Abscisic Acid Pathways Research Articles

The molecular mechanism by which heat stress during the grain filling period inhibits maize grain filling and reduces yield

High temperatures significantly impair plant growth and development by restricting maize grain filling; however, the molecular mechanisms underlying heat stress remain poorly understood. In this study, 350 maize inbred lines were evaluated under field conditions, leading to the identification of heat-tolerant Zheng58 and heat-sensitive Qi319. The two inbred lines were exposed to controlled conditions of 30°C/20°C (optimal) and 42°C/30°C (heat stress) during the grain filling period. Heat stress significantly reduced thousand-kernel weight and seed setting rates, with Qi319 experiencing more pronounced declines. In contrast, Zheng58 showed superior performance, with a grain filling rate 48% higher and seed setting rate 57% greater than Qi319. Transcriptome analysis showed that heat stress disrupted starch biosynthesis and hormonal homeostasis, notably affecting abscisic acid and auxin pathways. Additionally, photosynthetic and transpiration rates in panicle leaves were reduced due to the downregulation of genes related to light-harvesting complexes, photosystem I subunits, and water transport. These findings highlight the critical roles of starch metabolism, hormonal regulation, and photosynthetic efficiency in heat tolerance, offering valuable insights for developing heat-resilient maize varieties to mitigate yield losses under high-temperature conditions.

Involvement of endogenous IAA and ABA in the regulation of arbuscular mycorrhizal fungus on rooting of tea plant (Camellia sinensis L.) cuttings

BackgroundAdventitious root (AR) formation is the key step for successful cutting propagation of tea plants (Camellia sinensis L.). Studies showed that arbuscular mycorrhizal fungus (AMF) can promote the rooting ability, and auxin pathway in basal stem of cuttings was involved in this process. However, auxin and abscisic acid (another important regulator on AR formation) in the other parts of cuttings at different rooting stages responding to AMF inoculation are not well studied. Therefore, in this paper, contents, enzymes and genes related to these two plant hormones were comprehensively determined aiming to unveil how endogenous indole-3-acetic acid (IAA) and abscisic acid (ABA) involve in the AMF regulating AR development of tea cuttings.ResultsInoculating with AMF significantly increased the proportion of cuttings at S2 stage (AR formation), which was more than twice as much as the control. And the total rooting rate in mycorrhizal treatment was also higher than that in the control with an increase of 8.66%. Enzyme activity assays showed that except for decreased polyphenol oxidase (PPO) activity at the S3 stage and peroxidase (POD) activity in middle stem of S3 stage, AMF inoculation increased activities of POD, PPO, superoxide dismutase (SOD) and catalase (CAT) to varying degrees in leaf, middle stem and basal stem of tea cuttings. After inoculation with AMF, the indoleacetic acid oxidase (IAAO) activity decreased to a certain extent in the first three stages of tea cuttings, which showed a trend of ‘low-high-low’ in the basal stem of all treatments. Besides, there was a significantly positive correlation between SOD activity and AR formation, especially for the proportion of cuttings at S2 and S3 stages. Higher IAA level and IAA/ABA ratio was found in basal stem of cuttings at S1 stage induced by AMF, which promoting the AR formation as revealed by correlation analysis. At the same time, AMF significantly elevated the level of IAA in leaf at S1 stage. By screening differentially expressed genes (DEGs) related to IAA and ABA pathways, together with redundant analysis, it was indicated that auxin biosynthesis and transport, as well as ABA transport and signal transduction, were involved in AMF regulating the rooting of tea cuttings.ConclusionsOverall, both endogenous IAA and ABA played roles in the regulation of AR formation of tea cuttings by AMF inoculating, enriching the theoretical basis of AMF regulating rooting of cuttings and providing foundations for cutting propagation of tea plants.

MdHY5 positively regulates cold tolerance in apple by integrating the auxin and abscisic acid pathways.

