Molecular dynamics of pre-germinative metabolism in primed eggplant (Solanum melongena L.) seeds

Plant-Based Biostimulants for Seeds in the Context of Circular Economy and Sustainability

Plant-based biostimulants (PBs), agents rich in bioactive compounds, are emerging as key players able to sustainably improve plant growth and crop productivity to address food security. PBs are generally applied as foliar spray or soil irrigation, while more recently, the application as seed priming treatments is being envisaged as a highly sustainable method to also improve seed quality and germination. Therefore, this review proposes to explore the use of PBs for the seeds industry, specifically discussing about the relevance of product market values, sustainable methods for their production, why and how PBs are used for seed priming, and pinpointing specific strengths and challenges. The collected research studies indicate that PBs applied to seeds result in improved germination, seedling growth, and stress tolerance, although the molecular mechanisms at work are still largely overlooked. The high variability of bioactive molecules and used sources point towards a huge reservoir of nature-based solutions in support of sustainable agriculture practices.

Identification of Quantitative Trait Loci and Candidate Genes Controlling Seed Dormancy in Eggplant (Solanum melongena L.)

Seed dormancy is a life adaptation trait exhibited by plants in response to environmental changes during their growth and development. The dormancy of commercial seeds is the key factor affecting seed quality. Eggplant seed dormancy is controlled by quantitative trait loci (QTLs), but reliable QTLs related to eggplant dormancy are still lacking. In this study, F2 populations obtained through the hybridization of paternally inbred lines with significant differences in dormancy were used to detect regulatory sites of dormancy in eggplant seeds. Three QTLs (dr1.1, dr2.1, and dr6.1) related to seed dormancy were detected on three chromosomes of eggplant using the QTL-Seq technique. By combining nonsynonymous sites within the candidate regions and gene functional annotation analysis, nine candidate genes were selected from three QTL candidate regions. According to the germination results on the eighth day, the male parent was not dormant, but the female parent was dormant. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to verify the expression of nine candidate genes, and the Smechr0201082 gene showed roughly the same trend as that in the phenotypic data. We proposed Smechr0201082 as the potential key gene involved in regulating the dormancy of eggplant seeds. The results of seed experiments with different concentrations of gibberellin A3 (GA3) showed that, within a certain range, the higher the gibberellin concentration, the earlier the emergence and the higher the germination rate. However, higher concentrations of GA3 may have potential effects on eggplant seedlings. We suggest the use of GA3 at a concentration of 200-250 mg·L-1 to treat dormant seeds. This study provides a foundation for the further exploration of genes related to the regulation of seed dormancy and the elucidation of the molecular mechanism of eggplant seed dormancy and germination.

Seed longevity and genome damage

Seeds are the mode of propagation for most plant species and form the basis of both agriculture and ecosystems. Desiccation tolerant seeds, representative of most crop species, can survive maturation drying to become metabolically quiescent. The desiccated state prolongs embryo viability and provides protection from adverse environmental conditions, including seasonal periods of drought and freezing often encountered in temperate regions. However, the capacity of the seed to germinate declines over time and culminates in the loss of seed viability. The relationship between environmental conditions (temperature and humidity) and the rate of seed deterioration (ageing) is well defined, but less is known about the biochemical and genetic factors that determine seed longevity. This review will highlight recent advances in our knowledge that provide insight into the cellular stresses and protective mechanisms that promote seed survival, with a focus on the roles of DNA repair and response mechanisms. Collectively, these pathways function to maintain the germination potential of seeds. Understanding the molecular basis of seed longevity provides important new genetic targets for the production of crops with enhanced resilience to changing climates and knowledge important for the preservation of plant germplasm in seedbanks.

