Auxin controls seed dormancy through stimulation of abscisic acid signaling by inducing ARF-mediated ABI3 activation in Arabidopsis

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.

Endogenous cAMP elevation in Brassica napus causes changes in phytohormone levels

In higher plants, the regulatory roles of cAMP (cyclic adenosine 3',5'-monophosphate) signaling remain elusive until now. Cellular cAMP levels are generally much lower in higher plants than in animals and transiently elevated for triggering downstream signaling events. Moreover, plant adenylate cyclase (AC) activities are found in different moonlighting multifunctional proteins, which may pose additional complications in distinguishing a specific signaling role for cAMP. Here, we have developed rapeseed (Brassica napus L.) transgenic plants that overexpress an inducible plant-origin AC activity for generating high AC levels much like that in animal cells, which served the genetic model disturbing native cAMP signaling as a whole in plants. We found that overexpression of the soluble AC activity had significant impacts on the contents of indole-3-acetic acid (IAA) and stress phytohormones, i.e. jasmonic acid (JA), abscisic acid (ABA), and salicylic acid (SA) in the transgenic plants. Acute induction of the AC activity caused IAA overaccumulation, and upregulation of TAA1 and CYP83B1 in the IAA biosynthesis pathways, but also simultaneously the hyper-induction of PR4 and KIN2 expression indicating activation of JA and ABA signaling pathways. We observed typical overgrowth phenotypes related to IAA excess in the transgenic plants, including significant increases in plant height, internode length, width of leaf blade, petiole length, root length, and fresh shoot biomass, as well as the precocious seed development, as compared to wild-type plants. In addition, we identified a set of 1465 cAMP-responsive genes (CRGs), which are most significantly enriched in plant hormone signal transduction pathway, and function mainly in relevance to hormonal, abiotic and biotic stress responses, as well as growth and development. Collectively, our results support that cAMP elevation impacts phytohormone homeostasis and signaling, and modulates plant growth and development. We proposed that cAMP signaling may be critical in configuring the coordinated regulation of growth and development in higher plants.

Long days induce adaptive secondary dormancy in the seeds of the Mediterranean plant Aethionema arabicum

Secondary dormancy is an adaptive trait that increases reproductive success by aligning seed germination with permissive conditions for seedling establishment. Aethionema arabicum is an annual plant and member of the Brassicaceae that grows in environments characterized by hot and dry summers. Aethionema arabicum seeds may germinate in early spring when seedling establishment is permissible. We demonstrate that long-day light regimes induce secondary dormancy in the seeds of Aethionema arabicum (CYP accession), repressing germination in summer when seedling establishment is riskier. Characterization of mutants screened for defective secondary dormancy demonstrated that RGL2 mediates repression of genes involved in gibberellin (GA) signaling. Exposure to high temperature alleviates secondary dormancy, restoring germination potential. These data are consistent with the hypothesis that long-day-induced secondary dormancy and its alleviation by high temperatures may be part of an adaptive response limiting germination to conditions permissive for seedling establishment in spring and autumn.

Regulation of seed germination: ROS, epigenetic, and hormonal aspects

BACKGROUND

The whole life of a plant is regulated by complex environmental or hormonal signaling networks that control genomic stability, environmental signal transduction, and gene expression affecting plant development and viability. Seed germination, responsible for the transformation from seed to seedling, is a key initiation step in plant growth and is controlled by unique physiological and biochemical processes. It is continuously modulated by various factors including epigenetic modifications, hormone transport, ROS signaling, and interaction among them. ROS showed versatile crucial functions in seed germination including various physiological oxidations to nucleic acid, protein, lipid, or chromatin in the cytoplasm, cell wall, and nucleus.

AIM

of review: This review intends to provide novel insights into underlying mechanisms of seed germination especially associated with the ROS, and considers how these versatile regulatory mechanisms can be developed as useful tools for crop improvement.

KEY SCIENTIFIC CONCEPTS OF REVIEW

We have summarized the generation and elimination of ROS during seed germination, with a specific focus on uncovering and understanding the mechanisms of seed germination at the level of phytohormones, ROS, and epigenetic switches, as well as the close connections between them. The findings exhibit that ROS plays multiple roles in regulating the ethylene, ABA, and GA homeostasis as well as the Ca2+ signaling, NO signaling, and MAPK cascade in seed germination via either the signal trigger or the oxidative modifier agent. Further, ROS shows the potential in the nuclear genome remodeling and some epigenetic modifiers function, although the detailed mechanisms are unclear in seed germination. We propose that ROS functions as a hub in the complex network regulating seed germination.

Construction of a Membrane Yeast Two-Hybrid Library and Screening of MsPYR1-Like Interacting Proteins in Malus sieversii

To investigate the biological effects of the ABA receptor pyrabactin resistance 1-like (PYR1-like) in Malus sieversii seeds, the proteins interacting with MsPYR1-like were screened by the membrane yeast two-hybrid library based on the split-ubiquitin system, and to construct the bait vector pBT3-SUC-PYR1 for Malus sieversii cDNA library, which had no self-activating effect on the yeast cells of the pPR3-N membrane yeast two-hybrid library. The library titer assay showed that it could meet the requirements for membrane yeast two-hybrid library screening. After sequencing, GenBank database blast, and yeast rotary validation, 28 candidate proteins interacting with MsPYR1-like were obtained, including ribosomal proteins, late embryogenesis abundant proteins, F-actin-capping proteins, phytochrome-interacting proteins, low-temperature-inducible 65 kDa protein-like, senescence-associated, PP2C and SnRK2 family members, and unknown proteins. Gene ontology analysis of the interaction proteins was related to plant hormone response and negative regulation of seed germination, overexpression of MsPYR1-like in Arabidopsis negatively regulates seed germination, and the study of the biological roles of MsPYR1-like interacting proteins lays the foundation for revealing the lifting of seed dormancy in Malus sieversii.

The conversion of monolignans to sesquilignans and dilignans is closely correlated to the regulation of Arctium lappa seed germination

MAIN CONCLUSION

The secondary metabolic conversion of monolignans to sesquilignans/dilignans was closely related to seed germination and seedling establishment in Arctium lappa. Arctium lappa plants are used as a kind of traditional Chinese medicines for nearly 1500 years, and so far, only a few studies have put focus on the key secondary metabolic changes during seed germination and seedling establishment. In the current study, a combined approach was used to investigate the correlation among secondary metabolites, plant hormone signaling, and transcriptional profiles at the early critical stages of A. lappa seed germination and seedling establishment. Of 50 metabolites in methonolic extracts of A. lappa samples, 35 metabolites were identified with LC-MS/MS and 15 metabolites were identified with GC-MS. Their qualitative properties were examined according to the predicted chemical structures. The quantitative analysis was performed for deciphering their metabolic profiles, discovering that the secondary metabolic conversion from monolignans to sesquilignans/dilignans was closely correlated to the initiation of A. lappa seed germination and seedling establishment. Furthermore, the critical transcriptional changes in primary metabolisms, translational regulation at different cellular compartments, and multiple plant hormone signaling pathways were revealed. In addition, the combined approach provides unprecedented insights into key regulatory mechanisms in both gene transcription and secondary metabolites besides many known primary metabolites during seed germination of an important traditional Chinese medicinal plant species. The results not only provide new insights to understand the regulation of key medicinal components of 'ARCTII FRUCTUS', arctiin and arctigenin at the stages of seed germination and seedling establishment, but also potentially spur the development of seed-based cultivation in A. lappa plants.

Factors Influencing Seed Dormancy and Germination and Advances in Seed Priming Technology

Seed dormancy and germination play pivotal roles in the agronomic traits of plants, and the degree of dormancy intuitively affects the yield and quality of crops in agricultural production. Seed priming is a pre-sowing seed treatment that enhances and accelerates germination, leading to improved seedling establishment. Seed priming technologies, which are designed to partially activate germination, while preventing full seed germination, have exerted a profound impact on agricultural production. Conventional seed priming relies on external priming agents, which often yield unstable results. What works for one variety might not be effective for another. Therefore, it is necessary to explore the internal factors within the metabolic pathways that influence seed physiology and germination. This review unveils the underlying mechanisms of seed metabolism and germination, the factors affecting seed dormancy and germination, as well as the current seed priming technologies that can result in stable and better germination.

