Beyond gibberellins and abscisic acid: how ethylene and jasmonates control seed germination

The dimorphic diaspore model Aethionema arabicum (Brassicaceae): Distinct molecular and morphological control of responses to parental and germination temperatures

Plants in habitats with unpredictable conditions often have diversified bet-hedging strategies that ensure fitness over a wider range of variable environmental factors. A striking example is the diaspore (seed and fruit) heteromorphism that evolved to maximize species survival in Aethionema arabicum (Brassicaceae) in which external and endogenous triggers allow the production of two distinct diaspores on the same plant. Using this dimorphic diaspore model, we identified contrasting molecular, biophysical, and ecophysiological mechanisms in the germination responses to different temperatures of the mucilaginous seeds (M+ seed morphs), the dispersed indehiscent fruits (IND fruit morphs), and the bare non-mucilaginous M- seeds obtained by pericarp (fruit coat) removal from IND fruits. Large-scale comparative transcriptome and hormone analyses of M+ seeds, IND fruits, and M- seeds provided comprehensive datasets for their distinct thermal responses. Morph-specific differences in co-expressed gene modules in seeds, as well as in seed and pericarp hormone contents, identified a role of the IND pericarp in imposing coat dormancy by generating hypoxia affecting abscisic acid (ABA) sensitivity. This involved expression of morph-specific transcription factors, hypoxia response, and cell wall remodeling genes, as well as altered ABA metabolism, transport, and signaling. Parental temperature affected ABA contents and ABA-related gene expression and altered IND pericarp biomechanical properties. Elucidating the molecular framework underlying the diaspore heteromorphism can provide insight into developmental responses to globally changing temperatures.

Investigation of biological-rhythm patterns: physiological and biochemical effects in herbaceous plants exposed to low-level chronic radiation - part 1: nonirradiated seeds

HYPOTHESIS

Because reactive oxygen species are involved in the regulation of biological rhythms, we hypothesized that intra-annual variability of seed progeny quality at low doses of ionizing radiation (LDIRs) would differ from that of background plants.

MATERIALS AND METHODS

We conducted 12 consecutive experiments using the roll culture method by germinating seeds (monthly for 3 weeks) of six herbaceous plant species (Bromus inermis, Geum aleppicum, Plantago major, Rumex confertus, Silene latifolia, and Taraxacum officinale) growing under conditions of chronic radiation in the East Ural Radioactive Trace (EURT). We assessed physiological (seed viability and abnormality frequency) and biochemical (low-molecular-weight antioxidants, LMWAs) parameters of seedlings.

RESULTS

Total absorbed dose rates of maternal plants (TADRplants) and seed embryos (TADRseeds) in the EURT exceeded background levels by 1-3 and 1-2 orders of magnitude, respectively. Nonlinear dependencies on TADR were mainly characteristic of physiological and biochemical parameters. For most populations of the studied species (B. inermis, G. aleppicum, R. confertus, and S. latifolia), seedling survival and root length decreased in the autumn-winter period, while the frequency of abnormal seedlings increased. The content of LMWAs could be ranked as R. confertus > B. inermis > G. aleppicum > S. latifolia, in good agreement with the presence of anthocyanin pigmentation in the plants. The lowest synthesis of antioxidants in seedlings was observed in winter. A high LMWA content promoted growth and reduced the frequency of abnormal seedlings.

CONCLUSIONS

These results underscore a multistage nature of the impact of LDIRs on intra-annual biological rhythms in plants. High heterogeneity in reference group 'wild grasses' and diversity of their radiobiological effects should help to develop methods of radiation protection for natural ecosystems and facilitate approaches used by the International Commission on Radiological Protection.HighlightsAbsorbed dose rates for six plant species in the East Ural Radioactive Trace (EURT) area range from 0.11 to 73.89 µGy h-s (plants) and 0.11 to 6.88 µGy h-s (seed embryos).Intra-annual rhythms of physiological and biochemical parameters in the EURT zone differ from those in background seedlings.Plants in the EURT area exhibit a wide range of trait variability, asynchrony of the manifestation of the effects, nonlinear dose-response relations, and hormesis.A high content of low-molecular-weight antioxidants (LMWAs) is associated with low frequency of developmental abnormalities and high viability of seed progeny.

Comparative transcriptomics of seed nourishing tissues: uncovering conserved and divergent pathways in seed plants

The evolutionary and ecological success of spermatophytes is intrinsically linked to the seed habit, which provides a protective environment for the initial development of the new generation. This environment includes an ephemeral nourishing tissue that supports embryo growth. In gymnosperms this tissue originates from the asexual proliferation of the maternal megagametophyte, while in angiosperms it is a product of fertilization, and is called the endosperm. The emergence of these nourishing tissues is of profound evolutionary value, and they are also food staples for most of the world's population. Here, using Orthofinder to infer orthologue genes among newly generated and previously published datasets, we provide a comparative transcriptomic analysis of seed nourishing tissues from species of several angiosperm clades, including those of early diverging lineages, as well as of one gymnosperm. Our results show that, although the structure and composition of seed nourishing tissues has seen significant divergence along evolution, there are signatures that are conserved throughout the phylogeny. Conversely, we identified processes that are specific to species within the clades studied, and thus illustrate their functional divergence. With this, we aimed to provide a foundation for future studies on the evolutionary history of seed nourishing structures, as well as a resource for gene discovery in future functional studies.

Metabolome and transcriptome analyses reveal changes of rapeseed in response to ABA signal during early seedling development

Seed germination is an important development process in plant growth. The phytohormone abscisic acid (ABA) plays a critical role during seed germination. However, the mechanism of rapeseed in response to ABA is still elusive. In order to understand changes of rapeseed under exogenous ABA treatment, we explored differentially expressed metabolites (DEMs) and the differentially expressed genes (DEGs) between mock- and ABA-treated seedlings. A widely targeted LC-MS/MS based metabolomics were used to identify and quantify metabolic changes in response to ABA during seed germination, and a total of 186 significantly DEMs were identified. There are many compounds which are involved in ABA stimuli, especially some specific ABA transportation-related metabolites such as starches and lipids were screened out. Meanwhile, a total of 4440 significantly DEGs were identified by transcriptomic analyses. There was a significant enrichment of DEGs related to phenylpropanoid and cell wall organization. It suggests that exogenous ABA mainly affects seed germination by regulating cell wall loosening. Finally, the correlation analysis of the key DEMs and DEGs indicates that many DEGs play a direct or indirect regulatory role in DEMs metabolism. The integrative analysis between DEGs and DEMs suggests that the starch and sucrose pathways were the key pathway in ABA responses. The two metabolites from starch and sucrose pathways, levan and cellobiose, both were found significantly down-regulated in ABA-treated seedlings. These comprehensive metabolic and transcript analyses provide useful information for the subsequent post-transcriptional modification and post germination growth of rapeseed in response to ABA signals and stresses.

OsJMJ718, a histone demethylase gene, positively regulates seed germination in rice

Seed vigor has major impact on the rate and uniformity of seedling growth, crop yield, and quality. However, the epigenetic regulatory mechanism of crop seed vigor remains unclear. In this study, a (jumonji C) JmjC gene of the histone lysine demethylase OsJMJ718 was cloned in rice, and its roles in seed germination and its epigenetic regulation mechanism were investigated. OsJMJ718 was located in the nucleus and was engaged in H3K9 methylation. Histochemical GUS staining analysis revealed OsJMJ718 was highly expressed in seed embryos. Abiotic stress strongly induced the OsJMJ718 transcriptional accumulation level. Germination percentage and seedling vigor index of OsJMJ718 knockout lines (OsJMJ718-CR) were lower than those of the wild type (WT). Chromatin immunoprecipitation followed by sequencing (ChIP-seq) of seeds imbibed for 24 h showed an increase in H3K9me3 deposition of thousands of genes in OsJMJ718-CR. ChIP-seq results and transcriptome analysis showed that differentially expressed genes were enriched in ABA and ethylene signal transduction pathways. The content of ABA in OsJMJ718-CR was higher than that in WT seeds. OsJMJ718 overexpression enhanced sensitivity to ABA during germination and early seedling growth. In the seed imbibition stage, ABA and ethylene content diminished and augmented, separately, suggesting that OsJMJ718 may adjust rice seed germination through the ABA and ethylene signal transduction pathways. This study displayed the important function of OsJMJ718 in adjusting rice seed germination and vigor, which will provide an essential reference for practical issues, such as improving rice vigor and promoting direct rice sowing production.

