ABI4 regulates primary seed dormancy by regulating the biogenesis of abscisic acid and gibberellins in arabidopsis

OsHsp20-25, a small heat shock protein, from long-lived mRNA regulates seed size and germination rate in rice

MAIN CONCLUSION

The small heat shock protein OsHsp20-25, from long-lived mRNA, negatively regulates seed germination but positively regulates seed length. The mRNAs stored for a longer period in mature and dry seeds are called long-lived mRNA, which encodes diverse protein families and plays important roles in seed vigor. However, the specific contributions of individual mRNA populations to germination regulation remain poorly defined. In this study, we analyzed four small heat shock proteins, OsHsp20-17, OsHsp20-18, OsHsp20-20, and OsHsp20-25, from RNA sequencing data of rice seed. They were specifically expressed in the late stage of seed development and early stage of seed germination. Intriguingly, their transcripts retained detectable expression levels in one-year-old stored seeds. Four transgenic lines of OsHsp20s were generated, and only the OsHsp20-25 overexpression lines exhibited lower germination rates compared to the wild-type, accompanied by upregulated expression of OsABI5 and OsMFT2, and enhanced ABA sensitivity. Furthermore, OsHsp20-25-CRISPR mutants produced seeds of shorter length, but the overexpression line showed longer seeds. Biochemical and molecular evidence demonstrates that OsHsp20-25 interacted with OsHsp20-18, which also interacted with an F-box domain protein OsFBL45 in vivo and in vitro. Overall, OsHsp20, as a long-lived mRNA, plays important roles in seed development and seed germination.

The ubiquitin ligase SINA3 and the transcription factor WOX14 regulate tomato growth and development

In this study, we demonstrated that a regulatory module consisting of the SEVEN IN ABSENTIA (SINA) ubiquitin ligase SINA3 and the WUSCHEL homeobox-containing (WOX) transcription factor WOX14 fine-tunes tomato (Solanum lycopersicum) growth and development. Overexpression of SINA3 in tomato (SINA3-OX) resulted in dwarfism due to shortened internodes with smaller cells. SINA3 regulates WOX14 levels through ubiquitin-independent proteasome-mediated degradation, wherein SINA3 acts as a linker between WOX14 and the proteasome subunits REGULATORY PARTICLE NON-ATPASEs 9 and 13 (RPN9 and RPN13). Moreover, WOX14 knockout plants (WOX14-KO) exhibited dwarfism comparable to that of SINA3-OX plants. Genetic analyses showed that SINA3 controls vegetative growth by regulating WOX14 accumulation. Notably, WOX14 directly binds to the promoters of GA biosynthesis genes and activates their expression, thereby enhancing GA levels. Knockout of the GA biosynthesis gene GA3ox1 (GA3ox1-KO) caused growth retardation in tomato, similar to SINA3-OX and WOX14-KO transgenic plants. Bioactive GA levels were lower in SINA3-OX and WOX14-KO plants compared to the controls, and exogenous bioactive GA application partially restored their vegetative growth. This finding suggests that the SINA3-WOX14 module regulates vegetative growth in both GA-dependent and -independent manners. In addition, the SINA3-WOX14 module regulates GA-mediated reproductive growth and development, including fruit growth, seed set, seed growth, and maturation.

Identification of F-box proteins in ABA- and GA-regulated seed germination: interaction of GASA1 signalling peptide and ABA-induced ubiquitination

Large gene families and the frequent overlapping functions of homologous genes remain a major challenge for functional forward genetic screens in plants. The recent development of homology-based gene silencing using computationally generated artificial microRNAs (amiRNAs) has been demonstrated to be a promising tool for unbiased functional genomics in plants by circumventing redundancies and lethality. In this study, through a forward genetics screen, we isolated an abscisic acid (ABA)-insensitive amiRNA line targeting five previously uncharacterized F-box Insensitive to ABA (FIA) genes. Notably, a triple mutant in the identified FIA genes FIA1, FIA3 and FIA4 (f1/f3/f4), that are expressed in germinating seeds, exhibited insensitivity in ABA inhibition of seed germination. In contrast, this ABA insensitivity was not observed in a double mutant of two FIA genes FIA1 and FIA4. Further investigation of the FIA1 interactome using F-box decoy lines revealed the gibberellin (GA)-responsive GASA1 protein that has been reported to encode a small stress signalling peptide as an interacting partner. We found that ABA promoted the ubiquitination of GASA1 in Arabidopsis, leading to its degradation via the 26S proteasome pathway. Together, our study reveals that ABA represses seed germination through FIA proteins and regulates the FIA interactor, GA-responsive GASA1.This article is part of the theme issue 'Crops under stress: can we mitigate the impacts of climate change on agriculture and launch the 'Resilience Revolution'?'.

TaPP2C-a6 interacts with TaDOG1Ls and regulates seed dormancy and germination in wheat

Modern wheat cultivation requires seed to germinate rapidly and uniformly with weak dormancy. However, such varieties tend to undergo pre-harvest sprouting (PHS) if the harvest overlaps with the rainy season, causing substantial yield losses. Knowledge regarding the mechanisms of seed dormancy in wheat (Triticum aestivum L.) is limited, with only a few causal genes of the many PHS quantitative trait loci (QTLs) characterized. Here, we emphasize the involvement of ABA signalling core components in regulating seed dormancy and germination in wheat. TaPP2C-a6 was identified as the likely causal gene of wheat PHS-QTLs QPhs.wsu-1A/1B and QPhs1D.1_nwafu loci. Both TaPP2C-a6 and TaPP2C-a7 were highly expressed at embryonic developmental stages and germinating seeds, whereas TaPP2C-a6 was up-regulated during embryo maturation and seed germination. TaPP2C-a6 and TaPP2C-a7 were clade-A PP2Cs that interacted with TaPYLs and class III TaSnRK2s; however, TaPP2C-a6 showed stronger interactions with TaDOG1L members than those of TaPP2C-a7. TaPP2C-a6 overexpression in transgenic Arabidopsis thaliana caused a more severe reduction in ABA sensitivity than TaPP2C-a7 overexpression. Overexpression of TaPP2C-a6 in transgenic A. thaliana and wheat increased PHS levels, whereas TaPP2C-a7 transgenic A. thaliana did not affect PHS levels, confirming that TaPP2C-a6 is a novel regulator of wheat seed dormancy and germination. In summary, we demonstrated that leveraging the knowledge of seed dormancy and germination from model species could rapidly identify the causal genes of PHS-QTLs in wheat. Significantly, we showed that the TaPP2C-TaDOG1L interactions, particularly the interaction strength, could be a new aspect in the regulation of seed dormancy and germination.

Gamma-aminobutyric acid (GABA) releases seed dormancy by orchestrating abscisic acid and gibberellin metabolism and signaling

BACKGROUND

Seed dormancy release, regulated by abscisic acid (ABA) and gibberellin (GA), is essential for plant development and yield. Gamma-aminobutyric acid (GABA) is known to mediate plant stress responses; however, its role in seed dormancy release remains elusive.

RESULTS

Here, we reported that seed dormancy release was impaired in GAD2-deficient seeds lacking GABA biosynthesis while enhanced in GABA-T-deficient seeds with impaired GABA catabolism, indicating a positive regulatory role of GABA in seed dormancy release. Further, ABA antagonized GABA-facilitated seed dormancy release, and GABA failed to alleviate seed dormancy in the GA-deficient mutant ga1-t. Analysis of mutants defective in ABA and GA biosynthesis revealed that seed dormancy release, characterized as decreased ABA content and increased GA3 content, was suppressed in gad2 while enhanced in gaba-t1-1 mutant. Mechanistically, GABA promoted GA3 biosynthesis by upregulating GA20ox1 expression, while inhibited ABA biosynthesis by downregulating NCED6 and upregulating CYP707A2 transcription. GABA also amplified GA signaling and suppressed ABA signaling by downregulating genes expression of DELLAs and ABI3. Further, GABA-mediated seed dormancy alleviation was confirmed in seeds of pear, apple, and cherry, highlighting its broad applicability across diverse plant species.

CONCLUSION

Our findings not only advance our understanding on the mechanism of GABA-mediated seed dormancy release via coordinated regulation of abscisic acid and gibberellin pathways, but also highlight the potential of GABA as a natural alternative to synthetic chemicals for promoting sustainable and environmentally friendly agricultural practices.