Advances in the Modulation of Potato Tuber Dormancy and Sprouting

The post-harvest phase of potato tuber dormancy and sprouting are essential in determining the economic value. The intricate transition from dormancy to active growth is influenced by multiple factors, including environmental factors, carbohydrate metabolism, and hormonal regulation. Well-established environmental factors such as temperature, humidity, and light play pivotal roles in these processes. However, recent research has expanded our understanding to encompass other novel influences such as magnetic fields, cold plasma treatment, and UV-C irradiation. Hormones like abscisic acid (ABA), gibberellic acid (GA), cytokinins (CK), auxin, and ethylene (ETH) act as crucial messengers, while brassinosteroids (BRs) have emerged as key modulators of potato tuber sprouting. In addition, jasmonates (JAs), strigolactones (SLs), and salicylic acid (SA) also regulate potato dormancy and sprouting. This review article delves into the intricate study of potato dormancy and sprouting, emphasizing the impact of environmental conditions, carbohydrate metabolism, and hormonal regulation. It explores how various environmental factors affect dormancy and sprouting processes. Additionally, it highlights the role of carbohydrates in potato tuber sprouting and the intricate hormonal interplay, particularly the role of BRs. This review underscores the complexity of these interactions and their importance in optimizing potato dormancy and sprouting for agricultural practices.

Physiology and transcriptome of Sapindus mukorossi seeds at different germination stages

Sapindus mukorossi has a wide distribution range, high application value, and broad developmental potential. Previous studies have mostly focused on the medicinal and economic value of soapberry; however, few studies have been conducted on its seed germination. This study measured the physiological indicators and hormone content of soapberry seeds at different germination stages and preliminarily determined that abscisic acid (ABA) and indole-3-acetic acid (IAA) are the key hormones that affect the germination of soapberry seeds. Both Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG enrichment) analyses detected hormone transduction pathways, further confirming the key role of plant hormones in the germination process of soapberry seeds. Through transcriptome analysis, we speculated that CYP707A and IPA are key genes in the ABA and IAA synthesis pathways, respectively. This study revealed the close relationship between plant hormones and soapberry seed germination and provided new ideas for further exploration of the germination mechanism of soapberry seeds.

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.

Unraveling the role of PlARF2 in regulating deed formancy in Paeonia lactiflora

MAIN CONCLUSION

PlARF2 can positively regulate the seed dormancy in Paeonia lactiflora Pall. and bind the RY cis-element. Auxin, a significant phytohormone influencing seed dormancy, has been demonstrated to be regulated by auxin response factors (ARFs), key transcriptional modulators in the auxin signaling pathway. However, the role of this class of transcription factors (TFs) in perennials with complex seed dormancy mechanisms remains largely unexplored. Here, we cloned and characterized an ARF gene from Paeonia lactiflora, named PlARF2, which exhibited differential expression levels in the seeds during the process of seed dormancy release. The deduced amino acid sequence of PlARF2 had high homology with those of other plants and contained typical conserved Auxin_resp domain of the ARF family. Phylogenetic analysis revealed that PlARF2 was closely related to VvARF3 in Vitis vinifera. The subcellular localization and transcriptional activation assay showed that PlARF2 is a nuclear protein possessing transcriptional activation activity. The expression levels of dormancy-related genes in transgenic callus indicated that PlARF2 was positively correlated with the contents of PlABI3 and PlDOG1. The germination assay showed that PlARF2 promoted seed dormancy. Moreover, TF Centered Yeast one-hybrid assay (TF-Centered Y1H), electrophoretic mobility shift assay (EMSA) and dual-luciferase reporter assay analysis (Dual-Luciferase) provided evidence that PlARF2 can bind to the 'CATGCATG' motif. Collectively, our findings suggest that PlARF2, as TF, could be involved in the regulation of seed dormancy and may act as a repressor of germination.

ERECTA Modulates Seed Germination and Fruit Development via Auxin Signaling in Tomato

Tomato (Solanum lycopersicum) breeding for improved fruit quality emphasizes selecting for desirable taste and characteristics, as well as enhancing disease resistance and yield. Seed germination is the initial step in the plant life cycle and directly affects crop productivity and yield. ERECTA (ER) is a receptor-like kinase (RLK) family protein known for its involvement in diverse developmental processes. We characterized a Micro-Tom EMS mutant designated as a knock-out mutant of sler. Our research reveals that SlER plays a central role in controlling critical traits such as inflorescence development, seed number, and seed germination. The elevation in auxin levels and alterations in the expression of ABSCISIC ACID INSENSITIVE 3 (ABI3) and ABI5 in sler seeds compared to the WT indicate that SlER modulates seed germination via auxin and abscisic acid (ABA) signaling. Additionally, we detected an increase in auxin content in the sler ovary and changes in the expression of auxin synthesis genes YUCCA flavin monooxygenases 1 (YUC1), YUC4, YUC5, and YUC6 as well as auxin response genes AUXIN RESPONSE FACTOR 5 (ARF5) and ARF7, suggesting that SlER regulates fruit development via auxin signaling.

Allantoate Amidohydrolase OsAAH is Essential for Preharvest Sprouting Resistance in Rice

Preharvest sprouting (PHS) is an undesirable trait that decreases yield and quality in rice production. Understanding the genes and regulatory mechanisms underlying PHS is of great significance for breeding PHS-resistant rice. In this study, we identified a mutant, preharvest sprouting 39 (phs39), that exhibited an obvious PHS phenotype in the field. MutMap+ analysis and transgenic experiments demonstrated that OsAAH, which encodes allantoate amidohydrolase, is the causal gene of phs39 and is essential for PHS resistance. OsAAH was highly expressed in roots and leaves at the heading stage and gradually increased and then weakly declined in the seed developmental stage. OsAAH protein was localized to the endoplasmic reticulum, with a function of hydrolyzing allantoate in vitro. Disruption of OsAAH increased the levels of ureides (allantoate and allantoin) and activated the tricarboxylic acid (TCA) cycle, and thus increased energy levels in developing seeds. Additionally, the disruption of OsAAH significantly increased asparagine, arginine, and lysine levels, decreased tryptophan levels, and decreased levels of indole-3-acetic acid (IAA) and abscisic acid (ABA). Our findings revealed that the OsAAH of ureide catabolism is involved in the regulation of rice PHS via energy and hormone metabolisms, which will help to facilitate the breeding of rice PHS-resistant varieties.

Molecular mechanisms underlying the signal perception and transduction during seed germination

QuerySeed germination is a vital step in the life cycle of a plant, playing a significant role in seedling establishment and crop yield potential. It is also an important factor in the conservation of plant germplasm resources. This complex process is influenced by a myriad of factors, including environmental conditions, the genetic makeup of the seed, and endogenous hormones. The perception of these environmental signals triggers a cascade of intricate signal transduction events that determine whether a seed germinates or remains dormant. Despite considerable progress in uncovering the molecular mechanisms governing these processes, many questions remain unanswered. In this review, we summarize the current progress in the molecular mechanisms underlying the perception of environmental signals and consequent signal transduction during seed germination, and discuss questions that need to be addressed to better understand the process of seed germination and develop novel strategies for germplasm improvement.

Analysis of the global transcriptome and miRNAome associated with seed dormancy during seed maturation in rice (Oryza sativa L. cv. Nipponbare)

BACKGROUND

Seed dormancy is a biological mechanism that prevents germination until favorable conditions for the subsequent generation of plants are encountered. Therefore, this mechanism must be effectively established during seed maturation. Studies investigating the transcriptome and miRNAome of rice embryos and endosperms at various maturation stages to evaluate seed dormancy are limited. This study aimed to compare the transcriptome and miRNAome of rice seeds during seed maturation.

