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1.  Parental environment changes the dormancy state and karrikinolide response of Brassica tournefortii seeds 
Annals of Botany  2012;109(7):1369-1378.
Background and Aims
The smoke-derived chemical karrikinolide (KAR1) shows potential as a tool to synchronize the germination of seeds for weed management and restoration. To assess its feasibility we need to understand why seeds from different populations of a species exhibit distinct responses to KAR1. Environmental conditions during seed development, known as the parental environment, influence seed dormancy so we predicted that parental environment would also drive the KAR1-responses of seeds. Specifically, we hypothesized that (a) a common environment will unify the KAR1-responses of different populations, (b) a single population grown under different environmental conditions will exhibit different KAR1-responses, and (c) drought stress, as a particular feature of the parental environment, will make seeds less dormant and more responsive to KAR1.
Seeds of the weed Brassica tournefortii were collected from four locations in Western Australia and were sown in common gardens at two field sites, to test whether their KAR1-responses could be unified by a common environment. To test the effects of drought on KAR1-response, plants were grown in a glasshouse and subjected to water stress. For each trial, the germination responses of the next generation of seeds were assessed.
Key Results
The KAR1-responses of seeds differed among populations, but this variation was reduced when seeds developed in a common environment. The KAR1-responses of each population changed when seeds developed in different environments. Different parental environments affected germination responses of the populations differently, showing that parental environment interacts with genetics to determine KAR1-responses. Seeds from droughted plants were 5 % more responsive to KAR1 and 5 % less dormant than seeds from well-watered plants, but KAR1-responses and dormancy state were not intrinsically linked in all experiments.
The parental environment in which seeds develop is one of the key drivers of the KAR1-responses of seeds.
PMCID: PMC3359922  PMID: 22492259
Brassica tournefortii; butenolide; drought stress; germination; karrikinolide; maternal environment; parental environment; phenotypic plasticity; physiological dormancy; seed development; seed dormancy; weed seed bank
2.  Prior hydration of Brassica tournefortii seeds reduces the stimulatory effect of karrikinolide on germination and increases seed sensitivity to abscisic acid 
Annals of Botany  2010;105(6):1063-1070.
Background and Aims
The smoke-derived compound karrikinolide (KAR1) shows significant potential as a trigger for the synchronous germination of seeds in a variety of plant-management contexts, from weed seeds in paddocks, to native seeds when restoring degraded lands. Understanding how KAR1 interacts with seed physiology is a necessary precursor to the development of the compound as an efficient and effective management tool. This study tested the ability of KAR1 to stimulate germination of seeds of the global agronomic weed Brassica tournefortii, at different hydration states, to gain insight into how the timing of KAR1 applications in the field should be managed relative to rain events.
Seeds of B. tournefortii were brought to five different hydration states [equilibrated at 15 % relative humidity (RH), 47 % RH, 96 % RH, fully imbibed, or re-dried to 15 % RH following maximum imbibition] then exposed to 1 nm or 1 µm KAR1 for one of five durations (3 min, 1 h, 24 h, 14 d or no exposure).
Key Results
Dry seeds with no history of imbibition were the most sensitive to KAR1; sensitivity was lower in seeds that were fully imbibed or fully imbibed then re-dried. In addition, reduced sensitivity to KAR1 was associated with an increased sensitivity to exogenously applied abscisic acid (ABA).
Seed water content and history of imbibition were found to significantly influence whether seeds germinate in response to KAR1. To optimize the germination response of seeds, KAR1 should be applied to dry seeds, when sensitivity to ABA is minimized.
PMCID: PMC2876004  PMID: 20348089
Karrikinolide; karrikins; butenolide; smoke; germination stimulant; seed water content; abscisic acid; ABA; gibberellin; weed; Brassica tournefortii
3.  Comparison of germination responses of Anigozanthos flavidus (Haemodoraceae), Gyrostemon racemiger and Gyrostemon ramulosus (Gyrostemonaceae) to smoke-water and the smoke-derived compounds karrikinolide (KAR1) and glyceronitrile 
Annals of Botany  2013;111(3):489-497.
Background and Aims
A major germination-promoting chemical in smoke-water is 3-methyl-2H-furo[2,3-c]pyran-2-one (karrikinolide, KAR1). However, not all species that germinate in response to smoke-water are responsive to KAR1, such as Tersonia cyathiflora (Gyrostemonaceae). In this study, a test was made of whether two Gyrostemon species (Gyrostemonaceae) that have previously been shown to respond to smoke-water, respond to KAR1. If not, then the smoke-derived chemical that stimulates germination of these species is currently unknown. Recently, glyceronitrile was isolated from smoke-water and promoted the germination of certain Anigozanthos species (Haemodoraceae). Whether this chemical promotes Gyrostemon racemiger germination is also examined. Furthermore, an investigation was carried out into whether these species germinate in response to smoke-water derived from burning cellulose alone.
Methods Gyrostemon racemiger
and G. ramulosus seeds were buried after collection and retrieved in autumn the following year when dormancy was alleviated and seeds had become responsive to smoke-water. Anigozanthos flavidus seeds were after-ripened at 35 °C to alleviate dormancy. Gyrostemon and Anigozanthos seeds were then tested with ‘Seed Starter’ smoke-water, KAR1, glyceronitrile and cellulose-derived smoke-water.
Key Results
Although Gyrostemon racemiger, G. ramulosus and A. flavidus were all stimulated to germinate by ‘Seed Starter’ smoke-water, none of these species responded to KAR1. Gyrostemon racemiger germination was not promoted by glyceronitrile. This is in contrast to A. flavidus, where glyceronitrile, at concentrations of 1–500 µm, promoted germination, although seedling growth was inhibited at ≥400 µm. Maximum A. flavidus germination occurred at glyceronitrile concentrations of 25–300 µm. Some Gyrostemon germination was promoted by cellulose-derived smoke-water.
KAR1 and glyceronitrile, chemicals in smoke-water that are known to stimulate germination in other species, did not promote the germination of G. racemiger. This suggests that other chemical(s) which promote germination are present in smoke, and may be derived from burning cellulose alone.