Genotype-specific germination behavior induced by sustainable priming techniques in response to water deprivation stress in rice

Water stress brought about by climate change is among the major global concerns threatening food security. Rice is an important staple food which requires high water resources. Being a semi-aquatic plant, rice is particularly susceptible to drought. The aim of this work was to develop techniques directed to promote rice resilience to water deprivation stress during germination by implementing specific seed priming treatments. Five popular Italian rice varieties were subjected to priming treatments using novel, sustainable solutions, like poly-gamma-glutamic acid (γ-PGA), denatured γ-PGA (dPGA), and iron (Fe) pulsing, alone or in combination. The effect of the developed priming methods was tested under optimal conditions as well as under water deprivation stress imposed by polyethylene glycol (PEG) treatments. The priming efficacy was phenotypically determined in terms of germination behavior by measuring a series of parameters (germinability, germination index, mean germination time, seed vigor index, root and shoot length, germination stress tolerance index). Biochemical analyses were carried out to measure the levels of iron uptake and accumulation of reactive oxygen species (ROS). Integrative data analyses revealed that the rice varieties exhibited a strong genotype- and treatment-specific germination behavior. PEG strongly inhibited germination while most of the priming treatments were able to rescue it in all varieties tested except for Unico, which can be defined as highly stress sensitive. Molecular events (DNA repair, antioxidant response, iron homeostasis) associated with the transition from seed to seedling were monitored in terms of changes in gene expression profiles in two varieties sensitive to water deprivation stress with different responses to priming. The investigated genes appeared to be differentially expressed in a genotype-, priming treatment-, stress- and stage-dependent manner. The proposed seed priming treatments can be envisioned as sustainable and versatile agricultural practices that could help in addressing the impact of climate challenges on the agri-food system.

Base Excision DNA Repair in Plants: Arabidopsis and Beyond

Base excision DNA repair (BER) is a key pathway safeguarding the genome of all living organisms from damage caused by both intrinsic and environmental factors. Most present knowledge about BER comes from studies of human cells, E. coli, and yeast. Plants may be under an even heavier DNA damage threat from abiotic stress, reactive oxygen species leaking from the photosynthetic system, and reactive secondary metabolites. In general, BER in plant species is similar to that in humans and model organisms, but several important details are specific to plants. Here, we review the current state of knowledge about BER in plants, with special attention paid to its unique features, such as the existence of active epigenetic demethylation based on the BER machinery, the unexplained diversity of alkylation damage repair enzymes, and the differences in the processing of abasic sites that appear either spontaneously or are generated as BER intermediates. Understanding the biochemistry of plant DNA repair, especially in species other than the Arabidopsis model, is important for future efforts to develop new crop varieties.

Herbal and chemical seed potentiations improve the redox health of aged seeds of indigenous aromatic rice cultivars through regulation of oxidative window, gene expression, and restoration of hormonal homeostasis

Previous studies associated with seed potentiation support the critical role of metabolic readjustment in restricting the loss of seed vigor and viability of aged seeds. However, their exact role in the regulation of 'oxidative windows' of potentiated seeds is rarely studied and hence is the subject of the present investigation. Seed potentiation of two contrasting indigenous aromatic rice cultivars, differing in sensitivity towards redox attributes (Oryza sativa L., Cultivars Tulaipanji and Jamainadu), with standardized doses of hydrogen peroxide (20 mM), triadimefon (250 μM), herbal extract (1% aqueous extract of Lantana camara flower) and distilled water before accelerated aging (RH 92% and 41 °C for 24 h) found to have significant impact on redox regulation of aged seeds and improvement of germination phenotypes. The efficacy of integrated RBOH-ascorbate-glutathione/catalase pathway, redox status and other redox fingerprints in the metabolic landscape of potentiated-aged seeds vis-a-vis non-potentiated-aged seeds corroborate the impact of seed potentiation on the regulation of 'oxidative window' of experimental rice seeds. Gene expression analysis of central redox hub enzymes (Osrboh, OsAPx2, OsGRase, OsCatA) strongly substantiates the impact of seed potentiation on transcriptional regulation of genes for redox homeostasis in accelerated aged seeds. The novelty of the current effort is that it suggests a positive nexus between seed potentiation-induced redox regulation and hormonal homeostasis. The efficacy of seed potentiation on the redox regulation of experimental accelerated aged seeds is found to be cultivar-specific and comparatively better in the cultivar Tulaipanji as compared to the cultivar Jamainadu and in the order herbal extract, hydrogen peroxide, hydropriming and triadimefon.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01375-9.