Low-temperature stress causes various types of physiological and biochemical damage to plants. The basic leucine zipper (bZIP) family transcription factor HY5 plays a significant role in multiple stress responses in plants. Here, cold stress was found to induce the upregulation of MdHY5 expression, which, in turn, positively regulates the cold tolerance of apple (Malus domestica). MdHY5 directly interacts the promoters of MdGH3-2/12 (auxin-amido synthetase) and inhibits their expression. However, low-temperature stress inhibits the regulation of MdGH3-2/12 by MdHY5, which suppresses the increase in indole-3-acetic acid (IAA) mediated by the MdHY5-MdGH3-2/12 module. Alternatively, MdHY5 directly interacts with the promoter of MdNCED2, a crucial enzyme in the biosynthesis of abscisic acid (ABA), thereby activating its expression. Additionally, cold stress enhances the regulation of MdNCED2 by MdHY5, which leads to the promotion of the increase in ABA mediated by the MdHY5-MdNCED2 module. Therefore, under low-temperature stress, MdHY5 reduces the ratio of IAA : ABA within apple plants by regulating MdGH3-2/12 and MdNCED2, thereby indirectly promoting the accumulation of anthocyanins, which further improves the cold tolerance of apple. This study establishes a theoretical framework for the multiple roles and regulatory mechanisms of HY5 in integrating the IAA and ABA pathways under cold stress.

Comparative transcriptome profiling suggests the role of phytohormones in leaf stalk-stem angle in melon (Cucumis melo L.).

Leaf stalk-stem angle is an important agronomic trait influencing melon architecture, photosynthetic efficiency, and crop yield. However, the mechanisms governing leaf stalk-stem angle, particularly in melon, are not well understood. In this study, we explored the comparative transcriptome in the expanded architecture line Y164 and the compact plant architecture line Z151 at 30 days after pollination. Phytohormones were measured at the leaf stalk-angle site at the same time in these two lines using liquid chromatography (LC) tandem mass spectrometry (MS) (LC-MS/MS). The phytohormones and transcriptomes were jointly analyzed. Differential hormone profiling revealed that the levels of 1-aminocyclopropane-1-carboxylate (ACC) and 12-oxophytodienoic acid (OPDA) in the large-angled line Y164 were significantly higher than those in the small-angled line Z151. These differences were quantified as 2.1- and 2.8-fold increases, respectively. Conversely, the content of isopentenyl adenosine (IPA) was significantly elevated in Z151, with a 3.8-fold higher concentration relative to Y164. Transcriptome analysis identified a total of 1709 differently expressed genes (DEGs), with a predominant enrichment in the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to photosynthesis and plant hormone signal transduction. Similarly, photosynthesis and the hormone metabolic process were predominantly enriched in the biological process of Gene Ontology (GO) terms. Further integration of transcriptome and hormone analyses substantiated the close relationship between melon leaf stalk-stem angle and phytohormones, especially ACC, OPDA and IPA. Selected DEGs from phytohormone signal transduction were validated. Detailed analysis of DEGs highlighted the potential role of genes such as GH3s (LOC103490488, LOC103490483), SUARs (LOC107991561, LOC103497281 and LOC103489067), ARFs (LOC103503893, LOC103493078) and five genes in abscisic acid pathway. In summary, our findings strongly suggest a direct correlation between phytohormones and the leaf stalk-stem angles in melon.

Transcriptome Analysis Reveals the Crucial Role of Phenylalanine Ammonia-Lyase in Low Temperature Response in Ammopiptanthus mongolicus.

Background: Ammopiptanthus mongolicus is a rare temperate evergreen shrub with high tolerance to low temperature, and understanding the related gene expression regulatory network can help advance research on the mechanisms of plant tolerance to abiotic stress. Methods: Here, time-course transcriptome analysis was applied to investigate the gene expression network in A. mongolicus under low temperature stress. Results: A total of 12,606 differentially expressed genes (DEGs) were identified at four time-points during low temperature stress treatment, and multiple pathways, such as plant hormones, secondary metabolism, and cell membranes, were significantly enriched in the DEGs. Trend analysis found that the expression level of genes in cluster 19 continued to upregulate under low temperatures, and the genes in cluster 19 were significantly enriched in plant hormone signaling and secondary metabolic pathways. Based on the transcriptome data, the expression profiles of the genes in abscisic acid, salicylic acid, and flavonoid metabolic pathways were analyzed. It was found that biosynthesis of abscisic acid and flavonoids may play crucial roles in the response to low temperature stress. Furthermore, members of the phenylalanine ammonia-lyase (PAL) family in A. mongolicus were systematically identified and their structures and evolution were characterized. Analysis of cis-acting elements showed that the PAL genes in A. mongolicus were closely related to abiotic stress response. Expression pattern analysis showed that PAL genes responded to various environmental stresses, such as low temperature, supporting their involvement in the low temperature response in A. mongolicus. Conclusions: Our study provides important data for understanding the mechanisms of tolerance to low temperatures in A. mongolicus.