Aethionema arabicum dimorphic seed trait resetting during transition to seedlings

The transition from germinating seeds to emerging seedlings is one of the most vulnerable plant life cycle stages. Heteromorphic diaspores (seed and fruit dispersal units) are an adaptive bet-hedging strategy to cope with spatiotemporally variable environments. While the roles and mechanisms of seedling traits have been studied in monomorphic species, which produce one type of diaspore, very little is known about seedlings in heteromorphic species. Using the dimorphic diaspore model Aethionema arabicum (Brassicaceae), we identified contrasting mechanisms in the germination responses to different temperatures of the mucilaginous seeds (M+ seed morphs), the dispersed indehiscent fruits (IND fruit morphs), and the bare non-mucilaginous M- seeds obtained from IND fruits by pericarp (fruit coat) removal. What follows the completion of germination is the pre-emergence seedling growth phase, which we investigated by comparative growth assays of early seedlings derived from the M+ seeds, bare M- seeds, and IND fruits. The dimorphic seedlings derived from M+ and M- seeds did not differ in their responses to ambient temperature and water potential. The phenotype of seedlings derived from IND fruits differed in that they had bent hypocotyls and their shoot and root growth was slower, but the biomechanical hypocotyl properties of 15-day-old seedlings did not differ between seedlings derived from germinated M+ seeds, M- seeds, or IND fruits. Comparison of the transcriptomes of the natural dimorphic diaspores, M+ seeds and IND fruits, identified 2,682 differentially expressed genes (DEGs) during late germination. During the subsequent 3 days of seedling pre-emergence growth, the number of DEGs was reduced 10-fold to 277 root DEGs and 16-fold to 164 shoot DEGs. Among the DEGs in early seedlings were hormonal regulators, in particular for auxin, ethylene, and gibberellins. Furthermore, DEGs were identified for water and ion transporters, nitrate transporter and assimilation enzymes, and cell wall remodeling protein genes encoding enzymes targeting xyloglucan and pectin. We conclude that the transcriptomes of seedlings derived from the dimorphic diaspores, M+ seeds and IND fruits, undergo transcriptional resetting during the post-germination pre-emergence growth transition phase from germinated diaspores to growing seedlings.

Seed Longevity and Ageing: A Review on Physiological and Genetic Factors with an Emphasis on Hormonal Regulation

Upon storage, seeds inevitably age and lose their viability over time, which determines their longevity. Longevity correlates with successful seed germination and enhancing this trait is of fundamental importance for long-term seed storage (germplasm conservation) and crop improvement. Seed longevity is governed by a complex interplay between genetic factors and environmental conditions experienced during seed development and after-ripening that will shape seed physiology. Several factors have been associated with seed ageing such as oxidative stress responses, DNA repair enzymes, and composition of seed layers. Phytohormones, mainly abscisic acid, auxins, and gibberellins, have also emerged as prominent endogenous regulators of seed longevity, and their study has provided new regulators of longevity. Gaining a thorough understanding of how hormonal signalling genes and pathways are integrated with downstream mechanisms related to seed longevity is essential for formulating strategies aimed at preserving seed quality and viability. A relevant aspect related to research in seed longevity is the existence of significant differences between results depending on the seed equilibrium relative humidity conditions used to study seed ageing. Hence, this review delves into the genetic, environmental and experimental factors affecting seed ageing and longevity, with a particular focus on their hormonal regulation. We also provide gene network models underlying hormone signalling aimed to help visualize their integration into seed longevity and ageing. We believe that the format used to present the information bolsters its value as a resource to support seed longevity research for seed conservation and crop improvement.

Exogenous Nitric Oxide Alleviates Water Deficit and Increases the Seed Production of an Endemic Amazonian Canga Grass

Open pit mining can cause loss in different ecosystems, including damage to habitats of rare and endemic species. Understanding the biology of these species is fundamental for their conservation, and to assist in decision-making. Sporobolus multiramosus is an annual grass endemic to the Amazon canga ecosystems, which comprise rocky outcrop vegetation covering one of the world's largest iron ore reserves. Here, we evaluated whether nitric oxide aids S. multiramosus in coping with water shortages and examined the physiological processes behind these adaptations. nitric oxide application improved the water status, photosynthetic efficiency, biomass production, and seed production and germination of S. multiramosus under water deficit conditions. These enhancements were accompanied by adjustments in leaf and root anatomy, including changes in stomata density and size and root endodermis thickness and vascular cylinder diameter. Proteomic analysis revealed that nitric oxide promoted the activation of several proteins involved in the response to environmental stress and flower and fruit development. Overall, the results suggest that exogenous nitric oxide has the potential to enhance the growth and productivity of S. multiramosus. Enhancements in seed productivity have significant implications for conservation initiatives and can be applied to seed production areas, particularly for the restoration of native ecosystems.

ZmEREB92 plays a negative role in seed germination by regulating ethylene signaling and starch mobilization in maize

Rapid and uniform seed germination is required for modern cropping system. Thus, it is important to optimize germination performance through breeding strategies in maize, in which identification for key regulators is needed. Here, we characterized an AP2/ERF transcription factor, ZmEREB92, as a negative regulator of seed germination in maize. Enhanced germination in ereb92 mutants is contributed by elevated ethylene signaling and starch degradation. Consistently, an ethylene signaling gene ZmEIL7 and an α-amylase gene ZmAMYa2 are identified as direct targets repressed by ZmEREB92. OsERF74, the rice ortholog of ZmEREB92, shows conserved function in negatively regulating seed germination in rice. Importantly, this orthologous gene pair is likely experienced convergently selection during maize and rice domestication. Besides, mutation of ZmEREB92 and OsERF74 both lead to enhanced germination under cold condition, suggesting their regulation on seed germination might be coupled with temperature sensitivity. Collectively, our findings uncovered the ZmEREB92-mediated regulatory mechanism of seed germination in maize and provide breeding targets for maize and rice to optimize seed germination performance towards changing climates.

A non-JA producing oxophytodienoate reductase functions in salicylic acid-mediated antagonism with jasmonic acid during pathogen attack

Peroxisome-localized oxo-phytodienoic acid (OPDA) reductases (OPR) are enzymes converting 12-OPDA into jasmonic acid (JA). However, the biochemical and physiological functions of the cytoplasmic non-JA producing OPRs remain largely unknown. Here, we generated Mutator-insertional mutants of the maize OPR2 gene and tested its role in resistance to pathogens with distinct lifestyles. Functional analyses showed that the opr2 mutants were more susceptible to the (hemi)biotrophic pathogens Colletotrichum graminicola and Ustilago maydis, but were more resistant to the necrotrophic fungus Cochliobolus heterostrophus. Hormone profiling revealed that increased susceptibility to C. graminicola was associated with decreased salicylic acid (SA) but increased JA levels. Mutation of the JA-producing lipoxygenase 10 (LOX10) reversed this phenotype in the opr2 mutant background, corroborating the notion that JA promotes susceptibility to this pathogen. Exogenous SA did not rescue normal resistance levels in opr2 mutants, suggesting that this SA-inducible gene is the key downstream component of the SA-mediated defences against C. graminicola. Disease assays of the single and double opr2 and lox10 mutants and the JA-deficient opr7opr8 mutants showed that OPR2 negatively regulates JA biosynthesis, and that JA is required for resistance against C. heterostrophus. Overall, this study uncovers a novel function of a non-JA producing OPR as a major negative regulator of JA biosynthesis during pathogen infection, a function that leads to its contrasting contribution to either resistance or susceptibility depending on pathogen lifestyle.

Proteome Dynamics Analysis Reveals the Potential Mechanisms of Salinity and Drought Response during Seed Germination and Seedling Growth in Tamarix hispida

Understanding the molecular mechanisms of seed germination and seedling growth is vital for mining functional genes for the improvement of plant drought in a desert. Tamarix hispida is extremely resistant to drought and soil salinity perennial shrubs or trees. This study was the first to investigate the protein abundance profile of the transition process during the processes of T. hispida seed germination and seedling growth using label-free proteomics approaches. Our data suggested that asynchronous regulation of transcriptomics and proteomics occurs upon short-term seed germination and seedling growth of T. hispida. Enrichment analysis revealed that the main differentially abundant proteins had significant enrichment in stimulus response, biosynthesis, and metabolism. Two delta-1-pyrroline-5-carboxylate synthetases (P5CS), one Ycf3-interacting protein (Y3IP), one low-temperature-induced 65 kDa protein-like molecule, and four peroxidases (PRX) were involved in both water deprivation and hyperosmotic salinity responses. Through a comparative analysis of transcriptomics and proteomics, we found that proteomics may be better at studying short-term developmental processes. Our results support the existence of several mechanisms that enhance tolerance to salinity and drought stress during seedling growth in T. hispida.