PMCID: PMC3579451  PMID: 23299994
Butenolide; cyanohydrin; germination; glyceronitrile; karrikinolide; smoke; 2,3-dihydroxypropanenitrile; 3-methyl-2H-furo[2,3-c]pyran-2-one; Gyrostemonaceae; Anigozanthos flavidus; Gyrostemon racemiger; Gyrostemon ramulosus
4.  The fire ephemeral Tersonia cyathiflora (Gyrostemonaceae) germinates in response to smoke but not the butenolide 3-methyl-2H-furo[2,3-c]pyran-2-one 
Annals of Botany  2010;106(2):381-384.
Background and Aims
Tersonia cyathiflora (Gyrostemonaceae) is a fire ephemeral with an obligate requirement for smoke to germinate. Whether it is stimulated to germinate by 3-methyl-2H-furo[2,3-c]pyran-2-one (karrikinolide, KAR1), the butenolide isolated from smoke that stimulates the germination of many other smoke-responsive species, is tested.
Seeds of T. cyathiflora were buried in autumn following collection and were exhumed 1 year later, as this alleviates dormancy and enables seeds to germinate in response to smoke-water. Exhumed seeds were tested with smoke-water and KAR1. Fresh preparations of these solutions were again tested on seeds exhumed 2 months later under a broader range of conditions. They were also tested on Grevillea eriostachya (Proteaceae) and Stylidium affine (Stylidiaceae) to confirm the activity of KAR1.
Key Results
T. cyathiflora seeds germinated in response to smoke-water but not to KAR1. In contrast, G. eriostachya and S. affine germinated in response to both smoke-water and KAR1.
Although many smoke-responsive seeds germinate in the presence of KAR1, this does not apply universally. This suggests that other chemical(s) in smoke-water may play an important role in stimulating the germination of certain species.
PMCID: PMC2908171  PMID: 20605804
Butenolide; germination; karrikinolide; smoke; 3-methyl-2H-furo[2,3-c]pyran-2-one; Grevillea; Stylidium; Tersonia cyathiflora; Gyrostemonaceae
5.  The Changing Window of Conditions that Promotes Germination of Two Fire Ephemerals, Actinotus leucocephalus (Apiaceae) and Tersonia cyathiflora (Gyrostemonaceae) 
Annals of Botany  2005;96(7):1225-1236.
• Background and Aims Following a period of burial, more Actinotus leucocephalus (Apiaceae) and Tersonia cyathiflora (Gyrostemonaceae) seeds germinate in smoke water. The main aim of this study was to determine whether these fire-ephemeral seeds exhibit annual dormancy cycling during burial. This study also aimed to determine the effect of dormancy alleviation on the range of light and temperature conditions at which seeds germinate, and the possible factors driving changes in seed dormancy during burial.
• Methods Seeds were collected in summer, buried in soil in mesh bags in autumn and exhumed every 6 months for 24 months. Germination of exhumed and laboratory-stored (15 °C) seeds was assessed at 20 °C in water or smoke water. Germination response to light or dark conditions, incubation temperature (10, 15, 20, 25 and 30 °C), nitrate and gibberellic acid were also examined following burial or laboratory storage for 24 months. In the laboratory seeds were also stored at various temperatures (5, 15, 37 and 20/50 °C) for 1, 2 and 3 months followed by germination testing in water or smoke water.
• Key Results The two species exhibited dormancy cycling during soil burial, producing low levels of germination in response to smoke water when exhumed in spring and high levels of germination in autumn. In autumn, seeds germinated in both light and dark and at a broader range of temperatures than did laboratory-stored seeds, and some Actinotus leucocephalus seeds also germinated in water alone. Dormancy release of Actinotus leucocephalus was slow during dry storage at 15 °C and more rapid at higher temperatures (37 and 20/50 °C); weekly wet/dry cycles further accelerated the rate of dormancy release. Cold stratification (5 °C) induced secondary dormancy. By contrast, no Tersonia cyathiflora seeds germinated following any of the laboratory storage treatments.
• Conclusions Temperature and moisture influence dormancy cycling in Actinotus leucocephalus seeds. These factors alone did not simulate dormancy cycling of Tersonia cyathiflora seeds under the conditions tested.
PMCID: PMC4247073  PMID: 16199485
Dormancy cycling; fire ephemeral; germination stimulants; scarification; smoke water; soil burial; storage temperature; Actinotus leucocephalus; Tersonia cyathiflora
6.  The role of the persistent fruit wall in seed water regulation in Raphanus raphanistrum (Brassicaceae) 
Annals of Botany  2009;105(1):101-108.
Background and Aims
Dry fruits remain around the seeds at dispersal in a number of species, especially the Brassicaceae. Explanations for this vary, but usually involve mechanisms of innate dormancy. We speculate that, instead, a persistent fruit may give additional protection through control of dehydration, to species growing in arid or Mediterranean environments where water is sporadic.
X-rays and weight measurements were used to determine the extent to which Raphanus raphanistrum seeds within mature fruits imbibe water, and germination tests determined the roles of the fruit and seed coat in seed dormancy. Rates of water uptake and desiccation, and seedling emergence were compared with and without the fruit. Finally, germinability of seeds extracted from fruits was determined after various periods of moist conditions followed by a range of dry conditions.
Key Results
Most seeds rapidly take up water within the fruit, but they do not fully imbibe when compared with naked seeds. The seed coat is more important than the dry fruit wall in maintaining seed dormancy. The presence of a dry fruit slows emergence from the soil by up to 6–8 weeks. The fruit slows the rate of desiccation of the seed to a limited extent. The presence of the fruit for a few days during imbibition somehow primes more seeds to germinate than if the fruit is absent; longer moist periods within the pod appear to induce dormancy.
The fruit certainly modifies the seed environment as external conditions change between wet and dry, but not to a great extent. The major role seems to be: (a) the physical restriction of imbibition and germination; and (b) the release and then re-imposition of dormancy within the seed. The ecological significance of the results requires more research under field conditions.
PMCID: PMC2794069  PMID: 19889801
Wild radish; Raphanus raphanistrum; imbibition; desiccation; dry fruit wall; germination; dormancy; X-ray
7.  Kar4p, a karyogamy-specific component of the yeast pheromone response pathway. 
Molecular and Cellular Biology  1996;16(8):3990-4002.
