Proteomic insights into seed germination in response to environmental factors

Hallmarks of DNA Damage Response in Germination Across Model and Crop Species

DNA damage response (DDR) contributes to seed quality by guarding genome integrity in the delicate phases of pre- and post-germination. As a key determinant of stress tolerance and resilience, DDR has notable implications on the wider scale of the agroecosystems challenged by harsh climatic events. The present review focuses on the existing and documented links that interconnect DDR efficiency with an array of molecular hallmarks with biochemical, molecular, and physiological valence within the seed metabolic networks. The expression of genes encoding DDR sensors, transducers, mediators, and effectors is interpreted as a source of conserved hallmarks, along with markers of oxidative damage reflecting the seed's ability to germinate. Similarly, the accumulation patterns of proteins and metabolites that contribute to DNA stability are predictive of seed quality traits. While a list of candidates is presented from multiple models and crop species, their interaction with chromatin dynamics, cell cycle progression, and hormonal regulation provides further levels of analysis to investigate the seed stress response holistically. The identification of novel hallmarks of DDR in seeds constitutes a framework to prompt validation with different experimental systems, to refine the current models of pre-germinative metabolism, and to promote targeted approaches for seed quality evaluation.

ZmPTOX1, a plastid terminal oxidase, contributes to redox homeostasis during seed development and germination

Maize plastid terminal oxidase1 (ZmPTOX1) plays a pivotal role in seed development by upholding redox balance within seed plastids. This study focuses on characterizing the white kernel mutant 3735 (wk3735) mutant, which yields pale-yellow seeds characterized by heightened protein but reduced carotenoid levels, along with delayed germination compared to wild-type (WT) seeds. We successfully cloned and identified the target gene ZmPTOX1, responsible for encoding maize PTOX-a versatile plastoquinol oxidase and redox sensor located in plastid membranes. While PTOX's established role involves regulating redox states and participating in carotenoid metabolism in Arabidopsis leaves and tomato fruits, our investigation marks the first exploration of its function in storage organs lacking a photosynthetic system. Through our research, we validated the existence of plastid-localized ZmPTOX1, existing as a homomultimer, and established its interaction with ferredoxin-NADP+ oxidoreductase 1 (ZmFNR1), a crucial component of the electron transport chain (ETC). This interaction contributes to the maintenance of redox equilibrium within plastids. Our findings indicate a propensity for excessive accumulation of reactive oxygen species (ROS) in wk3735 seeds. Beyond its known role in carotenoids' antioxidant properties, ZmPTOX1 also impacts ROS homeostasis owing to its oxidizing function. Altogether, our results underscore the critical involvement of ZmPTOX1 in governing seed development and germination by preserving redox balance within the seed plastids.

Boosting Synergistic Antioxidant and Anti-Inflammatory Properties Blending Cereal-Based Nutraceuticals Produced Using Sprouting and Hydrolysis Tools

Nutraceuticals obtained from sprouted wheat and oat grains and processing by-products (bran and hull, respectively) naturally containing antioxidant and anti-inflammatory compounds were evaluated. The objective of this study was the development of a cereal-based nutraceutical formula combining extracts from sprouts and by-products and the exploration for potential synergetic effects in their bioactive properties. The antioxidant and anti-inflammatory capacities, glycemic index, phytic acid, and β-glucan of individual wheat bran hydrolysate (EH-WB), sprouted wheat (SW), oat hull hydrolysate (EH-OH), sprouted oat (SO), and combined ingredients (CI 1, CI 2, and CI3) were used to tailor an optimal nutraceutical formula. The three blend ingredients (CI 1, CI2, and CI3) were formulated at different ratios (EH-WB:SW:EH-OH:SO; 1:1:1:1, 2:1:2:1, and 1:2:1:2, w:w:w:w, respectively). The resulting mixtures showed total phenol (TPs) content ranging from 412.93 to 2556.66 µmol GAE 100 g-1 and antioxidant capacity values from 808.14 to 22,152.54 µmol TE 100 g-1 (ORAC) and 1914.05 to 7261.32 µmol TE 100 g-1 (ABTS•+), with Fe3+ reducing ability from 734. 02 to 8674.51 mmol reduced Fe 100 g-1 (FRAP) for the individual ingredients produced from EH-WB and EH-OH, where high antioxidant activity was observed. However, the anti-inflammatory results exhibited an interesting behavior, with a potentially synergistic effect of the individual ingredients. This effect was observed in CI2 and CI3, resulting in a higher ability to inhibit IL-6 and TNF-α than expected based on the anti-inflammatory values of their individual ingredients. Similar to the antioxidant properties, oat-based ingredients significantly contributed more to the anti-inflammatory properties of the overall mixture. This contribution is likely associated with the β-glucans and avenanthramides present in oats. To ensure the bioaccessibility of these ingredients, further studies including simulated digestion protocols would be necessary. The ingredient formulated with a 2:1 hydrolysate-to-sprout ratio was the most effective combination, reaching higher biological characteristics.

Comparative proteomic analysis of seed germination between allotetraploid cotton Gossypium hirsutum and Gossypium barbadense

Seed germination, a key initial event in the plant life cycle, directly affects cotton yield and quality. Gossypium barbadense and Gossypium hirsutum gradually evolved through polyploidization, resulting in different characteristics, and this interspecific variation lacks genetic and molecular explanation. This work aimed to compare the proteomes between G. barbadense and G. hirsutum during seed germination. Here, we identified 2740 proteins for G. barbadense and 3758 for G. hirsutum. In the initial state, proteins in two cotton involved similar bioprocess, such as sugar metabolism, DNA repairing, and ABA signaling pathway. However, in the post-germination stage, G. hirsutum expressed more protein related to redox homeostasis, peroxidase activity, and pathogen interactions. Analyzing the different expression patterns of 915 single-copy orthogroups between the two kinds of cotton indicated that most of the differentially expressed proteins in G. barbadense were related to carbon metabolism. In contrast, most proteins in G. hirsutum were associated with stress response. Besides that, by proteogenomic analysis, we found 349 putative non-canonical peptides, which may be involved in plant development. These results will help to understand the different characteristics of these two kinds of cotton, such as fiber quality, yield, and adaptability. SIGNIFICANCE STATEMENT: Cotton is the predominant natural fiber crop worldwide; Gossypium barbadense and Gossypium hirsutum have evolved through polyploidization to produce differing traits. However, given their specific features, the divergence of mechanisms underlying seed germination between G. hirsutum and G. barbadense has not been discussed. Here, we explore what protein contributes to interspecific differences between G. barbadense and G. hirsutum during the seed germination period. This study helps to elucidate the evolution and domestication history of cotton polyploids and may allow breeders to understand their domestication history better and improve fiber quality and adaptability.

Seeding alpine grasses in low altitude region increases global warming potential during early seedling growth

Introduction of alpine grasses to low altitude regions has long been a crucial strategy for enriching germplasm diversity, cultivating and acclimating high-quality species, enhancing ecosystem resilience and adaptability, as well as facilitating ecosystem restoration. However, there is an urgent need to investigate the impacts of planting Gramineae seeds on greenhouse gas (GHG) emissions, particularly during the critical stage of early plant growth. In this study, four species of grass seeds (Stipa breviflora, Poa pratensis, Achnatherum splendens, Elymus nutans) were collected from 19 high-altitude regions surrounding the Qinghai-Tibet Plateau and sown at low-altitude. Measurements of GHG emissions at early seedling growth in the mesocosm experiment using static chamber method showed a strong increase in the cumulative emissions of CO2 (5.71%-9.19%) and N2O (11.36%-13.64%) (p < 0.05), as well as an elevated CH4 uptake (2.75%-5.50%) in sites where the four grass species were introduced, compared to bare soil. Consequently, there was a substantial rise in global warming potential (13.87%-16.33%) (p < 0.05) at grass-introduced sites. Redundancy analysis showed that seed traits, plant biomass, and seedling emergence percentage were the main driving biotic factors of three GHGs fluxes. Our study unveils the potential risk of escalating GHG emissions induced by introducing high altitude grasses to low altitude bare soil, elucidating the mechanism through linking seed traits with seedling establishment and environmental feedback. Furthermore, this offers a new perspective for assessing the impact of grass introduction on ecological environment of introduced site.