Changes in Medicago truncatula seed proteome along the rehydration-dehydration cycle highlight new players in the genotoxic stress response

Introduction

Several molecular aspects underlying the seed response to priming and the resulting vigor profile are still poorly understood. Mechanisms involved in genome maintenance deserve attention since the balance between stimulation of germination and DNA damage accumulation versus active repair is a key determinant for designing successful seed priming protocols.

Methods

Changes in the Medicago truncatula seed proteome were investigated in this study, using discovery mass spectrometry and label-free quantification, along the rehydration-dehydration cycle of a standard vigorization treatment (hydropriming plus dry-back), and during post-priming imbibition.

Resuts and discussion

From 2056 to 2190 proteins were detected in each pairwise comparison, among which six were differentially accumulated and 36 were detected only in one condition. The following proteins were selected for further investigation: MtDRP2B (DYNAMIN-RELATED PROTEIN), MtTRXm4 (THIOREDOXIN m4), and MtASPG1 (ASPARTIC PROTEASE IN GUARD CELL 1) showing changes in seeds under dehydration stress; MtITPA (INOSINE TRIPHOSPHATE PYROPHOSPHORYLASE), MtABA2 (ABSCISIC ACID DEFICIENT 2), MtRS2Z32 (SERINE/ARGININE-RICH SPLICING FACTOR RS2Z32), and MtAQR (RNA HELICASE AQUARIUS) that were differentially regulated during post-priming imbibition. Changes in the corresponding transcript levels were assessed by qRT-PCR. In animal cells, ITPA hydrolyses 2'-deoxyinosine triphosphate and other inosine nucleotides, preventing genotoxic damage. A proof of concept was performed by imbibing primed and control M. truncatula seeds in presence/absence of 20 mM 2'-deoxyinosine (dI). Results from comet assay highlighted the ability of primed seeds to cope with dI-induced genotoxic damage. The seed repair response was assessed by monitoring the expression profiles of MtAAG (ALKYL-ADENINE DNA GLYCOSILASE) and MtEndoV (ENDONUCLEASE V) genes that participate in the repair of the mismatched I:T pair in BER (base excision repair) and AER (alternative excision repair) pathways, respectively.

Integrative Transcriptomics Data Mining to Explore the Functions of TDP1α and TDP1β Genes in the Arabidopsis thaliana Model Plant

The tyrosyl-DNA phosphodiesterase 1 (TDP1) enzyme hydrolyzes the phosphodiester bond between a tyrosine residue and the 3'-phosphate of DNA in the DNA-topoisomerase I (TopI) complex, being involved in different DNA repair pathways. A small TDP1 gene subfamily is present in plants, where TDP1α has been linked to genome stability maintenance, while TDP1β has unknown functions. This work aimed to comparatively investigate the function of the TDP1 genes by taking advantage of the rich transcriptomics databases available for the Arabidopsis thaliana model plant. A data mining approach was carried out to collect information regarding gene expression in different tissues, genetic backgrounds, and stress conditions, using platforms where RNA-seq and microarray data are deposited. The gathered data allowed us to distinguish between common and divergent functions of the two genes. Namely, TDP1β seems to be involved in root development and associated with gibberellin and brassinosteroid phytohormones, whereas TDP1α is more responsive to light and abscisic acid. During stress conditions, both genes are highly responsive to biotic and abiotic treatments in a time- and stress-dependent manner. Data validation using gamma-ray treatments applied to Arabidopsis seedlings indicated the accumulation of DNA damage and extensive cell death associated with the observed changes in the TDP1 genes expression profiles.