The ethylene receptor mutation etr2b reveals crosstalk between ethylene and ABA in the control of Cucurbita pepo germination

The enhanced salt tolerance of squash ethylene-insensitive mutants during germination and early stages of seedling development suggested that abscisic acid (ABA) could mediate this tolerance. To gain insight into the crosstalk between ethylene and ABA in seed germination, the germination rate and early seedling growth of wild type (WT) and ethylene-insensitive etr2b mutant were compared in seeds germinated under water and exogenous ABA treatment. The etr2b seeds germinated earlier than WT under both water and ABA, and the effect of ABA on radicle length and seedling growth of etr2b was lower than in WT, indicating that etr2b is also insensitive to ABA. The comparison of ABA and ethylene contents and ABA and ethylene gene expression profiles in WT and etr2b dry and imbibed seeds in either water, NaCl or ABA demonstrated a clear crosstalk between ethylene and ABA in germination. The expression profiles of ethylene genes in WT and etr2b indicated that the role of ethylene in seed germination does not appear to follow the canonical ethylene signaling pathway. Instead, etr2b reduces ABA content during formation of the seeds (dry seeds) and in response to seed imbibition and germination, which means diminished dormancy in the ethylene mutant. The etr2b mutation downregulated the expression of ABA biosynthesis and signaling genes during germination, demonstrating the positive role of ethylene receptor gene CpETR2B on seed germination and early seedling growth in squash is mediated by ABA. The reduced effect of exogenous ABA on ethylene production and ethylene gene expression in etr2b seeds suggests that this regulation is also dependent on ethylene.

Overexpression of acdS gene encoding 1-aminocyclopropane-1-carboxylic acid deaminase enzyme in petunia negatively affects seed germination

Overexpression of acdS in petunia negatively affects seed germination by suppression of ethylene biosynthesis and signaling genes and induction of abscisic acid biosynthesis genes in the seeds. The acdS gene, which encodes 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, has been overexpressed in horticultural crops to improve their tolerance to abiotic stress. However, the role of acdS in the germination of crop seeds has not been investigated, despite its suppression of ethylene production. In this study, acdS overexpression significantly reduced seed weight and germination rate in transgenic petunia cv. Merage Rose (T5, T7, and T12) relative to wild type via the suppression of ethylene biosynthesis and signaling genes and induction of abscisic acid (ABA) biosynthesis genes. The germination rate of T7 was significantly lower than those of T5 and T12, which was linked to higher expression of acdS in the former than the latter. The addition of exogenous ACC and gibberellic acid (GA₃) to the germination medium improved the germination rate of T5 seeds and GA₃ promoted the germination rate of T12 seeds. However, neither ACC nor GA₃ promoted the germination rate of T7 seeds. The improved germination rates in T5 and T12 were associated with the transcriptional regulation of ethylene biosynthesis genes, particularly that of the ACO1 gene, signaling genes, and ABA biosynthesis genes. In this study, we discovered a negative role of acdS in seed germination in petunia. Thus, we highlight the need to consider the negative effect of acdS on seed germination when overexpressing the gene in horticultural crops to improve tolerance to abiotic stress.

Effects of Seed Endophytic Bacteria on Life History and Reproductive Traits in a Cosmopolitan Weed, Capsella bursa-pastoris

Diverse bacteria inhabit plant seeds, and at least some of them can enhance plant performance at the early developmental stage. However, it is still inconclusive whether seed bacteria can influence post-germination traits and their contribution to plant fitness. To explore the evolutionary and ecological consequences of seed endophytic bacteria, we isolated four bacterial strains from the seeds of an annual weedy plant species, Capsella bursa-pastoris, and conducted a common garden experiment using seeds inoculated by isolated bacteria. Seeds infected by bacteria tended to germinate in spring rather than in autumn. Bacterial treatment also altered the expression of plant life history and reproductive traits, including flowering dates, rosette diameter at bolting, number of inflorescences, and fruit production. The results of the path analyses suggested that such effects of bacterial treatments were due to bacterial inoculation as well as germination delayed until spring. Spring germinants with bacterial infection showed a weaker association between post-germination traits and relative fitness than those without bacterial infection. These results suggest that seed bacteria likely affect the expression of post-germination traits directly or indirectly by delaying the germination season. An altered contribution of plant traits to relative fitness implies the influence of seed bacteria on the strength of natural selection.

Identification of miRNAs and their target genes associated with improved maize seed vigor induced by gibberellin

High seed vigor is crucial for agricultural production owing to its potential in high quality and yield of crops and a better understanding of the molecular mechanism associated with maize seed vigor is highly necessary. To better understand the involvement and regulatory mechanism of miRNAs correlated with maize seed vigor, small RNAs and degradome sequencing of two inbred lines Yu537A and Yu82 were performed. A total of 791 mature miRNAs were obtained with different expressions, among of which 505 miRNAs were newly identified and the rest miRNAs have been reported before by comparing the miRNAs with the sequences in miRbase database. Analysis of miRNA families showed maize seeds contain fewer miRNA families and larger miRNA families compared with animals, indicating that functions of miRNAs in maize seeds were more synergistic than animals. Degradome sequencing was used to identify the targets of miRNAs and the results showed a total of 6,196 targets were obtained. Function analysis of differentially expressed miRNAs and targets showed Glycan degradation and galactose metabolism were closely correlated with improved maize seed vigor. These findings provide valuable information to understand the involvement of miRNAs with maize seed vigor and these putative genes will be valuable resources for improving the seed vigor in future maize breeding.

Transcriptome Analyses Reveal the Role of Light in Releasing the Morphological Dormancy of Celery Seed by Integrating Plant Hormones, Sugar Metabolism and Endosperm Weakening

Celery seed is known to be difficult to germinate due to its morphological dormancy. Light is the key signal to release morphological dormancy and promote seed germination. However, this mechanism has rarely been studied. We performed physiological, transcriptome analyses on celery seed exposed to light and dark to decipher the mechanism by which light promotes germination of celery seed. The results showed that light significantly enhanced the expression of gibberellin synthesis genes and abscisic acid degradation genes and inhibited the expression of abscisic acid synthesis genes and gibberellin degradation genes. Moreover, gibberellin synthesis inhibitor could completely inhibit the germination capacity of celery seed, indicating that gibberellin is indispensable in the process of celery seed germination. Compared with dark, light also increased the activity of α-amylase and β-amylase and the expression of related coding genes and promoted the degradation of starch and the increase of soluble sugar content, suggesting that light enhanced the sugar metabolism of celery seed. In addition, transcriptome analysis revealed that many genes related to endosperm weakening (cell wall remodeling enzymes, extension proteins) were up-regulated under light. It was also found that light promoted the accumulation of hydrogen peroxide in the radicle, which promoted the endosperm weakening process of celery seed. Our results thus indicated that light signal may promote the release of morphological dormancy through the simultaneous action of multiple factors.

Maturation and Post-Harvest Resting of Fruits Affect the Macronutrients and Protein Content in Sweet Pepper Seeds

There are few studies about the influence of fruit maturation and post-harvest resting on seed composition, which can be necessary for seedling development and future establishment. Thus, the objective of this study was to evaluate the effect of maturation and post-harvest resting of fruits on the macronutrient and protein content of sweet pepper seeds. The experimental design was a randomized block, with eight treatments, in a 4 × 2 factorial arrangement. The first factor was fruit maturation stages (35, 50, 65 and 80 days after anthesis), and the second, with and without post-harvest resting of the fruits for 7 days. The characteristics evaluated in seeds were the dry weight of one thousand seeds, macronutrient content, and content of albumin, globulin, prolamin and glutelin proteins. There were reductions in K, Ca and Mg content, and an increase in seed content of albumin, globulin and prolamins as a function of the fruit maturation stage. Post-harvest resting of the fruits provided higher Ca content and protein albumin in seeds. The decreasing order of macronutrients and protein content in seeds, independent of fruit maturation and resting stage of the fruits, was N > K > P > Mg > S > Ca, and albumin > globulin ≈ glutelin > prolamine, respectively.

Underlying Biochemical and Molecular Mechanisms for Seed Germination

With the burgeoning population of the world, the successful germination of seeds to achieve maximum crop production is very important. Seed germination is a precise balance of phytohormones, light, and temperature that induces endosperm decay. Abscisic acid and gibberellins—mainly with auxins, ethylene, and jasmonic and salicylic acid through interdependent molecular pathways—lead to the rupture of the seed testa, after which the radicle protrudes out and the endosperm provides nutrients according to its growing energy demand. The incident light wavelength and low and supra-optimal temperature modulates phytohormone signaling pathways that induce the synthesis of ROS, which results in the maintenance of seed dormancy and germination. In this review, we have summarized in detail the biochemical and molecular processes occurring in the seed that lead to the germination of the seed. Moreover, an accurate explanation in chronological order of how phytohormones inside the seed act in accordance with the temperature and light signals from outside to degenerate the seed testa for the thriving seed’s germination has also been discussed.

