A Perspective on Secondary Seed Dormancy in Arabidopsis thaliana

A space for time. Exploring temporal regulation of plant development across spatial scales

Plants continuously undergo change during their life cycle, experiencing dramatic phase transitions altering plant form, and regulating the assignment and progression of cell fates. The relative timing of developmental events is tightly controlled and involves integration of environmental, spatial, and relative age-related signals and actors. While plant phase transitions have been studied extensively and many of their regulators have been described, less is known about temporal regulation on a smaller, cell-level scale. Here, using examples from both plant and animal systems, we outline time-dependent changes. Looking at systemic scale changes, we discuss the timing of germination, juvenile-to-adult transition, flowering, and senescence, together with regeneration timing. Switching to temporal regulation on a cellular level, we discuss several instances from the animal field in which temporal control has been examined extensively at this scale. Then, we switch back to plants and summarize examples where plant cell-level changes are temporally regulated. As time cannot easily be separated from signaling derived from the environment and tissue context, we next discuss factors that have been implicated in controlling the timing of developmental events, reviewing temperature, photoperiod, nutrient availability, as well as tissue context and mechanical cues on the cellular scale. Afterwards, we provide an overview of mechanisms that have been shown or implicated in the temporal control of development, considering metabolism, division control, mobile signals, epigenetic regulation, and the action of transcription factors. Lastly, we look at remaining questions for the future study of developmental timing in plants and how recent technical advancement can enable these efforts.

The BRAHMA-associated SWI/SNF chromatin remodeling complex controls Arabidopsis seed quality and physiology

The SWI/SNF (SWItch/Sucrose Non-Fermentable) chromatin remodeling complex is involved in various aspects of plant development and stress responses. Here, we investigated the role of BRM (BRAHMA), a core catalytic subunit of the SWI/SNF complex, in Arabidopsis thaliana seed biology. brm-3 seeds exhibited enlarged size, reduced yield, increased longevity, and enhanced secondary dormancy, but did not show changes in primary dormancy or salt tolerance. Some of these phenotypes depended on the expression of DOG1, a key regulator of seed dormancy, as they were restored in the brm-3 dog1-4 double mutant. Transcriptomic and metabolomic analyses revealed that BRM and DOG1 synergistically modulate the expression of numerous genes. Some of the changes observed in the brm-3 mutant, including increased glutathione levels, depended on a functional DOG1. We demonstrated that the BRM-containing chromatin remodeling complex directly controls secondary dormancy through DOG1 by binding and remodeling its 3' region, where the promoter of the long noncoding RNA asDOG1 is located. Our results suggest that BRM and DOG1 cooperate to control seed physiological properties and that BRM regulates DOG1 expression through asDOG1. This study reveals chromatin remodeling at the DOG1 locus as a molecular mechanism controlling the interplay between seed viability and dormancy.

Histone modifications affecting plant dormancy and dormancy release: common regulatory effects on hormone metabolism

As sessile organisms, plants enter periods of dormancy in response to environmental stresses to ensure continued growth and reproduction in the future. During dormancy, plant growth is suppressed, adaptive/survival mechanisms are exerted, and stress tolerance increases over a prolonged period until the plants resume their development or reproduction under favorable conditions. In this review, we focus on seed dormancy and bud dormancy, which are critical for adaptation to fluctuating environmental conditions. We provide an overview of the physiological characteristics of both types of dormancy as well as the importance of the phytohormones abscisic acid and gibberellin for establishing and releasing dormancy, respectively. Additionally, recent epigenetic analyses have revealed that dormancy establishment and release are associated with the removal and deposition of histone modifications at the loci of key regulatory genes influencing phytohormone metabolism and signaling, including DELAY OF GERMINATION 1 and DORMANCY-ASSOCIATED MADS-box genes. We discuss our current understanding of the physiological and molecular mechanisms required to establish and release seed dormancy and bud dormancy, while also describing how environmental conditions control dormancy depth, with a focus on the effects of histone modifications.

