Tomato PYR/PYL/RCAR abscisic acid receptors show high expression in root, differential sensitivity to the abscisic acid agonist quinabactin, and the capability to enhance plant drought resistance

The Abscisic Acid Receptor Gene StPYL8-like from Solanum tuberosum Confers Tolerance to Drought Stress in Transgenic Plants

Pyrabactin resistance 1-like (PYL) proteins are abscisic acid (ABA) receptors that play a crucial role in the plant's response to adverse environmental conditions. However, as of yet, there is limited research on the role of PYL proteins in potato. In this study, a potato PYL gene, StPYL8-like, was identified through transcriptome analysis under drought stress. Molecular characterization revealed that the StPYL8-like protein possesses a highly conserved PYL family domain. Evolutionary analysis demonstrated that StPYL8-like protein clusters with various PYL proteins are involved in stress responses across different species. Functional assays showed that StPYL8-like robustly responds to different abiotic stresses, including drought and ABA treatment. Furthermore, the transient and stable expressions of StPYL8-like in tobacco enhanced their drought resistance, leading to increased plant height, leaf number, and fresh weight, as well as an improved root system. Transgenic tobacco carrying the StPYL8-like gene exhibited lower malondialdehyde (MDA) levels and higher proline accumulation and antioxidant enzyme activity compared to wild-type plants under drought conditions. Moreover, StPYL8-like upregulated the expression of stress-responsive genes (NtRD29A, NtLEA5, NtP5CS, NtPOD, NtSOD, and NtCAT) in transgenic plants subjected to drought stress. Collectively, these findings highlight the positive regulatory role of the StPYL8-like gene in enhancing potato plants' response to drought stress.

Overexpression of Potato PYL16 Gene in Tobacco Enhances the Transgenic Plant Tolerance to Drought Stress

PYR/PYL/RCAR proteins are abscisic acid (ABA) receptors that play a crucial role in plant responses to abiotic stresses. However, there have been no research reports on potato PYL so far. In this study, a potato PYL gene named StPYL16 was identified based on transcriptome data under drought stress. Molecular characteristics analysis revealed that the StPYL16 protein possesses an extremely conserved PYL family domain. The tissue expression results indicated that the StPYL16 is predominantly expressed at high levels in the underground parts, particularly in tubers. Abiotic stress response showed that StPYL16 has a significant response to drought treatment. Further research on the promoter showed that drought stress could enhance the activation activity of the StPYL16 promoter on the reporter gene. Then, transient and stable expression of StPYL16 in tobacco enhanced the drought resistance of transgenic plants, resulting in improved plant height, stem thickness, and root development. In addition, compared with wild-type plants, StPYL16 transgenic tobacco exhibited lower malondialdehyde (MDA) content, higher proline accumulation, and stronger superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) activities. Meanwhile, StPYL16 also up-regulated the expression levels of stress-related genes (NtSOD, NtCAT, NtPOD, NtRD29A, NtLEA5, and NtP5CS) in transgenic plants under drought treatment. These findings indicated that the StPYL16 gene plays a positive regulatory role in potato responses to drought stress.

Genome-wide analysis of the PYL-PP2C-SnRK2s family in the ABA signaling pathway of pitaya reveals its expression profiles under canker disease stress

BACKGROUND

Abscisic acid (ABA) plays a crucial role in seed dormancy, germination, and growth, as well as in regulating plant responses to environmental stresses during plant growth and development. However, detailed information about the PYL-PP2C-SnRK2s family, a central component of the ABA signaling pathway, is not known in pitaya.