Microgreens on the rise: Expanding our horizons from farm to fork

Escalating public health concerns necessitate innovative approaches to food sources. Microgreens, nutrient-rich seedlings of vegetables and herbs, have gained recognition as functional foods. This review explores the evolution of microgreens, cultivation methods, biochemical changes during germination, nutritional content, health benefits, and commercial significance. Comprehensive studies have demonstrated that microgreens have an elevated level of various nutrients. Further, in vitro and in vivo research validated their antioxidant, anticancer, antibacterial, anti-inflammatory, anti-obesity, and antidiabetic properties. Microgreens, termed "desert food," show promise for sustainable food production in climate-vulnerable regions. This paper synthesizes recent research on microgreens, addressing challenges and gaps in understanding their nutritional content and health benefits. It contributes valuable insights for future research, fostering sustainable agriculture and enhancing understanding of microgreens in human health and nutrition.

Aging-Induced Reduction in Safflower Seed Germination via Impaired Energy Metabolism and Genetic Integrity Is Partially Restored by Sucrose and DA-6 Treatment

Seed storage underpins global agriculture and the seed trade and revealing the mechanisms of seed aging is essential for enhancing seed longevity management. Safflower is a multipurpose oil crop, rich in unsaturated fatty acids that are at high risk of peroxidation as a contributory factor to seed aging. However, the molecular mechanisms responsible for safflower seed viability loss are not yet elucidated. We used controlled deterioration (CDT) conditions of 60% relative humidity and 50 °C to reduce germination in freshly harvested safflower seeds and analyzed aged seeds using biochemical and molecular techniques. While seed malondialdehyde (MDA) and fatty acid content increased significantly during CDT, catalase activity and soluble sugar content decreased. KEGG analysis of gene function and qPCR validation indicated that aging severely impaired several key functional and biosynthetic pathways including glycolysis, fatty acid metabolism, antioxidant activity, and DNA replication and repair. Furthermore, exogenous sucrose and diethyl aminoethyl hexanoate (DA-6) treatment partially promoted germination in aged seeds, further demonstrating the vital role of impaired sugar and fatty acid metabolism during the aging and recovery processes. We concluded that energy metabolism and genetic integrity are impaired during aging, which contributes to the loss of seed vigor. Such energy metabolic pathways as glycolysis, fatty acid degradation, and the tricarboxylic acid cycle (TCA) are impaired, especially fatty acids produced by the hydrolysis of triacylglycerols during aging, as they are not efficiently converted to sucrose via the glyoxylate cycle to provide energy supply for safflower seed germination and seedling growth. At the same time, the reduced capacity for nucleotide synthesis capacity and the deterioration of DNA repair ability further aggravate the damage to DNA, reducing seed vitality.

Seed priming mitigates high salinity impact on germination of bread wheat (Triticum aestivum L.) by improving carbohydrate and protein mobilization

Salinity is increasingly considered as a major environmental issue, which threatens agricultural production by decreasing yield traits of crops. Seed priming is a useful and cost-effective technique to alleviate the negative effects of salinity and to enable a fast and uniform germination. In this context, we quantified the effects of priming with gibberellic acid (GP), calcium chloride (CP), and mannitol (MP) on seed germination of three bread wheat cultivars and investigated their response when grown at high salinity conditions (200 mM NaCl). Salt exposure strongly repressed seed imbibition and germination potential and extended germination time, whereas priming enhanced uniformity and seed vigor. Seed preconditioning alleviated the germination disruption caused by salt stress to varying degrees. Priming mitigating effect was agent-dependent with regard to water status (CP and MP), ionic imbalance (CP), and seed reserve mobilization (GP). Na+ accumulation in seedling tissues significantly impaired carbohydrate and protein mobilization by inhibiting amylase and proteases activities but had lesser effects on primed seeds. CP attenuated ionic imbalance by limiting sodium accumulation. Gibberellic acid was the most effective priming treatment for promoting the germination of wheat seeds under salt stress. Moreover, genotypic differences in wheat response to salinity stress were observed between varieties used in this study. Ardito, the oldest variety, seems to tolerate better salinity in priming-free conditions; Aubusson resulted the most salt-sensitive cultivar but showed a high germination recovery under priming conditions; Bologna showed an intermediate behavior.

Insights into the regulation of energy metabolism during the seed-to-seedling transition in marine angiosperm Zostera marina L.: Integrated metabolomic and transcriptomic analysis

Seed development is a crucial phase in the life cycle of seed-propagated plants. As the only group of angiosperms that evolved from terrestrial plants to complete their life cycle submerged in marine environments, the mechanisms underlying seed development in seagrasses are still largely unknown. In the present study, we attempted to combine transcriptomic, metabolomic, and physiological data to comprehensively analyze the molecular mechanism that regulates energy metabolism in Zostera marina seeds at the four major developmental stages. Our results demonstrated that seed metabolism was reprogrammed with significant alteration of starch and sucrose metabolism, glycolysis, the tricarboxylic acid cycle (TCA cycle), and the pentose phosphate pathway during the transition from seed formation to seedling establishment. The interconversion of starch and sugar provided energy storage substances in mature seeds and further acted as energy sources to support seed germination and seedling growth. The glycolysis pathway was active during Z. marina germination and seedling establishment, which provided pyruvate for TCA cycle by decomposing soluble sugar. Notably, the biological processes of glycolysis were severely inhibited during Z. marina seed maturation may have a positive effect on seed germination, maintaining a low level of metabolic activity during seed maturation to preserve seed viability. Increased acetyl-CoA and ATP contents were accompanied with the higher TCA cycle activity during seed germination and seedling establishment, indicating that the accumulations of precursor and intermediates metabolite that can strengthen the TCA cycle and facilitate energy supply for Z. marina seed germination and seedling growth. The large amount of oxidatively generated sugar phosphate promotes fructose 1,6-bisphosphate synthesis to feed back to glycolysis during seed germination, indicating that the pentose phosphate pathway not only provides energy for germination, but also complements the glycolytic pathway. Collectively, our findings suggest these energy metabolism pathways cooperate with each other in the process of seed transformation from maturity to seedling establishment, transforming seed from storage tissue to highly active metabolic tissue to meet the energy requirement seed development. These findings provide insights into the roles of the energy metabolism pathway in the complete developmental process of Z. marina seeds from different perspectives, which could facilitate habitat restoration of Z. marina meadows via seeds.

Non-target molecular network and putative genes of flavonoid biosynthesis in Erythrina velutina Willd., a Brazilian semiarid native woody plant

Erythrina velutina is a Brazilian native tree of the Caatinga (a unique semiarid biome). It is widely used in traditional medicine showing anti-inflammatory and central nervous system modulating activities. The species is a rich source of specialized metabolites, mostly alkaloids and flavonoids. To date, genomic information, biosynthesis, and regulation of flavonoids remain unknown in this woody plant. As part of a larger ongoing research goal to better understand specialized metabolism in plants inhabiting the harsh conditions of the Caatinga, the present study focused on this important class of bioactive phenolics. Leaves and seeds of plants growing in their natural habitat had their metabolic and proteomic profiles analyzed and integrated with transcriptome data. As a result, 96 metabolites (including 43 flavonoids) were annotated. Transcripts of the flavonoid pathway totaled 27, of which EvCHI, EvCHR, EvCHS, EvCYP75A and EvCYP75B1 were identified as putative main targets for modulating the accumulation of these metabolites. The highest correspondence of mRNA vs. protein was observed in the differentially expressed transcripts. In addition, 394 candidate transcripts encoding for transcription factors distributed among the bHLH, ERF, and MYB families were annotated. Based on interaction network analyses, several putative genes of the flavonoid pathway and transcription factors were related, particularly TFs of the MYB family. Expression patterns of transcripts involved in flavonoid biosynthesis and those involved in responses to biotic and abiotic stresses were discussed in detail. Overall, these findings provide a base for the understanding of molecular and metabolic responses in this medicinally important species. Moreover, the identification of key regulatory targets for future studies aiming at bioactive metabolite production will be facilitated.