Karyogamy is the process whereby two haploid nuclei fuse to form a diploid nucleus during mating in Saccharomyces cerevisiae. Here, we describe the characterization of the KAR4 gene, previously identified in a screen for new nuclear fusion-defective mutants. During mating, kar4 mutants were defective for the microtubule-dependent movement of nuclei, a phenotype identical to that of mutations in KAR3 and CIK1. Consistent with its mutant phenotype, we found that the kar4 mutation resulted in failure to induce KAR3 and CIK1 mRNA during mating. Expression of KAR3 and CIK1 under independent regulatory control suppressed the kar4 defect, indicating that KAR4 is required primarily for the induction of KAR3 and CIK1. KAR4 was also required for meiosis, during which it may regulate KAR3; however, mitotic expression of KAR3 and CIK1 during S/G2 phase was independent of KAR4. A 30-bp region upstream of KAR3 conferred both KAR4- and STE12-dependent induction by mating pheromone. This region contained one moderate and two weak matches to the consensus pheromone response element to which the Ste12p transcriptional activator binds and five repeats of the sequence CAAA(A). Overproduction of Ste12p suppressed the kar4 defect in KAR3 induction and nuclear fusion. In contrast, Ste12p-independent expression of Kar4p did not alleviate the requirement for Ste12p during KAR3 induction. We propose that Kar4p assists Ste12p in the pheromone-dependent expression of KAR3 and CIK1. KAR4 defines a novel level of regulation for the pheromone response pathway, acting at a subset of Stel2p-inducible genes required for karyogamy.
PMCID: PMC231395  PMID: 8754797
8.  Variation of seed heteromorphism in Chenopodium album and the effect of salinity stress on the descendants 
Annals of Botany  2010;105(6):1015-1025.
Background and Aims
Chenopodium album is well-known as a serious weed and is a salt-tolerant species inhabiting semi-arid and light-saline environments in Xinjiang, China. It produces large amounts of heteromorphic (black and brown) seeds. The primary aims of the present study were to compare the germination characteristics of heteromorphic seeds, the diversity of plant growth and seed proliferation pattern of the resulting plants, and the correlation between NaCl stress and variation of seed heteromorphism.
The phenotypic characters of heteromorphic seeds, e.g. seed morphology, seed mass and total seed protein were determined. The effects of dry storage at room temperature on dormancy behaviour, the germination response of seeds to salinity stress, and the effect of salinity on growth and seed proliferation with plants derived from different seed types were investigated.
Key Results
Black and brown seeds differed in seed morphology, mass, total seed protein, dormancy behaviour and salinity tolerance. Brown seeds were large, non-dormant and more salt tolerant, and could germinate rapidly to a high percentage in a wider range of environments; black seeds were salt-sensitive, and a large proportion of seeds were dormant. These characteristics varied between two populations. There was little difference in growth characteristics and seed output of plants produced from the two seed morphs except when plants were subjected to high salinity stress. Plants that suffered higher salinity stress produced more brown (salt-tolerant) seeds.
The two seed morphs of C. album exhibited distinct diversity in germination characteristics. There was a significant difference in plant development and seed proliferation pattern from the two types of seeds only when the parent plants were treated with high salinity. In addition, seed heteromorphism of C. album varied between the two populations, and such variation may be attributed, at least in part, to the salinity.
PMCID: PMC2876003  PMID: 20501882
Chenopodium album; development of descendants; salinity tolerance; seed germination; variation of seed heteromorphism
9.  Sympatric species of Hibbertia (Dilleniaceae) vary in dormancy break and germination requirements: implications for classifying morphophysiological dormancy in Mediterranean biomes 
Annals of Botany  2012;109(6):1111-1123.
Background and Aims
Several ecologically important plant families in Mediterranean biomes have seeds with morphophysiological dormancy (MPD) but have been poorly studied. The aim of this study was to understand the seed ecology of these species by focusing on the prominent, yet intractably dormant Australian genus Hibbertia. It was hypothesized that the slow germination in species of this genus is caused by a requirement for embryo growth inside the seed before germination, and that initiation of embryo growth is reliant upon a complex sequence of environmental cues including seasonal fluctuations in temperature and moisture, and an interplay with light and smoke. Using the results, the classification of the MPD level in species of Hibbertia is considered.
Four species of Hibbertia in winter rainfall south-western Australia were selected. These species, whilst differing in geographic distributions, are variously sympatric, and all are important understorey components of plant communities. The following aspects related to dormancy break, embryo growth and germination were investigated: temperature and moisture requirements; effects of karrikinolide, gibberellic acid and aerosol smoke; and phenology.
Key Results
Following exposure to wet/dry cycles at low or high temperatures, embryo growth and germination occurred, albeit slowly in all species at low temperatures when moisture was unlimited, corresponding to winter in south-west Australia. Photo regime influenced germination only in H. racemosa. Aerosol smoke triggered substantial germination during the 1st germination season in H. huegelii and H. hypericoides.
Although the study species are con-generic, sympatric and produce seeds of identical morphology, they possessed different dormancy-break and germination requirements. The physiological component of MPD was non-deep in H. racemosa but varied in the other three species where more deeply dormant seeds required >1 summer to overcome dormancy and, thus, germination was spread over time. Embryos grew during winter, but future studies need to resolve the role of cold versus warm stratification by using constant temperature regimes. To include Mediterranean species with MPD, some modifications to the current seed-dormancy classification system may need consideration: (a) wet/dry conditions for warm stratification and (b) a relatively long period for warm stratification. These outcomes have important implications for improving experimental approaches to resolve the effective use of broadcast seed for ecological restoration.
PMCID: PMC3336950  PMID: 22362661
Framework species; germination phenology; Hibbertia; karrikinolide; Mediterranean biome; morphophysiological dormancy; restoration; seeds; smoke; underdeveloped embryos
10.  Role of Transcription Factor Kar4 in Regulating Downstream Events in the Saccharomyces cerevisiae Pheromone Response Pathway▿  
Molecular and Cellular Biology  2006;27(3):818-829.