RESULTS

In this study, we identified 19 pyrabactin resistance-likes (PYLs), 70 type 2 C protein phosphatases (PP2Cs), and 14 SNF1-related protein kinase 2s (SnRK2s) from pitaya. In pitaya, tandem duplication was the primary mechanism for amplifying the PYL-PP2C-SnRK2s family. Co-linearity analysis revealed more homologous PYL-PP2C-SnRK2s gene pairs located in collinear blocks between pitaya and Beta vulgaris L. than that between pitaya and Arabidopsis. Transcriptome analysis showed that the PYL-PP2C-SnRK2s gene family plays a role in pitaya's response to infection by N. dimidiatum. By spraying ABA on pitaya and subsequently inoculating it with N. dimidiatum, we conducted qRT-PCR experiments to observe the response of the PYL-PP2C-SnRK2s gene family and disease resistance-related genes to ABA. These treatments significantly enhanced pitaya's resistance to pitaya canker. Further protein interaction network analysis helped us identify five key PYLs genes that were upregulated during the interaction between pitaya and N. dimidiatum, and their expression patterns were verified by qRT-PCR. Subcellular localization analysis revealed that the PYL (Hp1879) gene is primarily distributed in the nucleus.

CONCLUSION

This study enhances our understanding of the response of PYL-PP2C-SnRK2s to ABA and also offers a new perspective on pitaya disease resistance.

Genome-wide identification, abiotic stress, and expression analysis of PYL family in Tartary buckwheat (Fagopyrum tataricum (L.) Gaertn.) during grain development

BACKGROUND

Abscisic acid (ABA) is a plant hormone that plays an important role in plant resistance to drought, salinity, cold, and pathogens. It is also important for regulating plant growth and development. Pyrabactin resistance/pyr1-like/regulatory components of the ABA receptor (PYL/RCAR) are ABA receptor proteins in plants and the core of ABA signal transduction pathways in plant regulatory factors. At present, there are no reports on the PYL family of Tartary buckwheat.

RESULTS

In this study, 19 paralogous form PYL genes in buckwheat were identified at the whole-genome level and named FtPYL1-FtPYL19 according to their positions on chromosomes. We further analyzed the gene structure, conserved motifs, cis-acting elements, gene duplication, phylogenetic relationships, and expression patterns under different stress treatments and during grain development of the 19 paralogous form PYL genes in Tartary buckwheat. The FtPYL gene exhibits a single exonic gene structure for about 68.4% of the duplicated forms from the total paralogous forms. The remaining subfamilies, such as I and II, contain three exons and two exons (e.g., FtPYL19), respectively. Nineteen FtPYL genes were evenly distributed across the eight chromosomes, with at least one FtPYL gene on each chromosome. In the FtPYL gene family, there was one tandem repeat event and five gene duplication events. We investigated the gene expression levels of FtPYL gene under four abiotic stresses and different stages of grain development. Under drought stress (PEG6000), the relative expression levels of FtPYL14 and FtPYL15 increased by fourfold. Under high temperature stress (38℃), the relative expression level of FtPYL16 dropped to 0.12, and that of FtPYL17 fell to 0.22. At different stages of grain development, the gene expression level of FtPY15 is extremely high at 19 D. The relative expression level of FtPYL7 in roots and stems reaches up to approximately 450, and the relative expression level of FtPYL10 in 13 D also reaches up to 248. In this study, the PYL gene family of Tartary buckwheat was identified and analyzed based on the whole genome, and 19 paralogous form FtPYL genes of Tartary buckwheat were bioinformatically analyzed. The expression patterns of 19 paralogous form FtPYL genes in Tartary buckwheat cultivars under different stress treatments and during grain development were analyzed. It was found that the FtPYL gene played an important role in grain development.

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.

Transcriptome and metabolome analyses reveal the regulatory role of MdPYL9 in drought resistance in apple

BACKGROUND

The mechanisms by which the apple MdPYL9 gene mediates the response to drought stress remain unclear. Here, transcriptome and metabolome analyses of apple plants under drought were used to investigate the mechanisms by which MdPYL9 regulates the response to drought stress in apple. MdPYL9-overexpressed transgenic and non-transgenic apple histoculture seedlings were rooted, transplanted, and subjected to drought treatments to clarify the mechanisms underlying the responses of apples to drought stress through phenotypic observations, physiological and biochemical index measurements, and transcriptomic and metabolomic analyses.

