Despite the importance of secondary dormancy for plant life cycle timing and survival, there is insufficient knowledge about the (epigenetic) regulation of this trait at the molecular level. Our aim was to determine the role of (epi)genetic processes in the regulation of secondary seed dormancy using natural genotypes of the widely distributed Capsella bursa-pastoris. Seeds of nine ecotypes were exposed to control conditions or histone deacetylase inhibitors [trichostatin A (TSA), valproic acid] during imbibition to study the effects of hyper-acetylation on secondary seed dormancy induction and germination. Valproic acid increased secondary dormancy and both compounds caused a delay of t50 for germination (radicle emergence) but not of t50 for testa rupture, demonstrating that they reduced speed of germination. Transcriptome analysis of one accession exposed to valproic acid versus water showed mixed regulation of ABA, negative regulation of GAs, BRs and auxins, as well as up-regulation of SNL genes, which might explain the observed delay in germination and increase in secondary dormancy. In addition, two accessions differing in secondary dormancy depth (deep vs non-deep) were studied using RNA-seq to reveal the potential regulatory processes underlying this trait. Phytohormone synthesis or signalling was generally up-regulated for ABA (e.g. NCED6, NCED2, ABCG40, ABI3) and down-regulated for GAs (GA20ox1, GA20ox2, bHLH93), ethylene (ACO1, ERF4-LIKE, ERF105, ERF109-LIKE), BRs (BIA1, CYP708A2-LIKE, probable WRKY46, BAK1, BEN1, BES1, BRI1) and auxin (GH3.3, GH3.6, ABCB19, TGG4, AUX1, PIN6, WAT1). Epigenetic candidates for variation in secondary dormancy depth include SNL genes, histone deacetylases and associated genes (HDA14, HDA6-LIKE, HDA-LIKE, ING2, JMJ30), as well as sequences linked to histone acetyltransferases (bZIP11, ARID1A-LIKE), or to gene silencing through histone methylation (SUVH7, SUVH9, CLF). Together, these results show that phytohormones and epigenetic regulation play an important role in controlling differences in secondary dormancy depth between accessions.

Generally, orchids produce dust-like seeds in which endosperm reduction and embryo undifferentiation represent a derived state shared with species in about 11 other plant families. Orchid seeds are proposed to have a special kind of morphological or morphophysiological dormancy. We test this proposition, overcoming several design limitations of earlier studies, specifically that the in vitro germination method for orchid seeds uses pro-oxidants for disinfection and incorporates nitrate in the medium; both ‘treatments’ might contribute to dormancy breaking, potentially confounding judgement on the depth and nature of the dormant state. Seeds of the tropical orchid Dendrobium cruentum Rchb. f., were sown both in vitro, on a nutrient medium, and ex vitro, on plain agar omitting prior disinfection with sodium hypochlorite. Seeds previously stored and fresh seeds were incubated under combinations of vitro conditions, light treatments, constant or alternating temperatures and nitrate concentration. Seeds of D. cruentum are very small but have a large embryo that occupies most of the seed. Over a range of constant temperature seeds germinated to the spherical protocorm stage just as well ex vitro as in vitro. Neither light nor nitrate were prerequisites for ex vitro germination. The ability of D. cruentum seed to germinate in the absence of environmental or chemical stimuli suggests that mature seed can be non-dormant. Our results support the proposition that neither all DUST seed fit a dormancy class nor all orchids produce morphological or morphophysiological seeds. Finally, embryo/seed volume determinations in orchids may prove as valuable in studies on the evolution and ecology of germination and dormancy as embryo:seed ratios in other angiosperm species.

In small seeds, light often promotes germination and longer-term exposure to darkness reduces light sensitivity. In cacti inhabiting harsh environments, a rapid response to light exposure is potentially advantageous for seedling establishment. We exposed dark-imbibed seeds of the cactus Cereus repandus to doses of red (RED) light and far-red (FR) light. The seeds exhibited positive photoblastism to RED light. Although the initial levels of germination varied between seed lots, the sensitivity to increasing the RED dose did not. As little as 5 min per day for 4 d was sufficient to saturate the light requirement for germination. The effects of RED light were reversed by FR exposure as long as the interval between RED and FR did not extend to 2 d, by which time the seeds had ‘committed’ to germinate. Dark incubation for 1–2 weeks prior to RED exposure reduced light sensitivity in two seed lots, such that RED only promoted around 20% germination. Phytochrome is assumed to mediate the reversibility of the RED:FR response. High sensitivity to light spectral quality suggests that seeds of C. repandus are able to germinate quickly in high-quality microsites, but seed burial or shading may commit the seeds to form a soil seed bank. The light characteristics of the germination trait in this species are typical of many small seeded species of the drylands.