Different Responses of Invasive Weed Alternanthera philoxeroides and Oryza sativa to Plant Growth Regulators

Invasive plants cause a global loss of biodiversity, pose a major threat to the environment and economy, and also significantly affect agricultural production and food security. Plant growth regulators (PGRs) are widely used in agricultural production and might also affect invasive weeds distributed around crops in various ways. At present, there are few studies concerning whether there are significant effects of PGRs on invasive weeds. In this study, two widely used PGRs in paddy fields, gibberellic acid (GA) and paclobutrazol (PAC), were applied on Oryza sativa and a noxious weed Alternanthera philoxeroides, which is frequently distributed in paddy fields. The purpose of this study was to investigate if there are different responses of rice and weeds to these two plant regulators and the significant effects of PGRs on invasive weeds. The results showed that GA significantly promotes the total biomass of A. philoxeroides by 52.00%, but does not significantly affect that of O. sativa. GA significantly increases the growth of aboveground and belowground A. philoxeroides, but not that of O. sativa. On the other hand, PAC extremely inhibited the aboveground and belowground biomass of A. philoxeroides by more than 90%, but did not significantly inhibit the belowground biomass of O. sativa. PAC also enhanced the leaf nitrogen content and chlorophyll content of A. philoxeroides, but not the traits of O. sativa. Therefore, the effects of PGRs are significantly different between rice and the invasive weed. The potential promotion effects of PGRs on weeds that are frequently distributed in farmland warrant sufficient attention. This is probably one of the important reasons why invasive weeds can successfully invade the agricultural ecosystem with large human disturbance. This study might sound an alarm for weed control in paddy fields.

Reproductive Biology of Dry Grassland Specialist Ranunculus illyricus L. and Its Implications for Conservation

Simple Summary

The Ranunculus illyricus—Illyrian buttercup—is threatened with extinction in many countries and measures should be taken to protect it. In order to increase the effectiveness of such measures, it is necessary to know the methods of propagation and to evaluate their efficiency. R. illyricus reproduces generatively by seed and vegetatively by clusters of progeny tubers. The method and potential of vegetative propagation are described here for the first time and compared with the potential and actual effectiveness of generative propagation. Both the generative and vegetative propagation methods should be used to strengthen existing populations and create replacements.

Abstract

Ranunculus illyricus, a component of xerothermic grasslands, is a declining species and deserves active conservation treatments in many countries preceded by studies on the biology of its reproduction. So far, our knowledge of R. illyricus, a species with two modes of reproduction, has been fragmentary. The purpose of the studies presented here was to describe the annual development cycle of R. illyricus with particular emphasis on the production of underground tuber clusters that serve as vegetative propagation. Based on three-year-long observations in an ex situ collection, the efficiency of vegetative propagation was estimated and compared with the efficiency of generative propagation. It was found that in 3 years the best clones could produce up to 57 progeny clusters followed by flowering specimens in the first season. Meanwhile, the high potential for generative reproduction was suppressed by many limitations including fruit setting, the germination capacity of seeds, seedling survival rate, and additionally, the first flowering plant was observed only in the third year. It seems that the efficiency of vegetative propagation of this species can be higher than the efficiency of generative propagation. Moreover, vegets bloomed in the first year after emergence, whereas the first plant of generative origin was observed to bloom only after 3 years. A large proportion of individuals of vegetative origin can negatively affect the genetic diversity of the population but their survival rate against competing plants is higher. To enhance the existing populations or to create new ones, it would be best to use plants derived from clonal propagation of genets carried out in ex situ conditions.

Endosperm weakening: The gateway to a seed's new life

Seed germination is a crucial stage in a plant's life cycle, during which the embryo, surrounded by several tissues, undergoes a transition from the quiescent to a highly active state. Endosperm weakening, a key step in this transition, plays an important role in radicle protrusion. Endosperm weakening is initiated upon water uptake, followed by multiple key molecular events occurring within and outside endosperm cells. Although available transcriptomes have provided information about pivotal genes involved in this process, a complete understanding of the signaling pathways are yet to be elucidated. Much remains to be learnt about the diverse intercellular signals, such as reactive oxygen species-mediated redox signals, phytohormone crosstalk, environmental cue-dependent oxidative phosphorylation, peroxisomal-mediated pectin degradation, and storage protein mobilization during endosperm cell wall loosening. This review discusses the evidences from recent researches into the mechanism of endosperm weakening. Further, given that the endosperm has great potential for manipulation by crop breeding and biotechnology, we offer several novel insights, which will be helpful in this research field and in its application to the improvement of crop production.

Jasmonate regulates seed dormancy in wheat via modulating the balance between gibberellin and abscisic acid

Jasmonate (JA) regulates seed dormancy and germination; however, the underlying mechanisms remain poorly understood. Furthermore, it is unclear if JA is an essential regulator of dormancy and germination. We investigated whether the role of JA in regulating seed dormancy in wheat (Triticum aestivum L.) is mediated by modulation of gibberellin (GA)/abscisic acid (ABA) balance and if the reciprocal modulation of JA level and sensitivity is required for GA-mediated dormancy loss using physiological, pharmacological, and targeted transcriptomic and metabolomic approaches. JA-induced dormancy release in wheat seeds was associated with no change in GA level but up-regulation of GA signaling and ABA catabolism genes, and reduction of the ABA level. Although JA did not affect the expression levels of ABA signaling genes, up-regulation of germination-associated genes indicates a contribution of reduced ABA sensitivity to dormancy release. After-ripening-mediated dormancy loss was also associated with JA-GA synergistic and JA-ABA antagonistic interplays. The prevalence of no effect of GA, which effectively broke dormancy, on the JA-Ile level and expression patterns of JA biosynthesis/signaling and responsive genes reflects that GA-mediated dormancy release occurs independently of JA. Our study concludes that JA induces seed dormancy release in wheat via modulating ABA/GA balance; however, JA is not an essential regulator of dormancy and germination.

The sweet and musky scent of home: biogenic ethylene fine-tunes seed germination in wetlands

Wetlands are known for comparatively high production of biogenic ethylene from decomposed sediment. Because the gas has various well-documented effects on seed physiology, we asked whether it can be a vital seed germination cue for wetland plants. Specifically, we explored whether ethylene plays an ecological role in (i) breaking/weakening seed dormancy, (ii) broadening the germination niche width, (iii) promoting germination speed or (iv) altering the germination requirements of six plant species with different occurrence along a hydroperiod gradient. In a factorial experiment, both ethylene-treated and untreated seeds were incubated in combinations of temperature (constant versus fluctuating), illumination (light versus darkness) and oxygen (aerobic versus hypoxia) with and without cold stratification. Our results revealed seed exposure to ethylene did not weaken or break dormancy without cold stratification treatment. However, ethylene helped to broaden the germination niche width, increased overall germination percentage and speed of cold-stratified (non-dormant) seeds. This indicates that ethylene helps those seeds that lost dormancy (non-dormant) to sense favourable water-saturated versus flooded substrate depending on their requirement for aerobic versus hypoxic conditions to trigger germination. We conclude that ethylene does not interfere directly with the dormancy-breaking process in autumn-dispersed seeds that are naturally cold-stratified in winter and germinate in spring/summer. However, ethylene plays a crucial ecological role as a 'flood detector' for different wetland plant communities (reed, mudflat, swamp, shallow water) to synchronize germination of non-dormant seeds in the most suitable habitat at the right time.

Combined transcriptomic and metabolomic analysis reveals the potential mechanism of seed germination and young seedling growth in Tamarix hispida

Background

Seed germination is a series of ordered physiological and morphogenetic processes and a critical stage in plant life cycle. Tamarix hispida is one of the most salt-tolerant plant species; however, its seed germination has not been analysed using combined transcriptomics and metabolomics.

Results

Transcriptomic sequencing and widely targeted metabolomics were used to detect the transcriptional metabolic profiles of T. hispida at different stages of seed germination and young seedling growth. Transcriptomics showed that 46,538 genes were significantly altered throughout the studied development period. Enrichment study revealed that plant hormones, such as auxin, ABA, JA and SA played differential roles at varying stages of seed germination and post-germination. Metabolomics detected 1022 metabolites, with flavonoids accounting for the highest proportion of differential metabolites. Combined analysis indicated that flavonoid biosynthesis in young seedling growth, such as rhoifolin and quercetin, may improve the plant’s adaptative ability to extreme desert environments.

Conclusions

The differential regulation of plant hormones and the accumulation of flavonoids may be important for the seed germination survival of T. hispida in response to salt or arid deserts. This study enhanced the understanding of the overall mechanism in seed germination and post-germination. The results provide guidance for the ecological value and young seedling growth of T. hispida.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08341-x.