The Arabidopsis PM19L1 Protein Functions as a Regulator of Germination Under Osmotic Stress

How plants perceive and respond to water availability, especially during the critical stages of seed formation and germination, is key to their survival. During development, ripening, and germination, seeds undergo large changes in water content, down to around 10% during maturation and up to 90% again within 24 h of germination. However, the mechanisms by which plants perceive and respond to their osmotic environment remain largely unknown. The results presented here indicate that the osmotic environment of the seed is perceived by the PM19L1 protein. We find the Arabidopsis plasma membrane protein PM19L1 is evolutionarily conserved in all land plants, is highly expressed in seeds and seedlings, and regulates germination under osmotic stress, as shown by the reduced germination of the pm19l1 mutant under salt and osmotic stress. The PM19L1 protein structurally resembles the yeast osmosensor Sho1, and expression of PM19L1 in yeast will complement the osmosensitive sho1 mutant, thus PM19L1 can function as an osmosensor. In contrast to the Sho1-mediated mechanisms for osmotic tolerance in yeast, PM19L1 does not control osmolyte levels in plants, but is a regulator of genes governing abscisic acid and gibberellin synthesis, and of transcription factors that mediate the abscisic acid response. In the pm19l1 mutant, expression of genes for ABI3, LEC1, and FUS3, which promote the late maturation of the seed, is downregulated, whereas expression of the ABI4 and ABI5 transcription factors, which confer abscisic acid-dependent inhibition of germination, is upregulated. The role of PM19L1 as an osmosensor in the plant was verified by ectopic expression of PM19L1 which conferred the ability of vegetative plants to respond to imposed osmotic stress by enhanced expression of ABI3, LEC1, and FUS3. This suggests a function for PM19L1 as a factor that integrates information on the osmotic environment to modulate the developmental fate of the seed during development and germination. Analysis of endogenous hormone levels and phenotypes of digenic mutants, for example pm19l1/abi3 and pm19l1/abi4, will help confirm and refine this model. In a further parallel to ShoI osmosensing in yeast, intracellular signaling downstream of PM19L1 in the plant likely involves a MAP kinase signal transduction pathway, as shown by split ubiquitin analysis for protein-protein interactions, and by pull-down assays from plant extracts. The MAP kinase proteins AtMKK2 and AtMKK3 specifically bind to PM19L1, and the atmkk2, and atmkk3 mutants have strikingly similar germination and gene expression phenotypes to pm19l1; however, corroboration of the role of these proteins in the signaling pathway will require further analysis of knockout and gain of function MKK mutants in the pm19l1 background. These results have implications for the study of dormancy, drought, and salinity tolerance in land plants including crops, and may also provide an insight into evolutionary adaptation of plants to a terrestrial environment.

Map-based cloning of Zmccr3 and its network construction and validation for regulating maize seed germination

KEY MESSAGE

Map-based cloning of Zmccr3 for regulate SG and its molecular regulatory pathway was performed and validated. WGCNA, target genes/pathways during the process of seed dormancy formation were obtained. Seed dormancy (SD) and pre-harvest sprouting (PHS) affect the grain yield and quality of grain in cereal and hybrid seed production. Although the benefits of studying SD and seed germination (SG) during seed development are well established, research into the genetic variation and molecular regulation of SD, particularly during the transition from SD to SG, remains very limited. In this study, bulked segregant analysis (BSA) and linkage analysis were used to map the QTL for the maize vp16 mutant of PHS. Using genetic and biological methods, the candidate gene was identified as Zmccr3, encoding cinnamoyl-CoA reductase 3 (ccr3), which is involved in the phenylalanine pathway of lignin metabolism and affects SG. Based on RNA-seq (RNA sequencing) at two stages of grain development with extreme PHS traits, a weighted gene coexpression network analysis (WGCNA) related to SD and SG formation was constructed, and ten target genes and three pathways during the transition from SD to SG were identified. Simultaneously, the Zmccr3 pathway was established and validated, involving upstream lipid metabolism, redox modification and degradation of cell wall oligosaccharides (as electrophilic compounds), regulation of GA signaling and intracellular ROS homeostasis, and downstream oxidation of cell wall lignin units and synthesis of phenolic compounds that affect endosperm weakening and cell wall loosening, ultimately regulating SG or SD. Therefore, we propose the Zmccr3 hypothesis to elucidate its possible functions. These findings have important theoretical and practical implications for understanding the genetic basis of PHS and SD in maize, increasing genetic resources and improving traits.

Transcriptome and metabolite conjoint analysis reveals the seed dormancy release process of perilla

Seed dormancy is a common physiological phenomenon during storage which has a great impact on timely germination of seeds. An in-depth analysis of the physiological and molecular mechanisms of perilla seed dormancy release is of great significance for cultivating high-vigor perilla varieties. We used gibberellin A3-soaked seeds (GA), natural dormancy-release seeds (CK) and water-soaked seeds (WA) to study the changes in the transcriptome and metabolome of dormancy release. The germination test revealed that the optimum concentration of gibberellin A3 for releasing dormancy from perilla seeds was 200 mg/L. The results revealed that plant hormone signal transduction, starch and sucrose metabolism and citric acid cycle were significantly enriched metabolic pathways closely related to seed dormancy release. Perilla seeds release their dormancy by enhancing the expression of GID1, PIF3, SnRK2, IAA, ARR-A, GH3, MKK4_5, otsB, GN1_2_3, glgC, WAXY, inhibiting the expression of DELLA, PP2C, glga, bglX, and GN4, and regulating the content of gibberellin A4, abscisic acid, auxin, sucrose, maltose, trehalose, and α-D-glucose 1-phosphate. Auxin plays an important role in breaking perilla seed dormancy and promoting seed germination. The energy required for breaking seed dormancy and germination of perilla seeds is mainly provided through sucrose metabolism. Citric acid cycle (TCA cycle) is the main energy supply transformation pathway for seed germination.

MtCIR2 negatively regulates seed germination to salt stress by disrupting metabolisms and signaling of abscisic acid and gibberellins

Emerging evidence indicates that long non-coding RNAs (lncRNAs) play a regulatory role in plant response to environmental stresses. Seed germination is a complex physiological process modulated by many environmental and phytohormonal cues. However, how lncRNAs and phytohormones interactively regulate the response of seed germination to salt stress remain largely unknown. Here, we functionally characterized a salt-responsive lncRNA from legume species Medicago truncatula, referred to as MtCIR2, in response to salt stress during seed germination by heterologously expressing MtCIR2 in Arabidopsis in which none such homologous sequence was detected. Expressing MtCIR2 in Arabidopsis rendered the seed germination more sensitive to salt stress. We further evaluated whether and how abscisic acid (ABA) and gibberellin (GA) were involved in the MtCIR2-mediated seed germination in response to salt stress. We found that expression of MtCIR2 led to an increase in endogenous ABA concentration and a decrease in overall GA concentration due to enhanced expression of ABA catabolic gene CYP707A2 and suppressed expression of the genes of GA20ox1, GA20ox2, and GA20ox5 involved in GA synthesis under salt stress, respectively. The MtCIR2-dependent enhanced endogenous ABA and reduced endogenous GA concentrations in seeds resulted in greater suppression of seed germination in transgenic seeds than in wild-type seeds when exposed to salt stress. These findings highlight a regulatory role of lncRNAs in response to salt stress during seed germination.

Utilizing CRISPR-based genetic modification for precise control of seed dormancy: progress, obstacles, and potential directions

Seed dormancy, a complex trait that is influenced by both nuclear and cytoplasmic factors, poses a significant challenge to agricultural productivity. Conventional dormancy-breaking techniques, including mechanical, physiological, and chemical methods, often yield inconsistent results, impair seed quality, and lack precision. This has necessitated exploration of more targeted and efficient approaches. CRISPR-based gene editing has emerged as a promising tool for the precise regulation of seed dormancy without compromising seed viability or sustainability. Although CRISPR has been successfully applied to modify genes that govern physiological traits in various crops, its use in dormancy regulation remains in the early stages. This review examines recent advancements in CRISPR-based approaches for modulating seed dormancy and discusses key gene targets, modification techniques, and the resulting effects. We also consider the future potential of CRISPR to enhance dormancy control across diverse crop species.

The interplay of singlet oxygen and ABI4 in plant growth regulation

Abscisic acid (ABA) and the AP2/ERF (APETALA 2/ETHYLENE-RESPONSIVE FACTOR)-type transcription factor ABA INSENSITIVE 4 (ABI4) control plant growth and development. We review how singlet oxygen, which is produced in chloroplasts of the fluorescent mutant of Arabidopsis thaliana (arabidopsis), and ABI4 may cooperate in transcriptional and translational reprogramming to cause plants to halt growth or demise. Key elements of singlet oxygen- and ABI4-dependent chloroplast-to-nucleus retrograde signaling involve the chloroplast EXECUTER (EX) 1 and EX2 proteins as well as nuclear WRKY transcription factors. Mutants designed to study singlet oxygen signaling, that lack either ABI4 or the EX1 and EX2 proteins, do not show most of the growth effects of singlet oxygen. We propose a model that positions ABI4 downstream of WRKY transcription factors and EX1 and EX2.