Yeast Kar4 is a putative transcription factor required for karyogamy (the fusion of haploid nuclei during mating) and possibly other functions. Previously known to be required only for the transcriptional induction of KAR3 and CIK1, microarray experiments identified many genes regulated by Kar4 in both mating and mitosis. Several gene clusters are positively or negatively regulated by mating pheromone in a Kar4-dependent manner. Chromatin immunoprecipitation and gel shift assays confirmed that Kar4 binds to regulatory DNA sequences upstream of KAR3. Together with one-hybrid experiments, these data support a model in which both Kar4 and Ste12 bind jointly to the KAR3 promoter. Analysis of the upstream regions of Kar4-induced genes identified a DNA sequence motif that may be a binding site for Kar4. Mutation within the motif upstream of KAR3 eliminated pheromone induction. Genes regulated by Kar4, on average, are delayed in their temporal expression and exhibit a more stringent dose response to pheromone. Furthermore, the induction of Kar4 by pheromone is necessary for the delayed temporal induction of KAR3 and PRM2, genes required for efficient nuclear fusion during mating. Accordingly, we propose that Kar4 plays a critical role in the choreography of the mating response.
PMCID: PMC1800688  PMID: 17101777
11.  Mimicking a Semi-arid Tropical Environment Achieves Dormancy Alleviation for Seeds of Australian Native Goodeniaceae and Asteraceae 
Annals of Botany  2008;101(5):701-708.
Background and Aims
Seed physiological dormancy (PD) limits the use and conservation of some of Queensland's (Qld) native forb species. It was hypothesised that optimum dormancy-alleviating treatments would reflect environmental conditions that seeds experience in situ, and this premise was tested for PD seeds of four species native to south-west Qld.
High temperatures and increased rainfall during summer are characteristic of this semi-arid tropical environment. Ex situ treatments were designed to mimic conditions that seeds dispersed in spring experience during the summer months before germinating in cooler autumn temperatures. Seeds received between 4 and 20 weeks of a dry after-ripening (DAR), warm stratification or dry/wet cycling treatment (DAR interspersed with short periods of warm stratification), in darkness, before being transferred to germination test conditions. In addition, natural dormancy alleviation of one of the Goodeniaceae species was investigated in situ.
Key Results
Dry/wet cycling resulted in higher levels of germination of Actinobole uliginosum (Asteraceae), Goodenia cycloptera and Velleia glabrata (Goodeniaceae) when compared with constant DAR or stratification, while Goodenia fascicularis (Goodeniaceae) responded better to short durations of warm stratification. Long durations of DAR partially alleviated PD of A. uliginosum; however, stratification induced and maintained dormancy of this species. Modifications to the dry/wet cycling treatment and germination test conditions based on data collected in situ enabled germination of G. cycloptera and V. glabrata to be further improved.
Treatments designed using temperature, relative humidity and rainfall data for the period between natural seed dispersal and germination can successfully alleviate PD. Differences between the four species in conditions that resulted in maximum germination indicate that, in addition to responding to broad-scale climate patterns, species may be adapted to particular microsites and/or seasonal conditions.
PMCID: PMC2710182  PMID: 18245107
Seed dormancy; germination; dry after-ripening; dry/wet cycling; south-west Queensland; Australia; semi-arid tropical; Actinobole uliginosum; Asteraceae; Goodenia fascicularis; Goodenia cycloptera; Velleia glabrata; Goodeniaceae
12.  Germination traits explain soil seed persistence across species: the case of Mediterranean annual plants in cereal fields 
Annals of Botany  2011;107(3):415-426.
Background and Aims
Seed persistence in the soil under field conditions is an important issue for the maintenance of local plant populations and the restoration of plant communities, increasingly so in the light of rapidly changing land use and climate change. Whereas processes important for dispersal in space are well known, knowledge of processes governing dispersal in time is still limited. Data for morphological seed traits such as size have given contradictory results for prediction of soil seed persistence or cover only a few species. There have been few experimental studies on the role of germination traits in determining soil seed persistence, while none has studied their predictive value consistently across species. Delayed germination, as well as light requirements for germination, have been suggested to contribute to the formation of persistent seed banks. Moreover, diurnally fluctuating temperatures can influence the timing of germination and are therefore linked to seed bank persistence.
The role of germination speed measured by T50 (days to germination of 50 % of all germinated seeds), light requirement and reaction to diurnally fluctuating temperatures in determining seed persistence in the soil was evaluated using an experimental comparative data set of 25 annual cereal weed species.
Key Results
It is shown that light requirements and slow germination are important features to maintain seeds ungerminated just after entering the soil, and hence influence survival of seeds in the soil. However, the detection of low diurnally fluctuating temperatures enhances soil seed bank persistence by limiting germination. Our data further suggest that the effect of diurnally fluctuating temperatures, as measured on seeds after dispersal and dry storage, is increasingly important to prevent fatal germination after longer burial periods.
These results underline the functional role of delayed germination and light for survival of seeds in the soil and hence their importance for shaping the first part of the seed decay curve. Our analyses highlight the detection of diurnally fluctuating temperatures as a third mechanism to achieve higher soil seed persistence after burial which interacts strongly with season. We therefore advocate focusing future research on mechanisms that favour soil seed persistence after longer burial times and moving from studies of morphological features to exploration of germination traits such as reaction to diurnally fluctuating temperatures.
PMCID: PMC3043931  PMID: 21224268
Diurnally fluctuating temperatures; delayed germination; T50; gap detection; light requirement; dormancy; Asteraceae; Campanulaceae; Apiaceae; Papaveraceae; soil seed bank
13.  Transcriptome analysis of germinating maize kernels exposed to smoke-water and the active compound KAR1 
BMC Plant Biology  2010;10:236.
Smoke released from burning vegetation functions as an important environmental signal promoting the germination of many plant species following a fire. It not only promotes the germination of species from fire-prone habitats, but several species from non-fire-prone areas also respond, including some crops. The germination stimulatory activity can largely be attributed to the presence of a highly active butenolide compound, 3-methyl-2H-furo[2,3-c]pyran-2-one (referred to as karrikin 1 or KAR1), that has previously been isolated from plant-derived smoke. Several hypotheses have arisen regarding the molecular background of smoke and KAR1 action.
In this paper we demonstrate that although smoke-water and KAR1 treatment of maize kernels result in a similar physiological response, the gene expression and the protein ubiquitination patterns are quite different. Treatment with smoke-water enhanced the ubiquitination of proteins and activated protein-degradation-related genes. This effect was completely absent from KAR1-treated kernels, in which a specific aquaporin gene was distinctly upregulated.