Seed Dormancy Release and Germination Requirements of Cinnamomum migao, an Endangered and Rare Woody Plant in Southwest China

Seed dormancy is a complex adaptive trait of plants that are influenced by several physiological and environmental factors. The endangered plant Cinnamomum migao is also known to exhibit seed dormancy and low germination, which may influence its regeneration; however, these characteristics remain unexplored. To our knowledge, this study is the first to examine the type of dormancy and improve the germination percentage of C. migao seeds. We evaluated the structure and characteristics of the embryo and endocarp of C. migao seeds as well as the effects of endogenous inhibitors. Furthermore, we assessed the effects of light, stratification, alternating temperature, and gibberellic acid 3 (GA3) on the dormancy release of these seeds. The embryo was well developed the endocarp was water-permeable, and no obvious mechanical hindrance to germination was observed. However, the endocarp and embryo contained phenols and other germination inhibitors. The seed extracts of C. migao delayed the germination of cabbage and ryegrass seeds, which indicates the presence of endogenous inhibitors. These findings suggest that C. migao seeds exhibit physiological dormancy. Light and an alternating temperature (15/20°C) did not influence germination. However, GA3 pretreatment, alternating temperatures, and warm stratification relieved dormancy. GA3 pretreatment combined with the 15°C stratification treatment was most effective in rapidly releasing the C. migao seed dormancy. Our findings may facilitate the storage and conservation of this endangered plant, which is currently underrepresented in ex situ collections.

Editing of 1-aminocyclopropane-1-carboxylate oxidase genes negatively affects petunia seed germination

Editing of ACO genes involved in ethylene biosynthesis pathway reduces ethylene production in petunia seeds and inhibits seed germination. Ethylene production in the seeds of Petunia hybrida cv. 'Mirage Rose' was associated with expression of 1-aminocyclopropane-1-carboxylic acid (ACC) oxidase (ACO) genes (PhACO1, PhACO3, and PhACO4). Suppression of their expression by ethylene inhibitor silver thiosulphate (STS) significantly reduced ethylene production and inhibited seed germination. When it was combined with ethylene precursor ACC, ethylene production was re-promoted via activation of the genes and higher seed germination was restored. This was confirmed using the mutants editing the genes and WT. In the present study, compared with wild type plants, three different mutants (phaco1, phaco3, and phaco4) showed significantly decreased germination percentages as well as delayed germination time and seedling growth. These reductions were associated with lighter seed weight, lower ACO transcript levels, and lower ethylene production in mutants. Inhibited seed germination owing to reduced ethylene production was further verified by the supplementation of exogenous ACC and gibberellic acid (GA₃) to growth medium, which restored high seed germination activity in all mutants via enhanced ethylene production. In this study, we reported a key regulatory role of ethylene in seed germination mechanisms in petunia. Further, we highlighted on need to consider the negative effects of ethylene reduction in seed germination and plant growth when editing genes in the ethylene biosynthesis pathway for the maintenance of postharvest fruit, vegetable, and flower quality.

β-Carotene biofortification of chia sprouts with plant growth regulators

Chia (Salvia hispanica) is a native plant species from South America that is very appreciated for its oleaginous seeds in the agri-food field. Chia seeds are natural sources of many bioactive compounds which provide benefits to human health. Nevertheless, chia sprouts have better nutritional properties than seeds, such as antioxidants, essential amino acids, and phenolic compounds. Among all these beneficial compounds, β-carotene has not been studied in chia sprouts. β-carotene is a precursor of vitamin A, which contributes to maintaining our health status. In this study, to improve β-carotene content in chia sprouts, some plant growth regulators (abscisic acid, methyl jasmonate and methyl salicylate) were applied exogenously to germinating chia seeds. Gibberellins A4/A7 and cytokinin 6-benzyladenine (Promalin®) were also applied, combined with the other regulators, to antagonize a possible inhibition in the germination. Seeds were grown in darkness for 4 days, then seeds were exposed to a short light stimulus (30') and finally to a continued light stimulus (48h). β-carotene, xanthophylls, chlorophylls, de-epoxidation status of xanthophyll cycle (DPS), germination rate, and sprouts fresh weight were analysed. The results show that sprouts treated with methyl salicylate in-creased 2,35 fold their β-carotene content when they were exposed to light for 30'+48h. Sprouts fresh weight and germination were not affected by methyl salicylate. Although more research is needed before industrial application, it is concluded that methyl salicylate can be used to improve β-carotene contents in chia sprouts.

Transition from Seeds to Seedlings: Hormonal and Epigenetic Aspects

Transition from seed to seedling is one of the critical developmental steps, dramatically affecting plant growth and viability. Before plants enter the vegetative phase of their ontogenesis, massive rearrangements of signaling pathways and switching of gene expression programs are required. This results in suppression of the genes controlling seed maturation and activation of those involved in regulation of vegetative growth. At the level of hormonal regulation, these events are controlled by the balance of abscisic acid and gibberellins, although ethylene, auxins, brassinosteroids, cytokinins, and jasmonates are also involved. The key players include the members of the LAFL network-the transcription factors LEAFY COTYLEDON1 and 2 (LEC 1 and 2), ABSCISIC ACID INSENSITIVE3 (ABI3), and FUSCA3 (FUS3), as well as DELAY OF GERMINATION1 (DOG1). They are the negative regulators of seed germination and need to be suppressed before seedling development can be initiated. This repressive signal is mediated by chromatin remodeling complexes-POLYCOMB REPRESSIVE COMPLEX 1 and 2 (PRC1 and PRC2), as well as PICKLE (PKL) and PICKLE-RELATED2 (PKR2) proteins. Finally, epigenetic methylation of cytosine residues in DNA, histone post-translational modifications, and post-transcriptional downregulation of seed maturation genes with miRNA are discussed. Here, we summarize recent updates in the study of hormonal and epigenetic switches involved in regulation of the transition from seed germination to the post-germination stage.

Combinations of maternal-specific repressive epigenetic marks in the endosperm control seed dormancy

Polycomb Repressive Complex 2 (PRC2)-mediated trimethylation of histone H3 on lysine 27 (H3K27me3) and methylation of histone 3 on lysine 9 (H3K9me) are two repressive epigenetic modifications that are typically localized in distinct regions of the genome. For reasons unknown, however, they co-occur in some organisms and special tissue types. In this study, we show that maternal alleles marked by H3K27me3 in the Arabidopsis endosperm were targeted by the H3K27me3 demethylase REF6 and became activated during germination. In contrast, maternal alleles marked by H3K27me3, H3K9me2, and CHG methylation (CHGm) are likely to be protected from REF6 targeting and remained silenced. Our study unveils that combinations of different repressive epigenetic modifications time a key adaptive trait by modulating access of REF6.

Physiological and metabolic bases of increased growth in the tomato ethylene-insensitive mutant Never ripe: extending ethylene signaling functions

The tomato mutant Never ripe (Nr), a loss-of-function for the ethylene receptor SlETR3, shows enhanced growth, associated with increased carbon assimilation and a rewiring of the central metabolism. Compelling evidence has demonstrated the importance of ethylene during tomato fruit development, yet its role on leaf central metabolism and plant growth remains elusive. Here, we performed a detailed characterization of Never ripe (Nr) tomato, a loss-of-function mutant for the ethylene receptor SlETR3, known for its fruits which never ripe. However, besides fruits, the Nr gene is also constitutively expressed in vegetative tissues. Nr mutant showed a growth enhancement during both the vegetative and reproductive stage, without an earlier onset of leaf senescence, with Nr plants exhibiting a higher number of leaves and an increased dry weight of leaves, stems, roots, and fruits. At metabolic level, Nr also plays a significant role with the mutant showing changes in carbon assimilation, carbohydrates turnover, and an exquisite reprogramming of a large number of metabolite levels. Notably, the expression of genes related to ethylene signaling and biosynthesis are not altered in Nr. We assess our results in the context of those previously published for tomato fruits and of current models of ethylene signal transduction, and conclude that ethylene insensitivity mediated by Nr impacts the whole central metabolism at vegetative stage, leading to increased growth rates.