Molecular dynamics of seed priming at the crossroads between basic and applied research

The potential of seed priming is still not fully exploited. Our limited knowledge of the molecular dynamics of seed pre-germinative metabolism is the main hindrance to more effective new-generation techniques. Climate change and other recent global crises are disrupting food security. To cope with the current demand for increased food, feed, and biofuel production, while preserving sustainability, continuous technological innovation should be provided to the agri-food sector. Seed priming, a pre-sowing technique used to increase seed vigor, has become a valuable tool due to its potential to enhance germination and stress resilience under changing environments. Successful priming protocols result from the ability to properly act on the seed pre-germinative metabolism and stimulate events that are crucial for seed quality. However, the technique still requires constant optimization, and researchers are committed to addressing some key open questions to overcome such drawbacks. In this review, an update of the current scientific and technical knowledge related to seed priming is provided. The rehydration-dehydration cycle associated with priming treatments can be described in terms of metabolic pathways that are triggered, modulated, or turned off, depending on the seed physiological stage. Understanding the ways seed priming affects, either positively or negatively, such metabolic pathways and impacts gene expression and protein/metabolite accumulation/depletion represents an essential step toward the identification of novel seed quality hallmarks. The need to expand the basic knowledge on the molecular mechanisms ruling the seed response to priming is underlined along with the strong potential of applied research on primed seeds as a source of seed quality hallmarks. This route will hasten the implementation of seed priming techniques needed to support sustainable agriculture systems.

Noninvasive Methods to Detect Reactive Oxygen Species as a Proxy of Seed Quality

ROS homeostasis is crucial to maintain radical levels in a dynamic equilibrium within physiological ranges. Therefore, ROS quantification in seeds with different germination performance may represent a useful tool to predict the efficiency of common methods to enhance seed vigor, such as priming treatments, which are still largely empirical. In the present study, ROS levels were investigated in an experimental system composed of hydroprimed and heat-shocked seeds, thus comparing materials with improved or damaged germination potential. A preliminary phenotypic analysis of germination parameters and seedling growth allowed the selection of the best-per-forming priming protocols for species like soybean, tomato, and wheat, having relevant agroeconomic value. ROS levels were quantified by using two noninvasive assays, namely dichloro-dihydro-fluorescein diacetate (DCFH-DA) and ferrous oxidation-xylenol orange (FOX-1). qRT-PCR was used to assess the expression of genes encoding enzymes involved in ROS production (respiratory burst oxidase homolog family, RBOH) and scavenging (catalase, superoxide dismutase, and peroxidases). The correlation analyses between ROS levels and gene expression data suggest a possible use of these indicators as noninvasive approaches to evaluate seed quality. These findings are relevant given the centrality of seed quality for crop production and the potential of seed priming in sustainable agricultural practices.

Optimization of 'on farm' hydropriming conditions in wheat: Soaking time and water volume have interactive effects on seed performance

Seed priming is a simple and cost effective method to obtain a better plant stand under diverse environmental conditions. The current study was designed to determine the optimal priming duration and water volume for wheat seed. For this experiment, three wheat genotypes with distinct genetic and adaptive backgrounds were chosen. Seeds of each genotype were hydroprimed for 7 durations, i.e. 1, 2, 4, 8, 12, 16, and 20 hours, in three different water volumes, i.e. half, equal, and double volume with respect to seed weight and then surface dried for 1 hour. The control was unprimed (dry) seed. The germination characteristics and seedling vigour potential of hydroprimed seeds were evaluated in the lab by recording several parameters such as germination percentage and speed, seedling growth, and vigour indices at two different temperature levels. The results showed that optimal duration for hydropriming of wheat seed is 12 hours with an equal volume with respect to original seed weight, closely followed by 8 hours with double volume. Reduction in seed performance was observed at 16 and 20 hours priming particularly at double volume treatment. Effect of temperature on seed germination showed improvement in seedling vigour at 25°C when compared to 20°C, although effect on germination percentage was non-significant. Volume of water and priming duration showed significant interactive effects demonstrating that a higher volume can give equivalent results at a shorter duration and vice versa. Another experiment was also conducted to compare the on-farm priming (surface dried seed) with conventional priming (seed re-dried to original moisture) taking 3 potential durations i.e. 8, 12 and 16 hours. Results revealed that both priming methods were statistically at par in terms of germination percentage, while, surface drying resulted in better seedling vigour and speed of germination.