Our findings indicate that the array of bioactive compounds present in smoke-water form an environmental signal that may act together in germination stimulation. It is highly possible that the smoke/KAR1 'signal' is perceived by a receptor that is shared with the signal transduction system implied in perceiving environmental cues (especially stresses and light), or some kind of specialized receptor exists in fire-prone plant species which diverged from a more general one present in a common ancestor, and also found in non fire-prone plants allowing for a somewhat weaker but still significant response. Besides their obvious use in agricultural practices, smoke and KAR1 can be used in studies to gain further insight into the transcriptional changes during germination.
PMCID: PMC3095319  PMID: 21044315
14.  Seed dormancy in alpine species 
Flora  2011;206(10-3):845-856.
In alpine species the classification of the various mechanisms underlying seed dormancy has been rather questionable and controversial. Thus, we investigated 28 alpine species to evaluate the prevailing types of dormancy. Embryo type and water impermeability of seed coats gave an indication of the potential seed dormancy class. To ascertain the actual dormancy class and level, we performed germination experiments comparing the behavior of seeds without storage, after cold-dry storage, after cold-wet storage, and scarification. We also tested the light requirement for germination in some species. Germination behavior was characterized using the final germination percentage and the mean germination time. Considering the effects of the pretreatments, a refined classification of the prevailing dormancy types was constructed based on the results of our pretreatments. Only two out of the 28 species that we evaluated had predominantly non-dormant seeds. Physiological dormancy was prevalent in 20 species, with deep physiological dormancy being the most abundant, followed by non-deep and intermediate physiological dormancy. Seeds of four species with underdeveloped embryos were assigned to the morphophysiologial dormancy class. An impermeable seed coat was identified in two species, with no additional physiological germination block. We defined these species as having physical dormancy. Light promoted the germination of seeds without storage in all but one species with physiological dormancy. In species with physical dormancy, light responses were of minor importance. We discuss our new classification in the context of former germination studies and draw implications for the timing of germination in the field.
PMCID: PMC3886365  PMID: 24415831
CDSfresh, cold-dry storage of seeds before incubation under long-day conditions; CDSsc, scarification of seeds following cold-dry storage before incubation under long-day conditions; CWSfresh, cold-wet storage of seeds before incubation under long-day conditions; CWSsubs, cold-wet storage subsequent to a germination experiment before incubation under long-day conditions; FGP, final germination percentage; FRESHdark, seeds without storage incubated in darkness; FRESHsc, scarification of seeds without storage before incubation under long-day conditions; FRESHLD, seeds without storage incubated under long-day conditions; GA3, gibberellic acid; MD, morphological dormancy; MGT, mean germination time; MPD, morphophysiological dormancy; ND, non-dormant; PD, physiological dormancy; PY, physical dormancy; PY + PD, combinational dormancy of PY and PD; Cold-dry seed storage; Cold-wet seed storage; Dormancy classification; Embryo morphology; Light response; Scarification
15.  Germination parameterization and development of an after-ripening thermal-time model for primary dormancy release of Lithospermum arvense seeds 
Annals of Botany  2009;103(8):1291-1301.
Background and Aims
Models based on thermal-time approaches have been a useful tool for characterizing and predicting seed germination and dormancy release in relation to time and temperature. The aims of the present work were to evaluate the relative accuracy of different thermal-time approaches for the description of germination in Lithospermum arvense and to develop an after-ripening thermal-time model for predicting seed dormancy release.
Seeds were dry-stored at constant temperatures of 5, 15 or 24 °C for up to 210 d. After different storage periods, batches of 50 seeds were incubated at eight constant temperature regimes of 5, 8, 10, 13, 15, 17, 20 or 25 °C. Experimentally obtained cumulative-germination curves were analysed using a non-linear regression procedure to obtain optimal population thermal parameters for L. arvense. Changes in these parameters were described as a function of after-ripening thermal-time and storage temperature.
Key Results
The most accurate approach for simulating the thermal-germination response of L. arvense was achieved by assuming a normal distribution of both base and maximum germination temperatures. The results contradict the widely accepted assumption of a single Tb value for the entire seed population. The after-ripening process was characterized by a progressive increase in the mean maximum germination temperature and a reduction in the thermal-time requirements for germination at sub-optimal temperatures.
The after-ripening thermal-time model developed here gave an acceptable description of the observed field emergence patterns, thus indicating its usefulness as a predictive tool to enhance weed management tactics.
PMCID: PMC2685320  PMID: 19332426
Lithospermum arvense; winter annual weed; thermal-time model; cardinal temperatures; primary dormancy; after-ripening thermal-time; storage temperature; field germination; seedling emergence
16.  Do soil microbes and abrasion by soil particles influence persistence and loss of physical dormancy in seeds of tropical pioneers? 
Germination from the soil seed bank (SSB) is an important determinant of species composition in tropical forest gaps, with seed persistence in the SSB allowing trees to recruit even decades after dispersal. The capacity to form a persistent SSB is often associated with physical dormancy, where seed coats are impermeable at the time of dispersal. Germination literature often speculates, without empirical evidence, that dormancy-break in physically dormant seeds is the result of microbial action and/or abrasion by soil particles. We tested the microbial/soil abrasion hypothesis in four widely distributed neotropical pioneer tree species (Apeiba membranacea, Luehea seemannii, Ochroma pyramidale, and Cochlospermum vitifolium). Seeds were buried in five common gardens in a lowland tropical forest in Panama, and recovered at 1, 3, 6, and 12 months after burial. Seed permeability, microbial infection, seed coat thickness, and germination were measured. Parallel experiments compared the germination fraction of fresh and aged seeds without soil contact, and in seeds as a function of seed permeability. Contrary to the microbial/soil abrasion hypothesis the proportion of permeable seeds, and of seeds infected by cultivable microbes, decreased as a function of burial duration. Furthermore, seeds stored in dark and dry conditions for 2 years showed a higher proportion of seed germination than fresh seeds in identical germination conditions. We determined that permeable seeds of A. membranacea and O. pyramidale had cracks in the chalazal area or lacked the chalazal plug, whereas all surfaces of impermeable seeds were intact. Our results are inconsistent with the microbial/soil abrasion hypothesis of dormancy loss and instead suggest the existence of multiple dormancy phenotypes, where a fraction of each seed cohort is dispersed in a permeable state and germinates immediately, while the impermeable seed fraction accounts for the persistent SSB. Thus, we conclude that fluctuations in the soil temperature in the absence of soil abrasion and microbial infection are sufficient to break physical dormancy on seeds of tropical pioneer trees.