RESULTS

Oryza sativa L. cv. Nipponbare seeds were sampled for embryos and endosperms at three maturation stages: 30, 45, and 60 days after heading (DAH). The pre-harvest sprouting (PHS) assay was conducted to assess the level of dormancy in the seeds at each maturation stage. At 60 DAH, the PHS rate was significantly increased compared to those at 30 and 45 DAH, indicating that the dormancy is broken during the later maturation stage (45 DAH to 60 DAH). However, the largest number of differentially expressed genes (DEGs) and differentially expressed miRNAs (DEmiRs) were identified between 30 and 60 DAH in the embryo and endosperm, implying that the gradual changes in genes and miRNAs from 30 to 60 DAH may play a significant role in breaking seed dormancy. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses confirmed that DEGs related to plant hormones were most abundant in the embryo during 45 DAH to 60 DAH and 30 DAH to 60 DAH transitions. Alternatively, most of the DEGs in the endosperm were related to energy and abiotic stress. MapMan analysis and quantitative real-time polymerase chain reaction identified four newly profiled auxin-related genes (OsSAUR6/12/23/25) and one ethylene-related gene (OsERF087), which may be involved in seed dormancy during maturation. Additionally, miRNA target prediction (psRNATarget) and degradome dataset (TarDB) indicated a potential association between osa-miR531b and ethylene biosynthesis gene (OsACO4), along with osa-miR390-5p and the abscisic acid (ABA) exporter-related gene (OsMATE19) as factors involved in seed dormancy.

CONCLUSIONS

Analysis of the transcriptome and miRNAome of rice embryos and endosperms during seed maturation provided new insights into seed dormancy, particularly its relationship with plant hormones such as ABA, auxin, and ethylene.

Dynamic interactions between SPX proteins, the ubiquitination machinery, and signalling molecules for stress adaptation at a whole-plant level

The plant macronutrient phosphorus is a scarce resource and plant-available phosphate is limiting in most soil types. Generally, a gene regulatory module called the phosphate starvation response (PSR) enables efficient phosphate acquisition by roots and translocation to other organs. Plants growing on moderate to nutrient-rich soils need to co-ordinate availability of different nutrients and repress the highly efficient PSR to adjust phosphate acquisition to the availability of other macro- and micronutrients, and in particular nitrogen. PSR repression is mediated by a small family of single SYG1/Pho81/XPR1 (SPX) domain proteins. The SPX domain binds higher order inositol pyrophosphates that signal cellular phosphorus status and modulate SPX protein interaction with PHOSPHATE STARVATION RESPONSE1 (PHR1), the central transcriptional regulator of PSR. Sequestration by SPX repressors restricts PHR1 access to PSR gene promoters. Here we focus on SPX4 that primarily acts in shoots and sequesters many transcription factors other than PHR1 in the cytosol to control processes beyond the classical PSR, such as nitrate, auxin, and jasmonic acid signalling. Unlike SPX1 and SPX2, SPX4 is subject to proteasomal degradation not only by singular E3 ligases, but also by SCF-CRL complexes. Emerging models for these different layers of control and their consequences for plant acclimation to the environment will be discussed.

Genome-wide association mapping for pre-harvest sprouting in European winter wheat detects novel resistance QTL, pleiotropic effects, and structural variation in multiple genomes

Pre-harvest sprouting (PHS), germination of seeds before harvest, is a major problem in global wheat (Triticum aestivum L.) production, and leads to reduced bread-making quality in affected grain. Breeding for PHS resistance can prevent losses under adverse conditions. Selecting resistant lines in years lacking pre-harvest rain, requires challenging of plants in the field or in the laboratory or using genetic markers. Despite the availability of a wheat reference and pan-genome, linking markers, genes, allelic, and structural variation, a complete understanding of the mechanisms underlying various sources of PHS resistance is still lacking. Therefore, we challenged a population of European wheat varieties and breeding lines with PHS conditions and phenotyped them for PHS traits, grain quality, phenological and agronomic traits to conduct genome-wide association mapping. Furthermore, we compared these marker-trait associations to previously reported PHS loci and evaluated their usefulness for breeding. We found markers associated with PHS on all chromosomes, with strong evidence for novel quantitative trait locus/loci (QTL) on chromosome 1A and 5B. The QTL on chromosome 1A lacks pleiotropic effect, for the QTL on 5B we detected pleiotropic effects on phenology and grain quality. Multiple peaks on chromosome 4A co-located with the major resistance locus Phs-A1, for which two causal genes, TaPM19 and TaMKK3, have been proposed. Mapping markers and genes to the pan-genome and chromosomal alignments provide evidence for structural variation around this major PHS-resistance locus. Although PHS is controlled by many loci distributed across the wheat genome, Phs-A1 on chromosome 4A seems to be the most effective and widely deployed source of resistance, in European wheat varieties.

Development of PEG-mediated genetic transformation and gene editing system of Bryum argenteum as an abiotic stress tolerance model plant

KEY MESSAGE

To establish a sterile culture system and protoplast regeneration system for Bryum argenteum, and to establish and apply CRISPR/Cas9 system in Bryum argenteum. Bryum argenteum is a fascinating, cosmopolitan, and versatile moss species that thrives in various disturbed environments. Because of its comprehensive tolerance to the desiccation, high UV and extreme temperatures, it is emerging as a model moss for studying the molecular mechanisms underlying plant responses to abiotic stresses. However, the lack of basic tools such as gene transformation and targeted genome modification has hindered the understanding of the molecular mechanisms underlying the survival of B. argenteum in different environments. Here, we reported the protonema of B. argenteum can survive up to 95.4% water loss. In addition, the genome size of B. argenteum is approximately 313 Mb by kmer analysis, which is smaller than the previously reported 700 Mb. We also developed a simple method for protonema induction and an efficient protoplast isolation and regeneration protocol for B. argenteum. Furthermore, we established a PEG-mediated protoplast transient transfection and stable transformation system for B. argenteum. Two homologues of ABI3(ABA-INSENSITIVE 3) gene were successfully cloned from B. argenteum. To further investigate the function of the ABI3 gene in B. argenteum, we used the CRISPR/Cas9 genetic editing system to target the BaABI3A and BaABI3B gene in B. argenteum protoplasts. This resulted in mutagenesis at the target in about 2-5% of the regenerated plants. The isolated abi3a and abi3b mutants exhibited increased sensitivity to desiccation, suggesting that BaABI3A and BaABI3B play redundant roles in desiccation stress. Overall, our results provide a rapid and simple approach for molecular genetics in B. argenteum. This study contributes to a better understanding of the molecular mechanisms of plant adaptation to extreme environmental.

Unveiling Molecular Signatures in Light-Induced Seed Germination: Insights from PIN3, PIN7, and AUX1 in Arabidopsis thaliana

Light provides seeds with information that is essential for the adjustment of their germination to the conditions that are most favorable for the successful establishment of the future seedling. The promotion of germination depends mainly on environmental factors, like temperature and light, as well as internal factors associated with the hormonal balance between gibberellins (GA) and abscisic acid (ABA), although other hormones such as auxins may act secondarily. While transcriptomic studies of light-germinating Arabidopsis thaliana seeds suggest that auxins and auxin transporters are necessary, there are still no functional studies connecting the activity of the auxin transporters in light-induced seed germination. In this study, we investigated the roles of two auxin efflux carrier (PIN3 and PIN7) proteins and one auxin influx (AUX1) carrier protein during Arabidopsis thaliana seed germination. By using next-generation sequencing (RNAseq), gene expression analyses, hormonal sensitivity assays, and the quantification of indole-3-acetic acid (IAA) levels, we assessed the functional roles of PIN3, PIN7, and AUX1 during light-induced seed germination. We showed that auxin levels are increased 24 h after a red-pulse (Rp). Additionally, we evaluated the germination responses of pin3, pin7, and aux1 mutant seeds and showed that PIN3, PIN7, and AUX1 auxin carriers are important players in the regulation of seed germination. By using gene expression analysis in water, fluridone (F), and ABA+F treated seeds, we confirmed that Rp-induced seed germination is associated with auxin transport, and ABA controls the function of PIN3, PIN7, and AUX1 during this process. Overall, our results highlight the relevant and positive role of auxin transporters in germinating the seeds of Arabidopsis thaliana.

Identification of ARF genes in Cucurbita pepo L and analysis of expression patterns, and functional analysis of CpARF22 under drought, salt stress

BACKGROUND

Auxin transcription factor (ARF) is an important transcription factor that transmits auxin signals and is involved in plant growth and development as well as stress response. However, genome-wide identification and responses to abiotic and pathogen stresses of the ARF gene family in Cucurbita pepo L, especially pathogen stresses, have not been reported.