Clues on an intraspecific communication system in seed-seedling transition

How much interactivity is in a seed-seedling transition system? We hypothesize that seed-seed, seed-seedling, and seedling-seedling interactions can drive the early plant development in artificial growth systems directly due to mutual stimulation phenomena. To test the hypothesis, we performed seed germination measurements, gene expression in germination sensu stricto, water dynamics in germinating seeds, and information theory. For a biological model, we used Solanum lycocarpum A. St.-Hil. seeds. This is a neotropical species with high intraspecific variability in the seed sample. Our findings demonstrate that the dynamic and transient seed-seedling transition system is influenced by the number of individuals (seed or seedling) in the artificial system. In addition, we also discuss that: (1) the information entropy enables the quantification of system disturbance relative to individuals at the same physiological stage (seed-seed or seedling-seedling), which may be determinant for embryo growth during germination and (2) the intraspecific communication in seed-seedling transition systems formed by germinating seeds has the potential to alter the expression pattern of key genes for embryo development. Therefore, the phenomenon of mutual stimulation during the germination process can be an important aspect of seed-seedling transition, especially in laboratory conditions.

MES7 Modulates Seed Germination via Regulating Salicylic Acid Content in Arabidopsis

Seed germination is an important phase transitional period of angiosperm plants during which seeds are highly sensitive to different environmental conditions. Although seed germination is under the regulation of salicylic acid (SA) and other hormones, the molecular mechanism underlying these regulations remains mysterious. In this study, we determined the expression of SA methyl esterase (MES) family genes during seed germination. We found that MES7 expression decreases significantly in imbibed seeds, and the dysfunction of MES7 decreases SA content. Furthermore, MES7 reduces and promotes seed germination under normal and salt stress conditions, respectively. The application of SA restores the seed germination deficiencies of mes7 mutants under different conditions. Taking together, our observations uncover a MeSA hydrolytic enzyme, MES7, regulates seed germination via altering SA titer under normal and abiotic stress conditions.

Transcriptomes analysis reveals novel insight into the molecular mechanisms of somatic embryogenesis in Hevea brasiliensis

BACKGROUND

Somatic embryogenesis (SE) is a promising technology for plant vegetative propagation, which has an important role in tree breeding. Though rubber tree (Hevea brasiliensis Muell. Arg.) SE has been founded, few late SE-related genes have been identified and the molecular regulation mechanisms of late SE are still not well understood.

RESULTS

In this study, the transcriptomes of embryogenic callus (EC), primary embryo (PE), cotyledonary embryo (CE), abnormal embryo (AE), mature cotyledonary embryo (MCE) and withered abnormal embryo (WAE) were analyzed. A total of 887,852,416 clean reads were generated, 85.92% of them were mapped to the rubber tree genome. The de novo assembly generated 36,937 unigenes. The differentially expressed genes (DEGs) were identified in the pairwise comparisons of CE vs. AE and MCE vs. WAE, respectively. The specific common DEGs were mainly involved in the phytohormones signaling pathway, biosynthesis of phenylpropanoid and starch and sucrose metabolism. Among them, hormone signal transduction related genes were significantly enriched, especially the auxin signaling factors (AUX-like1, GH3.1, SAUR32-like, IAA9-like, IAA14-like, IAA27-like, IAA28-like and ARF5-like). The transcription factors including WRKY40, WRKY70, MYBS3-like, MYB1R1-like, AIL6 and bHLH93-like were characterized as molecular markers for rubber tree late SE. CML13, CML36, CAM-7, SERK1 and LEAD-29-like were also related to rubber tree late SE. In addition, histone modification had crucial roles during rubber tree late SE.

CONCLUSIONS

This study provides important information to elucidate the molecular regulation during rubber tree late SE.

Genome-Wide Association Mapping Unravels the Genetic Control of Seed Vigor under Low-Temperature Conditions in Rapeseed (Brassica napus L.)

Low temperature inhibits rapid germination and successful seedling establishment of rapeseed (Brassica napus L.), leading to significant productivity losses. Little is known about the genetic diversity for seed vigor under low-temperature conditions in rapeseed, which motivated our investigation of 13 seed germination- and emergence-related traits under normal and low-temperature conditions for 442 diverse rapeseed accessions. The stress tolerance index was calculated for each trait based on performance under non-stress and low-temperature stress conditions. Principal component analysis of the low-temperature stress tolerance indices identified five principal components that captured 100% of the seedling response to low temperature. A genome-wide association study using ~8 million SNP (single-nucleotide polymorphism) markers identified from genome resequencing was undertaken to uncover the genetic basis of seed vigor related traits in rapeseed. We detected 22 quantitative trait loci (QTLs) significantly associated with stress tolerance indices regarding seed vigor under low-temperature stress. Scrutiny of the genes in these QTL regions identified 62 candidate genes related to specific stress tolerance indices of seed vigor, and the majority were involved in DNA repair, RNA translation, mitochondrial activation and energy generation, ubiquitination and degradation of protein reserve, antioxidant system, and plant hormone and signal transduction. The high effect variation and haplotype-based effect of these candidate genes were evaluated, and high priority could be given to the candidate genes BnaA03g40290D, BnaA06g07530D, BnaA09g06240D, BnaA09g06250D, and BnaC02g10720D in further study. These findings should be useful for marker-assisted breeding and genomic selection of rapeseed to increase seed vigor under low-temperature stress.

BES1 negatively regulates the expression of ACC oxidase 2 to control the endogenous level of ethylene in Arabidopsis thaliana

Quantitative reverse transcription PCR (qRT-PCR) analysis and ProACO2::GUS expression showed that ACO2 was highly expressed in the shoots of Arabidopsis seedlings under light conditions. Exogenously applied aminocyclopropane-1-carboxylic acid (ACC) enhanced the expression of ACO2, whereas Co²⁺ ions suppressed its expression. In comparison with wild-type seedlings, the ACO2 knockdown mutant aco2-1 produced less ethylene, which resulted in the inhibited growth of Arabidopsis seedlings. Exogenously applied brassinolide reduced the expression of ACO2. ACO2 expression was increased in det2, a brassinosteroid (BR)-deficient mutant; however, it was decreased in bes1-D, a brassinosteroid insensitive 1-EMS-suppressor 1 (BES1)-dominant mutant. In the putative promoter region of ACO2, 11 E-box sequences for BES1 binding but not BR regulatory element sequences for brassinazole-resistant 1 (BZR1) binding were found. Chromatin immunoprecipitation assay showed that BES1 could directly bind to the E-boxes located in the putative promoter region of ACO4. Less ethylene was produced in bes1-D seedlings compared with wild-type seedlings, suggesting that the direct binding of BES1 to the ACO2 promoter may negatively regulate ACO2 expression to control the endogenous level of ethylene in Arabidopsis seedlings.

From the Outside to the Inside: New Insights on the Main Factors That Guide Seed Dormancy and Germination

The transition from a dormant to a germinating seed represents a crucial developmental switch in the life cycle of a plant. Subsequent transition from a germinating seed to an autotrophic organism also requires a robust and multi-layered control. Seed germination and seedling growth are multistep processes, involving both internal and external signals, which lead to a fine-tuning control network. In recent years, numerous studies have contributed to elucidate the molecular mechanisms underlying these processes: from light signaling and light-hormone crosstalk to the effects of abiotic stresses, from epigenetic regulation to translational control. However, there are still many open questions and molecular elements to be identified. This review will focus on the different aspects of the molecular control of seed dormancy and germination, pointing out new molecular elements and how these integrate in the signaling pathways already known.

Transcriptomic analysis of seed germination improvement of Andrographis paniculata responding to air plasma treatment

The plasma seed treatment is effective for promoting seed germination in many crops. However, the biological mechanism remains unclear. Therefore, mRNA sequencing was used to screen differentially expressed genes in the germination process of Andrographis paniculata seeds treated with air plasma (power density = 8.99 J/cm³). Following plasma treatment, the germination percentages were significantly higher than those of the control, they were 3.5±0.6% vs. 0 at 28 hours after sowing (HAS) and 50.3±2.6% vs. 37.3±1.7% at 48 HAS. After unigenes were assembled and annotated, 125 differentially expressed genes (DEGs) were detected at 28 HAS, compared with nine DEGs at 48 HAS, but no DEGs were detected at 0 HAS, indicating that air plasma treatment mainly changed the gene expression of A. paniculata seeds at 28 HAS. The NCED5 expression level of the treated group was less than one-fifth of the control, and the expressions of three ethylene response factors were significantly higher than the control at 28 HAS, indicating that lower abscisic acid levels play an important role and ethylene signal transduction also participates in radicle protrusion. ACO, NRT1 and PRP3 expressions were significantly higher than in the control at 48 HAS, suggesting that higher ethylene levels cause the endosperm cap to weaken and start to grow root hairs and lateral roots earlier. These findings reveal that plasma promotes seed germination mainly by regulating the expression of hormone-related genes. And the possible signal transduction of related hormones was discussed.