Influence of various temperatures, seed priming treatments and durations on germination and growth of the medicinal plant Aspilia africana

For millennia, Aspilia africana has been used across Africa to treat various diseases including malaria, wounds, and diabetes. In this study, temperature influenced the in vitro germination of A. africana with highest final germination percentage (FGP) and germination index (GI) of 65.0 ± 7.64% and 2.26 ± 0.223, respectively, at 19.8 °C. Priming seeds with H₂O, KNO_3, and GA₃ (gibberellic acid 3) improved both in vitro germination and ex vitro emergence of A. africana seeds. Seed priming with [Formula: see text] M GA₃ produced overall highest in vitro FGP (from 90.0 ± 4.08% to 100 ± 0.00%) and GI (from 2.97 ± 0.385 to 3.80 ± 0.239) across all priming durations. Seeds primed with KNO₃ had better germination parameters for 6 and 12 h compared to 18 and 24 h. Furthermore, the highest in vitro FGP (100 ± 0.00%) was observed in seeds primed for 12 h with [Formula: see text] M GA₃. Ex vitro A. africana seed emergence was significantly enhanced by GA₃ priming. Priming A. africana seeds with H₂O, KNO₃, and GA₃ improved their growth after 3 months, with the overall best growth for seeds primed with [Formula: see text] M GA₃. Seed priming of A. africana is a feasible approach for improving germination and seed emergence, and enhancing plant growth.

Changes in genotoxic stress response, ribogenesis and PAP (3'-phosphoadenosine 5'-phosphate) levels are associated with loss of desiccation tolerance in overprimed Medicago truncatula seeds

Re-establishment of desiccation tolerance is essential for the survival of germinated seeds facing water deficit in the soil. The molecular and ultrastructural features of desiccation tolerance maintenance and loss within the nuclear compartment are not fully resolved. In the present study, the impact of desiccation-induced genotoxic stress on nucleolar ultrastructure and ribogenesis was explored along the rehydration-dehydration cycle applied in standard seed vigorization protocols. Primed and overprimed Medicago truncatula seeds, obtained through hydropriming followed by desiccation (dry-back), were analysed. In contrast to desiccation-tolerant primed seeds, overprimed seeds enter irreversible germination and do not survive dry-back. Reactive oxygen species, DNA damage and expression profiles of antioxidant/DNA Damage Response genes were measured, as main hallmarks of the seed response to desiccation stress. Nuclear ultrastructural features were also investigated. Overprimed seeds subjected to dry-back revealed altered rRNA accumulation profiles and up-regulation of genes involved in ribogenesis control. The signal molecule PAP (3'-phosphoadenosine 5'-phosphate) accumulated during dry-back only in primed seeds, as a distinctive feature of desiccation tolerance. The presented results show the molecular and ultrastructural landscapes of the seed desiccation response, including substantial changes in nuclear organization.