RESULTS

Finally, 33 ARF genes (CpARF01 to CpARF33) were identified in C.pepo from the Cucurbitaceae genome database using bioinformatics methods. The putative protein contains 438 to 1071 amino acids, the isoelectric point is 4.99 to 8.54, and the molecular weight is 47759.36 to 117813.27 Da, the instability index ranged from 40.74 to 68.94, and the liposoluble index ranged from 62.56 to 76.18. The 33 genes were mainly localized in the nucleus and cytoplasm, and distributed on 16 chromosomes unevenly. Phylogenetic analysis showed that 33 CpARF proteins were divided into 6 groups. According to the amino acid sequence of CpARF proteins, 10 motifs were identified, and 1,3,6,8,10 motifs were highly conserved in most of the CpARF proteins. At the same time, it was found that genes in the same subfamily have similar gene structures. Cis-elements and protein interaction networks predicted that CpARF may be involved in abiotic factors related to the stress response. QRT-PCR analysis showed that most of the CpARF genes were upregulated under NaCl, PEG, and pathogen treatment compared to the control. Subcellular localization showed that CpARF22 was localized in the nucleus. The transgenic Arabidopsis thaliana lines with the CpARF22 gene enhanced their tolerance to salt and drought stress.

CONCLUSION

In this study, we systematically analyzed the CpARF gene family and its expression patterns under drought, salt, and pathogen stress, which improved our understanding of the ARF protein of zucchini, and laid a solid foundation for functional analysis of the CpARF gene.

Transcriptome analysis reveals the molecular mechanisms of rubber biosynthesis and laticifer differentiation during rubber seed germination

The molecular mechanisms underlying the initiation of natural rubber synthesis and laticifer differentiation have not been fully elucidated. In this study, we conducted a time-series transcriptome analysis of five rubber tree tissues at four stages of seed germination. A total of 161,199 DEGs were identified between the two groups, including most 16,673 DEGs (A3 vs B3 and A3 vs C3) and lest 1,210 DEGs (C2 vs D2). We found that the maturation of the seed is accompanied by the formation of laticifer cells in cotyledon. Meanwhile, the analysis of hormones related genes expression may provide effective clues for us to promote the differentiation of laticifer cells in seeds by hormones in the future. In this study, hormone-related gene enrichment analyses revealed that IAA, GA, and CTK were activated in laticifer containing tissues. Similarly, GO and GEGG analysis showed that hormone pathways, especially the auxin pathway, are enriched. Gene expression clustering was analyzed using the short time-series expression miner (STEM), and the analysis revealed four distinct trends in the gene expression profiles. Moreover, we enriched transcription factor (TF) enrichment in cotyledon and embryonic axis tissues, and the MYB type exhibited the most significant difference. Furthermore, our findings revealed that genes related to rubber synthesis exhibited tissue-specific expression patterns during seed germination. Notably, key genes associated with rubber biosynthesis, specifically small rubber particle protein (SRPP) and cis-prenyltransferase (CPT), exhibited significant changes in expression in cotyledon and embryonic axis tissues, suggesting synchronous rubber synthesis with seed germination. Our staining results reveled that laticifer cells were exits in the cotyledon before seed imbibition stage. In conclusion, these results lay the foundation for exploring the molecular mechanisms underlying laticifer differentiation and rubber synthesis during seed germination, deepening our understanding of the initiation stages of rubber biosynthesis and laticifer differentiation.

Regulatory function of the endogenous hormone in the germination process of quinoa seeds

The economic and health significance of quinoa is steadily growing on a global scale. Nevertheless, the primary obstacle to achieving high yields in quinoa cultivation is pre-harvest sprouting (PHS), which is intricately linked to seed dormancy. However, there exists a dearth of research concerning the regulatory mechanisms governing PHS. The regulation of seed germination by various plant hormones has been extensively studied. Consequently, understanding the mechanisms underlying the role of endogenous hormones in the germination process of quinoa seeds and developing strategies to mitigate PHS in quinoa cultivation are of significant research importance. This study employed the HPLC-ESI-MS/MS internal standard and ELISA method to quantify 8 endogenous hormones. The investigation of gene expression changes before and after germination was conducted using RNA-seq analysis, leading to the discovery of 280 differentially expressed genes associated with the regulatory pathway of endogenous hormones. Additionally, a correlation analysis of 99 genes with significant differences identified 14 potential genes that may act as crucial "transportation hubs" in hormonal interactions. Through the performance of an analysis on the modifications in hormone composition and the expression of associated regulatory genes, we posit a prediction that implies the presence of a negative feedback regulatory mechanism of endogenous hormones during the germination of quinoa seeds. This mechanism is potentially influenced by the unique structure of quinoa seeds. To shed light on the involvement of endogenous hormones in the process of quinoa seed germination, we have established a regulatory network. This study aims to offer innovative perspectives on the breeding of quinoa varieties that exhibit resistance to PHS, as well as strategies for preventing PHS.

Current research and future directions of melatonin's role in seed germination

Seed germination is a complex process regulated by internal and external factors. Melatonin (N-acetyl-5-methoxytryptamine) is a ubiquitous signaling molecule, playing an important role in regulating seed germination under normal and stressful conditions. In this review, we aim to provide a comprehensive overview on melatonin's effects on seed germination on the basis of existing literature. Under normal conditions, exogenous high levels of melatonin can suppress or delay seed germination, suggesting that melatonin may play a role in maintaining seed dormancy and preventing premature germination. Conversely, under stressful conditions (e.g., high salinity, drought, and extreme temperatures), melatonin has been found to accelerate seed germination. Melatonin can modulate the expression of genes involved in ABA and GA metabolism, thereby influencing the balance of these hormones and affecting the ABA/GA ratio. Melatonin has been shown to modulate ROS accumulation and nutrient mobilization, which can impact the germination process. In conclusion, melatonin can inhibit germination under normal conditions while promoting germination under stressful conditions via regulating the ABA/GA ratios, ROS levels, and metabolic enzyme activity. Further research in this area will deepen our understanding of melatonin's intricate role in seed germination and may contribute to the development of improved seed treatments and agricultural practices.

Abscisic acid biosynthesis is necessary for full auxin effects on hypocotyl elongation

In concert with other phytohormones, auxin regulates plant growth and development. However, how auxin and other phytohormones coordinately regulate distinct processes is not fully understood. In this work, we uncover an auxin-abscisic acid (ABA) interaction module in Arabidopsis that is specific to coordinating activities of these hormones in the hypocotyl. From our forward genetics screen, we determine that ABA biosynthesis is required for the full effects of auxin on hypocotyl elongation. Our data also suggest that ABA biosynthesis is not required for the inhibitory effects of auxin treatment on root elongation. Our transcriptome analysis identified distinct auxin-responsive genes in root and shoot tissues, which is consistent with differential regulation of growth in these tissues. Further, our data suggest that many gene targets repressed upon auxin treatment require an intact ABA pathway for full repression. Our results support a model in which auxin stimulates ABA biosynthesis to fully regulate hypocotyl elongation.

StSN2 interacts with the brassinosteroid signaling suppressor StBIN2 to maintain tuber dormancy

After harvest, potato tubers undergo an important period of dormancy, which significantly impacts potato quality and seed vigor. StSN2 has been reported as a key gene for maintaining tuber dormancy; in this study, we explored the molecular mechanism by which StSN2 maintains dormancy. StBIN2 was first identified as a candidate protein that interacts with StSN2 by co-immunoprecipitation/mass spectrometry, and both qPCR and enzyme activity experiments showed that StSN2 can promote the StBIN2 expression and activity. In addition, the interaction between StSN2 and StBIN2 was verified by yeast two-hybrid, luciferase complementation experiments and co-immunoprecipitation. Bioinformatics analysis and site-directed mutagenesis confirmed the critical role of cysteine residues of StBIN2 in its binding to StSN2. Similar to that of StSN2, overexpression of StBIN2 extended the dormancy of potato tuber. Interaction between StSN2 and StBIN2 increased the activity of the StBIN2 enzyme, inhibited the expression of StBZR1, and suppressed BR signaling. On the contrary, this interaction promoted the expression of StSnRK2.2/2.3/2.4/2.6 and StABI5, key genes of ABA signaling, and the phosphorylation of StSnRK2.3, thereby promoting ABA signaling. Altogether, our results indicate that StSN2 interacts with StBIN2 through key cysteine residues and StBIN2 maintains tuber dormancy by affecting ABA and BR signaling. Findings of this research offer new insights into the molecular mechanism by which StSN2 maintains potato tuber dormancy through interaction with StSIN2 and provide guidance for potato improvement.