LAFL Factors in Seed Development and Phase Transitions

Development is a chain reaction in which one event leads to another until the completion of a life cycle. Phase transitions are milestone events in the cycle of life. LEAFY COTYLEDON1 (LEC1), ABA INSENSITIVE3 (ABI3), FUSCA3 (FUS3), and LEC2 proteins, collectively known as LAFL, are master transcription factors (TFs) regulating seed and other developmental processes. Since the initial characterization of the LAFL genes, more than three decades of active research has generated tremendous amounts of knowledge about these TFs, whose roles in seed development and germination have been comprehensively reviewed. Recent advances in cell biology with genetic and genomic tools have allowed the characterization of the LAFL regulatory networks in previously challenging tissues at a higher throughput and resolution in reference species and crops. In this review, we provide a holistic perspective by integrating advances at the epigenetic, transcriptional, posttranscriptional, and protein levels to exemplify the spatiotemporal regulation of the LAFL networks in Arabidopsis seed development and phase transitions, and we briefly discuss the evolution of these TF networks.

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.

Effect of intraspecific seed trait variation on the germination of eight tropical dry forest species

Functional traits can have intraspecific and interspecific variations essential in the structure and dynamics of natural communities. These traits may have implications in the germination and seedling establishment phases in seeds. The objective of this study was to evaluate the effect of variations in mass, volume, and nutrient content (C, N, and P) on the germination of eight species representative of the tropical dry forest (TDF). Our results showed that seed size, both in terms of mass and volume, did not predict germination rates or percentages, nor were they related to nutrient content. In contrast, N content was the most important trait in the germination phase. Larger seeds did not germinate more or faster, but they could offer better resistance against desiccation, since they had higher C/N ratios in their tissues, a characteristic of orthodox seeds. The species A. guachapele, B. arborea, H. crepitans, and V. tortuosa presented a high biological potential in terms of their regeneration capacity, particularly, because the characteristics of their seeds, as well as the nutrient content, revealed consistent implications in their reproductive success, promoting high germination percentages in less time. In general, the results obtained in this study provide basic knowledge for future research, offering starting points for further exploration of species-specific adaptations and how they may be affected by the environment.

Dormancy heterogeneity among Arabidopsis thaliana seeds is linked to individual seed size

Production of morphologically and physiologically variable seeds is an important strategy that helps plants to survive in unpredictable natural conditions. However, the model plant Arabidopsis thaliana and most agronomically essential crops produce visually homogenous seeds. Using automated phenotype analysis, we observed that small seeds in Arabidopsis tend to have higher primary and secondary dormancy levels than large seeds. Transcriptomic analysis revealed distinct gene expression profiles between large and small seeds. Large seeds have higher expression of translation-related genes implicated in germination competence. By contrast, small seeds have elevated expression of many positive regulators of dormancy, including a key regulator of this process, the DOG1 gene. Differences in DOG1 expression are associated with differential production of its alternative cleavage and polyadenylation isoforms; in small seeds, the proximal poly(A) site is selected, resulting in a short mRNA isoform. Furthermore, single-seed RNA sequencing analysis demonstrated that large seeds resemble DOG1 knockout mutant seeds. Finally, on the single-seed level, expression of genes affected by seed size is correlated with expression of genes that position seeds on the path toward germination. Our results demonstrate an unexpected link between seed size and dormancy phenotypes in a species that produces highly homogenous seed pools, suggesting that the correlation between seed morphology and physiology is more widespread than initially assumed.

A method to determine antifungal activity in seed exudates by nephelometry

BACKGROUND

One of the levers towards alternative solutions to pesticides is to improve seed defenses against pathogens, but a better understanding is needed on the type and regulation of existing pathways during germination. Dormant seeds are able to defend themselves against microorganisms during cycles of rehydration and dehydration in the soil. During imbibition, seeds leak copious amounts of exudates. Here, we developed a nephelometry method to assay antimicrobial activity (AA) in tomato seed exudates as a proxy to assess level of defenses.

RESULTS

A protocol is described to determine the level of AA against the nonhost filamentous fungus Alternaria brassicicola in the exudates of tomato seeds and seedlings. The fungal and exudate concentrations can be adjusted to modulate the assay sensitivity, thereby providing a large window of AA detection. We established that AA in dormant seeds depends on the genotype. It ranged from very strong AA to complete absence of AA, even after prolonged imbibition. AA depends also on the stages of germination and seedling emergence. Exudates from germinated seeds and seedlings showed very strong AA, while those from dormant seeds exhibited less activity for the same imbibition time. The exudate AA did not impact the growth of a pathogenic fungus host of tomato, Alternaria alternata, illustrating the adaptation of this fungus to its host.