Omics based approaches to decipher the leaf ionome and transcriptome changes in Solanum lycopersicum L. upon Tomato Brown Rugose Fruit Virus (ToBRFV) infection.

The Tomato Brown Rugose Fruit Virus (ToBRFV) is a pathogen that mostly affects plants from the Solanaceae family. This virus severely affects the yield of tomato (Solanum lycopersicum L.) plants, thus creating an urgent need to research the basis of resistance to manage the disease. To understand the molecular basis of resistance, we employed omics-based approaches involving leaf ionomics and transcriptomics to help us decipher the interaction between elemental and nutritional composition and investigate its effect on the gene expression profile upon the ToBRFV infection in tomatoes. Ionomics was used to investigate the accumulation of trace elements in leaves, showcasing that the plants resistant to the virus had significantly higher concentrations of iron (p-value = 0.039) and nickel (p-value = 0.042) than the susceptible ones. By correlating these findings with transcriptomics, we identified some key genes involved in iron homeostasis and abscisic acid pathways, potentially responsible for conferring resistance against the pathogen. From the obtained list of differentially expressed genes, a panel of mutation profile was discovered with three important genes-Solyc02g068590.3.1 (K+ transporter), Solyc01g111890.3.1 (LRR), and Solyc02g061770.4.1 (Chitinase) showing persistent missense mutations. We ascertain the role of these genes and establish their association with plant resistance using genotyping assays in various tomato lines. The targeted selection of these genetic determinants can further enhance plant breeding and crop yield management strategies.

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.

Ubiquitin-Specific Protease 15 Plays an Important Role in Controlling the Tolerance to Salt, Drought and Abscisic Acid in Arabidopsis thaliana.

Ubiquitin-specific proteases (UBPs), the largest subfamily of deubiquitinating enzymes (DUBs), are critical for plant growth and development as well as abiotic-stress responses. In this study, we discovered that the expression of the ubiquitin-specific protease 15 (UBP15) gene of the gene ubiquitin-specific protease 15 (UBP15) was induced by salt, mannitol and abscisic acid (ABA) treatments. Further research revealed that UBP15 is involved in modulation of salt, drought tolerance and ABA signaling during seed germination, early seedling development, post-germination root growth or adult-plant stage. Enrichment analysis showed that many genes related to abiotic stresses and metabolic pathways were altered in the ubp15-1 mutant. Through the joint analysis of the quantitative real-time polymerase chain reaction (qRT-PCR) and differentially-expressed gene relationship network, we found that UBP15 may mainly regulate salt-stress tolerance by modulating the dwarf and delayed flowering 1 (DDF1) pathway through a cascade reaction. In the regulation of drought-stress responses, ring domain ligase1 (RGLG1) may be a direct substrate of UBP15. Moreover, we cannot exclude the possibility that UBP15 acts in a feed-forward loop mechanism in the regulation of drought-stress responses via ethylene response factor 53 (ERF53) and its ubiquitin (Ub) ligase RGLG1. In ABA signal transduction, UBP15 may play a role in at least three aspects of the ABA signaling pathway: ABA synthesis, stomatal closure regulated by ABA signaling, and transcription factors in the ABA pathway. Taken together, our results suggest that UBP15 is involved in salt, osmotic, and drought-stress tolerance and the ABA signaling pathway by directly regulating the stability of key substrates or indirectly affecting the expression of genes related to abiotic stresses in Arabidopsis thaliana. Our research provides new germplasm resources for stress-resistant crops cultivation. These results demonstrate that UBP15 is a key regulator of salt, drought and ABA tolerance in Arabidopsis.