RESULTS

Under drought stress treatment, transgenic plants were less affected by drought stress than non-transgenic plants. Decreases in the net photosynthetic rate, stomatal conductance, and transpiration rate of transgenic apple plants were less pronounced in transgenic plants than in non-transgenic plants, and increases in the intercellular CO2 concentration were less pronounced in transgenic plants than in non-transgenic plants. The relative electrical conductivity and content of malondialdehyde, superoxide anion, and hydrogen peroxide were significantly lower in transgenic plants than in non-transgenic plants, and the chlorophyll content and activities of antioxidant enzymes (superoxide dismutase, peroxidase, and catalase) were significantly higher in transgenic plants than in non-transgenic plants. The number of differentially expressed genes (DEGs) involved in the response to drought stress was lower in transgenic plants than in non-transgenic plants, and the most significant and highly annotated DEGs in the transgenic plants were involved in the flavonoid biosynthesis pathway, and the most significant and highly annotated DEGs in control plants were involved in the phytohormone signal transduction pathway. The number of differentially accumulated metabolites involved in the response to drought stress was lower in transgenic plants than in non-transgenic plants, and up-regulated metabolites were significantly enriched in apigenin-7-O-glucoside in transgenic plants and in abscisic acid in non-transgenic plants. In the flavonoid biosynthetic pathway, the expression of genes encoding chalcone synthase (CHS) and chalcone isomerase (CHI) was more significantly down-regulated in non-transgenic plants than in transgenic plants, and the expression of the gene encoding 4-coumarate-CoA ligase (4CL) was more significantly up-regulated in transgenic plants than in non-transgenic plants, which resulted in the significant up-regulation of apigenin-7-O-glucoside in transgenic plants.

CONCLUSIONS

The above results indicated that the over-expression of MdPYL9 increased the drought resistance of plants under drought stress by attenuating the down-regulation of the expression of genes encoding CHS and CHI and enhancing the up-regulated expression of the gene encoding 4CL, which enhanced the content of apigenin-7-O-glucoside.

Genome-Wide Identification of PYL/RCAR ABA Receptors and Functional Analysis of LbPYL10 in Heat Tolerance in Goji (Lycium barbarum)

The characterization of the PYL/RCAR ABA receptors in a great deal of plant species has dramatically advanced the study of ABA functions involved in key physiological processes. However, the genes in this family are still unclear in Lycium (Goji) plants, one of the well-known economically, medicinally, and ecologically valuable fruit crops. In the present work, 12 homologs of Arabidopsis PYL/RCAR ABA receptors were first identified and characterized from Lycium (L.) barbarum (LbPYLs). The quantitative real-time PCR (qRT-PCR) analysis showed that these genes had clear tissue-specific expression patterns, and most of them were transcribed in the root with the largest amount. Among the three subfamilies, while the Group I and Group III members were down-regulated by extraneous ABA, the Group II members were up-regulated. At 42 °C, most transcripts showed a rapid and violent up-regulation response to higher temperature, especially members of Group II. One of the genes in the Group II members, LbPYL10, was further functionally validated by virus-induced gene silencing (VIGS) technology. LbPYL10 positively regulates heat stress tolerance in L. barbarum by alleviating chlorophyll degradation, thus maintaining chlorophyll stability. Integrating the endogenous ABA level increase following heat stress, it may be concluded that LbPYL-mediated ABA signaling plays a vital role in the thermotolerance of L. barbarum plants. Our results highlight the strong potential of LbPYL genes in breeding genetically modified L. barbarum crops that acclimate to climate change.

Structural and functional characterization of genes PYL-PP2C-SnRK2s in the ABA signalling pathway of Cucurbita pepo

BACKGROUND

The core regulation of the abscisic acid (ABA) signalling pathway comprises the multigenic families PYL, PP2C, and SnRK2. In this work, we conducted a genome-wide study of the components of these families in Cucurbita pepo.