PMCID: PMC4292399  PMID: 25628640
Barro Colorado Island; germination cue; physical dormancy; pioneer plants; seed dormancy loss; seed persistence; soil seed bank
17.  Genetic Evidence for a Role of BiP/Kar2 That Regulates Ire1 in Response to Accumulation of Unfolded Proteins 
Molecular Biology of the Cell  2003;14(6):2559-2569.
In the unfolded protein response (UPR) signaling pathway, accumulation of unfolded proteins in the endoplasmic reticulum (ER) activates a transmembrane kinase/ribonuclease Ire1, which causes the transcriptional induction of ER-resident chaperones, including BiP/Kar2. It was previously hypothesized that BiP/Kar2 plays a direct role in the signaling mechanism. In this model, association of BiP/Kar2 with Ire1 represses the UPR pathway while under conditions of ER stress, BiP/Kar2 dissociation leads to activation. To test this model, we analyzed five temperature-sensitive alleles of the yeast KAR2 gene. When cells carrying a mutation in the Kar2 substrate-binding domain were incubated at the restrictive temperature, association of Kar2 to Ire1 was disrupted, and the UPR pathway was activated even in the absence of extrinsic ER stress. Conversely, cells carrying a mutation in the Kar2 ATPase domain, in which Kar2 poorly dissociated from Ire1 even in the presence of tunicamycin, a potent inducer of ER stress, were unable to activate the pathway. Our findings provide strong evidence in support of BiP/Kar2-dependent Ire1 regulation model and suggest that Ire1 associates with Kar2 as a chaperone substrate. We speculate that recognition of unfolded proteins is based on their competition with Ire1 for binding with BiP/Kar2.
PMCID: PMC194903  PMID: 12808051
18.  The autumn effect: timing of physical dormancy break in seeds of two winter annual species of Geraniaceae by a stepwise process 
Annals of Botany  2012;110(3):637-651.
Background and Aims
The involvement of two steps in the physical dormancy (PY)-breaking process previously has been demonstrated in seeds of Fabaceae and Convolvulaceae. Even though there is a claim for a moisture-controlled stepwise PY-breaking in some species of Geraniaceae, no study has evaluated the role of temperature in the PY-breaking process in this family. The aim of this study was to determine whether a temperature-controlled stepwise PY-breaking process occurs in seeds of the winter annuals Geranium carolinianum and G. dissectum.
Seeds of G. carolinianum and G. dissectum were stored under different temperature regimes to test the effect of storage temperature on PY-break. The role of temperature and moisture regimes in regulating PY-break was investigated by treatments simulating natural conditions. Greenhouse (non-heated) experiments on seed germination and burial experiments (outdoors) were carried out to determine the PY-breaking behaviour in the natural habitat.
Key Results
Irrespective of moisture conditions, sensitivity to the PY-breaking step in seeds of G. carolinianum was induced at temperatures ≥20 °C, and exposure to temperatures ≤20 °C made the sensitive seeds permeable. Sensitivity of seeds increased with time. In G. dissectum, PY-break occurred at temperatures ≥20 °C in a single step under constant wet or dry conditions and in two steps under alternate wet–dry conditions if seeds were initially kept wet.
Timing of seed germination with the onset of autumn can be explained by PY-breaking processes involving (a) two temperature-dependent steps in G. carolinianum and (b) one or two moisture-dependent step(s) along with the inability to germinate under high temperatures in G. dissectum. Geraniaceae is the third of 18 families with PY in which a two-step PY-breaking process has been demonstrated.
PMCID: PMC3400450  PMID: 22684684
Geraniaceae; Geranium; physical dormancy; stepwise process; the autumn effect;  timing of PY-break; two-step model; winter annual
19.  Occurrence of Physical Dormancy in Seeds of Australian Sapindaceae: A Survey of 14 Species in Nine Genera 
Annals of Botany  2008;101(9):1349-1362.
Background and Aims
Sapindaceae is one of 16 angiosperm families whose seeds have physical dormancy (PY). However, the extent and nature of PY within this family is poorly known. The primary aims of this study were: (1) to evaluate seed characteristics and determine presence (or not) of PY within nine genera of Australian Sapindaceae; and (2) to compare the frequency of PY across the phylogenetic tree within Australian Sapindaceae.
Viability, imbibition and seed characteristics were assessed for 14 taxa from nine genera of Sapindaceae. For five species of Dodonaea, optimal conditions for germination and dormancy break were evaluated. An in situ burial experiment was performed on D. hackettiana seeds to identify the factor(s) responsible for overcoming PY. Classes of dormancy and of non-dormancy for 26 genera of Sapindaceae were mapped onto a phylogenetic tree for the family.
Key Results
Mean seed viability across all taxa was 69·7 %. Embryos were fully developed and folded (seven genera) or bent (two genera); no endosperm was present. Seeds of all five Dodonaea spp. and of Distichostemon hispidulus had PY. Hot-water treatment released PY in these six species. Optimal germination temperature for seeds of the four Dodonaea spp. that germinated was 15–20 °C. Following 5 months burial in soil, 36·4 % of D. hackettiana seeds had lost PY and germinated by the beginning of the winter wet season (May). Laboratory and field data indicate that dormancy was broken by warm, moist temperatures (≥50 °C) during summer.
PY occurs infrequently in genera of Sapindaceae native to Australia. Seeds of Dodonaea and Distichostemon had PY, whereas those of the other seven genera did not. Seeds of these two genera and of Diplopeltis (a previous study) are the only three of the 20 native Australian genera of Sapindaceae for which germination has been studied that have PY; all three belong to subfamily Dodonaeoideae.
PMCID: PMC2710253  PMID: 18369237
Dodonaea spp.; physical dormancy; Sapindaceae; seed ecology; seed germination
20.  Kainate Receptor-Mediated Modulation of Hippocampal Fast Spiking Interneurons in a Rat Model of Schizophrenia 
PLoS ONE  2012;7(3):e32483.