Mining Aegilops tauschii genetic diversity in the background of bread wheat revealed a novel QTL for seed dormancy

Due to the low genetic diversity in the current wheat germplasm, gene mining from wild relatives is essential to develop new wheat cultivars that are more resilient to the changing climate. Aegilops tauschii, the D-genome donor of bread wheat, is a great gene source for wheat breeding; however, identifying suitable genes from Ae. tauschii is challenging due to the different morphology and the wide intra-specific variation within the species. In this study, we developed a platform for the systematic evaluation of Ae. tauschii traits in the background of the hexaploid wheat cultivar 'Norin 61' and thus for the identification of QTLs and genes. To validate our platform, we analyzed the seed dormancy trait that confers resistance to preharvest sprouting. We used a multiple synthetic derivative (MSD) population containing a genetic diversity of 43 Ae. tauschii accessions representing the full range of the species. Our results showed that only nine accessions in the population provided seed dormancy, and KU-2039 from Afghanistan had the highest level of seed dormancy. Therefore, 166 backcross inbred lines (BILs) were developed by crossing the synthetic wheat derived from KU-2039 with 'Norin 61' as the recurrent parent. The QTL mapping revealed one novel QTL, Qsd.alrc.5D, associated with dormancy explaining 41.7% of the phenotypic variation and other five unstable QTLs, two of which have already been reported. The Qsd.alrc.5D, identified for the first time within the natural variation of wheat, would be a valuable contribution to breeding after appropriate validation. The proposed platform that used the MSD population derived from the diverse Ae. tauschii gene pool and recombinant inbred lines proved to be a valuable platform for mining new and important QTLs or alleles, such as the novel seed dormancy QTL identified here. Likewise, such a platform harboring genetic diversity from wheat wild relatives could be a useful source for mining agronomically important traits, especially in the era of climate change and the narrow genetic diversity within the current wheat germplasm.

FUSCA3-induced AINTEGUMENTA-like 6 manages seed dormancy and lipid metabolism

FUSCA 3 (FUS3), a seed master regulator, plays critical role in seed dormancy and oil accumulation. However, its downstream regulation mechanisms remain poorly understood. Here, we explored the roles of AINTEGUMENTA-like 6 (AIL6), a seed transcription factor, in these processes. The activation of AIL6 by FUS3 was demonstrated by dual-LUC assay. Seeds of ail6 mutants showed alterations in fatty acid compositions, and both AtAIL6 (AIL6 from Arabidopsis thaliana) and BnaAIL6 (AIL6 from Brassica napus) rescued the phenotype. Over-expression (OE) of AIL6s reversed changes in seed fatty acid composition. Notably, OE lines showed low seed germination rates down to 12% compared to 100% of wild-type Col-0. Transcriptome analysis of the mutant and an OE line indicated widespread expression changes of genes involved in lipid metabolism and phytohormone pathways. In OE mature seeds, GA4 content decreased more than 15-fold, while abscisic acid and indole-3-acetic acid (IAA) contents clearly increased. Exogenous GA3 treatments did not effectively rescue the low germination rate. Nicking seed coats increased germination rates from 25% to nearly 80% while the wild-type rdr6-11 is 100% and 98% respectively, and elongation of storage time also improved seed germination. Furthermore, dormancy imposed by AIL6 was fully released in the della quintuple mutant. Together, our results indicate AIL6 acts as a manager downstream of FUS3 in seed dormancy and lipid metabolism.

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.

Comparative transcriptome analysis of grafting to improve chilling tolerance of cucumber

Grafting with pumpkin as rootstock could improve chilling tolerance of cucumber; however, the underlying mechanism of grafting-induced chilling tolerance remains unclear. Here, we analyzed the difference of physiological and transcriptional level between own-rooted (Cs/Cs) and hetero-grafted (Cs/Cm) cucumber seedlings under chilling stress. The results showed that grafting with pumpkin significantly alleviated the chilling injury as evidenced by slightly symptoms, lower contents of electrolyte leakage (EL), malondialdehyde (MDA), hydrogen peroxide (H2O2), and superoxide anion (O2-) and higher relative water content in Cs/Cm seedlings compared with Cs/Cs seedlings under chilling stress. RNA-seq data showed that grafting induced more DGEs at 8 °C/5 °C compared with 25 °C/18 °C. In accordance with the increase of the activities of antioxidant enzymes (SOD, POD, CAT, APX), grafting upregulated the expression of the regulated redox-related genes such as GST, SOD, and APX. Moreover, grafting increased the expression of genes participated in central carbon metabolism to promote the conversion and decomposition of sugar, which provided more energy for the growth of Cs/Cm seedlings under chilling stress. In addition, grafting regulated the genes involved in the intracellular signal transduction pathways such as calcium signal (CAML, CML, and CDPK) and inositol phospholipid signal (PLC), as well as changed the gene expression of plant hormone signal transduction pathways (ARF, GAI, ABF, and PYR/PYL). These results provide a physiological and transcriptional basis for the molecular mechanism of grafting-induced chilling tolerance of cucumber seedlings.

Comprehensive analysis of transcriptional data on seed germination of two maize inbred lines under low-temperature conditions

Seed germination directly affect maize yield and grain quality. Low-temperature reduces maize yield by affecting seed germination and seedling growth. However, the molecular mechanism of maize seed germination under low-temperature remains unclear. In this study, the transcriptome data of two maize inbred lines SCL127 (chilling-sensitive) and SCL326 (chilling-tolerant) were analyzed at five time points (0 H, 4 H, 12 H, 24 H, and 48 H) under low-temperature conditions. Through the comparison of SCL127-0 H-vs-SCL326-0 H (Group I), SCL127-4 H-vs-SCL326-4 H (Group Ⅱ), SCL127-12 H-vs-SCL326-12 H (Group Ⅲ), SCL127-24 H-vs-SCL326-24 H (Group Ⅳ), and SCL127-48 H-vs SCL326-48 H (Group Ⅴ), a total of 8,526 differentially expressed genes (DEGs) were obtained. Weighted correlation network analysis revealed that Zm00001d010445 was the hub gene involved in seed germination under low-temperature conditions. Zm00001d010445-based association analysis showed that Hap Ⅱ (G) was the excellent haplotype for seed germination under low-temperature conditions. These findings provide a new perspective for the study of the genetic architecture of maize tolerance to low-temperature and contribute to the cultivation of maize varieties with low-temperature tolerance.

A complex signaling trio in seed germination: Auxin-JA-ABA

Recently. Mei et al. discovered the molecular mechanism behind the synergistic action of auxins and jasmonates in enhancing the role of abscisic acid (ABA) in seed germination. They found that JASMONATE-ZIM DOMAIN (JAZ) proteins interact with AUXIN RESPONSE FACTOR (ARF)-16 to mediate auxin-jasmonic acid (JA) crosstalk. Furthermore, they revealed that ARF16 interacts with ABSCISIC ACID INSENSITIVE (ABI)-5 and positively modulates ABA responses at seed germination.