RESULTS

The bioinformatic analysis of the C. pepo genome resulted in the identification of 19 CpPYL, 102 CpPP2C and 10 CpSnRK2 genes. The investigation of gene structure and protein motifs allowed to define 4 PYL, 13 PP2C and 3 SnRK2 subfamilies. RNA-seq analysis was used to determine the expression of these gene families in different plant organs, as well as to detect their differential gene expression during germination, and in response to ABA and cold stress in leaves. The specific tissue expression of some gene members indicated the relevant role of some ABA signalling genes in plant development. Moreover, their differential expression under ABA treatment or cold stress revealed those ABA signalling genes that responded to ABA, and those that were up- or down-regulated in response to cold stress. A reduced number of genes responded to both treatments. Specific PYL-PP2C-SnRK2 genes that had potential roles in germination were also detected, including those regulated early during the imbibition phase, those regulated later during the embryo extension and radicle emergence phase, and those induced or repressed during the whole germination process.

CONCLUSIONS

The outcomes of this research open new research lines for agriculture and for assessing gene function in future studies.

Silicon nanoparticles improved the osmolyte production, antioxidant defense system, and phytohormone regulation in Elymus sibiricus (L.) under drought and salt stress

Drought and salt stress negatively influence the growth and development of various plant species. Thus, it is crucial to overcome these stresses for sustainable agricultural production and the global food chain. Therefore, the present study investigated the potential effects of exogenous silicon nanoparticles (SiNPs) on the physiological and biochemical parameters, and endogenous phytohormone contents of Elymus sibiricus under drought and salt stress. Drought stress was given as 45% water holding capacity, and salt stress was given as 120 mM NaCl. The seed priming was done with different SiNP concentrations: SiNP1 (50 mg L-1), SiNP2 (100 mg L-1), SiNP3 (150 mg L-1), SiNP4 (200 mg L-1), and SiNP5 (250 mg L-1). Both stresses imposed harmful impacts on the analyzed parameters of plants. However, SiNP5 increased the chlorophylls and osmolyte accumulation such as total proteins by 96% and 110% under drought and salt stress, respectively. The SiNP5 significantly decreased the oxidative damage and improved the activities of SOD, CAT, POD, and APX by 10%, 54%, 104%, and 211% under drought and 42%, 75%, 72%, and 215% under salt stress, respectively. The SiNPs at all concentrations considerably improved the level of different phytohormones to respond to drought and salt stress and increased the tolerance of Elymus plants. Moreover, SiNPs decreased the Na+ and increased K+ concentrations in Elymus suggesting the reduction in salt ion accumulation under salinity stress. Overall, exogenous application (seed priming/dipping) of SiNPs considerably enhanced the physio-biochemical and metabolic responses, resulting in an increased tolerance to drought and salt stresses. Therefore, this study could be used as a reference to further explore the impacts of SiNPs at molecular and genetic level to mitigate abiotic stresses in forages and related plant species.

Signalling mechanisms and agricultural applications of (Z)-3-hexenyl butyrate-mediated stomatal closure

Biotic and abiotic stresses can severely limit crop productivity. In response to drought, plants close stomata to prevent water loss. Furthermore, stomata are the main entry point for several pathogens. Therefore, the development of natural products to control stomata closure can be considered a sustainable strategy to cope with stresses in agriculture. Plants respond to different stresses by releasing volatile organic compounds. Green leaf volatiles, which are commonly produced across different plant species after tissue damage, comprise an important group within volatile organic compounds. Among them, (Z)-3-hexenyl butyrate (HB) was described as a natural inducer of stomatal closure, playing an important role in stomatal immunity, although its mechanism of action is still unknown. Through different genetic, pharmacological, and biochemical approaches, we here uncover that HB perception initiates various defence signalling events, such as activation of Ca2+ permeable channels, mitogen-activated protein kinases, and production of Nicotinamide adenine dinucleotide phosphate (NADPH) oxidase-mediated reactive oxygen species. Furthermore, HB-mediated stomata closure was found to be independent of abscisic acid biosynthesis and signalling. Additionally, exogenous treatments with HB alleviate water stress and improve fruit productivity in tomato plants. The efficacy of HB was also tested under open field conditions, leading to enhanced resistance against Phytophthora spp. and Pseudomonas syringae infection in potato and tomato plants, respectively. Taken together, our results provide insights into the HB signalling transduction pathway, confirming its role in stomatal closure and plant immune system activation, and propose HB as a new phytoprotectant for the sustainable control of biotic and abiotic stresses in agriculture.