Natural variation in OsMADS1 transcript splicing affects rice grain thickness and quality by influencing monosaccharide loading to the endosperm

Grain size, which encompasses grain length, width, and thickness, is a critical determinant of both grain weight and quality in rice. Despite the extensive regulatory networks known to determine grain length and width, the pathway(s) that regulate grain thickness remain to be clarified. Here, we present the map-based cloning and characterization of qGT3, a major quantitative trait locus for grain thickness in rice that encodes the MADS-domain transcription factor OsMADS1. Our findings demonstrate that OsMADS1 regulates grain thickness by affecting sugar delivery during grain filling, and we show that OsMADS1 modulates expression of the downstream monosaccharide transporter gene MST4. A natural variant leads to alternative splicing and thus to a truncated OsMADS1 protein with attenuated transcriptional repressor activity. The truncated OsMADS1 protein results in increased expression of MST4, leading to enhanced loading of monosaccharides into the developing endosperm and thereby increasing grain thickness and improving grain quality. In addition, our results reveal that NF-YB1 and NF-YC12 interact directly with OsMADS1, acting as cofactors to enhance its transcriptional activity toward MST4. Collectively, these findings reveal a novel molecular mechanism underlying grain thickness regulation that is controlled by the OsMADS1-NF-YB1-YC12 complex and has great potential for synergistic improvement of grain yield and quality in rice.

Physiology and transcriptome of Eucommia ulmoides seeds at different germination stages

E. ulmoides (Eucommia ulmoides) has significant industrial and medicinal value and high market demand. E. ulmoides grows seedlings through sowing. According to previous studies, plant hormones have been shown to regulate seed germination. To understand the relationship between hormones and E. ulmoides seed germination, we focused on examining the changes in various indicators during the germination stage of E. ulmoides seeds. We measured the levels of physiological and hormone indicators in E. ulmoides seeds at different germination stages and found that the levels of abscisic acid (ABA), gibberellin (GA), and indole acetic acid (IAA) significantly varied as the seeds germinated. Furthermore, we confirmed that ABA, GA, and IAA are essential hormones in the germination of E. ulmoides seeds using Gene Ontology and Kyoto Encyclopedia of Genes and Genomics enrichment analyses of the transcriptome. The discovery of hormone-related synthesis pathways in the control group of Eucommia seeds at different germination stages further confirmed this conclusion. This study provides a basis for further research into the regulatory mechanisms of E. ulmoides seeds at different germination stages and the relationship between other seed germination and plant hormones.

The RALF1 peptide-FERONIA complex phosphorylates the endosomal sorting protein FREE1 to attenuate abscisic acid signaling

The receptor-like kinase FERONIA (FER), together with its ligand rapid alkalinization factor 1 (RALF1) peptide, plays a crucial role in regulating stress responses, including its involvement in modulating abscisic acid (ABA) signaling. FER has been shown to activate ABA insensitive 2 in the cytoplasm, leading to the suppression of ABA signaling. However, its regulation of nucleus events in the ABA response remains unclear. FREE1, identified as a plant-specific component of the endosomal sorting complex required for transport in eukaryotes, serves as an important negative regulator in ABA signaling. In this study, we elucidate that upon RALF1 treatment, FER phosphorylates FREE1, promoting the accumulation of FREE1 protein in the nucleus in Arabidopsis (Arabidopsis thaliana). Consequently, FREE1 suppresses ABA sensitivity by inhibiting the expression of ABA-response genes. Mutating the 6 identified phosphorylation sites on FREE1, mediated by FER, to nonphosphorylable residues results in reduced nucleus localization of FREE1 and increased hypersensitivity to ABA. Our data also show that these 6 phosphorylation sites are likely involved in regulating plant survival under salt stress. Collectively, our study not only unveils an additional function of FER in attenuating ABA signaling in the nucleus but also provides a possible insight into the role of the RALF1-FER-FREE1 module in coordinating plant growth and salt stress tolerance.

Myosin-binding protein 13 mediates primary seed dormancy via abscisic acid biosynthesis and signaling in Arabidopsis

Dormancy is an essential characteristic that enables seeds to survive in unfavorable conditions while germinating when conditions are favorable. Myosin-binding proteins (MyoBs) assist in the movement of organelles along actin microfilaments by attaching to both organelles and myosins. In contrast to studies on yeast and metazoans, research on plant MyoBs is still in its early stages and primarily focuses on tip-growing cells. In this study, we found that Arabidopsis MyoB13 is highly expressed in dry mature seeds. The myob13 mutant, created using CRISPR/Cas9, exhibits a preharvest sprouting phenotype, which can be mitigated by after-ripening treatment, indicating that MyoB13 plays a positive role in primary seed dormancy. Furthermore, we show that MyoB13 negatively regulates ABA biosynthesis and signaling pathways. Notably, the expression of MyoB13 orthologs from maize and soybean can completely restore the phenotype of the Arabidopsis myob13 mutant, suggesting that the function of MyoB13 in ABA-induced seed dormancy is evolutionarily conserved. Therefore, the functional characterization of MyoB13 offers an additional genetic resource to help prevent vivipary in crop species.

PlZAT10 binds to the ABA catabolism gene PlCYP707A2 promoter to mediate seed dormancy release in Paeonia lactiflora

KEY MESSAGE

PlZAT10-PlCYP707A2 module promotes Paeonia lactiflora seeds germination. The herbaceous peony (Paeonia lactiflora) seeds exhibit double dormancy in the epicotyl and hypocotyl, which significantly inhibits the process of cultivation and breeding of new varieties. Nevertheless, the molecular mechanism underlying seed dormancy release in P. lactiflora remains to be fully identified. In this current study, we analyzed differentially expressed genes based on transcriptome data and selected the abscisic acid catabolic gene PlCYP707A2 for further investigation. The conserved domain of the protein indicated that PlCYP707A2 possessed a cytochrome P450 monooxygenase domain. Subcellular localization indicated that PlCYP707A2 was localized on the cytoplasm and cell membrane. Overexpression of PlCYP707A2 in P. lactiflora seeds decreased ABA contents and promoted seeds germination. The silencing of PlCYP707A2 resulted in seed dormancy and an alteration in the content of ABA. Moreover, yeast one-hybrid, electrophoretic mobility shift and dual-luciferase reporter assay revealed that PlZAT10 bound to the promoter of PlCYP707A2. In conclusion, the results demonstrated the mechanism of the PlZAT10-PlCYP707A2 module in regulating the dormancy release of P. lactiflora seeds, enriching relevant theories on seed dormancy and having significant implications for the herbaceous peony industry developing.

From Regulation to Application: The Role of Abscisic Acid in Seed and Fruit Development and Agronomic Production Strategies

Abscisic acid (ABA) is a crucial plant hormone that plays a decisive role in regulating seed and fruit development and is becoming increasingly important in agricultural applications. This article delves into ABA's regulatory functions in plant growth, particularly during the stages of seed and fruit development. In the seed phase, elevated ABA levels help maintain seed dormancy, aiding seed survival under unfavorable conditions. During fruit development, ABA regulates pigment synthesis and sugar accumulation, influencing the nutritional value and market quality of the fruit. This article highlights three main strategies for applying ABA in agricultural production: the use of ABA analogs, the development of ABA signal modulators, and breeding techniques based on ABA signaling. ABA analogs can mimic the natural functions of ABA, while ABA signal modulators, including enhancers and inhibitors, are used to finely tune plant responses to ABA, optimizing crop performance under specific growth conditions. Furthermore, breeding strategies based on ABA signaling aim to select crop varieties that effectively utilize ABA pathways through genetic engineering and other technologies. ABA is not only a key regulator of plant growth and development but also holds great potential for modern agricultural practices.

