with dry after-ripening partly as a consequence of differences in mRNA turnover.

Differentially expressed genes during the imbibition of dormant and after-ripened seeds - a reverse genetics approach

BACKGROUND

Seed dormancy, defined as the incapability of a viable seed to germinate under favourable conditions, is an important trait in nature and agriculture. Despite extensive research on dormancy and germination, many questions about the molecular mechanisms controlling these traits remain unanswered, likely due to its genetic complexity and the large environmental effects which are characteristic of these quantitative traits. To boost research towards revealing mechanisms in the control of seed dormancy and germination we depend on the identification of genes controlling those traits.

METHODS

We used transcriptome analysis combined with a reverse genetics approach to identify genes that are prominent for dormancy maintenance and germination in imbibed seeds of Arabidopsis thaliana. Comparative transcriptomics analysis was employed on freshly harvested (dormant) and after-ripened (AR; non-dormant) 24-h imbibed seeds of four different DELAY OF GERMINATION near isogenic lines (DOGNILs) and the Landsberg erecta (Ler) wild type with varying levels of primary dormancy. T-DNA knock-out lines of the identified genes were phenotypically investigated for their effect on dormancy and AR.

RESULTS

We identified conserved sets of 46 and 25 genes which displayed higher expression in seeds of all dormant and all after-ripened DOGNILs and Ler, respectively. Knock-out mutants in these genes showed dormancy and germination related phenotypes.

CONCLUSIONS

Most of the identified genes had not been implicated in seed dormancy or germination. This research will be useful to further decipher the molecular mechanisms by which these important ecological and commercial traits are regulated.

Transcriptional mechanisms associated with seed dormancy and dormancy loss in the gibberellin-insensitive sly1-2 mutant of Arabidopsis thaliana

While widespread transcriptome changes were previously observed with seed dormancy loss, this study specifically characterized transcriptional changes associated with the increased seed dormancy and dormancy loss of the gibberellin (GA) hormone-insensitive sleepy1-2 (sly1-2) mutant. The SLY1 gene encodes the F-box subunit of an SCF E3 ubiquitin ligase needed for GA-triggered proteolysis of DELLA repressors of seed germination. DELLA overaccumulation in sly1-2 seeds leads to increased dormancy that can be rescued without DELLA protein destruction either by overexpression of the GA receptor, GA-INSENSITIVE DWARF1b (GID1b-OE) (74% germination) or by extended dry after-ripening (11 months, 51% germination). After-ripening of sly1 resulted in different transcriptional changes in early versus late Phase II of germination that were consistent with the processes known to occur. Approximately half of the transcriptome changes with after-ripening appear to depend on SLY1-triggered DELLA proteolysis. Given that many of these SLY1/GA-dependent changes are genes involved in protein translation, it appears that GA signaling increases germination capacity in part by activating translation. While sly1-2 after-ripening was associated with transcript-level changes in 4594 genes over two imbibition timepoints, rescue of sly1-2 germination by GID1b-OE was associated with changes in only 23 genes. Thus, a big change in sly1-2 germination phenotype can occur with relatively little change in the global pattern of gene expression during the process of germination. Most GID1b-OE-responsive transcripts showed similar changes with after-ripening in early Phase II of imbibition, but opposite changes with after-ripening by late Phase II. This suggests that GID1b-OE stimulates germination early in imbibition, but may later trigger negative feedback regulation.