Desiccation-tolerant (DT) plant germplasm (i.e. seeds, pollen and spores) survive drying to low moisture contents, when cytoplasm solidifies, forming a glass, and chemical reactions are slowed. DT germplasm may survive for long periods in this state, though inter-specific and intra-specific variation occurs and is not currently explained. Such variability has consequences for agriculture, forestry and biodiversity conservation. Longevity was previously considered in the context of morphological features, cellular constituents or habitat characteristics. We suggest, however, that a biophysical perspective, which considers the molecular organization – or structure – within dried cytoplasm, can provide a more integrated understanding of the fundamental mechanisms that control ageing rates, hence the variation of longevity among species and cell types. Based on biochemical composition and physical–chemical properties of dried materials, we explore three types of the interplay between structural conformations of dried cytoplasm and ageing: (1) cells that lack chlorophyll and contain few storage lipids may exhibit long shelf life, with ageing probably occurring through slow autoxidative processes within the glassy matrix as it relaxes; (2) cells with active chlorophyll may die quickly, possibly because they are prone to oxidative stress promoted by the photosynthetic pigments in the absence of metabolic water and (3) cells that lack chloroplasts but contain high storage lipids may die quickly during storage at −20°C, possibly because lipids crystallize and destabilize the glassy matrix. Understanding the complex variation in structural conformation in space and time may help to design strategies that increase longevity in germplasm with generally poor shelf life.

Each taxon is characterized by a temperature range over which seed germination is possible and this may vary in space and time in relation to climate and ecological conditions. We used thermal modelling to test the hypothesis that thermal thresholds for seed germination can predict germination timing of Mediterranean species along an altitudinal and environmental gradient. Seeds of 18 species were collected in Sardinia from sea level to 1810 m above sea level, and germination tests were carried out at a range of constant (5 to 25°C) and alternating (25/10°C) temperatures. Different dormancy-breaking treatments [gibberellic acid (GA3), cold (C) and warm (W) stratifications and dry after ripening (DAR)] were applied. The annual pattern of soil temperatures was recorded using 24 data-loggers buried close to the study species. The logged soil temperatures distinguished ‘Mediterranean lowland’ from ‘Mediterranean mountain’ species. Although germination was >50% in untreated seeds of most species, GA3 had a positive effect in all species. C either inhibited or had a neutral effect on germination, W did not enhanced seed germination, while DAR had a positive effect only in species from coastal environments. The thermal time constant (S) for 50% germination ranged from 22 to 357°Cd (degree days) above base temperatures (Tb) of –9 to 9°C, depending on species and treatments. Mediterranean lowland species had lower Tb values compared with upland species. This study revealed significant differences in germination thresholds of Mediterranean lowland and mountain species in relation to Tb and S that probably have an impact on germination timing in the field and niche competitiveness.

Eugenia stipitata occurs along rivers in Western Amazonia and produces berry-type fruits with economic potential. Its large recalcitrant (i.e. desiccation-intolerant) seeds have been proposed as a model to study seed stress response, as no apparent differentiation between the embryonic axis and the fused cotyledons are visible. Here, the longevity of submerged seeds was analysed with a view to understanding adaptive mechanisms to seasonal flooding. Submerged seeds began germinating after 2 months. After 1 year, 87 and 96% total germination was reached when seeds were submerged under a water column of 6 cm (where seedlings could emerge from under the water) and 26 cm (where seedlings could not reach the water surface), respectively. Seedling morphology was altered underwater, with short internodes and rudimentary leaf blades, and when submersion was terminated, seedlings transplanted to nursery conditions recovered a normal phenotype. Furthermore, when seedlings were detached from the seeds, the ‘resown’ seeds produced a second, normal seedling within 9 months. Concentrations of the antioxidant glutathione, which was measured as a stress marker, increased with submersion time in water. Seeds that had developed roots and shoots underwater had higher concentrations of glutathione disulphide than non-germinated seeds, suggesting that the flooding stress was more intense for seedlings than seeds, although more oxidizing cellular redox environments are also consistent with the conditions required for differentiation. Submergence underwater is recommended for storage of the recalcitrant seeds of E. stipitata for up to 1 year.