Multi-Omics Approaches Unravel Specific Features of Embryo and Endosperm in Rice Seed Germination

Seed germination and subsequent seedling growth affect the final yield and quality of the crop. Seed germination is defined as a series of processes that begins with water uptake by a quiescent dry seed and ends with the elongation of embryonic axis. Rice is an important cereal crop species, and during seed germination, two tissues function in a different manner; the embryo grows into a seedling as the next generation and the endosperm is responsible for nutritional supply. Toward understanding the integrated roles of each tissue at the transcriptional, translational, and metabolic production levels during germination, an exhaustive "multi-omics" analysis was performed by combining transcriptomics, label-free shotgun proteomics, and metabolomics on rice germinating embryo and endosperm, independently. Time-course analyses of the transcriptome and metabolome in germinating seeds revealed a major turning point in the early phase of germination in both embryo and endosperm, suggesting that dramatic changes begin immediately after water imbibition in the rice germination program at least at the mRNA and metabolite levels. In endosperm, protein profiles mostly showed abundant decreases corresponding to 90% of the differentially accumulated proteins. An ontological classification revealed the shift from the maturation to the germination process where over-represented classes belonged to embryonic development and cellular amino acid biosynthetic processes. In the embryo, 19% of the detected proteins are differentially accumulated during germination. Stress response, carbohydrate, fatty acid metabolism, and transport are the main functional classes representing embryo proteome change. Moreover, proteins specific to the germinated state were detected by both transcriptomic and proteomic approaches and a major change in the network operating during rice germination was uncovered. In particular, concomitant changes of hormonal metabolism-related proteins (GID1L2 and CNX1) implicated in GAs and ABA metabolism, signaling proteins, and protein turnover events emphasized the importance of such biological networks in rice seeds. Using metabolomics, we highlighted the importance of an energetic supply in rice seeds during germination. In both embryo and endosperm, starch degradation, glycolysis, and subsequent pathways related to these cascades, such as the aspartate-family pathway, are activated during germination. A relevant number of accumulated proteins and metabolites, especially in embryos, testifies the pivotal role of energetic supply in the preparation of plant growth. This article summarizes the key genetic pathways in embryo and endosperm during rice seed germination at the transcriptional, translational, and metabolite levels and thereby, emphasizes the value of combined multi-omics approaches to uncover the specific feature of tissues during germination.

Plant Proteome Dynamics

Proteins are intimately involved in executing and controlling virtually all cellular processes. To understand the molecular mechanisms that underlie plant phenotypes, it is essential to investigate protein expression, interactions, and modifications, to name a few. The proteome is highly dynamic in time and space, and a plethora of protein modifications, protein interactions, and network constellations are at play under specific conditions and developmental stages. Analysis of proteomes aims to characterize the entire protein complement of a particular cell type, tissue, or organism-a challenging task, given the dynamic nature of the proteome. Modern mass spectrometry-based proteomics technology can be used to address this complexity at a system-wide scale by the global identification and quantification of thousands of proteins. In this review, we present current methods and technologies employed in mass spectrometry-based proteomics and provide examples of dynamic changes in the plant proteome elucidated by proteomic approaches.

Regeneration and Endogenous Phytohormone Responses to High-Temperature Stress Drive Recruitment Success in Hemiepiphytic Fig Species

Exposure to high-temperature stress (HTS) during early regeneration in plants can profoundly shape seed germination, seedling growth, and development, thereby providing stress resilience. In this study, we assessed how the timing of HTS, which was implemented as 8 h in 40°C, could affect the early regeneration stages and phytohormone concentration of four hemiepiphytic (Hs) and four non-hemiepiphytic (NHs) Ficus species. Their seed germination, seedling emergence, and seedling survival probabilities and the concentrations of three endogenous phytohormones, abscisic acid (ABA), indole-3-acetic acid (IAA), and salicylic acid (SA) were assessed after HTS imposed during imbibition, germination, and emergence. In both groups, seeds were more sensitive to HTS in the early regeneration process; stress experienced during imbibition affected emergence and survival, and stress experienced during germination affected subsequent emergence. There was no effect from HTS when received after emergence. Survival was highest in hemiepiphytes regardless of the HTS treatment. The phytohormones showed growth form- and regeneration stage-specific responses to HTS. Due to the HTS treatment, both SA and ABA levels decreased in non-hemiepiphytes during imbibition and germination; during germination, IAA increased in hemiepiphytes but was reduced in non-hemiepiphytes. Due to the HTS treatment experienced during emergence ABA and IAA concentrations were greater for hemiepiphytes but an opposite effect was seen in the two growth forms for the SA concentration. Our study showed that the two growth forms have different strategies for regulating their growth and development in the early regeneration stages in order to respond to HTS. The ability to respond to HTS is an ecologically important functional trait that allows plant species to appropriately time their seed germination and seedling development. Flexibility in modulating species regeneration in response to HTS in these subtropical and tropical Ficus species could provide greater community resilience under climate change.

Omics for the Improvement of Abiotic, Biotic, and Agronomic Traits in Major Cereal Crops: Applications, Challenges, and Prospects

Omics technologies, namely genomics, transcriptomics, proteomics, metabolomics, and phenomics, are becoming an integral part of virtually every commercial cereal crop breeding program, as they provide substantial dividends per unit time in both pre-breeding and breeding phases. Continuous advances in omics assure time efficiency and cost benefits to improve cereal crops. This review provides a comprehensive overview of the established omics methods in five major cereals, namely rice, sorghum, maize, barley, and bread wheat. We cover the evolution of technologies in each omics section independently and concentrate on their use to improve economically important agronomic as well as biotic and abiotic stress-related traits. Advancements in the (1) identification, mapping, and sequencing of molecular/structural variants; (2) high-density transcriptomics data to study gene expression patterns; (3) global and targeted proteome profiling to study protein structure and interaction; (4) metabolomic profiling to quantify organ-level, small-density metabolites, and their composition; and (5) high-resolution, high-throughput, image-based phenomics approaches are surveyed in this review.

A tubby-like protein CsTLP8 acts in the ABA signaling pathway and negatively regulates osmotic stresses tolerance during seed germination

BACKGROUND

TLPs (Tubby-like proteins) are widespread in eukaryotes and highly conserved in plants and animals. TLP is involved in many biological processes, such as growth, development, biotic and abiotic stress responses, while the underlying molecular mechanism remains largely unknown. In this paper we characterized the biological function of cucumber (Cucumis sativus L.) Tubby-like protein 8 (CsTLP8) in Arabidopsis.

RESULTS

In cucumber, the expression of the tubby-like protein CsTLP8 was induced by NaCl treatment, but reduced by PEG (Polyethylene Glycol) and ABA (Abscisic Acid) treatment. Subcellular localization and transcriptional activation activity analysis revealed that CsTLP8 possessed two characteristics of classical transcription factors: nuclear localization and trans-activation activity. Yeast two-hybrid assay revealed interactions of CsTLP8 with CsSKP1a and CsSKP1c, suggesting that CsTLP8 might function as a subunit of E3 ubiquitin ligase. The growth activity of yeast with ectopically expressed CsTLP8 was lower than the control under NaCl and mannitol treatments. Under osmotic and salt stresses, overexpression of CsTLP8 inhibited seed germination and the growth of Arabidopsis seedlings, increased the content of MDA (Malondialdehyde), and decreased the activities of SOD (Superoxide Dismutase), POD (Peroxidase) and CAT (Catalase) in Arabidopsis seedlings. Overexpression of CsTLP8 also increased the sensitivity to ABA during seed germination and ABA-mediated stomatal closure.

CONCLUSION

Under osmotic stress, CsTLP8 might inhibit seed germination and seedling growth by affecting antioxidant enzymes activities. CsTLP8 acts as a negative regulator in osmotic stress and its effects may be related to ABA.

Quantitative proteomics analysis reveals the response mechanism of peanut (Arachis hypogaea L.) to imbibitional chilling stress

Imbibitional chilling stress inhibits normal seed germination and seedling establishment and leads to large losses in peanut production. This is a major limiting factor when sowing peanut earlier and further north. To reveal the response mechanism of peanut to imbibitional chilling stress, a Tandem Mass Tag (TMT)-based quantitative proteomics analysis was conducted to identify differentially accumulated proteins (DAPs) under imbibitional chilling stress. Hormone profiling and transcriptional analysis were performed to confirm the proteomics data. Further seed priming analysis with exogenous cytokinins was conducted to validate the role of cytokinins in alleviating imbibitional chilling injury. A total of 5029 proteins were identified and quantified in all of the experimental groups. Among these, 104 proteins were DAPs as compared with the control. Enrichment analysis revealed that these DAPs were significant in various molecular functional and biological processes, especially for biosynthesis and metabolism of plant hormones. Hormone profiling and transcription analysis suggested that the reduced abundance of cytokinin oxidase may be caused by down-regulation of gene expression of the corresponding genes and leads to an elevated content of cytokinins under chilling stress. Seed priming analysis suggested that exogenous application of cytokinins may alleviate injury caused by imbibitional chilling. Our study provides a comprehensive proteomics analysis of peanut under imbibitional chilling stress, suggesting the role of plant hormones in the response mechanism. The results provide a better understanding of the imbibitional chilling stress response mechanism in peanut that will aid in peanut production.