CONCLUSIONS

We demonstrate that our nephelometry method is a simple yet powerful bioassay to quantify AA in seed exudates. Different developmental stages from dormant seed to seedlings show different levels of AA in the exudate that vary between genotypes, highlighting a genetic diversity x developmental stage interaction in defense. These findings will be important to identify molecules in the exudates conferring antifungal properties and obtain a better understanding of the regulatory and biosynthetic pathways through the lifecycle of seeds, from dormant seeds until seedling emergence.

Seed Germination of Three Milk Thistle (Silybum marianum (L.) Gaertn.) Populations of Greek Origin: Temperature, Duration, and Storage Conditions Effects

Milk thistle besides being a highly competitive weed is cultivated as a medicinal plant, and the seeds of which have been clinically utilized in several disorders caused in liver. The present study aims to evaluate the effect of duration and storage conditions, population, and temperature on seed germination. The experiment was conducted in Petri dishes with three replications and three factors: (a) wild populations of milk thistle (Palaionterveno, Mesopotamia, and Spata) originating from Greece, (b) duration and storage conditions (5 months at room temperature, 17 months at room temperature, and 29 months in the freezer at -18 °C), and (c) temperature (5 °C, 10 °C, 15 °C, 20 °C, 25 °C, and 30 °C). All three factors significantly affected germination percentage (GP), mean germination time (MGT), germination index (GI), radicle length (RL), and hypocotyl length (HL) and significant interactions among the treatments were noted. In specific, no seed germination was recorded at 5 °C, while the populations showed higher GP and GI at 20 °C and 25 °C after 5 months of storage. Prolonged storage negatively affected seed germination although, cold storage mitigated this effect. Moreover, higher temperatures reduced MGT and increased RL and HL with the populations reacting differently in storage and temperature regimes. The results of this study should be taken into consideration when proposing the appropriate sowing date and storage conditions of the seeds used as propagation material for crop establishment. Moreover, the effects of low temperatures such as 5 °C or 10 °C on seed germination as well as the high decline rate in germination percentage over time could be utilized in the design of integrated weed management systems thereby indicating the importance of the sowing time and the suitable crop rotation system to weed control.

A test of local adaptation to drought in germination and seedling traits in populations of two alpine forbs across a 2000 mm/year precipitation gradient

Seed regeneration is a critical stage in the life histories of plants, affecting species' abilities to maintain local populations, evolve, and disperse to new sites. In this study, we test for local adaptations to drought in germination and seedling growth of two alpine forbs with contrasting habitat preferences: the alpine generalist Veronica alpina and the snowbed specialist Sibbaldia procumbens. We sampled seeds of each species from four populations spanning a precipitation gradient from 1200 to 3400 mm/year in western Norway. In a growth chamber experiment, we germinated seeds from each population at 10 different water potentials under controlled light and temperature conditions. Drought led to lower germination percentage in both species, and additionally, slower germination, and more investment in roots for V. alpina. These responses varied along the precipitation gradient. Seeds from the driest populations had higher germination percentage, shorter time to germination, and higher investments in the roots under drought conditions than the seeds from the wettest populations - suggesting local adaption to drought. The snowbed specialist, S. procumbens, had lower germination percentages under drought, but otherwise did not respond to drought in ways that indicate physiological or morphological adaptions to drought. S. procumbens germination also did not vary systematically with precipitation of the source site, but heavier-seeded populations germinated to higher rates and tolerated drought better. Our study is the first to test drought effects on seed regeneration in alpine plants populations from high-precipitation regions. We found evidence that germination and seedling traits may show adaptation to drought even in populations from wet habitats. Our results also indicate that alpine generalists might be more adapted to drought and show more local adaptations in drought responses than snowbed specialists.