Orchid seeds are among the smallest seeds in nature and they are naturally rich in fatty acids. However, the fatty acid composition of orchid seeds has not been investigated because the sample masses utilized for widely used methods for fatty acid profiling would generally require prohibitively large numbers (i.e. 10,000s) of seeds. The present work aimed to develop a method for fatty acid analysis using gas chromatography–mass spectrometry on small quantities (mg) of seeds. The method was developed using the seeds of two species, Dactylorhiza fuchsii, a temperate terrestrial, and Grammatophyllum speciosum, a tropical epiphyte. A range of sample masses was tested to determine the minimum mass required to achieve reliable fatty acid composition data. A direct transesterification method was used, which did not require extraction of fatty acids from seeds prior to analysis, and the effects of seed processing (crushed versus intact seeds) and incubation time in toluene on fatty acid yield were tested. Stable fatty acid profiles were obtained using as little as 10 mg of seeds. Neither crushing the seeds nor extending the toluene incubation step had much effect on the fatty acid yield. The simple direct transesterification method presented will enable the fatty acid composition of orchid seeds, and possibly other small seeds, to be determined reliably for studies into seed development, storage and germination.

The ability of orthodox seeds to survive long-term dry storage is a key prerequisite for ex situ seed conservation in genebanks. However, only a few credible observations of seed survival for ≥ 200 years have been reported. In this paper, seed survival is shown for three species under suboptimal storage conditions for a documented time of ≥ 203 years and carbon dated at 218–270 years. Two species that germinated are in the Fabaceae (Liparia sp. and Acacia sp.). A water-impermeable seed coat, and hence an inability to equilibrate with ambient relative humidity, may contribute to long-term survival of these species. The third species that germinated (Leucospermum sp.) does not have a water-impermeable seed coat, and long-term survival may be linked to an oxygen-impermeable barrier in the seed. These results for species from the Cape Floristic Region, South Africa, suggest adaptation for extreme longevity in seeds of species of seasonally dry, Mediterranean environments.

For recalcitrant seeds, mortality curves of germination versus water content typically imply a wide range of desiccation sensitivities within a seed population. However, seed to seed differences in water content, during desiccation, may confound our interpretation of these mortality plots. Here, we illustrate this problem for two batches of Vitellaria paradoxa (Sapotaceae) seeds collected in 1996 and 2002. Whole seeds were desiccated to various target water contents (TWCs) using silica gel. During desiccation, smaller seeds in the population dried most rapidly. Consequently, there was a significant linear relationship between whole-seed water content and seed mass during the drying process. In addition, following desiccation to low TWCs, only the largest seeds in the population retained viability. Taken together, this suggests that the larger seeds survived, not as a consequence of great relative desiccation tolerance, but as a result of taking longer to desiccate. Subsequently, the critical water content (CWC) for viability loss was calculated, based on the assumptions that in the seed population whole-seed water content during desiccation was normally distributed and the smallest, and hence driest, seeds were killed first. Using this approach, the driest seeds in the population that were killed, at each TWC, were always below a single CWC (c. 20% and 26% in 1996 and 2002, respectively). In subsequent experiments the effect of seed size variation on the response to desiccation was confirmed by conducting desiccation screens on seeds sorted into two discrete size classes, i.e. the seed-lot heterogeneity in mass was reduced. Using this approach, the mortality curves had a steeper slope. Furthermore, data for 24 tropical tree species from the Database of Tropical Tree Seed Research (DABATTS) revealed that seed lots with less variability in mass had steeper mortality curves. Thus, taken together, the data suggest that, at least for whole seeds, the wide range of desiccation sensitivities typically inferred is an artefact of seed to seed variation in mass, and hence water contents, during drying.

The effects of desiccation and temperature on the germination capability of Carica papaya L. were investigated for seeds extracted from three commercial fruit batches. More than 50% of freshly isolated, cleaned (sarcotesta removed) but undried seeds germinated at 26°C. However, desiccation to approx. 20%seed RH reduced germination at this temperature to < 10%. A substantial increase in germination at alternating temperatures (33/19°C) indicated that desiccation induced seed dormancy rather than viability loss. Dormancy could be removed in a large proportion of the population by the application of a single heat shock to rehydrated seeds for 4 h at 36°C, with subsequent return to 26°C for germination. Longer (days) and shorter (minutes) periods of heat shock were less effective for releasing dormancy. Heat shock was generally applied 5 or 14 d after rehydration had started, but the treatment was equally effective after imbibition for only 1 d. Light was always applied during both imbibition and the post-heat shock treatment, but was not essential during the actual heat shock treatment. Rehydration and post-heat shock temperature treatments in the range of 16°C to 36°C revealed the same optima of 26°C. Dormancy was re-imposed in heat-shocked seeds when they were subsequently dried to seed relative humidities of 25 to 75%(5 to 11% moisture content [fresh weight basis]), but this state could be removed by a further heat shock. The longer heat-shocked seeds were held on agar-water at 26°C prior to re-drying, the greater the level of desiccation intolerance.