Insights into the genes involved in the ethylene biosynthesis pathway in Arabidopsis thaliana and Oryza sativa

Background

Ethylene is a gaseous plant hormone that acts as a requisite role in many aspects of the plant life cycle, and it is also a regulator of plant responses to abiotic and biotic stresses. In this study, we attempt to provide comprehensive information through analyses of existing data using bioinformatics tools to compare the identified ethylene biosynthesis genes between Arabidopsis (as dicotyledonous) and rice (as monocotyledonous).

Results

The results exposed that the Arabidopsis proteins of the ethylene biosynthesis pathway had more potential glycosylation sites than rice, and 1-aminocyclopropane-1-carboxylate oxidase proteins were less phosphorylated than 1-aminocyclopropane-1-carboxylate synthase and S-adenosylmethionine proteins. According to the gene expression patterns, S-adenosylmethionine genes were more involved in the rice-ripening stage while in Arabidopsis, ACS2, and 1-aminocyclopropane-1-carboxylate oxidase genes were contributed to seed maturity. Furthermore, the result of miRNA targeting the transcript sequences showed that ath-miR843 and osa-miR1858 play a key role to regulate the post-transcription modification of S-adenosylmethionine genes in Arabidopsis and rice, respectively. The discovered cis- motifs in the promoter site of all the ethylene biosynthesis genes of A. thaliana genes were engaged to light-induced response in the cotyledon and root genes, sulfur-responsive element, dehydration, cell cycle phase-independent activation, and salicylic acid. The ACS4 protein prediction demonstrated strong protein-protein interaction in Arabidopsis, as well as, SAM2, Os04T0578000, Os01T0192900, and Os03T0727600 predicted strong protein-protein interactions in rice.

Conclusion

In the current study, the complex between miRNAs with transcript sequences of ethylene biosynthesis genes in A. thaliana and O. sativa were identified, which could be helpful to understand the gene expression regulation after the transcription process. The binding sites of common transcription factors such as MYB, WRKY, and ABRE that control target genes in abiotic and biotic stresses were generally distributed in promoter sites of ethylene biosynthesis genes of A. thaliana. This was the first time to wide explore the ethylene biosynthesis pathway using bioinformatics tools that markedly showed the capability of the in silico study to integrate existing data and knowledge and furnish novel insights into the understanding of underlying ethylene biosynthesis pathway genes that will be helpful for more dissection.

Ethylene Sensor-Enabled Dynamic Monitoring and Multi-Strategies Control for Quality Management of Fruit Cold Chain Logistics

Due to the presence of bioactive compounds, fruits are an essential part of people’s healthy diet. However, endogenous ethylene produced by climacteric fruits and exogenous ethylene in the microenvironment could play a pivotal role in the physiological and metabolic activities, leading to quality losses during storage or shelf life. Moreover, due to the variety of fruits and complex scenarios, different ethylene control strategies need to be adapted to improve the marketability of fruits and maintain their high quality. Therefore, this study proposed an ethylene dynamic monitoring based on multi-strategies control to reduce the post-harvest quality loss of fruits, which was evaluated here for blueberries, sweet cherries, and apples. The results showed that the ethylene dynamic monitoring had rapid static/dynamic response speed (2 ppm/s) and accurately monitoring of ethylene content (99% accuracy). In addition, the quality parameters evolution (firmness, soluble solids contents, weight loss rate, and chromatic aberration) showed that the ethylene multi-strategies control could effectively reduce the quality loss of fruits studied, which showed great potential in improving the quality management of fruits in the supply chain.

Seed Transcriptome Annotation Reveals Enhanced Expression of Genes Related to ROS Homeostasis and Ethylene Metabolism at Alternating Temperatures in Wild Cardoon

The association among environmental cues, ethylene response, ABA signaling, and reactive oxygen species (ROS) homeostasis in the process of seed dormancy release is nowadays well-established in many species. Alternating temperatures are recognized as one of the main environmental signals determining dormancy release, but their underlying mechanisms are scarcely known. Dry after-ripened wild cardoon achenes germinated poorly at a constant temperature of 20, 15, or 10 °C, whereas germination was stimulated by 80% at alternating temperatures of 20/10 °C. Using an RNA-Seq approach, we identified 23,640 and annotated 14,078 gene transcripts expressed in dry achenes and achenes exposed to constant or alternating temperatures. Transcriptional patterns identified in dry condition included seed reserve and response to dehydration stress genes (i.e., HSPs, peroxidases, and LEAs). At a constant temperature, we observed an upregulation of ABA biosynthesis genes (i.e., NCED9), ABA-responsive genes (i.e., ABI5 and TAP), as well as other genes previously related to physiological dormancy and inhibition of germination. However, the alternating temperatures were associated with the upregulation of ethylene metabolism (i.e., ACO1, 4, and ACS10) and signaling (i.e., EXPs) genes and ROS homeostasis regulators genes (i.e., RBOH and CAT). Accordingly, the ethylene production was twice as high at alternating than at constant temperatures. The presence in the germination medium of ethylene or ROS synthesis and signaling inhibitors reduced significantly, but not completely, germination at 20/10 °C. Conversely, the presence of methyl viologen and salicylhydroxamic acid (SHAM), a peroxidase inhibitor, partially increased germination at constant temperature. Taken together, the present study provides the first insights into the gene expression patterns and physiological response associated with dormancy release at alternating temperatures in wild cardoon (Cynara cardunculus var. sylvestris).

Symbiotic and Asymbiotic Germination of Dendrobium officinale (Orchidaceae) Respond Differently to Exogenous Gibberellins

Seeds of almost all orchids depend on mycorrhizal fungi to induce their germination in the wild. The regulation of this symbiotic germination of orchid seeds involves complex crosstalk interactions between mycorrhizal establishment and the germination process. The aim of this study was to investigate the effect of gibberellins (GAs) on the symbiotic germination of Dendrobium officinale seeds and its functioning in the mutualistic interaction between orchid species and their mycobionts. To do this, we used liquid chromatograph-mass spectrometer to quantify endogenous hormones across different development stages between symbiotic and asymbiotic germination of D. officinale, as well as real-time quantitative PCR to investigate gene expression levels during seed germination under the different treatment concentrations of exogenous gibberellic acids (GA3). Our results showed that the level of endogenous GA3 was not significantly different between the asymbiotic and symbiotic germination groups, but the ratio of GA3 and abscisic acids (ABA) was significantly higher during symbiotic germination than asymbiotic germination. Exogenous GA3 treatment showed that a high concentration of GA3 could inhibit fungal colonization in the embryo cell and decrease the seed germination rate, but did not significantly affect asymbiotic germination or the growth of the free-living fungal mycelium. The expression of genes involved in the common symbiotic pathway (e.g., calcium-binding protein and calcium-dependent protein kinase) responded to the changed concentrations of exogenous GA3. Taken together, our results demonstrate that GA3 is probably a key signal molecule for crosstalk between the seed germination pathway and mycorrhiza symbiosis during the orchid seed symbiotic germination.

Jasmonate induced alternative splicing responses in Arabidopsis

Jasmonate is an essential phytohormone regulating plant growth, development, and defense. Alternative splicing (AS) in jasmonate ZIM-domain (JAZ) repressors is well-characterized and plays an important role in jasmonate signaling regulation. However, it is unknown whether other genes in the jasmonate signaling pathway are regulated by AS. We explore the potential for AS regulation in three Arabidopsis genotypes (WT, jaz2, jaz7) in response to methyl jasmonate (MeJA) treatment with respect to: (a) differential AS, (b) differential miRNA targeted AS, and (c) AS isoforms with novel functions. AS events identified from transcriptomic data were validated with proteomic data. Protein interaction networks identified two genes, SKIP and ALY4 whose products have both DNA- and RNA-binding affinities, as potential key regulators mediating jasmonate signaling and AS regulation. We observed cases where AS alone, or AS and transcriptional regulation together, can influence gene expression in response to MeJA. Twenty-one genes contain predicted miRNA target sites subjected to AS, which implies that AS is coupled to miRNA regulation. We identified 30 cases where alternatively spliced isoforms may have novel functions. For example, AS of bHLH160 generates an isoform without a basic domain, which may convert it from an activator to a repressor. Our study identified potential key regulators in AS regulation of jasmonate signaling pathway. These findings highlight the importance of AS regulation in the jasmonate signaling pathway, both alone and in collaboration with other regulators.

SIGNIFICANCE STATEMENT

By exploring alternative splicing, we demonstrate its regulation in the jasmonate signaling pathway alone or in collaboration with other posttranscriptional regulations such as nonsense and microRNA-mediated decay. A signal transduction network model for alternative splicing in jasmonate signaling pathway was generated, contributing to our understanding for this important, prevalent, but relatively unexplored regulatory mechanism in plants.