Kainate receptor (KAR) subunits are believed to be involved in abnormal GABAergic neurotransmission in the hippocampus (HIPP) in schizophrenia (SZ) and bipolar disorder. Postmortem studies have shown changes in the expression of the GluR5/6 subunits of KARs in the stratum oriens (SO) of sectors CA2/3, where the basolateral amygdala (BLA) sends a robust projection. Previous work using a rat model of SZ demonstrated that BLA activation leads to electrophysiological changes in fast-spiking interneurons in SO of CA2/3. The present study explores KAR modulation of interneurons in CA2/3 in response to BLA activation. Intrinsic firing properties of these interneurons through KAR-mediated activity were measured with patch-clamp recordings from rats that received 15 days of picrotoxin infusion into the BLA. Chronic BLA activation induced changes in the firing properties of CA2/3 interneurons associated with modifications in the function of KARs. Specifically, the responsiveness of these interneurons to activation of KARs was diminished in picrotoxin-treated rats, while the after-hyperpolarization (AHP) amplitude was increased. In addition, we tested blockers of KAR subunits which have been shown to have altered gene expression in SO sector CA2/3 of SZ subjects. The GluR5 antagonist UBP296 further decreased AP frequency and increased AHP amplitude in picrotoxin-treated rats. Application of the GluR6/7 antagonist NS102 suggested that activation of GluR6/7 KARs may be required to maintain the high firing rates in SO interneurons in the presence of KA. Moreover, the GluR6/7 KAR-mediated signaling may be suppressed in PICRO-treated rats. Our findings indicate that glutamatergic activity from the BLA may modulate the firing properties of CA2/3 interneurons through GluR5 and GluR6/7 KARs. These receptors are expressed in GABAergic interneurons and play a key role in the synchronization of gamma oscillations. Modulation of interneuronal activity through KARs in response to amygdala activation may lead to abnormal oscillatory rhythms reported in SZ subjects.
PMCID: PMC3291556  PMID: 22396770
21.  Regulation of Wheat Seed Dormancy by After-Ripening Is Mediated by Specific Transcriptional Switches That Induce Changes in Seed Hormone Metabolism and Signaling 
PLoS ONE  2013;8(2):e56570.
Treatments that promote dormancy release are often correlated with changes in seed hormone content and/or sensitivity. To understand the molecular mechanisms underlying the role of after-ripening (seed dry storage) in triggering hormone related changes and dormancy decay in wheat (Triticum aestivum), temporal expression patterns of genes related to abscisic acid (ABA), gibberellin (GA), jasmonate and indole acetic acid (IAA) metabolism and signaling, and levels of the respective hormones were examined in dormant and after-ripened seeds in both dry and imbibed states. After-ripening mediated developmental switch from dormancy to germination appears to be associated with declines in seed sensitivity to ABA and IAA, which are mediated by transcriptional repressions of PROTEIN PHOSPHATASE 2C, SNF1-RELATED PROTEIN KINASE2, ABA INSENSITIVE5 and LIPID PHOSPHATE PHOSPHTASE2, and AUXIN RESPONSE FACTOR and RELATED TO UBIQUITIN1 genes. Transcriptomic analysis of wheat seed responsiveness to ABA suggests that ABA inhibits the germination of wheat seeds partly by repressing the transcription of genes related to chromatin assembly and cell wall modification, and activating that of GA catabolic genes. After-ripening induced seed dormancy decay in wheat is also associated with the modulation of seed IAA and jasmonate contents. Transcriptional control of members of the ALLENE OXIDE SYNTHASE, 3-KETOACYL COENZYME A THIOLASE, LIPOXYGENASE and 12-OXOPHYTODIENOATE REDUCTASE gene families appears to regulate seed jasmonate levels. Changes in the expression of GA biosynthesis genes, GA 20-OXIDASE and GA 3-OXIDASE, in response to after-ripening implicate this hormone in enhancing dormancy release and germination. These findings have important implications in the dissection of molecular mechanisms underlying regulation of seed dormancy in cereals.
PMCID: PMC3577873  PMID: 23437172
22.  Influence of Environmental Factors on the Germination of Urena lobata L. and Its Response to Herbicides 
PLoS ONE  2014;9(3):e90305.
Urena lobata is becoming a noxious and invasive weed in rangelands, pastures, and undisturbed areas in the Philippines. This study determined the effects of seed scarification, light, salt and water stress, amount of rice residue, and seed burial depth on seed germination and emergence of U. lobata; and evaluated the weed's response to post-emergence herbicides. Germination was stimulated by both mechanical and chemical seed scarifications. The combination of the two scarification methods provided maximum (99%) seed germination. Germination was slightly stimulated when seeds were placed in light (65%) compared with when seeds were kept in the dark (46%). Sodium chloride concentrations ranging from 0 to 200 mM and osmotic potential ranging from 0 to −1.6 MPa affected the germination of U. lobata seeds significantly. The osmotic potential required for 50% inhibition of the maximum germination was −0.1 MPa; however, some seeds germinated at −0.8 MPa, but none germinated at −1.6 MPa. Seedling emergence and biomass increased with increase in rice residue amount up to 4 t ha−1, but declined beyond this amount. Soil surface placement of weed seeds resulted in the highest seedling emergence (84%), which declined with increase in burial depth. The burial depth required for 50% inhibition of maximum emergence was 2 cm; emergence was greatly reduced (93%) at burial depth of 4 cm or more. Weed seedling biomass also decreased with increase in burial depth. Bispyribac-sodium, a commonly used herbicide in rice, sprayed at the 4-leaf stage of the weed, provided 100% control, which did not differ much with 2,4-D (98%), glyphosate (97%), and thiobencarb + 2,4-D (98%). These herbicides reduced shoot and root biomass by 99–100%.
PMCID: PMC3962347  PMID: 24658143
23.  The resemblance and disparity of gene expression in dormant and non-dormant seeds and crown buds of leafy spurge (Euphorbia esula) 
BMC Plant Biology  2014;14(1):216.