Comparative proteomics reveals new insights into the endosperm responses to drought, salinity and submergence in germinating wheat seeds

Beyond the role of a nutrient reservoir during germination, the endosperm of wheat seeds also responds to different abiotic stresses via modification of the protein profiles. The endosperm is the main component of wheat seeds. During seed germination, it provides nutrients to support the embryo development, and its constituents vary under environmental stresses such as drought, salinity and submergence that are associated with disordered water supply. However, the molecular mechanism of these stress responses remains unclear. In this study, a comparative label-free proteomic analysis was performed on endosperm from the germinating wheat seeds subjected to PEG, NaCl and submergence treatments. In total, 2273 high confidence proteins were detected, and 234, 207 and 209 of them were identified as differentially expressed proteins (DEPs) under the three stresses, respectively. Functional classification revealed that the DEPs were mainly involved in protein, amino acid and organic acid metabolic process in all stress treatments. While some other metabolic processes were highlighted in one or two of the stresses specifically, such as oxidative phosphorylation in PEG and submergence, and β-alanine metabolism in PEG and NaCl treatments. The identification of a series of stress-related proteins and their biased expression in different stresses indicates the active stress-responding role of endosperm beyond a simple nutrient reservoir during germination, while the overall stress responses of the endosperm were found to be moderate and lag behind the embryo. Besides, some fundamental processes and DEPs shared by the three stresses could be selected priorly for future molecular breeding researches. Our results provide new insights into the mechanism of endosperm responses to abiotic stresses during seed germination.

Transcriptome and metabolite analysis reveal the drought tolerance of foxtail millet significantly correlated with phenylpropanoids-related pathways during germination process under PEG stress

BACKGROUND

Foxtail millet [Setaria italica (L.) P. Beauv.] is an excellent crop known for its superior level of drought tolerance across the world. Especially, less water is needed during its germination period than the other cereal crops. However, the knowledge of the mechanisms underlying the abiotic stress effects on seed germination of foxtail millet is largely unknown.

RESULTS

The water uptake pattern of foxtail millet seeds was ploted during germination period, according to which the germination time course of millet was separated into three phases. We sequenced the transcriptome of foxtail millet seeds, which were treated by PEG during different germination phases after sowing. The transcriptional studies revealed that more DEGs were identified during the further increase in water uptake period (phase III) than during the rapid initial uptake period (phase I) and the plateau period (phase II) under PEG stress. The pathway analysis of DEGs showed that the highly enriched categories were related to phenylpropanoid biosynthesis, plant hormone signal transduction and phenylalanine metabolism during phase III. The 20 phenylpropanoids-related genes of germinating foxtail millet were found to be down-regulated during the further increase in water uptake period under PEG stress. Further expression analysis identified 4 genes of phenylalanine ammonia-lyase, 4-coumarate-CoA ligase 3, cinnamoyl-CoA reductase 1, cationic peroxidase SPC4 in phenylpropanoids-related pathway, which played important roles in foxtail millet in response to PEG stress during different germination periods. The studies of metabolites in phenylpropanoid biosynthesis pathway revealed that higher amount of cinnamic acid was accumulated in germinating seeds under PEG stress, while the contents of p-coumaric acid, caffeic acid, ferulic acid and sinapic acid were decreased. And the effects of five phenolic compounds on germination and growth of foxtail millet showed that 1 mM concentration of cinnamic acid inhibited shoot and root growth, especially root development. Ferulic acid, caffeic acid, sinapic acid and p-coumaric acid could increase the root length and root/sprout in lower concentration.

CONCLUSIONS

These findings suggest that key genes and metabolites of foxtail millet related with phenylpropanoids pathway may play prominent roles in the regulation of resistance to drought during germination. Foxtail millet can probably avoid drought by regulating the levels of endogenous allelochemicals.

Quantitative Metabonomic Analysis Reveals the Germination-Associated Dynamic and Systemic Biochemical Changes for Mung-Bean (Vigna radiata) Seeds

Seed germination is essential for plant survival, germplasm resource preservation, and worldwide food supplies, although the germination-associated seed biochemical variations are not fully understood. With the NMR-based metabonomics, we quantitatively analyzed the comprehensive metabolite composition (metabonome) of mung-bean (Vigna radiata) seeds at eight time points of germination covering all three phases. We found that mung-bean seed metabonomes were dominated by 63 metabolites including lipids, amino acids, oligo-/monosaccharides, cyclitols, cholines, organic acids, nucleotides/-sides, nicotinates, and the shikimate pathway-mediated secondary metabolites. During germination, metabolic changes included mainly the degradation of proteins and raffinose family oligosaccharides, glycolysis, tricarboxylic acid (TCA) cycle, anaerobic respiration, biosynthesis of osmolytes and antioxidants together with the metabolisms of nucleotides/-sides, nicotinates, and amino acids. Oligosaccharide degradation was the primary energy source for germination, which coupled with the mobilization of starch and protein storages to produce sugars and amino acids for biomaterial and energy generations. Osmotic and redox regulations were prerequisites for seed germination together with mitochondrial reparations and generations to enable TCA cycle. During the postgermination growth stage (phase-3), the use of small molecules including amino acids and saccharides was switched to meet the growth demands of radicle cells. Small metabolites passed freely through seed testa leaking into the culture media during early germination but were reabsorbed by seed cells around the postgermination growth stage. Extra after-ripening accelerated these metabolic processes of seeds in phase-1, especially the biosynthesis of cyclitols, choline, and nicotinates, increasing the germination uniformity in terms of speed and percentage. Germination-resistant seeds were incapable of activating the germination-associated metabolic processes.

A multiscale approach reveals regulatory players of water stress responses in seeds during germination

Seed germination is regulated by environmental factors, particularly water availability. Water deficits at the time of sowing impair the establishment of crop plants. Transcriptome and proteome profiling was used to document the responses of sunflower (Helianthus annuus) seeds to moderate water stress during germination in two hybrids that are nominally classed as drought sensitive and drought tolerant. Differences in the water stress-dependent accumulation reactive oxygen species and antioxidant enzymes activities were observed between the hybrids. A pathway-based analysis of the hybrid transcriptomes demonstrated that the water stress-dependent responses of seed metabolism were similar to those of the plant, with a decreased abundance of transcripts encoding proteins associated with metabolism and cell expansion. Moreover, germination under water stress conditions was associated with increased levels of transcripts encoding heat shock proteins. Exposure of germinating seeds to water stress specifically affected the abundance of a small number of proteins, including heat shock proteins. Taken together, these data not only identify factors that are likely to play a key role in drought tolerance during seed germination, but they also demonstrate the importance of the female parent in the transmission of water stress tolerance.

Dehydration Sensitivity at the Early Seedling Establishment Stages of the European Beech (Fagus sylvatica L.)

Shortage of water is a limiting factor for the growth and development of plants, particularly at early developmental stages. We focused on the European beech (Fagus sylvatica L.), which produces seeds and further seedlings in large intervals of up to ten years. To explore the beech seedling establishment process, six stages referring to embryo expansion were studied to determine sensitivity to dehydration. The characterization of the response of elongating embryonic axes and cotyledons included a viability test before and after dehydration and measurement of the amounts of electrolyte leakage, concentration, and arrangement of storage materials, changes in chaperone proteins related to water deficit, and accumulation of hydrogen peroxide and superoxide anion radicals. Elongating embryonic axes and cotyledons differed in water content, dehydration rates, membrane permeability before and after dehydration, protein, and lipid decomposition pattern, and amount of 44-kDa dehydrin and 22-kDa small heat shock protein (sHSP). Protruding embryonic axes were more sensitive to dehydration than cotyledons, although dehydration caused transient reinduction of three dehydrin-like proteins and sHSP synthesis, which accompany desiccation tolerance. Extended deterioration, including overproduction of hydrogen peroxide and depletion of superoxide anion radicals, was reported in dehydrated embryonic axes longer than 10 mm characterized by highly elevated cellular leakage. The apical part elongating embryonic axes consisting of the radicles was the most sensitive part of the seed to dehydration, and the root apical meristem area was the first to become inviable. The effects of severe dehydration involving ROS imbalance and reduced viability in beech seedlings with embryonic axes longer than 10 mm might help to explain the difficulties in beech seedling establishment observed in drought-affected environments. The conversion of environmental drought into climate-originated oxidative stress affecting beech seedling performance is discussed in this report.