Physiological and molecular aspects of seed longevity: exploring intra-species variation in eight Pisum sativum L. accessions

Conservation of plant genetic diversity is fundamental for crop improvement, increasing agricultural production and sustainability, especially in the face of climatic changes. Although seed longevity is essential for the management of seed banks, few studies have, so far, addressed differences in this trait among the accessions of a single species. Eight Pisum sativum L. (pea) accessions were investigated to study the impact of long-term (approximately 20 years) storage, aiming to reveal contrasting seed longevity and clarify the causes for these differences. The outstanding seed longevity observed in the G4 accession provided a unique experimental system. To characterize the biochemical and physical status of stored seeds, reactive oxygen species, lipid peroxidation, tocopherols, free proline and reducing sugars were measured. Thermoanalytical measurements (thermogravimetry and differential scanning calorimetry) and transmission electron microscopy combined with immunohistochemical analysis were performed. The long-lived G4 seeds neither consumed tocopherols during storage nor showed free proline accumulation, as a deterioration hallmark, whereas reducing sugars were not affected. Thermal decomposition suggested a biomass composition compatible with the presence of low molecular weight molecules. Expansion of heterochromatic areas and reduced occurrence of γH2AX foci were highlighted in the nucleus of G4 seeds. The longevity of G4 seeds correlates with the occurrence of a reducing cellular environment and a nuclear ultrastructure favourable to genome stability. This work brings novelty to the study of within-species variations in seed longevity, underlining the relevance of multidisciplinary approaches in seed longevity research.

Hydropriming Applied on Fast Germinating Solanum villosum Miller Seeds: Impact on Pre-germinative Metabolism

Seed priming can circumvent poor germination rate and uniformity, frequently reported in eggplant (Solanum melongena L.) and its crop wild relatives (CWRs). However, there is still a gap of knowledge on how these treatments impact the pre-germinative metabolism in a genotype- and/or species-dependent manner. The CWR Solanum villosum Miller (hairy nightshade) investigated in this study showed a quite unique profile of fast germination. Although this accelerated germination profile would not apparently require further improvement, we wanted to test whether priming would still be able to impact the pre-germinative metabolism, eventually disclosing the predominant contribution of specific antioxidant components. Hydropriming followed by dry-back resulted in synchronized germination, as revealed by the lowest MGR (Mean Germination Rate) and U (Uncertainty) values, compared to unprimed seeds. No significant changes in ROS (reactive oxygen species) were observed throughout the treatment. Increased tocopherols levels were detected at 2 h of hydropriming whereas, overall, a low lipid peroxidation was evidenced by the malondialdehyde (MDA) assay. Hydropriming resulted in enhanced accumulation of the naturally occurring antioxidant phenolic compounds chlorogenic acid and iso-orientin, found in the dry seeds and ex novo accumulation of rutin. The dynamic changes of the pre-germinative metabolism induced by hydropriming are discussed in view of future applications that might boost the use of eggplant CWRs for breeding, upon upgrade mediated by seed technology.

A New Intra-Specific and High-Resolution Genetic Map of Eggplant Based on a RIL Population, and Location of QTLs Related to Plant Anthocyanin Pigmentation and Seed Vigour

Eggplant is the second most important solanaceous berry-producing crop after tomato. Despite mapping studies based on bi-parental progenies and GWAS approaches having been performed, an eggplant intraspecific high-resolution map is still lacking. We developed a RIL population from the intraspecific cross ‘305E40’, (androgenetic introgressed line carrying the locus Rfo-Sa1 conferring Fusarium resistance) x ‘67/3’ (breeding line whose genome sequence was recently released). One hundred and sixty-three RILs were genotyped by a genotype-by-sequencing (GBS) approach, which allowed us to identify 10,361 polymorphic sites. Overall, 267 Gb of sequencing data were generated and ~773 M Illumina paired end (PE) reads were mapped against the reference sequence. A new linkage map was developed, including 7249 SNPs assigned to the 12 chromosomes and spanning 2169.23 cM, with iaci@liberoan average distance of 0.4 cM between adjacent markers. This was used to elucidate the genetic bases of seven traits related to anthocyanin content in different organs recorded in three locations as well as seed vigor. Overall, from 7 to 17 QTLs (at least one major QTL) were identified for each trait. These results demonstrate that our newly developed map supplies valuable information for QTL fine mapping, candidate gene identification, and the development of molecular markers for marker assisted selection (MAS) of favorable alleles.