Leafy spurge (Euphorbia esula L.) is a herbaceous perennial weed and dormancy in both buds and seeds is an important survival mechanism. Bud dormancy in leafy spurge exhibits three well-defined phases of para-, endo- and ecodormancy; however, seed dormancy for leafy spurge is classified as physiological dormancy that requires after-ripening and alternating temperature for maximal germination. Overlaps in transcriptome profiles between different phases of bud and seed dormancy have not been determined. Thus, we compared various phases of dormancy between seeds and buds to identify common genes and molecular processes, which should provide new insights about common regulators of dormancy.
Cluster analysis of expression profiles for 201 selected genes indicated bud and seed samples clustered separately. Direct comparisons between buds and seeds are additionally complicated since seeds incubated at a constant temperature of 20°C for 21 days (21d C) could be considered paradormant (Para) because seeds may be inhibited by endosperm-generated signals, or ecodormant (Eco) because seeds germinate after being subjected to alternating temperature of 20:30°C. Since direct comparisons in gene expression between buds and seeds were problematic, we instead examined commonalities in differentially-expressed genes associated with different phases of dormancy. Comparison between buds and seeds (‘Para to Endo buds’ and ‘21d C to 1d C seeds’), using endodormant buds (Endo) and dormant seeds (1d C) as common baselines, identified transcripts associated with cell cycle (HisH4), stress response/transcription factors (ICE2, ERFB4/ABR1), ABA and auxin response (ABA1, ARF1, IAA7, TFL1), carbohydrate/protein degradation (GAPDH_1), and transport (ABCB2). Comparison of transcript abundance for the ‘Eco to Endo buds’ and ‘21d C to 1d C seeds’ identified transcripts associated with ABA response (ATEM6), auxin response (ARF1), and cell cycle (HisH4). These results indicate that the physiological state of 21d C seeds is more analogous to paradormant buds than that of ecodormant buds.
Combined results indicate that common molecular mechanisms associated with dormancy transitions of buds and seeds involve processes associated with ABA and auxin signaling and transport, cell cycle, and AP2/ERF transcription factors or their up-stream regulators.
Electronic supplementary material
The online version of this article (doi:10.1186/s12870-014-0216-4) contains supplementary material, which is available to authorized users.
PMCID: PMC4256794  PMID: 25112962
Leafy spurge; Bud dormancy; Seed dormancy; Gene expression; Hormones; Transcription factors
24.  ABA crosstalk with ethylene and nitric oxide in seed dormancy and germination 
Dormancy is an adaptive trait that enables seed germination to coincide with favorable environmental conditions. It has been clearly demonstrated that dormancy is induced by abscisic acid (ABA) during seed development on the mother plant. After seed dispersal, germination is preceded by a decline in ABA in imbibed seeds, which results from ABA catabolism through 8′-hydroxylation. The hormonal balance between ABA and gibberellins (GAs) has been shown to act as an integrator of environmental cues to maintain dormancy or activate germination. The interplay of ABA with other endogenous signals is however less documented. In numerous species, ethylene counteracts ABA signaling pathways and induces germination. In Brassicaceae seeds, ethylene prevents the inhibitory effects of ABA on endosperm cap weakening, thereby facilitating endosperm rupture and radicle emergence. Moreover, enhanced seed dormancy in Arabidopsis ethylene-insensitive mutants results from greater ABA sensitivity. Conversely, ABA limits ethylene action by down-regulating its biosynthesis. Nitric oxide (NO) has been proposed as a common actor in the ABA and ethylene crosstalk in seed. Indeed, convergent evidence indicates that NO is produced rapidly after seed imbibition and promotes germination by inducing the expression of the ABA 8′-hydroxylase gene, CYP707A2, and stimulating ethylene production. The role of NO and other nitrogen-containing compounds, such as nitrate, in seed dormancy breakage and germination stimulation has been reported in several species. This review will describe our current knowledge of ABA crosstalk with ethylene and NO, both volatile compounds that have been shown to counteract ABA action in seeds and to improve dormancy release and germination.
PMCID: PMC3607800  PMID: 23531630
abscisic acid; dormancy; ethylene; germination; hormone; nitric oxide; seed
25.  Interaction Between Seed Dormancy-release Mechanism, Environment and Seed Bank Strategy for a Widely Distributed Perennial Legume, Parkinsonia aculeata (Caesalpinaceae) 
Annals of Botany  2008;102(2):255-264.
Background and Aims
Parkinsonia aculeata (Caesalpinaceae) is a perennial legume with seeds that have hard-seeded (physical) dormancy and are potentially very long-lived. Seed dormancy is a characteristic that can both help maximize the probability of seedling establishment and spread the risk of recruitment failure across years (bet-hedging). In this study, dormancy-release patterns are described across the diverse environments in which this species occurs in order to test whether wet heat (incubation under wet, warm-to-hot, conditions) alone can explain those patterns, and in order to determine the likely ecological role of physical dormancy across this species distribution.
A seed burial trial was conducted across the full environmental distribution of P. aculeata in Australia (arid to wet-dry tropics, uplands to wetlands, soil surface to 10 cm deep).
Key Results
Wet heat explained the pattern of dormancy release across all environments. Most seeds stored in the laboratory remained dormant throughout the trial (at least 84 %). Dormancy release was quickest for seeds buried during the wet season at relatively high rainfall, upland sites (only 3 % of seeds remained dormant after 35 d). The longest-lived seeds were in wetlands (9 % remained dormant after almost 4 years) and on the soil surface (57 % after 2 years). There was no consistent correlation between increased aridity and rate of dormancy release.
The results suggest that physical dormancy in P. aculeata is a mechanism for maximizing seedling establishment rather than a bet-hedging strategy. However, seed persistence can occur in environmental refuges where dormancy-release cues are weak and conditions for germination and establishment are poor (e.g. under dense vegetation or in more arid micro-environments) or unsuitable (e.g. when seeds are inundated or on the soil surface). Risks of recruitment failure in suboptimal environments could therefore be reduced by inter-year fluctuations in microclimate or seed movement.
PMCID: PMC2712363  PMID: 18558626
Bet-hedging; dormancy-release mechanisms; environmental refuges; legume; Parkinsonia aculeata; physical dormancy; seed bank persistence; seed burial depth; seed dormancy; tropical wetlands; wet heat; variable environment

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