Comparative analyses of albumin/globulin grain proteome fraction in differentially salt-tolerant Tunisian barley landraces reveals genotype-specific and defined abundant proteins

Salinity is one of the major abiotic stresses threatening crop production and yield worldwide. Breeding programmes are therefore needed to improve yield under cultivation in soil. Traits from locally adopted landraces provide a resource to assist breeding of novel elite genotypes. Here, we examine differentially expressed proteins by performing comparative proteomic profiling of the albumin/globulin grain fraction of Tunisian barley genotype landraces with contrasting salinity tolerance. Tunisian barley Boulifa (B, tolerant) and Testour (T, sensitive) mature grains were assessed in 2-DE profiles. Differentially expressed spots, with an abundance enhanced 1.5-fold in the grain, were subjected to MALDI TOF/TOF MS for identification. Distinctiveness between tolerant and sensitive genotypes was proved in the albumin/globulin fraction using PCA; 64 spots showed significant differential abundance. Increased accumulation of 40 spots was confirmed in Boulifa with, interestingly, four genotype-specific spots. Two of these four spots were sHSP. Proteins with highest abundance were serpin Z7, 16.9 KDa Class I HSP and phosphogluconolactonase 2. Proteins such as expansin, kiwellin, kinesin and succinyl-CoA ligase were identified for the first time in barley grain. Moreover, ß-amylase, LEA family and others were identified as abundant in Boulifa. On the other hand, proteins more accumulated in Testour are implicated mainly in ROS scavenging and protease inhibition. Our results clearly indicate proteomic contrast between the two selected genotypes. With identification of specific HSP, high abundant stress-protective and other defined proteins, we provide biochemical traits that will support breeding programmes to address the threat of salinity in agricultural production.

Sprouted Grains: A Comprehensive Review

In the last decade, there has been an increase in the use of sprouted grains in human diet and a parallel increase in the scientific literature dealing with their nutritional traits and phytochemical contents. This review examines the physiological and biochemical changes during the germination process, and the effects on final sprout composition in terms of macro- and micro-nutrients and bioactive compounds. The main factors affecting sprout composition are taken into consideration: genotype, environmental conditions experimented by the mother plant, germination conditions. In particular, the review deepens the recent knowledge on the possible elicitation factors useful for increasing the phytochemical contents. Microbiological risks and post-harvest technologies are also evaluated, and a brief summary is given of some important in vivo studies matching with the use of grain sprouts in the diet. All the species belonging to Poaceae (Gramineae) family as well as pseudocereals species are included.

Toward characterizing germination and early growth in the non-orthodox forest tree species Quercus ilex through complementary gel and gel-free proteomic analysis of embryo and seedlings

By using two complementary proteomics, gel-based and gel-free (shotgun) approaches, the protein profiles of the non-orthodox forest tree species Quercus ilex seeds during germination and early seedling growth have been compared. Proteins were extracted from embryo axis, radicle and shoot tissues at different developmental stages. Proteins were subjected to one- and two-dimensional gel electrophoresis. A multivariate analysis (PCA) revealed that SDS-PAGE clearly separated germination (0-24 h post-imbibition), postgermination (72-216 h post-imbibition) and early seedling growth stages (2 weeks post-imbibition). Image analysis of the two-dimensional gels revealed a total of 732 spots, 103 of which were significantly variable among developmental stages. After MALDI-TOF/TOF MS analysis, 90 spots were identified, belonging to six main functional categories: carbohydrate, amino acids, energy, and protein metabolism, biosynthesis of secondary metabolites, and redox processes. The gel-based approach disclosed important metabolic changes that occurred in the holm oak seed after the germination. However, few proteins were significantly altered during the germination period (from 0 h to 24 h post imbibition) and, because of that, a further shotgun analysis was therefore used to analyse changes in the protein profile during seed germination. Up to 1250 proteins could be confidently identified, with 153 being variable. They belonged to the main functional categories of carbohydrate, amino acids and secondary metabolism, protein degradation, and responses to abiotic stress. The accumulation of proteases and amino acids metabolism proteins in mature seeds can be reflecting the production of energy from the mobilization of storage proteins to start germination. These results, therefore, corroborate the hypothesis that the mature non-orthodox seeds of Q. ilex have all the machinery necessary for rapidly resuming metabolic activities and starting the germination process, in contrast to that occurs in orthodox seeds, which metabolic activity ceases in mature dry seeds. The use of a genus-specific database combined with the public Viridiplantae database improved the quality and quantity of protein identification in this orphan species. In addition, both proteomics approaches (gel-based and shotgun) were complementary, with shotgun increasing by over two-fold the coverage of the proteome analysed. Both approaches provided similar results and supported the same conclusions on the metabolic switch experienced by the seed upon germination. SIGNIFICANCE: The optimal seed germination is a prerequisite for successful seedling establishment and plant vigour, being of great relevance in the case of crops and commercial woody plants. By using a complementary gel-based and gel-free proteomic strategy we have study the protein profiles of the non-orthodox forest tree species Quercus ilex seeds during germination and early seedling growth. The contribution of this work is of great importance, due to the complemented proteomic approaches giving similar clues to the metabolic state of the mature Q. ilex seed before the germination starts, and the metabolic switch experienced by the imbibed acorn until the seedling is established.

High salinity impacts germination of the halophyte Cakile maritima but primes seeds for rapid germination upon stress release

Seed germination recovery aptitude is an adaptive trait of overriding significance for the successful establishment and dispersal of extremophile plants in their native ecosystems. Cakile maritima is an annual halophyte frequent on Mediterranean coasts, which produces transiently dormant seeds under high salinity, that germinate fast when soil salinity is lowered by rainfall. Here, we report ecophysiological and proteomic data about (1) the effect of high salt (200 mM NaCl) on the early developmental stages (germination and seedling) and (2) the seed germination recovery capacity of this species. Upon salt exposure, seed germination was severely inhibited and delayed and seedling length was restricted. Interestingly, non-germinated seeds remained viable, showing high germination percentage and faster germination than the control seeds after their transfer onto distilled water. The plant phenotypic plasticity during germination was better highlighted by the proteomic data. Salt exposure triggered (1) a marked slower degradation of seed storage reserves and (2) a significant lower abundance of proteins involved in several biological processes (primary metabolism, energy, stress-response, folding and stability). Yet, these proteins showed strong increased abundance early after stress release, thereby sustaining the faster seed storage proteins mobilization under recovery conditions compared to the control. Overall, as part of the plant survival strategy, C. maritima seems to avoid germination and establishment under high salinity. However, this harsh condition may have a priming-like effect, boosting seed germination and vigor under post-stress conditions, sustained by active metabolic machinery.

Impact of geography on adaptation of Phyllanthus amarus seeds

The present study was aimed to evaluate adaptive mechanism in terms of seed characters of Phyllanthus amarus collected from ten different locations of Tamil Nadu, India. The adaptive variations among the collected populations were assessed based on the sink and float percentages of the seeds in water, the percentage of seed germination, total protein, carbohydrates and their seedling's growth ability such as shoot and root lengths. From this, we observed that the population had a significantly higher germination percentage of sinking seeds that were attributed to its relatively higher carbohydrate and protein contents than the floating seeds. A comparison of the seed population by cluster analysis and principal coordinate analysis showed that the Chennai population constituted a single clade that was very distinct from the other nine populations, which were further grouped into two sub-clusters. They exhibited a trend consistent with their geographical proximity. Standardised Mantel's t tests had revealed that the adaptive diversity of the P. amarus population was significantly affected by the geographic distance (r = 0.78, t = 2.68, P > 0.001), altitude (r = 0.35, t = 21.53, P > 0.05), minimum temperature (r = 0.43, t = 1.49, P > 0.01) and maximum temperature (r = 0.49, t = 1.67, P > 0.001). Seed's characteristics and geographical conditions were correlated along with 19 bioclimatic variables. In dry season, the seedling's rooting ability showed positive correlation, while its protein content exhibited a negative correlation. It is clearly evident from this study that the geographical variables significantly influence the adaptive ability of the P. amarus.