Protein phosphatases type 2C regulate branches by interacting with DgLsL and participating in abscisic acid pathway in Chrysanthemum × morifolium

Chrysanthemum(Chrysanthemum × morifolium) branching is an important ornamental trait, which directly determines its ornamental quality and production. In this study, CmPP2C1 and CmPP2C2 were identified as interacting proteins of DgLsL and its function in branches was analyzed. Yeast two-hybrid assay (Y2H) and Luciferase complementation imaging assay (LCA) were used to demonstrate the interaction. The expression of CmPP2C1 and CmPP2C2 were significantly increased after decapitation. In addition, CmPP2C1 overexpression led to a significant decrease in endogenous abscisic acid (ABA) content and expression of related synthetic genes. This implies that CmPP2C1 and DgLsL may regulate chrysanthemum branching by participating in the ABA pathway. Taken together, our results revealed that protein phosphatases type 2C regulate branches by interacting with DgLsL and regulating Abscisic acid synthesis in Chrysanthemum × morifolium ‘Jinba’, which provides an important theoretical basis for the molecular breeding and production of the chrysanthemum.

Environmental Pollutant Anthracene Induces ABA-Dependent Transgenerational Effects on Gemmae Dormancy in Marchantia polymorpha.

Anthracene, a polycyclic aromatic hydrocarbon (PAH) from fossil fuel combustion, poses significant environmental threats. This study investigates the role of abscisic acid (ABA) in the anthracene tolerance of the liverwort Marchantia polymorpha using mutants deficient in ABA perception (Mppyl1) or biosynthesis (Mpaba1). In this study, we monitored the role of ABA in the anthracene tolerance response by tracking two ABA-controlled traits: plant growth inhibition and gemmae dormancy. We found that the anthracene-induced inhibition of plant growth is dose-dependent, similar to the growth-inhibiting effect of ABA, but independent of ABA pathways. However, gemmae dormancy was differentially affected by anthracene in ABA-deficient mutants. We found that gemmae from anthracene-exposed WT plants exhibited reduced germination compared to those from mock-treated plants. This suggests that the anthracene exposure of mother plants induces a transgenerational effect, resulting in prolonged dormancy in their asexual propagules. While Mppyl1 gemmae retained a dormancy delay when derived from anthracene-exposed thalli, the ABA biosynthesis mutant Mpaba1 did not display any significant dormancy delay as a consequence of anthracene exposure. These results, together with the strong induction of ABA marker genes upon anthracene treatment, imply that anthracene-induced germination inhibition relies on ABA synthesis in the mother plant, highlighting the critical role of MpABA1 in the tolerance response. These findings reveal a complex interplay between anthracene stress and ABA signaling, where anthracene triggers ABA-mediated responses, influencing reproductive success and highlighting the potential for leveraging genetic and hormonal pathways to enhance plant resilience in contaminated habitats.

Combined transcriptomic and metabolomic analysis of the mechanism by which Bacillus velezensis induces resistance to anthracnose in walnut.

Walnut (Juglans spp.), a significant deciduous tree of economic and ecological importance, faces substantial threats from walnut anthracnose, primarily caused by Colletotrichum gloeosporioides. Bacillus velezensis has shown promise in mitigating this fungal pathogen. To delve deeper into the induction mechanism of B. velezensis on walnut plant resistance, we conducted a metabolomic analysis on walnut leaves from six different treatment groups. Specifically, the groups were defined as follows: Group B.v. was inoculated with B. velezensis alone, Group CK served as the blank control, and Group C.g. was inoculated solely with C. gloeosporioides. Group B.v.-C.g. received B. velezensis followed by C. gloeosporioides inoculation. Group B.v.+C.g. underwent simultaneous inoculation with both B. velezensis and C. gloeosporioides, while Group C.g.-B.v. was treated first with C. gloeosporioides then B. velezensis. A total of 1,503 metabolites were detected, mainly including flavonoids, terpenoids, and steroids. The results revealed that B. velezensis spraying not only enhanced the inherent resistance of walnut plants but also significantly regulated walnut plants already infected with C. gloeosporioides. This was mainly achieved by inducing walnut plants to adjust their metabolic pathways such as salicylic acid, jasmonic acid, and abscisic acid, thereby strengthening their stress response. Transcriptomic and metabolomic correlation analyses showed that in the comparisons of B.v. vs. CK, C.g. vs. CK, and C.g.-B.v. vs. C.g., 59, 244, and 122 differential abundance metabolites were detected, along with 7860, 3677, and 5587 differential genes, respectively. Amino acid synthesis, starch and sucrose metabolism, photosynthesis, phenylpropane metabolism, purine metabolism, and glutathione metabolism played crucial roles in walnut's disease resistance mechanism. Further analysis revealed that B. velezensis induced walnut plants to regulate multiple genes, such as LOC109005403, LOC108985444 and LOC118344177, resulting in the production of defensive metabolites such as palmitic acid, coumarin and ferulic acid, thereby enhancing their resistance to C. gloeosporioides. In summary, B. velezensis induces systemic resistance in walnut plants by modulating the metabolic pathways of salicylic acid, jasmonic acid, and abscisic acid. It enhances this resistance by strengthening cell walls, synthesizing defensive secondary metabolites, and regulating energy metabolism and stress responses. These findings provide a solid theoretical foundation for the future field application of B. velezensis in controlling walnut anthracnose.

