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.

ABA and GA4 dynamic modulates secondary dormancy and germination in Syngonanthus verticillatus seeds.

MAIN CONCLUSION: ABA and GA metabolism during incubation rather than hormone contents in dry seeds is the key to understanding secondary dormancy and germination of Syngonanthus verticillatus seeds. The mechanism of seed dormancy cycle, although very important for preventing germination during unfavorable periods for seedling establishment, is poorly understood in tropical species. Here, we used a perennial tropical species of the Brazilian campo rupestre, Syngonanthus verticillatus (Eriocaulaceae), to investigate the involvement of ABA and GA in modulating secondary dormancy of seeds buried in situ over time and the dynamic of these hormones during the incubation of dormant and non-dormant seeds. Hormone analyses were carried out with freshly harvested seeds and on buried seeds exhumed after 3, 6 and 9 months. Dynamics of ABA and GAs in dormant and non-dormant seeds during incubation (0, 12, 24 and 36 h) under favorable conditions for germination (at 20 °C in the presence of light) were also investigated. In addition, the effects of GA4 and fluridone were evaluated for overcoming secondary dormancy. Our results showed that changes in the contents of both ABA and GA4 occurred after burial, suggesting they may be related to the modulation of secondary dormancy/germination of S. verticillatus seeds. The application of fluridone was more effective than GA4 at overcoming secondary dormancy. We conclude that during incubation, de novo ABA synthesis and its consequent maintenance at high contents regulate the inhibition of germination in dormant seeds, while GA4 synthesis and ABA catabolism modulate the germination of non-dormant seeds. ABA and GA metabolism during incubation of both dormant and non-dormant seeds rather than hormone contents of dry seeds in the field is thought to be the key to understanding secondary dormancy and germination.

Trait analysis reveals DOG1 determines initial depth of seed dormancy, but not changes during dormancy cycling that result in seedling emergence timing.

Seedling emergence timing is crucial in competitive plant communities and so contributes to species fitness. To understand the mechanistic basis of variation in seedling emergence timing, we exploited the contrasting behaviour of two Arabidopsis thaliana ecotypes: Cape Verde Islands (Cvi) and Burren (Bur-0). We used RNA-Seq analysis of RNA from exhumed seeds and quantitative trait loci (QTL) analyses on a mapping population from crossing the Cvi and Bur-0 ecotypes. We determined genome-wide expression patterns over an annual dormancy cycle in both ecotypes, identifying nine major clusters based on the seasonal timing of gene expression, and variation in behaviour between them. QTL were identified for depth of seed dormancy and seedling emergence timing (SET). Both analyses showed a key role for DOG1 in determining depth of dormancy, but did not support a direct role for DOG1 in generating altered seasonal patterns of seedling emergence. The principle QTL determining SET (SET1: dormancy cycling) is physically close on chromosome 5, but is distinct from DOG1. We show that SET1 and two other SET QTLs each contain a candidate gene (AHG1, ANAC060, PDF1 respectively) closely associated with DOG1 and abscisic acid signalling and suggest a model for the control of SET in the field.

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.

DNA damage checkpoint kinase ATM regulates germination and maintains genome stability in seeds.

Genome integrity is crucial for cellular survival and the faithful transmission of genetic information. The eukaryotic cellular response to DNA damage is orchestrated by the DNA damage checkpoint kinases ATAXIA TELANGIECTASIA MUTATED (ATM) and ATM AND RAD3-RELATED (ATR). Here we identify important physiological roles for these sensor kinases in control of seed germination. We demonstrate that double-strand breaks (DSBs) are rate-limiting for germination. We identify that desiccation tolerant seeds exhibit a striking transcriptional DSB damage response during germination, indicative of high levels of genotoxic stress, which is induced following maturation drying and quiescence. Mutant atr and atm seeds are highly resistant to aging, establishing ATM and ATR as determinants of seed viability. In response to aging, ATM delays germination, whereas atm mutant seeds germinate with extensive chromosomal abnormalities. This identifies ATM as a major factor that controls germination in aged seeds, integrating progression through germination with surveillance of genome integrity. Mechanistically, ATM functions through control of DNA replication in imbibing seeds. ATM signaling is mediated by transcriptional control of the cell cycle inhibitor SIAMESE-RELATED 5, an essential factor required for the aging-induced delay to germination. In the soil seed bank, seeds exhibit increased transcript levels of ATM and ATR, with changes in dormancy and germination potential modulated by environmental signals, including temperature and soil moisture. Collectively, our findings reveal physiological functions for these sensor kinases in linking genome integrity to germination, thereby influencing seed quality, crucial for plant survival in the natural environment and sustainable crop production.