Proteomics in commercial crops: An overview

Proteomics is a rapidly growing area of biological research that is positively affecting plant science. Recent advances in proteomic technology, such as mass spectrometry, can now identify a broad range of proteins and monitor their modulation during plant growth and development, as well as during responses to abiotic and biotic stresses. In this review, we highlight recent proteomic studies of commercial crops and discuss the advances in understanding of the proteomes of these crops. We anticipate that proteomic-based research will continue to expand and contribute to crop improvement.

SIGNIFICANCE

Plant proteomics study is a rapidly growing area of biological research that is positively impacting plant science. With the recent advances in new technologies, proteomics not only allows us to comprehensively analyses crop proteins, but also help us to understand the functions of the genes. In this review, we highlighted recent proteomic studies in commercial crops and updated the advances in our understanding of the proteomes of these crops. We believe that proteomic-based research will continue to grow and contribute to the improvement of crops.

Systems biology and genome-wide approaches to unveil the molecular players involved in the pre-germinative metabolism: implications on seed technology traits

The pre-germinative metabolism is among the most fascinating aspects of seed biology. The early seed germination phase, or pre-germination, is characterized by rapid water uptake (imbibition), which directs a series of dynamic biochemical events. Among those are enzyme activation, DNA damage and repair, and use of reserve storage compounds, such as lipids, carbohydrates and proteins. Industrial seedling production and intensive agricultural production systems require seed stocks with high rate of synchronized germination and low dormancy. Consequently, seed dormancy, a quantitative trait related to the activation of the pre-germinative metabolism, is probably the most studied seed trait in model species and crops. Single omics, systems biology, QTLs and GWAS mapping approaches have unveiled a list of molecules and regulatory mechanisms acting at transcriptional, post-transcriptional and post-translational levels. Most of the identified candidate genes encode for regulatory proteins targeting ROS, phytohormone and primary metabolisms, corroborating the data obtained from simple molecular biology approaches. Emerging evidences show that epigenetic regulation plays a crucial role in the regulation of these mentioned processes, constituting a still unexploited strategy to modulate seed traits. The present review will provide an up-date of the current knowledge on seed pre-germinative metabolism, gathering the most relevant results from physiological, genetics, and omics studies conducted in model and crop plants. The effects exerted by the biotic and abiotic stresses and priming are also addressed. The possible implications derived from the modulation of pre-germinative metabolism will be discussed from the point of view of seed quality and technology.

Proteomic analysis reveals a role of melatonin in promoting cucumber seed germination under high salinity by regulating energy production

Seed germination is a critical and complex process in the plant life cycle. Although previous studies have found that melatonin can promote seed germination under salt stress, the involvement of melatonin in the regulation of proteomic changes remains poorly understood. In this study, a total of 157 proteins were significantly influenced (ratio ≥ 2 or ≤ -2) by melatonin during seed germination under salt stress using a label-free quantitative technique. Our GO analysis revealed that several pathways were obviously regulated by melatonin, including ribosome biosynthesis, lipid metabolism, carbohydrate metabolism, and storage protein degradation. Not only stress-tolerant proteins but also proteins that produce ATP as part of glycolysis, the citric acid cycle, and the glyoxylate cycle were upregulated by melatonin. Overall, this study provides new evidence that melatonin alleviates the inhibitory effects of NaCl stress on seed germination by promoting energy production. This study is the first to provide insights at the proteomic level into the molecular mechanism of melatonin in response to salt stress in cucumber seeds. This may be helpful to further understand the role of melatonin in cucumber seed germination under stress conditions.

Dissection of brassinosteroid-regulated proteins in rice embryos during germination by quantitative proteomics

Brassinosteroids (BRs), essential plant-specific steroidal hormones, function in a wide spectrum of plant growth and development events, including seed germination. Rice is not only a monocotyledonous model plant but also one of the most important staple food crops of human beings. Rice seed germination is a decisive event for the next-generation of plant growth and successful seed germination is critical for rice yield. However, little is known about the molecular mechanisms on how BR modulates seed germination in rice. In the present study, we used isobaric tags for relative and absolute quantification (iTRAQ) based proteomic approach to study BR-regulated proteome during the early stage of seed germination. The results showed that more than 800 BR-responsive proteins were identified, including 88 reliable target proteins responsive to stimuli of both BR-deficiency and BR-insensitivity. Moreover, 90% of the 88 target proteins shared a similar expression change pattern. Gene ontology and string analysis indicated that ribosomal structural proteins, as well as proteins involved in protein biosynthesis and carbohydrate metabolisms were highly clustered. These findings not only enrich BR-regulated protein database in rice seeds, but also allow us to gain novel insights into the molecular mechanism of BR regulated seed germination.

Mitochondrial Proteome Studies in Seeds during Germination

Seed germination is considered to be one of the most critical phases in the plant life cycle, establishing the next generation of a plant species. It is an energy-demanding process that requires functioning mitochondria. One of the earliest events of seed germination is progressive development of structurally simple and metabolically quiescent promitochondria into fully active and cristae-containing mitochondria, known as mitochondrial biogenesis. This is a complex and tightly regulated process, which is accompanied by sequential and dynamic gene expression, protein synthesis, and post-translational modifications. The aim of this review is to give a comprehensive summary of seed mitochondrial proteome studies during germination of various plant model organisms. We describe different gel-based and gel-free proteomic approaches used to characterize mitochondrial proteomes of germinating seeds as well as challenges and limitations of these proteomic studies. Furthermore, the dynamic changes in the abundance of the mitochondrial proteomes of germinating seeds are illustrated, highlighting numerous mitochondrial proteins involved in respiration, tricarboxycylic acid (TCA) cycle, metabolism, import, and stress response as potentially important for seed germination. We then review seed mitochondrial protein carbonylation, phosphorylation, and S-nitrosylation as well as discuss the possible link between these post-translational modifications (PTMs) and the regulation of seed germination.

Shotgun proteomic analysis of soybean embryonic axes during germination under salt stress

Seed imbibition and radicle emergence are generally less affected by salinity in soybean than in other crop plants. In order to unveil the mechanisms underlying this remarkable salt tolerance of soybean at seed germination, a comparative label-free shotgun proteomic analysis of embryonic axes exposed to salinity during germination sensu stricto (GSS) was conducted. The results revealed that the application of 100 and 200 mmol/L NaCl stress was accompanied by significant changes (>2-fold, P<0.05) of 97 and 75 proteins, respectively. Most of these salt-responsive proteins (70%) were classified into three major functional categories: disease/defense response, protein destination and storage and primary metabolism. The involvement of these proteins in salt tolerance of soybean was discussed, and some of them were suggested to be potential salt-tolerant proteins. Furthermore, our results suggest that the cross-protection against aldehydes, oxidative as well as osmotic stress, is the major adaptive response to salinity in soybean.

Source-Sink Communication: Regulated by Hormone, Nutrient, and Stress Cross-Signaling

Communication between source organs (exporters of photoassimilates) and sink organs (importers of fixed carbon) has a pivotal role in carbohydrate assimilation and partitioning during plant growth and development. Plant productivity is enhanced by sink strength and source activity, which are regulated by a complex signaling network encompassing sugars, hormones, and environmental factors. However, key components underlying the signaling pathways that regulate source-sink communication are only now beginning to be discovered. Here, we discuss recent advances in our understanding of the molecular mechanisms regulating sugar mobilization during seed development and seedling establishment in cereals, which provide the majority of nutrition for humans. Insights into these mechanisms may provide strategies for improving crop productivity.

Proteomic Analysis Reveals Key Proteins and Phosphoproteins upon Seed Germination of Wheat (Triticum aestivum L.)