Gaining or cutting SLAC: the evolution of plant guard cell signalling pathways.

The evolution of adjustable stomatal pores, enabling CO2 acquisition, was one of the most significant events in the development of life on land. Here, we investigate how the guard cell signalling pathways that regulate stomatal movements evolved. We compare fern and angiosperm guard cell transcriptomes and physiological responses, and examine the functionality of ion channels from diverse plant species. We find that, despite conserved expression in guard cells, fern anion channels from the SLAC/SLAH family are not activated by the same abscisic acid (ABA) pathways that provoke stomatal closure in angiosperms. Accordingly, we find an insensitivity of fern stomata to ABA. Moreover, our analysis points to a complex evolutionary history, featuring multiple gains and/or losses of SLAC activation mechanisms, as these channels were recruited to a role in stomatal closure. Our results show that the guard cells of flowering and nonflowering plants share similar core features, with lineage-specific and ecological niche-related adaptations, likely underlying differences in behaviour.

Hormonal signaling regulates photosynthetic function of alfalfa (Medicago sativa L.) under NaHCO3 stress

The physiological and molecular mechanisms underlying salt-alkali tolerance in Medicago sativa are of significant importance for the development of animal husbandry on salt-alkali lands and the restoration of vegetation in such areas. This study utilized salt-alkali tolerance Medicago sativa 'Zhaodong' (ZD) and salt-alkali sensitive variety M. sativa 'Zhongmu No.1′ (ZM) as materials. Physiological analyses, transcriptomic sequencing, and hormone-targeted metabolomics techniques were employed to investigate the differential responses of the two alfalfa varieties to NaHCO3 stress in terms of morphology, photosynthetic functionality, and oxidative damage indicators. Additionally, weighted gene co-expression network analysis (WGCNA) was utilized to elucidate key mechanisms underlying salt-alkali tolerance in alfalfa. The results indicate that NaHCO3 stress leads to photosynthetic inhibition and oxidative damage in alfalfa leaves. Under NaHCO3 stress, PSI in alfalfa leaves exhibits higher stability compared to PSII. The salt-alkali tolerance alfalfa variety ZD demonstrates stronger tolerance compared to the salt-alkali sensitive variety ZM. Furthermore, differentially expressed genes (DEGs) between the two varieties under NaHCO3 stress are primarily enriched in KEGG pathways such as chlorophyll synthesis, photosynthesis, carbon fixation, and plant hormone synthesis and signaling. Weighted gene co-expression network analysis (WGCNA) was conducted based on physiological and transcriptomic data. Most differentially expressed genes (DEGs) in the top two modules with the highest correlation to physiological indicators such as photosynthesis are enriched in hormone synthesis and signal transduction pathways. Additionally, key transcription factors involved in hormone signal transduction were identified within these modules, such as MYC2 and ABI5, which regulate jasmonic acid (JA) and abscisic acid (ABA) signaling, respectively. These findings suggest that plant hormone signaling may play a critical role in regulating salt-alkali tolerance in alfalfa. Further analysis was conducted on plant hormone levels and gene expression involved in biosynthesis and signal transduction processes. The results indicate that NaHCO3 stress leads to significant accumulation of ABA and JA content in alfalfa leaves. The biosynthesis and signal transduction pathways of ABA and JA are activated under NaHCO3 stress. Additionally, the salt-alkali tolerance alfalfa variety ZD exhibits a more sensitive response to ABA and JA signals compared to ZM. Salicylic acid (SA) shows a positive response to NaHCO3 stress only in the ZD variety, which may be one of the key reasons for its stronger salt-alkali tolerance. Under NaHCO3 stress, overall growth-promoting hormones (IAA, GA, CK) are downregulated in ZD but upregulated in ZM, indicating that the salt-alkali tolerance alfalfa variety ZD mainly regulates the balance between growth and resistance by modulating the ratio of growth-promoting and stress-related hormones in response to NaHCO3 stress. This study reveals that hormone signaling plays a key role in regulating the photosynthetic function of alfalfa in response to salt-alkali stress, which provides theoretical basis and clues for the molecular breeding of alfalfa for salt-alkali tolerance.