Methodological and physiological study of seed dormancy release in Tilia henryana

Tilia henryana is a rare tree of the Tilia family, found exclusively in China. Its seeds have severe dormancy features that limit its normal conditions of reproduction and renewal. Its seeds have severe dormant characteristics that limit its normal conditions of reproduction and renewal. The Dormancy in T. henryana seeds is a comprehensive dormancy (PY + PD) caused by mechanical and permeability barriers of seed coat and the presence of germination inhibitor in endosperm. L9 (34) orthogonal test was used to determine the best procedure for releasing the dormancy of T. henryana seeds, that is, first treating the seeds with H2SO4 for 15 min, followed by the application of 1 g L-1 GA3, stratification at 5 °C for 45 days, and finally germination at 20 °C, which can achieve a 98% seed germination rate. Large amounts of fat are consumed throughout the dormancy release process. As quantities of protein and starch marginally increase, soluble sugars are continuously decreased. Acid phosphatase and amylase activities increased rapidly, and the combined enzyme activities of G-6-PDH and 6-PGDH related to the PPP were also significantly increased. The levels of GA and ZR continued to increase, while the levels of ABA and IAA gradually decreased, among which GA and ABA changed most rapidly. The total amino acids content continued to decrease. Asp, Cys, Leu, Phe, His, Lys and Arg decreased with dormancy release, while Ser, Glu, Ala, Ile, Pro and Gaba showed an upward trend. The physical dormancy of T. henryana seeds is broken with H2SO4 in order to make the seed coat more permeable, which is a prerequisite for germination. As a result, the seeds can absorb water and engage in physiological metabolic activities, particularly the hydrolysis and metabolism of fat, which supply a significant amount of energy for dormancy release. In addition, rapid variations in the levels of different endogenous hormones and free amino acids, induced by cold stratification and GA3 application, are another important factor promoting the quick physiological activation of seeds and breaking the endosperm barrier.

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.

The Knockdown of AUXIN RESPONSE FACTOR 2 Confers Enhanced Tolerance to Salt and Drought Stresses in Tomato (Solanum lycopersicum L.)

Auxin response factors (ARFs) act as key elements of the auxin-signaling pathway and play important roles in the process of a plant's growth, development, and response to environmental conditions. We studied the implication of the SlARF2 gene in the tomato response to salt (150 mM of NaCl) and drought (15% PEG 20000) stresses. The functional characterization of SlARF2 knockdown tomato mutants revealed that the downregulation of this gene enhanced primary root length and root branching and reduced plant wilting. At the physiological level, the arf2 mutant line displayed higher chlorophyll, soluble sugars, proline, and relative water contents as well as lower stomatal conductance and a decreased malondialdehyde content. Moreover, SlARF2 knockdown tomato mutants demonstrated higher activities of the antioxidant enzymes superoxide dismutase (SOD) and catalase (CAT) under salt and drought stresses than the wild type. Indeed, the stress tolerance of the arf2 mutant was also reflected by the upregulation of stress-related genes involved in ROS scavenging and plant defense, including SOD, CAT, dehydration-responsive element-binding protein, and early responsive to dehydration, which can ultimately result in a better resistance to salt and drought stresses. Furthermore, the transcriptional levels of the Δ1-pyrroline-5-carboxylate synthase (P5CS) gene were upregulated in the arf2 mutant after stress, in correlation with the higher levels of proline. Taken together, our findings reveal that SlARF2 is implicated in salt and drought tolerance in tomato and provides some considerable elements for improving the abiotic stress tolerance and increasing the crop yields of tomato.

Ethrel-induced release of fresh seed dormancy causes remodelling of amylase activity, proteomics, phytohormone and fatty acid profile of groundnut (Arachis hypogaea L.)

It is important to have a short period of fresh seed dormancy in some of the groundnut species to counter pre-harvest sprouting (PHS). One of the main causes of PHS is the activation of ethylene-mediated pathways. To determine the effect of ethylene, the study was conducted and alterations in amylase, proteins and fatty acids were observed at the 0, 6, 12, and 24 h stages after ethrel administration. The result showed an increase in amylase activity, and the fatty acids profile showed a unique alteration pattern at different germination stages. Two-dimensional gel electrophoresis (2DGE) revealed differential expression of proteins at each stage. The trypsin digestion following spectral development through UPLC-MS/MS enabled identification of number of differentially expressed proteins. A total of 49 proteins were identified from 2DGE excised spots. The majority were belonged to seed storage-related proteins like Arah1, Arah2, AAI- domain containing protein, conglutin, Arah3/4, arachin, glycinin. Expression of lipoxygenase1, lipoxygenase9 and Arah2 genes were further confirmed by qRT-PCR which showed its involvement at transcript level. Up-regulation of lipoxygenase9 is correlated with decreased content of fatty acids during germination. Phytohormone detection revealed decrease in ABA, SA and JA content which are generally inhibitor of seed germination while GA, IAA and kinetin concentration increased revealing positive regulation of seed germination. We present an integrated view of proteomics, phytohormone profile, carbohydrate and lipid metabolism to unravel mechanism of fresh seed dormancy.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01332-6.

SlMYB99-mediated auxin and abscisic acid antagonistically regulate ascorbic acids biosynthesis in tomato

Ascorbic acid (AsA) is a water-soluble antioxidant that plays important roles in plant development and human health. Understanding the regulatory mechanism underlying AsA biosynthesis is imperative to the development of high AsA plants. In this study, we reveal that the auxin response factor SlARF4 transcriptionally inhibits SlMYB99, which subsequently modulates AsA accumulation via transcriptional activation of AsA biosynthesis genes GPP, GLDH, and DHAR. The auxin-dependent transcriptional cascade of SlARF4-SlMYB99-GPP/GLDH/DHAR modulates AsA synthesis, while mitogen-activated protein kinase SlMAPK8 not only phosphorylates SlMYB99, but also activates its transcriptional activity. Both SlMYB99 and SlMYB11 proteins physically interact with each other, thereby synergistically regulating AsA biosynthesis by upregulating the expression of GPP, GLDH, and DHAR genes. Collectively, these results demonstrate that auxin and abscisic acid antagonistically regulate AsA biosynthesis during development and drought tolerance in tomato via the SlMAPK8-SlARF4-SlMYB99/11 module. These findings provide new insights into the mechanism underlying phytohormone regulation of AsA biosynthesis and provide a theoretical basis for the future development of high AsA plants via molecular breeding.

Transcriptome profile analysis of Indian mustard (Brassica juncea L.) during seed germination reveals the drought stress-induced genes associated with energy, hormone, and phenylpropanoid pathways

Indian mustard (Brassica juncea L. Czern and Coss) is an important oil and vegetable crop frequently affected by seasonal drought stress during seed germination, which retards plant growth and causes yield loss considerably. However, the gene networks regulating responses to drought stress in leafy Indian mustard remain elusive. Here, we elucidated the underlying gene networks and pathways of drought response in leafy Indian mustard using next-generation transcriptomic techniques. Phenotypic analysis showed that the drought-tolerant leafy Indian mustard cv. 'WeiLiang' (WL) had a higher germination rate, antioxidant capacity, and better growth performance than the drought-sensitive cv. 'ShuiDong' (SD). Transcriptome analysis identified differentially expressed genes (DEGs) in both cultivars under drought stress during four germination time points (i.e., 0, 12, 24, and 36 h); most of which were classified as drought-responsive, seed germination, and dormancy-related genes. In the Kyoto Encyclopedia of Genes and Genome (KEGG) analyses, three main pathways (i.e., starch and sucrose metabolism, phenylpropanoid biosynthesis, and plant hormone signal transduction) were unveiled involved in response to drought stress during seed germination. Furthermore, Weighted Gene Co-expression Network Analysis (WGCNA) identified several hub genes (novel.12726, novel.1856, BjuB027900, BjuA003402, BjuA021578, BjuA005565, BjuB006596, novel.12977, and BjuA033308) associated with seed germination and drought stress in leafy Indian mustard. Taken together, these findings deepen our understanding of the gene networks for drought responses during seed germination in leafy Indian mustard and provide potential target genes for the genetic improvement of drought tolerance in this crop.