QTL mapping and transcriptome analysis of seed germination under PEG-induced water stress in Lactuca spp

The impact of limited water availability on lettuce growth has been well documented. However, the mechanisms by which lettuce controls seed germination under water stress remain unknown. Germination percentage was evaluated in the cv. Salinas (Lactuca sativa) (L. sativa) × US96UC23 (Lactuca serriola) (L. serriola) recombinant inbred line (RIL) population and USDA germplasm collection using 10% polyethylene glycol (PEG). About 50% of both populations displayed less than 90% germination. The average broad-sense heritability (H2) for germination percentage was 0.81 across both populations. Two quantitative trait loci (QTL) for germination percentage were identified on chromosomes 4 and 8 in the RIL population. The RNA-Seq and network analyses of wild lettuce, US96UC23, were performed using the control (distilled water, dH2O) and treatment (10% PEG) datasets. The number of differentially expressed genes (DEGs) was 4,095. The top 20 gene ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were assessed by enrichment analysis. The consensus network analysis captured 44 modules. Gene networks were constructed for the top 20 hub genes in 10 significant modules from each dataset. This study comprehensively explains QTL, GO terms, KEGG pathways, and gene networks associated with lettuce seed germination under osmotic stress.

Rice seed storability: From molecular mechanisms to agricultural practices

The storability of rice seeds is crucial for ensuring flexible planting options, agricultural seed security, and global food safety. With the intensification of global climate change and the constant fluctuations in agricultural production conditions, enhancing the storability of rice seeds has become particularly important. Seed storability is a complex quantitative trait regulated by both genetic and environmental factors. This article reviews the main regulatory mechanisms of rice seed storability, including the accumulation of seed storage proteins, late embryogenesis abundant (LEA) proteins, heat shock proteins, sugar signaling, hormonal regulation by gibberellins and abscisic acid, and the role of the ubiquitination pathway. Additionally, this article explores the improvement of storability using wild rice genes, molecular marker-assisted selection, and gene editing techniques such as CRISPR/Cas9 in rice breeding. By providing a comprehensive scientific foundation and practical guidance, this review aims to promote the development of rice varieties with enhanced storability to meet evolving agricultural demands.

The SINA1-BSD1 Module Regulates Vegetative Growth Involving Gibberellin Biosynthesis in Tomato

In plants, vegetative growth is controlled by synergistic and/or antagonistic effects of many regulatory factors. Here, the authors demonstrate that the ubiquitin ligase seven in absentia1 (SINA1) mammalian BTF2-like transcription factors, Drosophila synapse-associated proteins, and yeast DOS2-like proteins (BSD1) function as a regulatory module to control vegetative growth in tomato via regulation of the production of plant growth hormone gibberellin (GA). SINA1 negatively regulates the protein level of BSD1 through ubiquitin-proteasome-mediated degradation, and the transgenic tomato over-expressing SINA1 (SINA1-OX) resembles the dwarfism phenotype of the BSD1-knockout (BSD1-KO) tomato plant. BSD1 directly activates expression of the BSD1-regulated gene 1 (BRG1) via binding to a novel core BBS (standing for BSD1 binding site) binding motif in the BRG1 promoter. Knockout of BRG1 (BRG1-KO) in tomato also results in a dwarfism phenotype, suggesting BRG1 plays a positive role in vegetative growth as BSD1 does. Significantly, GA contents are attenuated in transgenic SINA1-OX, BSD1-KO, and BRG1-KO plants exhibiting dwarfism phenotype and exogenous application of bioactive GA3 restores their vegetative growth. Moreover, BRG1 is required for the expression of multiple GA biosynthesis genes and BSD1 activates three GA biosynthesis genes promoting GA production. Thus, this study suggests that the SINA1-BSD1 module controls vegetative growth via direct and indirect regulation of GA biosynthesis in tomato.

The phosphatidylethanolamine-binding proteins OsMFT1 and OsMFT2 regulate seed dormancy in rice

Seed dormancy is crucial for optimal plant life-cycle timing. However, domestication has largely diminished seed dormancy in modern cereal cultivars, leading to challenges such as preharvest sprouting (PHS) and subsequent declines in yield and quality. Therefore, it is imperative to unravel the molecular mechanisms governing seed dormancy for the development of PHS-resistant varieties. In this study, we screened a mutant of BASIC HELIX-LOOP-HELIX TRANSCRIPTION FACTOR4 (OsbHLH004) with decreased seed dormancy and revealed that OsbHLH004 directly regulates the expression of 9-CIS-EPOXYCAROTENOID DIOXYGENASE3 (OsNCED3) and GIBBERELLIN 2-OXIDASE6 (OsGA2ox6) in rice (Oryza sativa). Additionally, we determined that two phosphatidylethanolamine-binding proteins, MOTHER OF FT AND TFL1 and 2 (OsMFT1 and OsMFT2; hereafter OsMFT1/2) interact with OsbHLH004 and Ideal Plant Architecture 1 (IPA1) to regulate their binding capacities on OsNCED3 and OsGA2ox6, thereby promoting seed dormancy. Intriguingly, FT-INTERACTING PROTEIN1 (OsFTIP1) interacts with OsMFT1/2 and affects their nucleocytoplasmic translocation into the nucleus, where OsMFT1/2-OsbHLH004 and OsMFT1/2-IPA1 antagonistically modulate the expression of OsNCED3 and OsGA2ox6. Our findings reveal that OsFTIP1-mediated inhibition of nuclear translocation of OsMFT1/2 and the dynamic transcriptional modulation of OsNCED3 and OsGA2ox6 by OsMFT1/2-OsbHLH004 and OsMFT1/2-IPA1 complexes in seed dormancy in rice.

OsRAV1 Regulates Seed Vigor and Salt Tolerance During Germination in Rice

Seed vigor is a complex trait encompassing seed germination, seedling emergence, growth, seed longevity, and stress tolerance, all are crucial for direct seeding in rice. Here, we report that the AP2/ERF transcription factor OsRAV1 (RELATED TO ABI3 AND VP1) positively regulates seed germination, vigor, and salt tolerance. Additionally, OsRAV1 was differently expressed in embryo and endosperm, with the OsRAV1 localized in the nucleus. Transcriptomic analysis revealed that OsRAV1 modulates seed vigor through plant hormone signal transduction and phenylpropanoid biosynthesis during germination. Haplotype analysis showed that rice varieties carrying Hap3 displayed enhanced salt tolerance during seed germination. These findings suggest that OsRAV1 is a potential target in breeding rice varieties with high seed vigor suitable for direct seeding cultivation.

Regulation of cryptochrome-mediated blue light signaling by the ABI4-PIF4 module

ABSCISIC ACID-INSENSITIVE 4 (ABI4) is a pivotal transcription factor which coordinates multiple aspects of plant growth and development as well as plant responses to environmental stresses. ABI4 has been shown to be involved in regulating seedling photomorphogenesis; however, the underlying mechanism remains elusive. Here, we show that the role of ABI4 in regulating photomorphogenesis is generally regulated by sucrose, but ABI4 promotes hypocotyl elongation of Arabidopsis seedlings under blue (B) light under all tested sucrose concentrations. We further show that ABI4 physically interacts with PHYTOCHROME INTERACTING FACTOR 4 (PIF4), a well-characterized growth-promoting transcription factor, and post-translationally promotes PIF4 protein accumulation under B light. Further analyses indicate that ABI4 directly interacts with the B light photoreceptors cryptochromes (CRYs) and inhibits the interactions between CRYs and PIF4, thus relieving CRY-mediated repression of PIF4 protein accumulation. In addition, while ABI4 could directly activate its own expression, CRYs enhance, whereas PIF4 inhibits, ABI4-mediated activation of the ABI4 promoter. Together, our study demonstrates that the ABI4-PIF4 module plays an important role in mediating CRY-induced B light signaling in Arabidopsis.

Molecular mechanism of vivipary as revealed by the genomes of viviparous mangroves and non-viviparous relatives

Vivipary is a prominent feature of mangroves, allowing seeds to complete germination while attached to the mother plant, and equips propagules to endure and flourish in challenging coastal intertidal wetlands. However, vivipary-associated genetic mechanisms remain largely elusive. Genomes of two viviparous mangrove species and a non-viviparous inland relative were sequenced and assembled at the chromosome level. Comparative genomic analyses between viviparous and non-viviparous genomes revealed that DELAY OF GERMINATION 1 (DOG1) family genes (DFGs), the proteins from which are crucial for seed dormancy, germination, and reserve accumulation, are either lost or dysfunctional in the entire lineage of true viviparous mangroves but are present and functional in their inland, non-viviparous relatives. Transcriptome dynamics at key stages of vivipary further highlighted the roles of phytohormonal homeostasis, proteins stored in mature seeds, and proanthocyanidins in vivipary under conditions lacking DFGs. Population genomic analyses elucidate dynamics of syntenic regions surrounding the missing DFGs. Our findings demonstrated the genetic foundation of constitutive vivipary in Rhizophoraceae mangroves.