Seed dormancy cycling and the regulation of dormancy mechanisms to time germination in variable field environments.

Many molecular mechanisms that regulate dormancy have been identified individually in controlled laboratory studies. However, little is known about how the seed employs this complex suite of mechanisms during dormancy cycling in the variable environment of the soil seed bank. Nevertheless, this behaviour is essential to ensure germination takes place in a favourable habitat and climate space, and in the correct season for the resulting plant to complete its life cycle. During their time in the soil seed bank, seeds continually adjust their dormancy status by sensing a range of environmental signals. Those related to slow seasonal change (e.g. temperature) are used for temporal sensing to determine the time of year and depth of dormancy. This alters their sensitivity to signals related to their spatial environment (e.g. light, nitrate, and water potential) that indicate that conditions are suitable for germination, and so trigger the termination of dormancy. We review work on the physiological, molecular, and ecological aspects of seed dormancy in Arabidopsis and interpret it in the context of dormancy cycling in the soil seed bank. This approach has provided new insight into the co-ordination of mechanisms and signalling networks, and the multidimensional sensing that regulates dormancy cycling in a variable environment.

Seed dormancy cycling in Arabidopsis: chromatin remodelling and regulation of DOG1 in response to seasonal environmental signals.

The involvement of chromatin remodelling in dormancy cycling in the soil seed bank (SSB) is poorly understood. Natural variation between the winter and summer annual Arabidopsis ecotypes Cvi and Bur was exploited to investigate the expression of genes involved in chromatin remodelling via histone 2B (H2B) ubiquitination/de-ubiquitination and histone acetylation/deacetylation, the repressive histone methyl transferases CURLY LEAF (CLF) and SWINGER (SWN), and the gene silencing repressor ROS1 (REPRESSOR OF SILENCING1) and promoter of silencing KYP/SUVH4 (KRYPTONITE), during dormancy cycling in the SSB. ROS1 expression was positively correlated with dormancy while the reverse was observed for CLF and KYP/SUVH4. We propose ROS1 dependent repression of silencing and a sequential requirement of CLF and KYP/SUVH4 dependent gene repression and silencing for the maintenance and suppression of dormancy during dormancy cycling. Seasonal expression of H2B modifying genes was correlated negatively with temperature and positively with DOG1 expression, as were histone acetyltransferase genes, with histone deacetylases positively correlated with temperature. Changes in the histone marks H3K4me3 and H3K27me3 were seen on DOG1 (DELAY OF GERMINATION1) in Cvi during dormancy cycling. H3K4me3 activating marks remained stable along DOG1. During relief of dormancy, H3K27me3 repressive marks slowly accumulated and accelerated on exposure to light completing dormancy loss. We propose that these marks on DOG1 serve as a thermal sensing mechanism during dormancy cycling in preparation for light repression of dormancy. Overall, chromatin remodelling plays a vital role in temporal sensing through regulation of gene expression.

Seed dormancy cycling and mortality differ between two locally adapted populations of Arabidopsis thaliana.