Transcriptome Analysis of Rice Embryo and Endosperm during Seed Germination

Seed germination is a complex, multistage developmental process that is an important step in plant development. In this study, RNA-Seq was conducted in the embryo and endosperm of unshelled germinating rice seeds. A total of 14,391 differentially expressed genes (DEGs) were identified between the dry seeds and the germinating seeds. Of these DEGs, 7109 were identified in both the embryo and endosperm, 3953 were embryo specific, and 3329 were endosperm specific. The embryo-specific DEGs were enriched in the plant-hormone signal-transduction pathway, while the endosperm-specific DEGs were enriched in phenylalanine, tyrosine, and tryptophan biosynthesis. We categorized these DEGs into early-, intermediate-, and late-stage genes, as well as consistently responsive genes, which can be enriched in various pathways related to seed germination. Transcription-factor (TF) analysis showed that 643 TFs from 48 families were differentially expressed during seed germination. Moreover, 12 unfolded protein response (UPR) pathway genes were induced by seed germination, and the knockout of OsBiP2 resulted in reduced germination rates compared to the wild type. This study enhances our understanding of gene responses in the embryo and endosperm during seed germination and provides insight into the effects of UPR on seed germination in rice.

Multiomics strategies for decoding seed dormancy breakdown in Paris polyphylla

BACKGROUND

The disruption of seed dormancy is a complicated process and is controlled by various factors. Among these factors, membrane lipids and plant hormones are two of the most important ones. Paris polyphylla is an important Chinese herbaceous species, and the dormancy trait of its seed limits the cultivation of this herb.

RESULTS

In this study, we investigate the global metabolic and transcriptomic profiles of Paris polyphylla during seed dormancy breaking. Widely targeted metabolomics revealed that lysophospholipids (lysoPLs) increased during P. polyphylla seed dormancy breaking. The expression of phospholipase A2 (PLA2), genes correlated to the production of lysoPLs, up-regulated significantly during this process. Abscisic acid (ABA) decreased dramatically during seed dormancy breaking of P. polyphylla. Changes of different GAs varied during P. polyphylla seeds dormancy breaking, 13-OH GAs, such as GA₅₃ were not detected, and GA₃ decreased significantly, whereas 13-H GAs, such as GA₁₅, GA₂₄ and GA₄ increased. The expression of CYP707As was not synchronous with the change of ABA content, and the expression of most UGTs, GA20ox and GA3ox up-regulated during seed dormancy breaking.

CONCLUSIONS

These results suggest that PLA2 mediated production of lysoPLs may correlate to the seed dormancy breaking of P. polyphylla. The conversion of ABA to ABA-GE catalysed by UGTs may be the main cause of ABA degradation. Through inhibition the expression of genes related to the synthesis of 13-OH GAs and up-regulation genes related to the synthesis of 13-H GAs, P. polyphylla synthesized more bioactive 13-H GA (GA₄) to break its seed dormancy.

Insights into cryptochrome modulation of ABA signaling to mediate dormancy regulation in Marchantia polymorpha

The acquisition of dormancy capabilities has enabled plants to survive in adverse terrestrial environmental conditions. Dormancy accumulation and release is coupled with light signaling, which is well studied in Arabidopsis, but it is unclear in the distant nonvascular relative. We study the characteristics and function on dormancy regulation of a blue light receptor cryptochrome in Marchantia polymorpha (MpCRY). Here, we identified MpCRY via bioinformatics and mutant complement analysis. The biochemical characteristics were assessed by multiple protein-binding assays. The function of MpCRY in gemma dormancy was clarified by overexpression and mutation of MpCRY, and its mechanism was analyzed via RNA sequencing and quantitative PCR analyses associated with hormone treatment. We found that the unique MpCRY protein in M. polymorpha undergoes both blue light-promoted interaction with itself (self-interaction) and blue light-dependent phosphorylation. MpCRY has the specific characteristics of blue light-induced nuclear localization and degradation. We further demonstrated that MpCRY transcriptionally represses abscisic acid (ABA) signaling-related gene expression to suppress gemma dormancy, which is dependent on blue light signaling. Our findings indicate that MpCRY possesses specific biochemical and molecular characteristics, and modulates ABA signaling under blue light conditions to regulate gemma dormancy in M. polymorpha.

The dynamics of Arabidopsis H2A.Z on SMALL AUXIN UP RNAs regulates abscisic acid-auxin signaling crosstalk

Extreme environmental changes threaten plant survival and worldwide food production. In response to osmotic stresses, plant hormone ABA activates stress responses and restricts plant growth. However, the epigenetic regulation of the ABA signaling and ABA-auxin crosstalk are not well known. Here we report that the histone variant H2A.Z knockdown mutant in Arabidopsis Col-0 ecotype, h2a.z-kd, has altered ABA signaling and stress performances. RNA-sequencing data showed that a majority of stress related genes are activated in h2a.z-kd. In addition, we revealed that ABA directly promotes the deposition of H2A.Z on SMALL AUXIN UP RNAs (SAURs), which is involved in ABA-repressed SAUR expression. Moreover, we found that ABA represses the transcription of H2A.Z genes through suppressing ARF7/19-HB22/25 module. Our results shed light on a dynamic and reciprocal regulation hub through H2A.Z deposition on SAURs and ARF7/19-HB22/25-mediated H2A.Z transcription to integrate ABA/auxin signaling and regulate stress responses in Arabidopsis.

A transcription factor WRKY36 interacts with AFP2 to break primary seed dormancy by progressively silencing DOG1 in Arabidopsis

The phytohormones abscisic acid (ABA) and gibberellic acid (GA) antagonistically control the shift between seed dormancy and its alleviation. DELAY OF GERMINATION1 (DOG1) is a critical regulator that determines the intensity of primary seed dormancy, but its underlying regulatory mechanism is unclear. In this study, we combined physiological, biochemical, and genetic approaches to reveal that a bHLH transcriptional factor WRKY36 progressively silenced DOG1 expression to break seed dormancy through ABI5-BINDING PROTEIN 2 (AFP2) as the negative regulator of ABA signal. AFP2 interacted with WRKY36, which recognizes the W-BOX in the DOG1 promoter to suppress its expression; Overexpressing WRKY36 broke primary seed dormancy, whereas wrky36 mutants showed strong primary seed dormancy. In addition, AFP2 recruited the transcriptional corepressor TOPLESS-RELATED PROTEIN2 (TPR2) to reduce histone acetylation at the DOG1 locus, ultimately mediating WRKY36-dependent inhibition of DOG1 expression to break primary seed dormancy. Our result proposes that the WRKY36-AFP2-TPR2 module progressively silences DOG1 expression epigenetically, thereby fine-tuning primary seed dormancy.

Abscisic acid promotes auxin biosynthesis to inhibit primary root elongation in rice

Soil compaction is a global problem causing inadequate rooting and poor yield in crops. Accumulating evidence indicates that phytohormones coordinately regulate root growth via regulating specific growth processes in distinct tissues. However, how abscisic acid (ABA) signaling translates into auxin production to control root growth during adaptation to different soil environments is still unclear. In this study, we report that ABA has biphasic effects on primary root growth in rice (Oryza sativa) through an auxin biosynthesis-mediated process, causing suppression of root elongation and promotion of root swelling in response to soil compaction. We found that ABA treatment induced the expression of auxin biosynthesis genes and auxin accumulation in roots. Conversely, blocking auxin biosynthesis reduced ABA sensitivity in roots, showing longer and thinner primary roots with larger root meristem size and smaller root diameter. Further investigation revealed that the transcription factor basic region and leucine zipper 46 (OsbZIP46), involved in ABA signaling, can directly bind to the YUCCA8/rice ethylene-insensitive 7 (OsYUC8/REIN7) promoter to activate its expression, and genetic analysis revealed that OsYUC8/REIN7 is located downstream of OsbZIP46. Moreover, roots of mutants defective in ABA or auxin biosynthesis displayed the enhanced ability to penetrate compacted soil. Thus, our results disclose the mechanism in which ABA employs auxin as a downstream signal to modify root elongation and radial expansion, resulting in short and swollen roots impaired in their ability to penetrate compacted soil. These findings provide avenues for breeders to select crops resilient to soil compaction.