Interactions between Brassinosteroids and Strigolactones in Alleviating Salt Stress in Maize.

Exogenous brassinolide (BR) and strigolactones (SLs) play an important role in alleviating salt stress in maize. We studied the morphological and physiological responses of the salt-sensitive genotype PH4CV and salt-tolerant genotype Zheng58 to BR (1.65 nM), SL (1 µM), and BS (1.65 nM BR + 1 µM SL) under salt stress. Phenotypic analysis showed that salt stress significantly inhibited the growth of maize seedlings and significantly increased the content of Na+ in the roots. Exogenous hormones increased oxidase activity and decreased Na+ content in the roots and mitigated salt stress. Transcriptome analysis showed that the interaction of BR and SL is involved in photosynthesis-antenna proteins, the TCA cycle, and plant hormone signal transduction pathways. This interaction influences the expression of chlorophyll a/b-binding protein and glucose-6-phosphate isomerase 1 chloroplastic, and aconitase genes are affected. Furthermore, the application of exogenous hormones regulates the expression of genes associated with the signaling pathways of cytokinin (CK), gibberellins (GA), auxin (IAA), brassinosteroid (BR), abscisic acid (ABA), and jasmonic acid (JA). Additionally, exogenous hormones inhibit the expression of the AKT2/3 genes, which are responsible for regulating ion transduction and potassium ion influx. Four candidate genes that may regulate the seedling length of maize were screened out through WGCNA. Respective KOG notes concerned inorganic ion transport and metabolism, signal transduction mechanisms, energy production and conversion, and amino acid transport and metabolism. The findings of this study provide a foundation for the proposition that BR and SL can be employed to regulate salt stress alleviation in maize.

Transcriptomic and coexpression network analyses revealed the regulatory mechanism of Cydia pomonella infestation on the synthesis of phytohormones in walnut husks

The codling moth (Cydia pomonella) has a major effect on the quality and yield of walnut fruit. Plant defences respond to insect infestation by activating hormonal signalling and the flavonoid biosynthetic pathway. However, little is known about the role of walnut husk hormones and flavonoid biosynthesis in response to C. pomonella infestation. The phytohormone content assay revealed that the contents of salicylic acid (SA), abscisic acid (ABA), jasmonic acid (JA), jasmonic acid-isoleucine conjugate (JA-ILE), jasmonic acid-valine (JA-Val) and methyl jasmonate (MeJA) increased after feeding at different time points (0, 12, 24, 36, 48, and 72 h) of walnut husk. RNA-seq analysis of walnut husks following C. pomonella feeding revealed a temporal pattern in differentially expressed genes (DEGs), with the number increasing from 3,988 at 12 h to 5,929 at 72 h postfeeding compared with the control at 0 h postfeeding. Walnut husks exhibited significant upregulation of genes involved in various defence pathways, including flavonoid biosynthesis (PAL, CYP73A, 4CL, CHS, CHI, F3H, ANS, and LAR), SA (PAL), ABA (ZEP and ABA2), and JA (AOS, AOC, OPR, JAZ, and MYC2) pathways. Three gene coexpression networks that had a significant positive association with these hormonal changes were constructed based on the basis of weighted gene coexpression network analysis (WGCNA). We identified several hub transcription factors, including the turquoise module (AIL6, MYB4, PRE6, WRKY71, WRKY31, ERF003, and WRKY75), the green module (bHLH79, PCL1, APRR5, ABI5, and ILR3), and the magenta module (ERF27, bHLH35, bHLH18, TIFY5A, WRKY31, and MYB44). Taken together, these findings provide useful genetic resources for exploring the defence response mediated by phytohormones in walnut husks.