An Updated Overview on the Regulation of Seed Germination

The ability of a seed to germinate and establish a plant at the right time of year is of vital importance from an ecological and economical point of view. Due to the fragility of these early growth stages, their swiftness and robustness will impact later developmental stages and crop yield. These traits are modulated by a continuous interaction between the genetic makeup of the plant and the environment from seed production to germination stages. In this review, we have summarized the established knowledge on the control of seed germination from a molecular and a genetic perspective. This serves as a “backbone” to integrate the latest developments in the field. These include the link of germination to events occurring in the mother plant influenced by the environment, the impact of changes in the chromatin landscape, the discovery of new players and new insights related to well-known master regulators. Finally, results from recent studies on hormone transport, signaling, and biophysical and mechanical tissue properties are underscoring the relevance of tissue-specific regulation and the interplay of signals in this crucial developmental process.

Role of ethylene crosstalk in seed germination and early seedling development: A review

Seed germination and early seedling development are two critical phases in plant lifecycle that largely determine crop yield. Phytohormones play an essential role in governing these developmental processes; of these, ethylene (ET; C₂H₄), the smallest gaseous hormone, plays a major role via crosstalk with other hormones. Typically, the mechanism of hormone (for instance, auxin, cytokinins, ET, and gibberellins) action is determined by cellular context, revealing either synergistic or antagonistic relations. Significant progress has been made, so far, on unveiling ET crosstalk with other hormones and environmental signals, such as light. In particular, stimulatory and inhibitory effects of ET on hypocotyl growth in light and dark, respectively, and its interaction with other hormones provide an ideal model to study the growth-regulatory pathways. In this review, we aim at exploring the mechanisms of multifarious phenomena that occur via ET crosstalk during the germination of seeds (overcoming dormancy), and all through the development of seedlings. Understanding the remarkably complex mechanism of ET crosstalk that emerges from the interaction between hormones and other molecular players to modulate plant growth, remains a challenge in plant developmental biology.

Factors affecting the dormancy and germination of bleeding heart [Lamprocapnos spectabilis (L.) Fukuhara] seeds

Information on the optimal conditions to promote the germination of Lamprocapnos spectabilis (L.) Fukuhara seeds is limited; consequently, this study was conducted to establish the requirements to break seed dormancy and promote germination. The selected seeds had morphophysiological dormancy and had not begun embryo development. To study the dormancy breaking and embryo development processes, seeds were subjected to constant or changing temperature treatments during moist stratification. High temperature and humidity resulted in vigorous embryo growth, with the longest embryos occurring after 1 month of incubation at 20 °C. At 4 °C, the seeds required incubation period of at least 3 months to germinate. Embryo growth and germination were higher with changing high and low temperatures than under a constant temperature, and changing temperatures also considerably changed the endogenous hormone levels, embryo development and germination. Bioactive gibberellin (GA) content was higher in seeds incubated at 20 °C for 1 month, then at 4 °C for 2 months. The content of endogenous abscisic acid in seeds subjected to the same treatment decreased by 97.6% compared with that of the untreated seeds. Embryo growth and seed germination require changing high and low temperatures; however, exogenous GA₃ could substitute for high temperatures, as it also causes accelerated germination. In this study, the seeds of L. spectabilis were identified as an intermediate simple type, a sub-level of morphophysiologically dormant seeds.

Ethylene regulates post-germination seedling growth in wheat through spatial and temporal modulation of ABA/GA balance

This study aimed to gain insights into the molecular mechanisms underlying the role of ethylene in regulating germination and seedling growth in wheat by combining pharmacological, molecular, and metabolomics approaches. Our study showed that ethylene does not affect radicle protrusion but controls post-germination endospermic starch degradation through transcriptional regulation of specific α-amylase and α-glucosidase genes, and this effect is mediated by alteration of endospermic bioactive gibberellin (GA) levels, and GA sensitivity via expression of the GA signaling gene, TaGAMYB. Our data implicated ethylene as a positive regulator of embryo axis and coleoptile growth through transcriptional regulation of specific TaEXPA genes. These effects were associated with modulation of GA levels and sensitivity, through expression of GA metabolism (TaGA20ox1, TaGA3ox2, and TaGA2ox6) and signaling (TaGAMYB) genes, respectively, and/or the abscisic acid (ABA) level and sensitivity, via expression of specific ABA metabolism (TaNCED2 or TaCYP707A1) and signaling (TaABI3) genes, respectively. Ethylene appeared to regulate the expression of TaEXPA3 and thereby root growth through its control of coleoptile ABA metabolism, and root ABA signaling via expression of TaABI3 and TaABI5. These results show that spatiotemporal modulation of ABA/GA balance mediates the role of ethylene in regulating post-germination storage starch degradation and seedling growth in wheat.

Integrated Transcriptomic and Metabolic Framework for Carbon Metabolism and Plant Hormones Regulation in Vigna radiata during Post-Germination Seedling Growth

During mung bean post-germination seedling growth, various metabolic and physiological changes occurred, leading to the improvement of its nutritional values. Here, transcriptomic and metabolomic analyses of mung bean samples from 6-hour, 3-day and 6-day after imbibition (6-HAI, 3-DAI, and 6-DAI) were performed to characterize the regulatory mechanism of the primary metabolites during the post-germination seedling growth. From 6-HAI to 3-DAI, rapid changes in transcript level occurred, including starch and sucrose metabolism, glycolysis, citrate cycle, amino acids synthesis, and plant hormones regulation. Later changes in the metabolites, including carbohydrates and amino acids, appeared to be driven by increases in transcript levels. During this process, most amino acids and monosaccharides kept increasing, and accumulated in 6-day germinated sprouts. These processes were also accompanied with changes in hormones including abscisic acid, gibberellin, jasmonic acid, indole-3-acetic acid, etc. Overall, these results will provide insights into molecular mechanisms underlying the primary metabolic regulation in mung bean during post-germination seedling growth.

Identification of Quantitative Trait Loci Controlling Ethylene Production in Germinating Seeds in Maize (Zea mays L.)

Plant seed germination is a crucial developmental event that has significant effects on seedling establishment and yield production. This process is controlled by multiple intrinsic signals, particularly phytohormones. The gaseous hormone ethylene stimulates seed germination; however, the genetic basis of ethylene production in maize during seed germination remains poorly understood. In this study, we quantified the diversity of germination among 14 inbred lines representing the parental materials corresponding to multiple recombinant inbred line (RIL) mapping populations. Quantitative trait loci (QTLs) controlling ethylene production were then identified in germinating seeds from an RIL population constructed from two parental lines showing differences in both germination speed and ethylene production during germination. To explore the possible genetic correlations of ethylene production with other traits, seed germination and seed weight were evaluated using the same batch of samples. On the basis of high-density single nucleotide polymorphism-based genetic linkage maps, we detected three QTLs for ethylene production in germinating seeds, three QTLs for seed germination, and four QTLs for seed weight, with each QTL explaining 5.8%–13.2% of the phenotypic variation of the trait. No QTLs were observed to be co-localized, suggesting that the genetic bases underlying the three traits are largely different. Our findings reveal three chromosomal regions responsible for ethylene production during seed germination, and provide a valuable reference for the future investigation of the genetic mechanism underlying the role of the stress hormone ethylene in maize germination control under unfavourable external conditions.

Transgenerational impacts of herbivory and inbreeding on reproductive output in Solanum carolinense

PREMISE

Plant maternal effects on offspring phenotypes are well documented. However, little is known about how herbivory on maternal plants affects offspring fitness. Furthermore, while inbreeding is known to reduce plant reproductive output, previous studies have not explored whether and how such effects may extend across generations. Here, we addressed the transgenerational consequences of herbivory and maternal plant inbreeding on the reproduction of Solanum carolinense offspring.

METHODS

Manduca sexta caterpillars were used to inflict weekly damage on inbred and outbred S. carolinense maternal plants. Cross-pollinations were performed by hand to produce seed from herbivore-damaged outbred plants, herbivore-damaged inbred plants, undamaged outbred plants, and undamaged inbred plants. The resulting seeds were grown in the greenhouse to assess emergence rate and flower production in the absence of herbivores. We also grew offspring in the field to examine reproductive output under natural conditions.

RESULTS

We found transgenerational effects of herbivory and maternal plant inbreeding on seedling emergence and reproductive output. Offspring of herbivore-damaged plants had greater emergence, flowered earlier, and produced more flowers and seeds than offspring of undamaged plants. Offspring of outbred maternal plants also had greater seedling emergence and reproductive output than offspring of inbred maternal plants, even though all offspring were outbred. Moreover, the effects of maternal plant inbreeding were more severe when plant offspring were grown in field conditions.

CONCLUSIONS

This study demonstrates that both herbivory and inbreeding have fitness consequences that extend across generations even in outbred progeny.