Assessing Seedbank Longevity and Seed Persistence of the Invasive Tussock Grass Nassella trichotoma Using in-Field Burial and Laboratory-Controlled Ageing

The ability to produce highly dense and persistent seedbanks is a major contributor to the successful widespread establishment of invasive plants. This study seeks to identify seed persistence and seedbank longevity for the invasive tussock grass Nassella trichotoma (Nees.) Hack. ex Arechav in order to recommend management strategies for preventing re-emergence from the seedbank. To determine the seedbank longevity and persistence, two experiments were conducted: (i) seeds were buried at four depths (0, 1, 2, and 4 cm) and collected and assessed for viability, seed decay, and in-field germination after 6, 9, 12, 15, and 18 months of field burial; and (ii) seeds were exposed to artificial ageing conditions (60% RH and 45 °C) for 1, 2, 5, 9, 20, 30, 50, 75, 100, and 120 days, and viability was determined through germination tests and tetrazolium tests. Less than 10% of the seeds collected after 12 months of in-field burial were viable. The artificial ageing treatment found germination declined to 50% after 5.8 days, further suggesting that N. trichotoma seeds are short lived. The results from both experiments indicate that N. trichotoma has a transient seedbank, with less than 10% of the seeds demonstrating short-term persistence. It is likely the persistent seeds beyond 12 months were exhibiting secondary dormancy as viable seeds did not germinate under optimal germination conditions. The "Best Practice Guidelines" recommend monitoring for seedbank recruitment for at least three years after treating N. trichotoma infestations. The results of this study support this recommendation as a small proportion of the seeds demonstrated short-term persistence.

The membrane associated NAC transcription factors ANAC060 and ANAC040 are functionally redundant in the inhibition of seed dormancy in Arabidopsis thaliana

The NAC family of transcription factors is involved in plant development and various biotic and abiotic stresses. The Arabidopsis thaliana ANAC genes ANAC060, ANAC040, and ANAC089 are highly homologous based on protein and nucleotide sequence similarity. These three genes are predicted to be membrane bound transcription factors (MTFs) containing a conserved NAC domain, but divergent C-terminal regions. The anac060 mutant shows increased dormancy when compared with the wild type. Mutations in ANAC040 lead to higher seed germination under salt stress, and a premature stop codon in ANAC089 Cvi allele results in seeds exhibiting insensitivity to high concentrations of fructose. Thus, these three homologous MTFs confer distinct functions, although all related to germination. To investigate whether the differences in function are caused by a differential spatial or temporal regulation, or by differences in the coding sequence (CDS), we performed swapping experiments in which the promoter and CDS of the three MTFs were exchanged. Seed dormancy and salt and fructose sensitivity analyses of transgenic swapping lines in mutant backgrounds showed that there is functional redundancy between ANAC060 and ANAC040, but not between ANAC060 and ANAC089.

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.

Parental and Environmental Control of Seed Dormancy in Arabidopsis thaliana

Seed dormancy-the absence of seed germination under favorable germination conditions-is a plant trait that evolved to enhance seedling survival by avoiding germination under unsuitable environmental conditions. In Arabidopsis, dormancy levels are influenced by the seed coat composition, while the endosperm is essential to repress seed germination of dormant seeds upon their imbibition. Recent research has shown that the mother plant modulates its progeny seed dormancy in response to seasonal temperature changes by changing specific aspects of seed coat and endosperm development. This process involves genomic imprinting by means of epigenetic marks deposited in the seed progeny and regulators previously known to regulate flowering time. This review discusses and summarizes these discoveries and provides an update on our present understanding of the role of DOG1 and abscisic acid, two key contributors to dormancy.