Identification of VvAGL Genes Reveals Their Network's Involvement in the Modulation of Seed Abortion via Responding Multi-Hormone Signals in Grapevines.

The formation of seedless traits is regulated by multiple factors. AGLs, which belong to the MADS-box family, were reported to be important regulators in this process; however, the underlying mechanism remains elusive. Here, we identified the VvAGL sub-family genes during the seed abortion process in seedless grapevine cv. 'JingkeJing' and found 40 differentially expressed VvAGL members and 1069 interacting proteins in this process. Interestingly, almost all members and their interacting proteins involved in the tryptophan metabolic pathway (K14486) and participated in the phytohormone signalling (KO04075) pathway, including the growth hormone (IAA), salicylic acid (SA), abscisic acid (ABA), cytokinin (CTK), and ethylene signalling pathways. The promoters of AGL sub-family genes contain cis-elements in response to hormones such as IAA, ABA, CTK, SA, and ETH, implying that they might respond to multi-hormone signals and involve in hormone signal transductions. Further expression analysis revealed VvAGL6-2, VvAGL11, VvAGL62-11, and VvAGL15 had the highest expression at the critical period of seed abortion, and there were positive correlations between ETH-VvAGL15-VvAGL6-2, ABA-VvAGL80, and SA-VvAGL62 in promoting seed abortion but negative feedback between IAA-VvAGL15-VvAGL6-2 and CTK-VvAGL11. Furthermore, many genes in the IAA, ABA, SA, CTK, and ETH pathways had a special expressional pattern in the seed, whereby we developed a regulatory network mediated by VvAGLs by responding to multihormonal crosstalk during grape seed abortion. Our findings provide new insights into the regulatory network of VvAGLs in multi-hormone signalling to regulate grape seed abortion, which could be helpful in the molecular breeding of high-quality seedless grapes.

Deciphering physiological and transcriptional mechanisms of maize seed germination.

Maize is a valuable raw material for feed and food production. Healthy seed germination is important for improving the yield and quality of maize. Seed aging occurs relatively fast in crops and it is a process that delays germination as well as reduces its rate and even causes total loss of seed viability. However, the physiological and transcriptional mechanisms that regulate maize seeds, especially aging seed germination remain unclear. Coronatine (COR) which is a phytotoxin produced by Pseudomonas syringae and a new type of plant growth regulator can effectively regulate plant growth and development, and regulate seed germination. In this study, the physiological and transcriptomic mechanisms of COR-induced maize seed germination under different aging degrees were analyzed. The results showed that 0.001-0.01μmol/L COR could promote the germination of aging maize seed and the growth of primary roots and shoots. COR treatment increased the content of gibberellins (GA3) and decreased the content of abscisic acid (ABA) in B73 seeds before germination. The result of RNA-seq analysis showed 497 differentially expressed genes in COR treatment compared with the control. Three genes associated with GA biosynthesis (ZmCPPS2, ZmD3, and ZmGA2ox2), and two genes associated with GA signaling transduction (ZmGID1 and ZmBHLH158) were up-regulated. Three genes negatively regulating GA signaling transduction (ZmGRAS48, ZmGRAS54, and Zm00001d033369) and two genes involved in ABA biosynthesis (ZmVP14 and ZmPCO14472) were down-regulated. The physiological test results also showed that the effects of GA and ABA on seed germination were similar to those of high and low-concentration COR, respectively, which indicated that the effect of COR on seed germination may be carried out through GA and ABA pathways. In addition, GO and KEGG analysis suggested that COR is also highly involved in antioxidant enzyme systems and secondary metabolite synthesis to regulate maize seed germination processes. These findings provide a valuable reference for further research on the mechanisms of maize seed germination.

Contrasted NCED gene expression across conifers with rising and peaking abscisic acid responses to drought

Conifer trees have diverse strategies to cope with drought. They accumulate the plant hormone abscisic acid (ABA) following a range of profiles from constantly rising to peaking and falling (R- and P-type) with direct effect on foliar transpiration. The molecular basis of this adaptive diversification among species is largely unknown. Here, we analysed the sequences of candidate ABA biosynthesis and catabolism genes and monitored their expression in response to intensifying drought. We studied young trees from Cupressaceae, Pinaceae, and Taxaceae under controlled drought conditions and compared changes in water status, ABA profiles and gene-specific transcript levels. Our data indicate that R-type and P-type ABA profiles may be controlled by divergent expression of genes involved in the biosynthetic and catabolic pathways of ABA, respectively, and emphasize a key role of nine-cis-epoxycarotenoid dioxygenases (NCED) genes. Our results open the doors to understanding the molecular basis of contrasted drought response strategies across conifer taxa, which we expect will help foresters grow more drought-resilient trees.