Melatonin Priming Promotes Crop Seed Germination and Seedling Establishment Under Flooding Stress by Mediating ABA, GA, and ROS Cascades

Both seed germination and subsequent seedling establishment are key checkpoints during the life cycle of seed plants, yet flooding stress markedly inhibits both processes, leading to economic losses from agricultural production. Here, we report that melatonin (MT) seed priming treatment enhances the performance of seeds from several crops, including soybean, wheat, maize, and alfalfa, under flooding stress. Transcriptome analysis revealed that MT priming promotes seed germination and seedling establishment associated with changes in abscisic acid (ABA), gibberellin (GA), and reactive oxygen species (ROS) biosynthesis and signaling pathways. Real-time quantitative RT-PCR (qRT-PCR) analysis confirmed that MT priming increases the expression levels of GA biosynthesis genes, ABA catabolism genes, and ROS biosynthesis genes while decreasing the expression of positive ABA regulatory genes. Further, measurements of ABA and GA concentrations are consistent with these trends. Following MT priming, quantification of ROS metabolism-related enzyme activities and the concentrations of H2O2 and superoxide anions (O2 -) after MT priming were consistent with the results of transcriptome analysis and qRT-PCR. Finally, exogenous application of GA, fluridone (an ABA biosynthesis inhibitor), or H2O2 partially rescued the poor germination of non-primed seeds under flooding stress. Collectively, this study uncovers the application and molecular mechanisms underlying MT priming in modulating crop seed vigor under flooding stress.

Overexpression of RPOTmp Being Targeted to Either Mitochondria or Chloroplasts in Arabidopsis Leads to Overall Transcriptome Changes and Faster Growth

The transcription of Arabidopsis organellar genes is performed by three nuclear-encoded RNA polymerases: RPOTm, RPOTmp, and RPOTp. The RPOTmp protein possesses ambiguous transit peptides, allowing participation in gene expression control in both mitochondria and chloroplasts, although its function in plastids is still under discussion. Here, we show that the overexpression of RPOTmp in Arabidopsis, targeted either to mitochondria or chloroplasts, disturbs the dormant seed state, and it causes the following effects: earlier germination, decreased ABA sensitivity, faster seedling growth, and earlier flowering. The germination of RPOTmp overexpressors is less sensitive to NaCl, while rpotmp knockout is highly vulnerable to salt stress. We found that mitochondrial dysfunction in the rpotmp mutant induces an unknown retrograde response pathway that bypasses AOX and ANAC017. Here, we show that RPOTmp transcribes the accD, clpP, and rpoB genes in plastids and up to 22 genes in mitochondria.

Lipid remodelling and the conversion of lipids into sugars associated with tolerance to cadmium toxicity during white clover seed germination

Cadmium (Cd) is a leading environmental issue worldwide. The current study was conducted to investigate Cd tolerance of 10 commercial white clover (Trifolium repens) cultivars during seed germination and to further explore differences in lipid remodelling, glycometabolism, and the conversion of lipids into sugars contributing to Cd tolerance in the early phase of seedling establishment as well as the accumulation of Cd in seedlings and mature plants. The results show that Cd stress significantly reduced seed germination of 10 cultivars. Compared to Cd-sensitive Sulky, Cd-tolerant Pixie accelerated amylolysis to produce more glucose, fructose, and sucrose by maintaining higher amylase and sucrase activities under Cd stress. Pixie maintained higher contents of various lipids, higher DGDG/MGDG ratio, and lower unsaturation levels of lipids, which could be beneficial to membrane stability and integrity as well as signal transduction in cells after being subjected to Cd stress. In addition, Pixie upregulated expression levels of key genes (TrACX1, TrACX4, TrSDP6, and TrPCK1) involved in the conversion of lipids into sugars for early seedling establishment under Cd stress. These findings indicate that lipid remodelling, enhanced glycometabolism, and accelerated conversion of lipids into sugars are important adaptive strategies for white clover seed germination and subsequent seedling establishment under Cd stress. In addition, Pixie not only accumulated more Cd in seedlings and mature plants than Sulky but also had significantly better growth and phytoremediation efficiency under Cd stress. Pixie could be used as a suitable and critical germplasm for the rehabilitation and re-establishment of Cd-contaminated areas.

PIF4 interacts with ABI4 to serve as a transcriptional activator complex to promote seed dormancy by enhancing ABA biosynthesis and signaling

Transcriptional regulation plays a key role in the control of seed dormancy, and many transcription factors (TFs) have been documented. However, the mechanisms underlying the interactions between different TFs within a transcriptional complex regulating seed dormancy remain largely unknown. Here, we showed that TF PHYTOCHROME-INTERACTING FACTOR4 (PIF4) physically interacted with the abscisic acid (ABA) signaling responsive TF ABSCISIC ACID INSENSITIVE4 (ABI4) to act as a transcriptional complex to promote ABA biosynthesis and signaling, finally deepening primary seed dormancy. Both pif4 and abi4 single mutants exhibited a decreased primary seed dormancy phenotype, with a synergistic effect in the pif4/abi4 double mutant. PIF4 binds to ABI4 to form a heterodimer, and ABI4 stabilizes PIF4 at the protein level, whereas PIF4 does not affect the protein stabilization of ABI4. Subsequently, both TFs independently and synergistically promoted the expression of ABI4 and NCED6, a key gene for ABA anabolism. The genetic evidence is also consistent with the phenotypic, physiological and biochemical analysis results. Altogether, this study revealed a transcriptional regulatory cascade in which the PIF4-ABI4 transcriptional activator complex synergistically enhanced seed dormancy by facilitating ABA biosynthesis and signaling.

A commitment for life: Decades of unraveling the molecular mechanisms behind seed dormancy and germination

Seeds are unique time capsules that can switch between 2 complex and highly interlinked stages: seed dormancy and germination. Dormancy contributes to the survival of plants because it allows to delay germination to optimal conditions. The switch between dormancy and germination occurs in response to developmental and environmental cues. In this review we provide a comprehensive overview of studies that have helped to unravel the molecular mechanisms underlying dormancy and germination over the last decades. Genetic and physiological studies provided a strong foundation for this field of research and revealed the critical role of the plant hormones abscisic acid and gibberellins in the regulation of dormancy and germination, and later natural variation studies together with quantitative genetics identified previously unknown genetic components that control these processes. Omics technologies like transcriptome, proteome, and translatomics analysis allowed us to mechanistically dissect these processes and identify new components in the regulation of seed dormancy and germination.

Genome-Wide Identification of GAST Family Members and Their Potential Roles in Epicotyl Dormancy in Chinese Cork Oak (Quercus variabilis)

Chinese cork oak (Quercus variabilis Blume) is a widespread tree species with high economic and ecological values. Chinese cork oak exhibits epicotyl dormancy, causing emergence heterogeneity and affecting the quality of seedling cultivation. Gibberellic acid-stimulated transcript (GAST) is a plant-specific protein family that plays a crucial regulatory role in plant growth, development, and seed germination. However, their evolution in Chinese cork oak and roles in epicotyl dormancy are still unclear. Here, a genome-wide identification of the GAST gene family was conducted in Chinese cork oak. Ten QvGAST genes were identified, and nine of them were expressed in seed. The physicochemical properties and promoter cis-acting elements of the selected Chinese cork oak GAST family genes indicated that the cis-acting elements in the GAST promoter are involved in plant development, hormone response, and stress response. Germinated seeds were subjected to gibberellins (GAs), abscisic acid (ABA), and fluridone treatments to show their response during epicotyl dormancy release. Significant changes in the expression of certain QvGAST genes were observed under different hormone treatments. QvGAST1, QvGAST2, QvGAST3, and QvGAST6 exhibited upregulation in response to gibberellin. QvGAST2 was markedly upregulated during the release of epicotyl dormancy in response to GA. These findings suggested that QvGAST2 might play an important role in epicotyl dormancy release. This study provides a basis for further analysis of the mechanisms underlying the alleviation of epicotyl dormancy in Chinese cork oak by QvGASTs genes.