Transcriptional control of Arabidopsis seed development

The entire process of embryo development is under the tight control of various transcription factors. Together with other proteins, they act in a combinatorial manner and control distinct events during embryo development. Seed development is a complex process that proceeds through sequences of events regulated by the interplay of various genes, prominent among them being the transcription factors (TFs). The members of WOX, HD-ZIP III, ARF, and CUC families have a preferential role in embryonic patterning. While WOX TFs are required for initiating body axis, HD-ZIP III TFs and CUCs establish bilateral symmetry and SAM. And ARF5 performs a major role during embryonic root, ground tissue, and vasculature development. TFs such as LEC1, ABI3, FUS3, and LEC2 (LAFL) are considered the master regulators of seed maturation. Furthermore, several new TFs involved in seed storage reserves and dormancy have been identified in the last few years. Their association with those master regulators has been established in the model plant Arabidopsis. Also, using chromatin immunoprecipitation (ChIP) assay coupled with transcriptomics, genome-wide target genes of these master regulators have recently been proposed. Many seed-specific genes, including those encoding oleosins and albumins, have appeared as the direct target of LAFL. Also, several other TFs act downstream of LAFL TFs and perform their function during maturation. In this review, the function of different TFs in different phases of early embryogenesis and maturation is discussed in detail, including information about their genetic and molecular interactors and target genes. Such knowledge can further be leveraged to understand and manipulate the regulatory mechanisms involved in seed development. In addition, the genomics approaches and their utilization to identify TFs aiming to study embryo development are discussed.

ABA Metabolism and Homeostasis in Seed Dormancy and Germination

Abscisic acid (ABA) is a key hormone that promotes dormancy during seed development on the mother plant and after seed dispersal participates in the control of dormancy release and germination in response to environmental signals. The modulation of ABA endogenous levels is largely achieved by fine-tuning, in the different seed tissues, hormone synthesis by cleavage of carotenoid precursors and inactivation by 8'-hydroxylation. In this review, we provide an overview of the current knowledge on ABA metabolism in developing and germinating seeds; notably, how environmental signals such as light, temperature and nitrate control seed dormancy through the adjustment of hormone levels. A number of regulatory factors have been recently identified which functional relationships with major transcription factors, such as ABA INSENSITIVE3 (ABI3), ABI4 and ABI5, have an essential role in the control of seed ABA levels. The increasing importance of epigenetic mechanisms in the regulation of ABA metabolism gene expression is also described. In the last section, we give an overview of natural variations of ABA metabolism genes and their effects on seed germination, which could be useful both in future studies to better understand the regulation of ABA metabolism and to identify candidates as breeding materials for improving germination properties.

Temperate Fruit Trees under Climate Change: Challenges for Dormancy and Chilling Requirements in Warm Winter Regions

Adequate chill is of great importance for successful production of deciduous fruit trees. However, temperate fruit trees grown under tropical and subtropical regions may face insufficient winter chill, which has a crucial role in dormancy and productivity. The objective of this review is to discuss the challenges for dormancy and chilling requirements of temperate fruit trees, especially in warm winter regions, under climate change conditions. After defining climate change and dormancy, the effects of climate change on various parameters of temperate fruit trees are described. Then, dormancy breaking chemicals and organic compounds, as well as some aspects of the mechanism of dormancy breaking, are demonstrated. After this, the relationships between dormancy and chilling requirements are delineated and challenging aspects of chilling requirements in climate change conditions and in warm winter environments are demonstrated. Experts have sought to develop models for estimating chilling requirements and dormancy breaking in order to improve the adaption of temperate fruit trees under tropical and subtropical environments. Some of these models and their uses are described in the final section of this review. In conclusion, global warming has led to chill deficit during winter, which may become a limiting factor in the near future for the growth of temperate fruit trees in the tropics and subtropics. With the increasing rate of climate change, improvements in some managing tools (e.g., discovering new, more effective dormancy breaking organic compounds; breeding new, climate-smart cultivars in order to solve problems associated with dormancy and chilling requirements; and improving dormancy and chilling forecasting models) have the potential to solve the challenges of dormancy and chilling requirements for temperate fruit tree production in warm winter fruit tree growing regions.

Time to Wake Up: Epigenetic and Small-RNA-Mediated Regulation during Seed Germination

Plants make decisions throughout their lifetime based on complex networks. Phase transitions during seed growth are not an exception. From embryo development through seedling growth, several molecular pathways control genome stability, environmental signal transduction and the transcriptional landscape. Particularly, epigenetic modifications and small non-coding RNAs (sRNAs) have been extensively studied as significant handlers of these processes in plants. Here, we review key epigenetic (histone modifications and methylation patterns) and sRNA-mediated regulatory networks involved in the progression from seed maturation to germination, their relationship with seed traits and crosstalk with environmental inputs.