BACKGROUND AND AIMS: Intraspecific variation in seed bank dynamics should contribute to local adaptation, but is not well studied. The extent to which genetic and environmental factors affect dormancy cycling and seed mortality was investigated in the annual herb Arabidopsis thaliana by conducting a reciprocal seed burial experiment. METHODS: Seeds from two locally adapted populations (from Italy and Sweden) were buried at both of the sites of origin, and seed mortality and germinability were determined during the following 2 years for initially non-dormant glasshouse-matured seeds and dormant field-matured seeds. KEY RESULTS: Mean soil temperature was higher at the Italian site compared with the Swedish site throughout the year, and the germination proportions were in general higher for seeds buried in Italy than in Sweden. The rate of secondary dormancy induction of the Italian genotype was faster than that of the Swedish genotype at both sites, while the opposite was true for the rate of dormancy release, at least at the Swedish site. The comparison of non-dormant glasshouse seeds with dormant field seeds demonstrated that A. thaliana seeds can adjust their dormancy levels to current environmental conditions, and suggests that maternal environmental conditions have only minor effects on dormancy cycles. At both sites, locally produced seeds had low germinability in the first year compared with the second year, suggesting that a considerable fraction of the seeds would enter the seed bank. In Italy, but not in Sweden, seed mortality increased rapidly during the second year of burial. CONCLUSIONS: This is the first demonstration of intraspecific genetic differentiation in the annual seed dormancy cycle of any species, and the documented difference is likely to contribute to local adaptation. The results suggest that the contribution of a seed bank to seedling recruitment should vary among environments due to differences in the rate of seed mortality.

Environment sensing in spring-dispersed seeds of a winter annual Arabidopsis influences the regulation of dormancy to align germination potential with seasonal changes.

Seed dormancy cycling plays a crucial role in the lifecycle timing of many plants. Little is known of how the seeds respond to the soil seed bank environment following dispersal in spring into the short-term seed bank before seedling emergence in autumn. Seeds of the winter annual Arabidopsis ecotype Cvi were buried in field soils in spring and recovered monthly until autumn and their molecular eco-physiological responses were recorded. DOG1 expression is initially low and then increases as dormancy increases. MFT expression is negatively correlated with germination potential. Abscisic acid (ABA) and gibberellin (GA) signalling responds rapidly following burial and adjusts to the seasonal change in soil temperature. Collectively these changes align germination potential with the optimum climate space for seedling emergence. Seeds naturally dispersed to the soil in spring enter a shallow dormancy cycle dominated by spatial sensing that adjusts germination potential to the maximum when soil environment is most favourable for germination and seedling emergence upon soil disturbance. This behaviour differs subtly from that of seeds overwintered in the soil seed bank to spread the period of potential germination in the seed population (existing seed bank and newly dispersed). As soil temperature declines in autumn, deep dormancy is re-imposed as seeds become part of the persistent seed bank.

Dormancy cycling and persistence of seeds in soil of a cold desert halophyte shrub.

BACKGROUND AND AIMS: Formation of seed banks and dormancy cycling are well known in annual species, but not in woody species. In this study it was hypothesized that the long-lived halophytic cold desert shrub Kalidium gracile has a seed bank and dormancy cycling, which help restrict germination to a favourable time for seedling survival. METHODS: Fresh seeds were buried in November 2009 and exhumed and tested for germination monthly from May 2010 to December 2011 over a range of temperatures and salinities. Germination recovery and viability were determined after exposure to salinity and water stress. Seedling emergence and dynamics of the soil seed bank were investigated in the field. KEY RESULTS: Seeds of K. gracile had a soil seed bank of 7030 seeds m(-2) at the beginning of the growing season. About 72 % of the seeds were depleted from the soil seed bank during a growing season, and only 1·4 % of them gave rise to seedlings that germinated early enough to reach a stage of growth at which they could survive to overwinter. About 28 % of the seeds became part of a persistent soil seed bank. Buried seeds exhibited an annual non-dormancy/conditional dormancy (ND/CD) cycle, and germination varied in sensitivity to salinity during the cycle. Dormancy cycling is coordinated with seasonal environmental conditions in such a way that the seeds germinate in summer, when there is sufficient precipitation for seedling establishment. CONCLUSIONS: Kalidium gracile has three life history traits that help ensure persistence at a site: a polycarpic perennial life cycle, a persistent seed bank and dormancy cycling. The annual ND/CD cycle in seeds of K. gracile contributes to seedling establishment of this species in the unpredictable desert environment and to maintenance of a persistent soil seed bank. This is the first report of a seed dormancy cycle in a cold desert shrub.

Long days induce adaptive secondary dormancy in the seeds of the Mediterranean plant Aethionema arabicum.