Wheat (Triticum aestivum L.) is one of the oldest cultivated crops and the second most important food crop in the world. Seed germination is the key developmental process in plant growth and development, and poor germination directly affects plant growth and subsequent grain yield. In this study, we performed the first dynamic proteome analysis of wheat seed germination using a two-dimensional differential gel electrophoresis (2D-DIGE)-based proteomic approach. A total of 166 differentially expressed protein (DEP) spots representing 73 unique proteins were identified, which are mainly involved in storage, stress/defense/detoxification, carbohydrate metabolism, photosynthesis, cell metabolism, and transcription/translation/transposition. The identified DEPs and their dynamic expression profiles generally correspond to three distinct seed germination phases after imbibition: storage degradation, physiological processes/morphogenesis, and photosynthesis. Some key DEPs involved in storage substance degradation and plant defense mechanisms, such as globulin 3, sucrose synthase type I, serpin, beta-amylase, and plastid ADP-glucose pyrophosphorylase (AGPase) small subunit, were found to be phosphorylated during seed germination. Particularly, the phosphorylation site Ser(355) was found to be located in the enzyme active region of beta-amylase, which promotes substrate binding. Phosphorylated modification of several proteins could promote storage substance degradation and environmental stress defense during seed germination. The central metabolic pathways involved in wheat seed germination are proposed herein, providing new insights into the molecular mechanisms of cereal seed germination.

De novo assembly and characterization of germinating lettuce seed transcriptome using Illumina paired-end sequencing

At supraoptimal temperature, germination of lettuce (Lactuca sativa L.) seeds exhibits a typical germination thermoinhibition, which can be alleviated by sodium nitroprusside (SNP) in a nitric oxide-dependent manner. However, the molecular mechanism of seed germination thermoinhibition and its alleviation by SNP are poorly understood. In the present study, the lettuce seeds imbibed at optimal temperature in water or at supraoptimal temperature with or without 100 μM SNP for different periods of time were used as experimental materials, the total RNA was extracted and sequenced, we gained 147,271,347 raw reads using Illumina paired-end sequencing technique and assembled the transcriptome of germinating lettuce seeds. A total of 51,792 unigenes with a mean length of 849 nucleotides were obtained. Of these unigenes, a total of 29,542 unigenes were annotated by sequence similarity searching in four databases, NCBI non-redundant protein database, SwissProt protein database, euKaryotic Ortholog Groups database, and NCBI nucleotide database. Among the annotated unigenes, 22,276 unigenes were assigned to Gene Ontology database. When all the annotated unigenes were searched against the Kyoto Encyclopedia of Genes and Genomes Pathway database, a total of 8,810 unigenes were mapped to 5 main categories including 260 pathways. We first obtained a lot of unigenes encoding proteins involved in abscisic acid (ABA) signaling in lettuce, including 11 ABA receptors, 94 protein phosphatase 2Cs and 16 sucrose non-fermenting 1-related protein kinases. These results will help us to better understand the molecular mechanism of seed germination, thermoinhibition of seed germination and its alleviation by SNP.

Seed priming: state of the art and new perspectives

Priming applied to commercial seed lots is widely used by seed technologists to enhance seed vigour in terms of germination potential and increased stress tolerance. Priming can be also valuable to seed bank operators who need improved protocols of ex situ conservation of germplasm collections (crop and native species). Depending on plant species, seed morphology and physiology, different priming treatments can be applied, all of them triggering the so-called 'pre-germinative metabolism'. This physiological process takes place during early seed imbibition and includes the seed repair response (activation of DNA repair pathways and antioxidant mechanisms), essential to preserve genome integrity, ensuring proper germination and seedling development. The review provides an overview of priming technology, describing the range of physical-chemical and biological treatments currently available. Optimised priming protocols can be designed using the 'hydrotime concept' analysis which provides the theoretical bases for assessing the relationship between water potential and germination rate. Despite the efforts so far reported to further improve seed priming, novel ideas and cutting-edge investigations need to be brought into this technological sector of agri-seed industry. Multidisciplinary translational research combining digital, bioinformatic and molecular tools will significantly contribute to expand the range of priming applications to other relevant commercial sectors, e.g. the native seed market.

Cytological and Proteomic Analyses of Osmunda cinnamomea Germinating Spores Reveal Characteristics of Fern Spore Germination and Rhizoid Tip Growth

Fern spore is a good single-cell model for studying the sophisticated molecular networks in asymmetric cell division, differentiation, and polar growth. Osmunda cinnamomea L. var. asiatica is one of the oldest fern species with typical separate-growing trophophyll and sporophyll. The chlorophyllous spores generated from sporophyll can germinate without dormancy. In this study, the spore ultrastructure, antioxidant enzyme activities, as well as protein and gene expression patterns were analyzed in the course of spore germination at five typical stages (i.e. mature spores, rehydrated spores, double-celled spores, germinated spores, and spores with protonemal cells). Proteomic analysis revealed 113 differentially expressed proteins, which were mainly involved in photosynthesis, reserve mobilization, energy supplying, protein synthesis and turnover, reactive oxygen species scavenging, signaling, and cell structure modulation. The presence of multiple proteoforms of 25 differentially expressed proteins implies that post-translational modification may play important roles in spore germination. The dynamic patterns of proteins and their encoding genes exhibited specific characteristics in the processes of cell division and rhizoid tip growth, which include heterotrophic and autotrophic metabolisms, de novo protein synthesis and active protein turnover, reactive oxygen species and hormone (brassinosteroid and ethylene) signaling, and vesicle trafficking and cytoskeleton dynamic. In addition, the function skew of proteins in fern spores highlights the unique and common mechanisms when compared with evolutionarily divergent spermatophyte pollen. These findings provide an improved understanding of the typical single-celled asymmetric division and polar growth during fern spore germination.

Cytological and proteomic analyses of horsetail (Equisetum arvense L.) spore germination

Spermatophyte pollen tubes and root hairs have been used as single-cell-type model systems to understand the molecular processes underlying polar growth of plant cells. Horsetail (Equisetum arvense L.) is a perennial herb species in Equisetopsida, which creates separately growing spring and summer stems in its life cycle. The mature chlorophyllous spores produced from spring stems can germinate without dormancy. Here we report the cellular features and protein expression patterns in five stages of horsetail spore germination (mature spores, rehydrated spores, double-celled spores, germinated spores, and spores with protonemal cells). Using 2-DE combined with mass spectrometry, 80 proteins were found to be abundance changed upon spore germination. Among them, proteins involved in photosynthesis, protein turnover, and energy supply were over-represented. Thirteen proteins appeared as proteoforms on the gels, indicating the potential importance of post-translational modification. In addition, the dynamic changes of ascorbate peroxidase, peroxiredoxin, and dehydroascorbate reductase implied that reactive oxygen species homeostasis is critical in regulating cell division and tip-growth. The time course of germination and diverse expression patterns of proteins in photosynthesis, energy supply, lipid and amino acid metabolism indicated that heterotrophic and autotrophic metabolism were necessary in light-dependent germination of the spores. Twenty-six proteins were involved in protein synthesis, folding, and degradation, indicating that protein turnover is vital to spore germination and rhizoid tip-growth. Furthermore, the altered abundance of 14-3-3 protein, small G protein Ran, actin, and caffeoyl-CoA O-methyltransferase revealed that signaling transduction, vesicle trafficking, cytoskeleton dynamics, and cell wall modulation were critical to cell division and polar growth. These findings lay a foundation toward understanding the molecular mechanisms underlying fern spore asymmetric division and rhizoid polar growth.

A proteomic analysis of rice seed germination as affected by high temperature and ABA treatment

Seed germination is a critical phase in the plant life cycle, but the specific events associated with seed germination are still not fully understood. In this study, we used two-dimensional gel electrophoresis followed by mass spectrometry to investigate the changes in the proteome during imbibition of Oryza sativa seeds at optimal temperature with or without abscisic acid (ABA) and high temperature (germination thermoinhibition) to further identify and quantify key proteins required for seed germination. A total of 121 protein spots showed a significant change in abundance (1.5-fold increase/decrease) during germination under all conditions. Among these proteins, we found seven proteins specifically associated with seed germination including glycosyl hydrolases family 38 protein, granule-bound starch synthase 1, Os03g0842900 (putative steroleosin-B), N-carbamoylputrescine amidase, spermidine synthase 1, tubulin α-1 chain and glutelin type-A; and a total of 20 imbibition response proteins involved in energy metabolism, cell growth, cell defense and storage proteins. High temperature inhibited seed germination by decreasing the abundance of proteins involved in methionine metabolism, amino acid biosynthesis, energy metabolism, reserve degradation, protein folding and stress responses. ABA treatment inhibited germination and decreased the abundance of proteins associated with methionine metabolism, energy production and cell division. Our results show that changes in many biological processes including energy metabolism, protein synthesis and cell defense and rescue occurred as a result of all treatments, while enzymes involved in methionine metabolism and weakening of cell wall specifically accumulated when the seeds germinated at the optimal temperature.