Auxin contributes to jasmonate-mediated regulation of abscisic acid signaling during seed germination in Arabidopsis

Abscisic acid (ABA) represses seed germination and postgerminative growth in Arabidopsis thaliana. Auxin and jasmonic acid (JA) stimulate ABA function; however, the possible synergistic effects of auxin and JA on ABA signaling and the underlying molecular mechanisms remain elusive. Here, we show that exogenous auxin works synergistically with JA to enhance the ABA-induced delay of seed germination. Auxin biosynthesis, perception, and signaling are crucial for JA-promoted ABA responses. The auxin-dependent transcription factors AUXIN RESPONSE FACTOR10 (ARF10) and ARF16 interact with JASMONATE ZIM-DOMAIN (JAZ) repressors of JA signaling. ARF10 and ARF16 positively mediate JA-increased ABA responses, and overaccumulation of ARF16 partially restores the hyposensitive phenotype of JAZ-accumulating plants defective in JA signaling in response to combined ABA and JA treatment. Furthermore, ARF10 and ARF16 physically associate with ABSCISIC ACID INSENSITIVE5 (ABI5), a critical regulator of ABA signaling, and the ability of ARF16 to stimulate JA-mediated ABA responses is mainly dependent on ABI5. ARF10 and ARF16 activate the transcriptional function of ABI5, whereas JAZ repressors antagonize their effects. Collectively, our results demonstrate that auxin contributes to the synergetic modulation of JA on ABA signaling, and explain the mechanism by which ARF10/16 coordinate with JAZ and ABI5 to integrate the auxin, JA, and ABA signaling pathways.

Effects of High Voltage Electrical Discharge (HVED) on Endogenous Hormone and Polyphenol Profile in Wheat

High voltage electrical discharge (HVED) is an eco-friendly low-cost method based on the creation of plasma-activated water (PAW) through the release of electrical discharge in water which results in the formation of reactive particles. Recent studies have reported that such novel plasma technologies promote germination and growth but their hormonal and metabolic background is still not known. In the present work, the HVED-induced hormonal and metabolic changes were studied during the germination of wheat seedlings. Hormonal changes including abscisic acid (ABA), gibberellic acids (GAs), indol acetic acid (IAA) and jasmonic acid (JA) and the polyphenol responses were detected in the early (2nd day) and late (5th day) germination phases of wheat as well as their redistribution in shoot and root. HVED treatment significantly stimulated germination and growth both in the shoot and root. The root early response to HVED involved the upregulation of ABA and increased phaseic and ferulic acid content, while the active form of gibberellic acid (GA1) was downregulated. In the later phase (5th day of germination), HVED had a stimulatory effect on the production of benzoic and salicylic acid. The shoot showed a different response: HVED induced the synthesis of JA_Le_Ile, an active form of JA, and provoked the biosynthesis of cinnamic, p-coumaric and caffeic acid in both phases of germination. Surprisingly, in 2-day-old shoots, HVED decreased the GA20 levels, being intermediate in the synthesis of bioactive gibberellins. These HVED-provoked metabolic changes indicated a stress-related response that could contribute to germination in wheat.

Transcriptome and proteome analyses reveal the potential mechanism of seed dormancy release in Amomum tsaoko during warm stratification

BACKGROUND

In Amomum tsaoko breeding, the low germination rate is the major limitation for their large-scale reproduction. We found that warm stratification was an effective treatment to break the seed dormancy of A. tsaoko prior to sowing and could be an important component of improving breeding programs. The mechanism of seed dormancy release during warm stratification remains unclear. Therefore, we studied the differences between transcripts and proteomes at 0, 30, 60, and 90 days of warm stratification, to identify some regulatory genes and functional proteins that may cause seed dormancy release in A. tsaoko and reveal their regulatory mechanism.

RESULTS

RNA-seq was performed for the seed dormancy release process, and the number of differentially expressed genes (DEGs) was 3196 in three dormancy release periods. Using TMT-labelling quantitative proteome analysis, a total of 1414 proteins were defined as differentially expressed proteins (DEPs). Functional enrichment analyses revealed that the DEGs and DEPs were mainly involved in signal transduction pathways (MAPK signaling, hormone) and metabolism processes (cell wall, storage and energy reserves), suggesting that these differentially expressed genes and proteins are somehow involved in response to seed dormancy release process, including MAPK, PYR/PYL, PP2C, GID1, GH3, ARF, AUX/IAA, TPS, SPS, and SS. In addition, transcription factors ARF, bHLH, bZIP, MYB, SBP, and WRKY showed differential expression during the warm stratification stage, which may relate to dormancy release. Noteworthy, XTH, EXP, HSP and ASPG proteins may be involved in a complex network to regulate cell division and differentiation, chilling response and the seed germination status in A. tsaoko seed during warm stratification.

CONCLUSION

Our transcriptomic and proteomic analysis highlighted specific genes and proteins that warrant further study in fully grasping the precise molecular mechanisms that control the seed dormancy and germination of A. tsaoko. A hypothetical model of the genetic regulatory network provides a theoretical basis for overcoming the physiological dormancy in A. tsaoko in the future.

Advances in structure and function of auxin response factor in plants

Auxin is a crucial phytohormone that has various effects on the regulators of plant growth and development. Auxin signal transduction is mainly controlled by two gene families: auxin response factor (ARF) and auxin/indole-3-acetic acid (Aux/IAA). ARFs are plant-specific transcription factors that bind directly to auxin response elements in the promoters of auxin-responsive genes. ARF proteins contain three conserved regions: a conserved N-terminal B3 DNA-binding domain, a variable intermediate middle region domain that functions in activation or repression, and a C-terminal domain including the Phox and Bem1p region for dimerization, similar to the III and IV elements of Aux/IAA, which facilitate protein-protein interaction through homodimerization of ARF proteins or heterodimerization of ARF and Aux/IAA proteins. In the two decades following the identification of the first ARF, 23 ARF members have been identified and characterized in Arabidopsis. Using whole-genome sequencing, 22, 25, 23, 25, and 36 ARF genes have been identified in tomato, rice, wheat, sorghum, and maize, respectively, in addition to which the related biofunctions of some ARFs have been reported. ARFs play crucial roles in regulating the growth and development of roots, leaves, flowers, fruits, seeds, responses to biotic and abiotic stresses, and phytohormone signal crosstalk. In this review, we summarize the research progress on the structures and functions of ARFs in Arabidopsis, tomato, and cereal crops, to provide clues for future basic research on phytohormone signaling and the molecular design breeding of crops.

Exogenous abscisic acid prolongs the dormancy of recalcitrant seed of Panax notoginseng

The seeds of Panax notoginseng (Burk.) F. H. Chen are typically characterized by their recalcitrance and after-ripening process and exhibit a high water content at harvest as well as a high susceptibility to dehydration. Storage difficulty and the low germination of recalcitrant seeds of P. notoginseng are known to cause an obstacle to agricultural production. In this study, the ratio of embryo to endosperm (Em/En) in abscisic acid (ABA) treatments (1 mg·l^-1 and 10 mg·l^-1, LA and HA) was 53.64% and 52.34%, respectively, which were lower than those in control check (CK) (61.98%) at 30 days of the after-ripening process (DAR). A total of 83.67% of seeds germinated in the CK, 49% of seeds germinated in the LA treatment, and 37.33% of seeds germinated in the HA treatment at 60 DAR. The ABA, gibberellin (GA), and auxin (IAA) levels were increased in the HA treatment at 0 DAR, while the jasmonic acid (JA) levels were decreased. ABA, IAA, and JA were increased, but GA was decreased with HA treatment at 30 DAR. A total of 4,742, 16,531, and 890 differentially expressed genes (DEGs) were identified between the HA-treated and CK groups, respectively, along with obvious enrichment in the ABA-regulated plant hormone pathway and the mitogen-activated protein kinase (MAPK) signaling pathway. The expression of pyracbactin resistance-like (PYL) and SNF1-related protein kinase subfamily 2 (SnRK2s) increased in the ABA-treated groups, whereas the expression of type 2C protein phosphatase (PP2C) decreased, both of which are related to the ABA signaling pathway. As a result of the changes in expression of these genes, increased ABA signaling and suppressed GA signaling could inhibit the growth of the embryo and the expansion of developmental space. Furthermore, our results demonstrated that MAPK signaling cascades might be involved in the amplification of hormone signaling. Meanwhile, our study uncovered that the exogenous hormone ABA could inhibit embryonic development, promote dormancy, and delay germination in recalcitrant seeds. These findings reveal the critical role of ABA in regulating the dormancy of recalcitrant seeds, and thereby provide a new insight into recalcitrant seeds in agricultural production and storage.