The ABI4-RGL2 module serves as a double agent to mediate the antagonistic crosstalk between ABA and GA signals

Abscisic acid (ABA) and gibberellins (GA) antagonistically mediate several biological processes, including seed germination, but the molecular mechanisms underlying ABA/GA antagonism need further investigation, particularly any role mediated by a transcription factors module. Here, we report that the DELLA protein RGL2, a repressor of GA signaling, specifically interacts with ABI4, an ABA signaling enhancer, to act as a transcription factor complex to mediate ABA/GA antagonism. The rgl2, abi3, abi4 and abi5 mutants rescue the non-germination phenotype of the ga1-t. Further, we demonstrate that RGL2 specifically interacts with ABI4 to form a heterodimer. RGL2 and ABI4 stabilize one another, and GA increases the ABI4-RGL2 module turnover, whereas ABA decreases it. At the transcriptional level, ABI4 enhances the RGL2 expression by directly binding to its promoter via the CCAC cis-element, and RGL2 significantly upregulates the transcriptional activation ability of ABI4 toward its target genes, including ABI5 and RGL2. Abscisic acid promotes whereas GA inhibits the ability of ABI4-RGL2 module to activate transcription, and ultimately ABA and GA antagonize each other. Genetic analysis demonstrated that both ABI4 and RGL2 are essential for the activity of this transcription factor module. These results suggest that the ABI4-RGL2 module mediates ABA/GA antagonism by functioning as a double agent.

Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition

Translation of seed stored mRNAs is essential to trigger germination. However, when RNAPII re-engages RNA synthesis during the seed-to-seedling transition has remained in question. Combining csRNA-seq, ATAC-seq and smFISH in Arabidopsis thaliana we demonstrate that active transcription initiation is detectable during the entire germination process. Features of non-coding regulation such as dynamic changes in chromatin accessible regions, antisense transcription, as well as bidirectional non-coding promoters are widespread throughout the Arabidopsis genome. We show that sensitivity to exogenous ABSCISIC ACID (ABA) during germination depends on proximal promoter accessibility at ABA-responsive genes. Moreover, we provide genetic validation of the existence of divergent transcription in plants. Our results reveal that active enhancer elements are transcribed producing non-coding enhancer RNAs (eRNAs) as widely documented in metazoans. In sum, this study defining the extent and role of coding and non-coding transcription during key stages of germination expands our understanding of transcriptional mechanisms underlying plant developmental transitions.

Pectin methylesterase 31 is transcriptionally repressed by ABI5 to negatively regulate ABA-mediated inhibition of seed germination

Pectin methylesterase (PME), a family of enzymes that catalyze the demethylation of pectin, influences seed germination. Phytohormone abscisic acid (ABA) inhibits seed germination. However, little is known about the function of PMEs in response to ABA-mediated seed germination. In this study, we found the role of PME31 in response to ABA-mediated inhibition of seed germination. The expression of PME31 is prominent in the embryo and is repressed by ABA treatment. Phenotype analysis showed that disruption of PME31 increases ABA-mediated inhibition of seed germination, whereas overexpression of PME31 attenuates this effect. Further study found that ABI5, an ABA signaling bZIP transcription factor, is identified as an upstream regulator of PME31. Genetic analysis showed that PME31 functions downstream of ABI5 in ABA-mediated seed germination. Detailed studies showed that ABI5 directly binds to the PME31 promoter and inhibits its expression. In the plants, PME31 expression is reduced by ABI5 in ABA-mediated seed germination. Taken together, PME31 is transcriptionally inhibited by ABI5 and negatively regulates ABA-mediated seed germination inhibition. These findings shed new light on the mechanisms of PMEs in response to ABA-mediated seed germination.

S-nitrosylation of the transcription factor MYB30 facilitates nitric oxide-promoted seed germination in Arabidopsis

The gaseous signaling molecule nitric oxide (NO) plays an important role in breaking seed dormancy. NO induces a decrease in abscisic acid (ABA) content by transcriptionally activating its catabolic enzyme, the ABA 8'-hydroxylase CYP707A2. However, the underlying mechanism of this process remains unclear. Here, we report that the transcription factor MYB30 plays a critical role in NO-induced seed germination in Arabidopsis (Arabidopsis thaliana). MYB30 loss-of-function attenuates NO-mediated seed dormancy breaking. MYB30 triggers a NO-induced decrease in ABA content during germination by directly promoting CYP707A2 expression. NO induces S-nitrosylation at Cys-49 of MYB30 and enhances its transcriptional activity. Conversely, the ABA receptors PYRABACTIN RESISTANCE1 (PYR1)/PYR1-LIKE (PYL)/REGULATORY COMPONENTS OF ABA RECEPTORS (RCAR) interact with MYB30 and repress its transcriptional activity. ABA promotes the interaction between PYL4 and MYB30, whereas S-nitrosylation releases the PYL4-mediated inhibition of MYB30 by interfering with the PYL4-MYB30 interaction. Genetic analysis showed that MYB30 functions downstream of PYLs during seed dormancy and germination in response to NO. Furthermore, MYB30 mutation significantly represses the reduced dormancy phenotype and the enhanced CYP707A2 expression of the pyr1 pyl1 pyl2 pyl4 quadruple mutant. Our findings reveal that S-nitrosylation of MYB30 precisely regulates the balance of seed dormancy and germination, providing insights into the underlying mechanism of NO-promoted seed germination.

Involvement of Abscisic Acid in Transition of Pea (Pisum sativum L.) Seeds from Germination to Post-Germination Stages

The transition from seed to seedling represents a critical developmental step in the life cycle of higher plants, dramatically affecting plant ontogenesis and stress tolerance. The release from dormancy to acquiring germination ability is defined by a balance of phytohormones, with the substantial contribution of abscisic acid (ABA), which inhibits germination. We studied the embryonic axis of Pisum sativum L. before and after radicle protrusion. Our previous work compared RNA sequencing-based transcriptomics in the embryonic axis isolated before and after radicle protrusion. The current study aims to analyze ABA-dependent gene regulation during the transition of the embryonic axis from the germination to post-germination stages. First, we determined the levels of abscisates (ABA, phaseic acid, dihydrophaseic acid, and neo-phaseic acid) using ultra-high-performance liquid chromatography-tandem mass spectrometry. Second, we made a detailed annotation of ABA-associated genes using RNA sequencing-based transcriptome profiling. Finally, we analyzed the DNA methylation patterns in the promoters of the PsABI3, PsABI4, and PsABI5 genes. We showed that changes in the abscisate profile are characterized by the accumulation of ABA catabolites, and the ABA-related gene profile is accompanied by the upregulation of genes controlling seedling development and the downregulation of genes controlling water deprivation. The expression of ABI3, ABI4, and ABI5, which encode crucial transcription factors during late maturation, was downregulated by more than 20-fold, and their promoters exhibited high levels of methylation already at the late germination stage. Thus, although ABA remains important, other regulators seems to be involved in the transition from seed to seedling.

Catalase associated with antagonistic changes of abscisic acid and gibberellin response, biosynthesis and catabolism is involved in eugenol-inhibited seed germination in rice

KEY MESSAGE

The inhibitory effect of eugenol on rice germination is mediated by a two-step modulatory process: Eugenol first regulates the antagonism of GA and ABA, followed by activation of catalase activity. The natural monoterpene eugenol has been reported to inhibit preharvest sprouting in rice. However, the inhibitory mechanism remains obscure. In this study, simultaneous monitoring of GA and ABA responses by the in vivo GA and ABA-responsive dual-luciferase reporter system showed that eugenol strongly inhibited the GA response after 6 h of imbibition, whereas eugenol significantly enhanced the ABA response after 12 h of imbibition. Gene expression analysis revealed that eugenol significantly induced the ABA biosynthetic genes OsNCED2, OsNCED3, and OsNCED5, but notably suppressed the ABA catabolic genes OsABA8ox1 and OsABA8ox2. Conversely, eugenol inhibited the GA biosynthetic genes OsGA3ox2 and OsGA20ox4 but significantly induced the GA catabolic genes OsGA2ox1 and OsGA2ox3 during imbibition. OsABI4, the key signaling regulator of ABA and GA antagonism, was notably induced before 12 h and suppressed after 24 h by eugenol. Moreover, eugenol markedly reduced the accumulation of H2O2 in seeds after 36 h of imbibition. Further analysis showed that eugenol strongly induced catalase activity, protein accumulation, and the expression of three catalase genes. Most importantly, mitigation of eugenol-inhibited seed germination was found in the catc mutant. These findings indicate that catalase associated with antagonistic changes of ABA and GA is involved in the sequential regulation of eugenol-inhibited seed germination in rice.

Advance Research on the Pre-Harvest Sprouting Trait in Vegetable Crop Seeds

Pre-harvest sprouting (PHS), the germination of seeds on the plant prior to harvest, poses significant challenges to agriculture. It not only reduces seed and grain yield, but also impairs the commodity quality of the fruit, ultimately affecting the success of the subsequent crop cycle. A deeper understanding of PHS is essential for guiding future breeding strategies, mitigating its impact on seed production rates and the commercial quality of fruits. PHS is a complex phenomenon influenced by genetic, physiological, and environmental factors. Many of these factors exert their influence on PHS through the intricate regulation of plant hormones responsible for seed germination. While numerous genes related to PHS have been identified in food crops, the study of PHS in vegetable crops is still in its early stages. This review delves into the regulatory elements, functional genes, and recent research developments related to PHS in vegetable crops. Meanwhile, this paper presents a novel understanding of PHS, aiming to serve as a reference for the study of this trait in vegetable crops.