Studies on the molecular mechanisms of seed germination

Seed germination that begins with imbibition and ends with radicle emergence is the first step for plant growth. Successful germination is not only crucial for seedling establishment but also important for crop yield. After being dispersed from mother plant, seed undergoes continuous desiccation in ecosystem and selects proper environment to trigger germination. Owing to the contribution of transcriptomic, proteomic, and molecular biological studies, molecular aspect of seed germination is elucidated well in Arabidopsis. Recently, more and more proteomic and genetic studies concerning cereal seed germination were performed on rice (Oryza sativa) and barley (Hordeum vulgare), which possess completely different seed structure and domestication background with Arabidopsis. In this review, both the common features and the distinct mechanisms of seed germination are compared among different plant species including Arabidopsis, rice, and maize. These features include morphological changes, cell and its related structure recovery, metabolic activation, hormone behavior, and transcription and translation activation. This review will provide more comprehensive insights into the molecular mechanisms of seed germination.

Fourteen years of plant proteomics reflected in Proteomics: moving from model species and 2DE-based approaches to orphan species and gel-free platforms

In this article, the topic of plant proteomics is reviewed based on related papers published in the journal Proteomics since publication of the first issue in 2001. In total, around 300 original papers and 41 reviews published in Proteomics between 2000 and 2014 have been surveyed. Our main objective for this review is to help bridge the gap between plant biologists and proteomics technologists, two often very separate groups. Over the past years a number of reviews on plant proteomics have been published . To avoid repetition we have focused on more recent literature published after 2010, and have chosen to rather make continuous reference to older publications. The use of the latest proteomics techniques and their integration with other approaches in the "systems biology" direction are discussed more in detail. Finally we comment on the recent history, state of the art, and future directions of plant proteomics, using publications in Proteomics to illustrate the progress in the field. The review is organized into two major blocks, the first devoted to provide an overview of experimental systems (plants, plant organs, biological processes) and the second one to the methodology.

Proteomics of seed development, desiccation tolerance, germination and vigor

Proteomics, the large-scale study of the total complement of proteins in a given sample, has been applied to all aspects of seed biology mainly using model species such as Arabidopsis or important agricultural crops such as corn and rice. Proteins extracted from the sample have typically been separated and quantified by 2-dimensional polyacrylamide gel electrophoresis followed by liquid chromatography and mass spectrometry to identify the proteins in the gel spots. In this way, qualitative and quantitative changes in the proteome during seed development, desiccation tolerance, germination, dormancy release, vigor alteration and responses to environmental factors have all been studied. Many proteins or biological processes potentially important for each seed process have been highlighted by these studies, which greatly expands our knowledge of seed biology. Proteins that have been identified to be particularly important for at least two of the seed processes are involved in detoxification of reactive oxygen species, the cytoskeleton, glycolysis, protein biosynthesis, post-translational modifications, methionine metabolism, and late embryogenesis-abundant (LEA) proteins. It will be useful for molecular biologists and molecular plant breeders to identify and study genes encoding particularly interesting target proteins with the aim to improve the yield, stress tolerance or other critical properties of our crop species.

Gel-based comparative phosphoproteomic analysis on rice embryo during germination

Seed germination is a well regulated process, which incorporates many events including signal transduction, mobilization of reserves, reactive oxygen species scavenging and cell division. Although many transcriptomic and proteomic studies have been conducted on this process, regulation of protein modification has not been studied. To better understand the mechanism, a gel-based comparative phosphoproteomic study was performed on rice embryo during the germination process. In total, 168 protein spots exhibited significantly changed Pro-Q staining intensity during germination. Using matrix-assisted laser deionization-time of flight/time of flight mass spectrometry (MALDI-TOF/TOF MS) analysis, 193 proteins were identified. By combining Pro-Q and Coomassie brilliant blue stain intensity analyses, 109 proteins were verified to be phosphorylation regulation proteins. Functional analyses indicated that phosphorylation of proteins involved in stress response and storage was gradually enhanced. Phosphorylation of signal transduction proteins was mainly activated during the early stage of germination, while stress response and storage protein phosphorylation were enhanced at the late stage. Enzyme assays proved that the phosphorylation of fructokinase, pyruvate kinase, malate dehydrogenase, GDP-mannose 3,5-epimerase1, ascorbate peroxidase and glutathione S-transferase could consistently enhance their activity. This study showed the dynamic changes of protein phosphorylation status in rice embryo during germination and provided new insight into understanding the mechanism underlying this process.

Comparative analysis of metabolic proteome variation in ascorbate-primed and unprimed wheat seeds during germination under salt stress

Seed priming with ascorbic acid improves salt tolerance in durum wheat. For understanding the potential mechanisms underlying this priming effect a gel-free shotgun proteomic analysis was performed comparing unprimed to ascorbate-primed wheat seed during germination under saline and non-saline conditions. Since seed germination is the result of interplay or cross-talk between embryo and embryo-surrounding tissues, we studied the variation of metabolic proteome in both tissues separately. 167 of 697 identified and 69 of 471 identified proteins increase or decrease in abundance significantly in response to priming and/or salinity compared to untreated, unstressed control in embryo and embryo-surrounding tissues, respectively. In untreated wheat embryo salt stress was accompanied by change in 129 proteins, most of which are belonging to metabolism, energy, disease/defense, protein destination and storage categories. Ascorbate pretreatment prevents and counteracts the effects of salinity upon most of these proteins and changes specifically the abundance of 35 others proteins, most of which are involved in metabolism, protein destination and storage categories. Hierarchical clustering analysis revealed three and two major clusters of protein expression in embryo and embryo-surrounding tissues, respectively. This study opens promising new avenues to understand priming-induced salt tolerance in plants.

BIOLOGICAL SIGNIFICANCE

To clearly understand how ascorbate-priming enhance the salt tolerance of durum wheat during germination, we performed for the first time a comparative shotgun proteomic analysis between unprimed and ascorbate-primed wheat seeds during germination under saline and non-saline conditions. Furthermore, since seed germination is the result of interplay or cross-talk between embryo and embryo-surrounding tissues we analyzed the variation of metabolic proteome in both tissues separately. 1168 proteins exhibiting greater molecular weight diversity (ranging from 5 to 258kDa) were identified. Among them, 167 and 69 proteins were increased or decreased in abundance significantly by priming and/or salinity as compared to control, in embryo and embryo-surrounding tissues respectively. Ascorbate pretreatment alleviates the effects of salinity upon most of these proteins, particularly those involved in metabolism, energy, disease/defense, protein destination and storage functions. Hierarchical clustering analysis revealed three and two major clusters of protein accumulation in embryo and embryo-surrounding tissues, respectively. These results may provide new avenues for understanding and advancing priming-induced salt tolerance in crop plants.

A systematic proteomic analysis of NaCl-stressed germinating maize seeds

Salt (NaCl) is a common physiological stressor of plants. To better understand how germinating seeds respond to salt stress, we examined the changes that occurred in the proteome of maize seeds during NaCl-treated germination. Phenotypically, salt concentrations less than 0.2 M appear to delay germination, while higher concentrations disrupt development completely, leading to seed death. The identities of 96 proteins with expression levels altered by NaCl-incubation were established using 2-DE-MALDI-TOF-MS and 2-DE-MALDI-TOF-MS/MS. Of these 96 proteins, 79 were altered greater than twofold when incubated with a 0.2 M salt solution, while 51 were altered when incubated with a 0.1 M salt solution. According to their functional annotations in the Swiss-Prot protein-sequence databases, these proteins are mainly involved in seed storage, energy metabolism, stress response, and protein metabolism. Notably, the expression of proteins that respond to abscisic acid signals increased in response to salt stress. The results of this study provide important clues as to how NaCl stresses the physiology of germinating maize seeds.