Secondary dormancy is an adaptive trait that increases reproductive success by aligning seed germination with permissive conditions for seedling establishment. Aethionema arabicum is an annual plant and member of the Brassicaceae that grows in environments characterized by hot and dry summers. Aethionema arabicum seeds may germinate in early spring when seedling establishment is permissible. We demonstrate that long-day light regimes induce secondary dormancy in the seeds of Aethionema arabicum (CYP accession), repressing germination in summer when seedling establishment is riskier. Characterization of mutants screened for defective secondary dormancy demonstrated that RGL2 mediates repression of genes involved in gibberellin (GA) signaling. Exposure to high temperature alleviates secondary dormancy, restoring germination potential. These data are consistent with the hypothesis that long-day-induced secondary dormancy and its alleviation by high temperatures may be part of an adaptive response limiting germination to conditions permissive for seedling establishment in spring and autumn.

A Travel through Landscapes of Seed Dormancy.

Basic features of seed dormancy are illustrated. The seed overall regulatory network governs seed metabolism and development, and it is coordinated by plant hormones. A functional model focused on abscisic acid (ABA), the foremost plant hormone in dormancy, is used as a framework to critically discuss the literature. Gibberellins (GAs) have a main role in germination, and the ABA-GAs balance is a typical feature of the seed state: ABA dominates during dormancy and GAs prevail through germination. Thus, the literature converges toward envisaging the development switch between dormancy and germination as represented by the ABA/GAs ratio. The ABA-GAs antagonism is based on mutual inhibition, a feature of the regulatory network architecture that characterizes development trajectories based on a regulatory circuit with a bistable switch. Properties of such kind of regulatory architecture are introduced step by step, and it is shown that seed development-toward either dormancy or germination-is more properly represented by a tristable regulatory circuit, whose intermediate metastable states ultimately take one or the other development trajectory. Although the ABA/GAs ratio can conveniently represent the state of the seed overall regulatory network along the seed development trajectory, specific (unknown) dormancy factors are required to determine the development trajectory. The development landscape is shown to provide a well-suited representation of seed states travelling along developmental trajectories, particularly when the states are envisioned as regulatory circuits. Looking at seed dormancy in terms of regulatory circuits and development landscapes offers a valuable perspective to improve our understanding of this biological phenomenon.

Seed Germination and Seed Bank Dynamics of Eruca sativa (Brassicaceae): A Weed on the Northeastern Edge of Tibetan Plateau.

As a versatile cruciferous species, Eruca sativa is widely cultivated, but in some areas, it has become an invasive weed. There are few studies on its seed dormancy and soil seed bank. This research examined seed dormancy, germination, and dynamics of the soil seed bank of E. sativa, with a view to provide support for its prevention and control. We tested the effects of temperature, light, storage, water, and salinity stress on seed germination and burial depth on seedling emergence of E. sativa. Dynamics of the soil seed bank were determined with a 24 month in situ seed-burial study. Seeds of E. sativa can germinate in a temperature range of 5-35°C; moreover, they exhibited non-deep physiological dormancy (NDPD) at maturity, which can be broken by dry storage or exposure to low temperature in winter. Germination of E. sativa seeds was sensitive to water and salinity stress, and most seeds did not germinate at -0.3 MPa. When buried in soil in the field, seeds exhibited an annual dormancy/non-dormancy cycle and formed at least a short-term persistent soil seed bank. Seeds buried deeper than 5 cm can hardly emerge. Seeds of E. sativa have a wide germination temperature range and exhibited dormancy cycling, which promotes the formation of a persistent soil seed bank and enables it to better adapt to the harsh low-temperature climate of the Qinghai-Tibet Plateau. No-tillage would be a good management strategy for this species.

Evidence for physiological seed dormancy cycling in the woody shrub Asterolasia buxifolia and its ecological significance in fire-prone systems.