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

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

Comprehensive Functional Analysis of the bZIP Family in Bletilla striata Reveals That BsbZIP13 Could Respond to Multiple Abiotic Stresses

Basic leucine zipper (bZIP) transcription factors (TFs) are one of the largest families involved in plant physiological processes such as biotic and abiotic responses, growth, and development, etc. In this study, 66 members of the bZIP family were identified in Bletilla striata, which were divided into 10 groups based on their phylogenetic relationships with AtbZIPs. A structural analysis of BsbZIPs revealed significant intron-exon differences among BsbZIPs. A total of 63 bZIP genes were distributed across 16 chromosomes in B. striata. The tissue-specific and germination stage expression patterns of BsbZIPs were based on RNA-seq. Stress-responsive expression analysis revealed that partial BsbZIPs were highly expressed under low temperatures, wounding, oxidative stress, and GA treatments. Furthermore, subcellular localization studies indicated that BsbZIP13 was localized in the nucleus. Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays suggested that BsbZIP13 could interact with multiple BsSnRK2s. The results of this study provide insightful data regarding bZIP TF as one of the stress response regulators in B. striata, while providing a theoretical basis for transgenic and functional studies of the bZIP gene family in B. striata.

Enhancement of osmotic stress tolerance in soybean seed germination by bacterial bioactive extracts

Soybean (Glycine max (L.) Merr.) is important to the global food industry; however, its productivity is affected by abiotic stresses such as osmosis, flooding, heat, and cold. Here, we evaluated the bioactive extracts of two biostimulant bacterial strains, Bacillus butanolivorans KJ40 and B. siamensis H30-3, for their ability to convey tolerance to osmotic stress in soybean seeds during germination. Soybean seeds were dip-treated in extracts of KJ40 (KJ40E) or H30-3 (H30-3E) and incubated with either 0% or 20% polyethylene glycol 6000 (PEG), simulating drought-induced osmotic stress. We measured malondialdehyde content as a marker for lipid peroxidation, as well as the activity of antioxidant enzymes, including catalase, glutathione peroxidase, and glutathione reductase, together with changes in sugars content. We also monitored the expression of genes involved in the gibberellic acid (GA)-biosynthesis pathway, and abscisic acid (ABA) signaling. Following osmotic stress in the extract-treated seeds, malondialdehyde content decreased, while antioxidant enzyme activity increased. Similarly, the expression of GA-synthesis genes, including GmGA2ox1 and GmGA3 were upregulated in KJ40E-dipped seeds at 12 or 6 h after treatment, respectively. The ABA signaling genes GmABI4 and GmDREB1 were upregulated in H30-3E- and KJ40E-treated seeds at 0 and 12 h after treatment under osmotic stress; however, GmABI5, GmABI4, and GmDREB1 levels were also elevated in the dip-treated seeds in baseline conditions. The GA/ABA ratio increased only in KJ40E-treated seeds undergoing osmotic stress, while glucose content significantly decreased in H30-3E-treated seeds at 24 h after treatment. Collectively, our findings indicated that dip-treatment of soybean seeds in KJ40E and H30-3E can enhance the seeds' resistance to osmotic stress during germination, and ameliorate cellular damage caused by secondary oxidative stress. This seed treatment can be used agriculturally to promote germination under drought stress and lead to increase crop yield and quality.

Insights from multi-omics integration into seed germination of Taxus chinensis var mairei

The transition from deep dormancy to seed germination is essential for the life cycle of plants, but how this process occurs in the gymnosperm Chinese yew (Taxus chinensis var mairei), the natural source of the anticancer drug paclitaxel, remains unclear. Herein, we analyse the transcriptome, proteome, spatial metabolome, and spatial lipidome of the Chinese yew and present the multi-omics profiles of dormant and germinating seeds. Our results show that abscisic acid and gibberellic acid 12 homoeostasis is closely associated with gene transcription and protein translation, and the balance between these phytohormones thereby determines if seeds remain dormant or germinate. We find that an energy supply of carbohydrates from glycolysis and the TCA cycle feed into the pentose phosphate pathway during seed germination, and energy supplied from lipids are mainly derived from the lipolysis of triacylglycerols. Using mass spectrometry imaging, we demonstrate that the spatial distribution of plant hormones and phospholipids has a remarkable influence on embryo development. We also provide an atlas of the spatial distribution of paclitaxel C in Chinese yew seeds for the first time. The data from this study enable exploration of the germination mechanism of Chinese yew seeds across several omics levels.

The DELLA-ABI4-HY5 module integrates light and gibberellin signals to regulate hypocotyl elongation

Plant growth is coordinately controlled by various environmental and hormonal signals, of which light and gibberellin (GA) signals are two critical factors with opposite effects on hypocotyl elongation. Although interactions between the light and GA signaling pathways have been studied extensively, the detailed regulatory mechanism of their direct crosstalk in hypocotyl elongation remains to be fully clarified. Previously, we reported that ABA INSENSITIVE 4 (ABI4) controls hypocotyl elongation through its regulation of cell-elongation-related genes, but whether it is also involved in GA signaling to promote hypocotyl elongation is unknown. In this study, we show that promotion of hypocotyl elongation by GA is dependent on ABI4 activation. DELLAs interact directly with ABI4 and inhibit its DNA-binding activity. In turn, ABI4 combined with ELONGATED HYPOCOTYL 5 (HY5), a key positive factor in light signaling, feedback regulates the expression of the GA2ox GA catabolism genes and thus modulates GA levels. Taken together, our results suggest that the DELLA-ABI4-HY5 module may serve as a molecular link that integrates GA and light signals to control hypocotyl elongation.

Abscisic Acid Is Involved in the Resistance Response of Arabidopsis thaliana Against Meloidogyne paranaensis

Abscisic acid (ABA) is a classical hormone involved in the plant defense against abiotic stresses, especially drought. However, its role in the defense response against biotic stresses is controversial: it can induce resistance to some pathogens but can also increase the susceptibility to other pathogens. Information regarding the effect of ABA on the relationship between plants and sedentary phytonematodes, such as Meloidogyne paranaensis, is scarce. In this study, we found that ABA changed the susceptibility level of Arabidopsis thaliana against M. paranaensis. The population of M. paranaensis was reduced by 58.3% with the exogenous application of ABA 24 h before the nematode inoculation, which demonstrated that ABA plays an important role in the preinfectional defense of A. thaliana against M. paranaensis. The increase in the nematode population density in the ABA biosynthesis mutant, aba2-1, corroborated the results observed with the exogenous application of ABA. The phytohormone did not show nematicide or nematostatic effects on M. paranaensis juveniles in in vitro tests, indicating that the response is linked to intrinsic plant factors, which was corroborated by the decrease in the number of nematodes in the abi4-1 mutant. This reduction indicates that the gene expression regulation by transcript factors is possibly related to regulatory cascades mediated by ABA in the response of A. thaliana against M. paranaensis.

WEAK SEED DORMANCY 1, an aminotransferase protein, regulates seed dormancy in rice through the GA and ABA pathways

Seed dormancy is a critical trait that enhances plant survival by preventing seed germination at the wrong time or under unsuitable conditions. Lack of seed dormancy in rice can lead to pre-harvest sprouting on mother plants leading to reduced yield and seed quality. Although some genes have been identified, knowledge of regulation of seed dormancy is limited. Here, we characterized a weak seed dormancy mutant named weak seed dormancy 1 (wsd1) that showed a higher seed germination percentage than the wild-type following the harvest ripeness. We cloned the WSD1 encoding an aminotransferase protein using a MutMap approach. WSD1 was stably expressed after imbibition and its protein was localized in the endoplasm reticulum. A widely targeted metabolomics assay and amino acid analysis showed that WSD1 had a role in regulating homeostasis of amino acids. PAC treatment and RNA-seq analysis showed that WSD1 regulates seed dormancy by involvement in the GA biosynthesis pathway. GA1 content and expression of GA biosynthesis-related genes were increased in the wsd1 mutant compared with the wild-type. The wsd1 mutant had reduced sensitivity to ABA. Our overall results indicated that WSD1 regulates seed dormancy by balancing the ABA and GA pathways.