A novel Microbacterium strain SRS2 promotes the growth of Arabidopsis and MicroTom (S. lycopersicum) under normal and salt stress conditions.

Microbacterium strain SRS2 promotes growth and induces salt stress resistance in Arabidopsis and MicroTom in various growth substrates via the induction of the ABA pathway. Soil salinity reduces plant growth and development and thereby decreases the value and productivity of soils. Plant growth-promoting rhizobacteria (PGPR) have been shown to support plant growth such as in salt stress conditions. Here, Microbacterium strain SRS2, isolated from the root endosphere of tomato, was tested for its capability to help plants cope with salt stress. In a salt tolerance assay, SRS2 grew well up to medium levels of NaCl, but the growth was inhibited at high salt concentrations. SRS2 inoculation led to increased biomass of Arabidopsis and MicroTom tomato in various growth substrates, in the presence and in the absence of high NaCl concentrations. Whole-genome analysis revealed that the strain contains several genes involved in osmoregulation and reactive oxygen species (ROS) scavenging, which could potentially explain the observed growth promotion. Additionally, we also investigated via qRT-PCR, promoter::GUS and mutant analyses whether the abscisic acid (ABA)-dependent or -independent pathways for tolerance against salt stress were involved in the model plant, Arabidopsis. Especially in salt stress conditions, the plant growth-promotion effect of SRS2 was lost in aba1, abi4-102, abi3, and abi5-1 mutant lines. Furthermore, ABA genes related to salt stress in SRS2-inoculated plants were transiently upregulated compared to mock under salt stress conditions. Additionally, SRS2-inoculated ABI4::GUS and ABI5::GUS plants were slightly more activated compared to the uninoculated control under salt stress conditions. Together, these assays show that SRS2 promotes growth in normal and in salt stress conditions, the latter possibly via the induction of ABA-dependent and -independent pathways.

RiceMetaSys: Drought-miR, a one-stop solution for drought responsive miRNAs-mRNA module in rice.

MicroRNAs are key players involved in stress responses in plants and reports are available on the role of miRNAs in drought stress response in rice. This work reports the development of a database, RiceMetaSys: Drought-miR, based on the meta-analysis of publicly available sRNA datasets. From 28 drought stress-specific sRNA datasets, we identified 216 drought-responsive miRNAs (DRMs). The major features of the database include genotype-, tissue- and miRNA ID-specific search options and comparison of genotypes to identify common miRNAs. Co-localization of the DRMs with the known quantitative trait loci (QTLs), i.e., meta-QTL regions governing drought tolerance in rice pertaining to different drought adaptive traits, narrowed down this to 37 promising DRMs. To identify the high confidence target genes of DRMs under drought stress, degradome datasets and web resource on drought-responsive genes (RiceMetaSys: DRG) were used. Out of the 216 unique DRMs, only 193 had targets with high stringent parameters. Out of the 1081 target genes identified by Degradome datasets, 730 showed differential expression under drought stress in at least one accession. To retrieve complete information on the target genes, the database has been linked with RiceMetaSys: DRG. Further, we updated the RiceMetaSys: DRGv1 developed earlier with the addition of DRGs identified from RNA-seq datasets from five rice genotypes. We also identified 759 putative novel miRNAs and their target genes employing stringent criteria. Novel miRNA search has all the search options of known miRNAs and additionally, it gives information on their in silico validation features. Simple sequence repeat markers for both the miRNAs and their target genes have also been designed and made available in the database. Network analysis of the target genes identified 60 hub genes which primarily act through abscisic acid pathway and jasmonic acid pathway. Co-localization of the hub genes with the meta-QTL regions governing drought tolerance narrowed down this to 16 most promising DRGs. Database URL: http://14.139.229.201/RiceMetaSys_miRNA Updated database of RiceMetaSys URL: http://14.139.229.201/RiceMetaSysA/Drought/.