Dormancy cycling is a key mechanism that contributes to the maintenance of long-term persistent soil seed banks, but has not been recorded in long-lived woody shrub species from fire-prone environments. Such species rely on seed banks and dormancy break as important processes for post-fire recruitment and recovery. We used germination experiments with smoke treatments on fresh seeds and those buried for 1 year (retrieved in spring) and 1.5 years (retrieved the following late autumn) to investigate whether Asterolasia buxifolia, a shrub from fire-prone south-eastern Australia with physiologically dormant seeds, exhibited dormancy cycling. All seeds had an obligation for winter seasonal temperatures and smoke to promote germination, even after ageing in the soil. A high proportion of germination was recorded from fresh seeds. but germination after the first retrieval was significantly lower, despite high seed viability. After the second retrieval, germination returned to the initial level. This indicates a pattern of annual dormancy cycling; one of the few observations, to our knowledge, for a perennial species. Additionally, A. buxifolia's winter temperature and smoke requirements did not change over time, highlighting the potential for seeds to remain conditionally dormant (i.e. restricted to a narrow range of germination conditions) for long periods. For physiologically dormant species, such as A. buxifolia, we conclude that dormancy cycling is an important driver of successful regeneration, allowing seed bank persistence, sometimes for decades, during fire-free periods unsuitable for successful recruitment, while ensuring that a large proportion of seeds are available for recruitment when a fire occurs.

A Perspective on Secondary Seed Dormancy in Arabidopsis thaliana.

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

Seed dormancy regulates germination response to smoke and temperature in a rhizomatous evergreen perennial.

Seed dormancy status regulates the response of seeds to environmental cues that can trigger germination. Anigozanthos flavidus (Haemodoraceae) produces seeds with morphophysiological dormancy (MPD) that are known to germinate in response to smoke, but embryo growth dynamics and germination traits in response to temperatures and after-ripening have not been well characterized. Seeds of A. flavidus, after-ripened for 28 months at 15 °C/15 % relative humidity, were incubated on water agar, water agar containing 1 µM karrikinolide (KAR1) or 50 µM glyceronitrile at 5, 10, 15, 20, 25, 20/10 and 25/15 °C for 28 days. After incubation at 5, 10 and 25 °C for 28 days, seeds were transferred to 15 °C for another 28 days. Embryo growth dynamics were tested at 5, 10, 15 and 25 °C. Results demonstrated that fresh seeds of A. flavidus had MPD and the physiological dormancy (PD) component could be broken by either glyceronitrile or dry after-ripening. After-ripened seeds germinated to ≥80 % at 15-20 °C while no additional benefit of germination was observed in the presence of the KAR1 or glyceronitrile. Embryo length significantly increased at 10 °C, and only slightly increased at 5 °C, while growth did not occur at 25 °C. When un-germinated seeds were moved from 5-10 °C to 15 °C for a further 28 days, germination increased from 0 to >80 % in significantly less time indicating that cold stratification may play a key role in the germination process during winter and early spring in A. flavidus. The lower germination (<50 %) of seeds moved from 25 to 15 °C was produced by the induction of secondary dormancy. Induction of secondary dormancy in seeds exposed to warm stratification, a first report for Anigozanthos species, suggests that cycling of PD may be an important mechanism of controlling germination timing in the field.

Ecological longevity of Polaskia chende (Cactaceae) seeds in the soil seed bank, seedling emergence and survival.

Soil seed banks are essential elements of plant population dynamics, enabling species to maintain genetic variability, withstand periods of adversity and persist over time, including for cactus species. However knowledge of the soil seed bank in cacti is scanty. In this study, over a 5-year period we studied the seed bank dynamics, seedling emergence and nurse plant facilitation of Polaskia chende, an endemic columnar cactus of central Mexico. P. chende seeds were collected for a wild population in Puebla, Mexico. Freshly collected seeds were sown at 25 °C and 12-h photoperiod under white light, far-red light and darkness. The collected seeds were divided in two lots, the first was stored in the laboratory and the second was use to bury seeds in open areas and beneath a shrub canopy. Seeds were exhumed periodically over 5 years. At the same time seeds were sown in open areas and beneath shrub canopies; seedling emergence and survival were recorded over different periods of time for 5 years. The species forms long-term persistent soil seed banks. The timing of seedling emergence via germination in the field was regulated by interaction between light, temperature and soil moisture. Seeds entered secondary dormancy at specific times according to the expression of environmental factors, demonstrating irregular dormancy cycling. Seedling survival of P. chende was improved under Acacia constricta nurse plants. Finally, plant facilitation affected the soil seed bank dynamics as it promoted the formation of a soil seed bank, but not its persistence.