Genome-wide characterization of the PLATZ gene family in watermelon (Citrullus lanatus L.) with putative functions in biotic and abiotic stress response

Plant AT-rich sequence and zinc-binding (PLATZ) proteins are plant-specific transcription factors involved in growth, development, and stress responses. Here, we conducted a genome-wide characterization of the watermelon ClPLATZ family and examined its expression responsiveness to defense hormones and pathogen infection along with putative functions in biotic and abiotic stress responses. The watermelon genome contains 12 putative ClPLATZ genes, encoding proteins with a characteristic PLATZ domain, and their promoters contain various cis-elements related to plant growth, development, phytohormones and stress response. The ClPLATZ genes, except ClPLATZ6, are differentially expressed in response to defense hormones (e.g., salicylic acid and methyl jasmonate) and fungal infections caused by Fusarium oxysporum f. sp. niveum and Stagonosporopsis cucurbitacearum. Most ClPLATZ proteins interact with other proteins (viz., ClDP, ClRPT2a, and ClRPC53). Among ClPLATZ proteins, ClPLATZ8, 9, 10, and 11 are predominately localized in the nucleus. ClPLATZ3 and 8 positively, but ClPLATZ11 negatively regulate resistance against Pseudomonas syringe pv. tomato DC3000 in transgenic Arabidopsis lines. ClPLATZ8 and 11 positively regulate stress tolerance to NaCl and mannitol during seed germination in transgenic Arabidopsis. In conclusion, the characterization of the ClPLATZ family provides insights into the biological functions of ClPLATZ genes in growth, development, and stress response in watermelon. Further, the involvement of certain ClPLATZ genes in biotic and abiotic stress response in transgenic Arabidopsis suggests their potential application in engineering stress-tolerant crops.

A mulberry 9-cis-epoxycarotenoid dioxygenase gene MaNCED1 is involved in plant growth regulation and confers salt and drought tolerance in transgenic tobacco

The phytohormone abscisic acid (ABA) is vital in regulating root elongation, seed germination, and abiotic stress responses in plants. Conversely, the mechanisms of ABA in mulberry root growth, seed germination, and abiotic stress responses are poorly understood. Here, we reported that exogenous ABA and drought treatment inhibited the growth of mulberry seedlings but significantly increased the ratio of root/stem. Inhibition of ABA synthesis by fluridone and sodium tungstate resulted in the decrease of root/stem ratio. We also showed that the expression of MaNCED1 in the root was strongly induced by drought and salt stress. Increasing the expression of MaNCED1 in tobacco using overexpression leads to increased root elongation and reduced seed germination. Compared with the wild type, the accumulation of H2O2 and MDA was reduced, while the POD activity and proline content was increased in the transgenic plants after drought and salt treatment. Further studies revealed increased resistance to drought and salt stress in MaNCED1 overexpressed tobaccos. Meanwhile, the auxin and ethylene signal pathway-related gene expression levels increased in MaNCED1 overexpressed tobaccos. This study demonstrated the roles of mulberry MaNCED1 in regulating plant development and abiotic stress responses. It gave further insights into the coordinated regulation of ABA, auxin, and ethylene in seed growth and germination.

OsMFT1 Inhibits Seed Germination by Modulating Abscisic Acid Signaling and Gibberellin Biosynthesis under Salt Stress in Rice

Seed dormancy and germination are regulated by endogenous gene expression as well as hormonal and environmental conditions, such as salinity, which greatly inhibits seed germination. MOTHER OF FT AND TFL1 (MFT), which encodes a phosphatidylethanolamine-binding protein, is a key regulator of seed germination in Arabidopsis thaliana. There are two orthologous genes of AtMFT in rice (Oryza sativa), namely, OsMFT1 and OsMFT2. However, the functions of these two genes in regulating rice seed germination under salt stress remain unknown. In this study, we found that seeds of loss-of-function osmft1 mutants germinated faster than wild-type (WT) seeds under salt stress, but this was not the case for loss-of-function osmft2 mutants. Overexpression of OsMFT1 (OsMFT1OE) or OsMFT2 increased the sensitivity to salt stress during seed germination. Transcriptome comparisons of osmft1 vs WT in the absence and presence of salt stress yielded several differentially expressed genes, which were associated with salt stress, plant hormone metabolism and signaling pathways, such as B-BOX ZINC FINGER 6, O. sativa bZIP PROTEIN 8 and GIBBERELLIN (GA) 20-oxidase 1. In addition, the sensitivity of OsMFT1OE seeds to GA and osmft1 seeds to abscisic acid (ABA) during seed germination increased under salt stress. Overall, our results indicate that ABA and GA metabolism and their signaling pathways are regulated by OsMFT1, modulating seed germination in rice under salt stress.

Triphosphate Tunnel Metalloenzyme 2 Acts as a Downstream Factor of ABI4 in ABA-Mediated Seed Germination

Seed germination is a complex process that is regulated by various exogenous and endogenous factors, in which abscisic acid (ABA) plays a crucial role. The triphosphate tunnel metalloenzyme (TTM) superfamily exists in all living organisms, but research on its biological role is limited. Here, we reveal that TTM2 functions in ABA-mediated seed germination. Our study indicates that TTM2 expression is enhanced but repressed by ABA during seed germination. Promoted TTM2 expression in 35S::TTM2-FLAG rescues ABA-mediated inhibition of seed germination and early seedling development and ttm2 mutants exhibit lower seed germination rate and reduced cotyledon greening compared with the wild type, revealing that the repression of TTM2 expression is required for ABA-mediated inhibition of seed germination and early seedling development. Further, ABA inhibits TTM2 expression by ABA insensitive 4 (ABI4) binding of TTM2 promoter and the ABA-insensitive phenotype of abi4-1 with higher TTM2 expression can be rescued by mutation of TTM2 in abi4-1 ttm2-1 mutant, indicating that TTM2 acts downstream of ABI4. In addition, TTM1, a homolog of TTM2, is not involved in ABA-mediated regulation of seed germination. In summary, our findings reveal that TTM2 acts as a downstream factor of ABI4 in ABA-mediated seed germination and early seedling growth.

MIW1 participates in ABA signaling through the regulation of MYB30 in Arabidopsis

Seed germination and seedling establishment are critical biological processes, and their underlying molecular mechanisms have practical implications. The ABA signaling during seed germination and early seedling development is negatively regulated by transcription factor MYB30, but its interaction partners and downstream targets are not fully understood. In this study, we identified MIW1 (MYB30-interacting WD40 protein 1), a WD40 protein that could interact with MYB30 and promote its degradation. In the miw1 mutant, the MYB30 protein became more stable. MIW1 enhanced the ABA-mediated inhibition of postgerminative development. The miw1 mutants became hyposensitive to exogenous ABA, and this effect was suppressed by mutations in MYB30. Furthermore, we found that MYB30 negatively regulated the expression of the ABA receptor genes PYR1/PYL/RCARs. The changes in PYLs expression during early seedling development or under ABA treatment became more pronounced in the myb30 mutant. ChIP-qPCR analyses showed MYB30 could directly bind to the promoters of PYL11 and PYL12. Our study reveals that the WD40 protein MIW1 promotes the expression of PYLs by destabilizing MYB30, thus positively regulating the ABA signaling during postgermination in Arabidopsis.

Intra-Specific Variation in Desiccation Tolerance of Citrus sinensis 'bingtangcheng' (L.) Seeds under Different Environmental Conditions in China

Intra-specific variation in seed storage behaviour observed in several species has been related to different maternal environments. However, the particular environmental conditions and molecular processes involved in intra-specific variation of desiccation tolerance remain unclear. We chose Citrus sinensis 'bingtangcheng' for the present study due to its known variability in desiccation tolerance amongst seed lots. Six seed lots of mature fruits were harvested across China and systematically compared for drying sensitivity. Annual sunshine hours and average temperature from December to May showed positive correlations with the level of seed survival of dehydration. Transcriptional analysis indicated significant variation in gene expression between relatively desiccation-tolerant (DT) and -sensitive (DS) seed lots after harvest. The major genes involved in late seed maturation, such as heat shock proteins, showed higher expression in the DT seed lot. Following the imposition of drying, 80% of stress-responsive genes in the DS seed lot changed to the stable levels seen in the DT seed lot prior to and post-desiccation. However, the changes in expression of stress-responsive genes in DS seeds did not improve their tolerance to desiccation. Thus, higher desiccation tolerance of Citrus sinensis 'bingtangcheng' seeds is modulated by the maternal environment (e.g., higher annual sunshine hours and seasonal temperature) during seed development and involves stable expression levels of stress-responsive genes.