Genome-wide identification of PYL/PYR-PP2C (A)-SnRK2 genes in Eutrema and their co-expression analysis in response to ABA and abiotic stresses

ABA signaling core components PYR/PYL, group A PP2C and SnRK2 play important roles in various environmental stress responses of plants. This study identified 14 PYR/PYL, 9 PP2C (A), and 10 SnRK2 genes from halophytic Eutrema. Phylogenetic analysis showed 4 EsPYR/PYL, 4 EsPP2C (A) and 3 EsSnRK2 subfamilies characterized, which was supported by their gene structures and protein motifs. Large-scale segmental duplication event was demonstrated to be a major contributor to expansion of the EsPYL-PP2C (A)-SnRK2 gene families. Synteny relationship analysis revealed more orthologous PYL-PP2C (A)-SnRK2 gene pairs located in collinear blocks between Eutrema and Brassica than that between Eutrema and Arabidopsis. RNA-seq and qRT-PCR revealed EsABI1, EsABI2 and EsHAL2 showed a significantly up-regulated expression in leaves and roots in response to ABA, NaCl or cold stress. Three markedly co-expression modules of ABA/R-brown, NaCl/L-lightsteelblue1 and Cold/R-lightgreen were uncovered to contain EsPYL-PP2C (A)-SnRK2 genes by WGCNA analysis. GO and KEGG analysis indicated that the genes of ABA/R-brown module containing EsHAB1, EsHAI2 and EsSnRK2.6 were enriched in proteasome pathway. Further, EsHAI2-OE transgenic Arabidopsis lines showed significantly enhanced seeds germination and seedlings growth. This work provides a new insight for elucidating potential molecular functions of PYL-PP2C (A)-SnRK2 responding to ABA and abiotic stresses.

ABA signaling branches out: emerging ABA-related signaling functions in Solanum tuberosum

This article comments on:

Liu T, Dong L, Wang E, Liu S, Cheng Y, Zhao J, Xu S, Liang Z, Ma H, Nie B, Song B. 2023. StHAB1, a negative regulatory factor in abscisic acid signaling, plays crucial roles in potato drought tolerance and shoot branching. Journal of Experimental Botany 74, 6708–6721.

CePP2C19 confers tolerance to drought by regulating the ABA sensitivity in Cyperus esculentus

BACKGROUND

Tiger nut (Cyperus esculentus) is widely known as an additional source of food, oil and feed worldwide. The agricultural production of tiger nut has been greatly hindered by drought stress, reducing both yield and quality. Protein phosphatase 2 C (PP2Cs) plays an important role in plant responses to drought stress however, the molecular mechanism of PP2Cs in tiger nuts still unclear.

RESULTS

In this study, we identified a putative group A PP2C-encoding gene (CePP2C19) from tiger nut using transcriptome analysis, which is highly induced by drought stress. The transient expression assay suggested that CePP2C19 was localized to nucleus. Furthermore, the interaction between CePP2C19 and CePYR1, a coreceptor for ABA signaling, was first detected using a yeast two-hybrid assay and then verified using a bimolecular fluorescence complementation (BiFC) analysis. In addition, the transgenic Arabidopsis lines overexpressing CePP2C19 exhibited extreme tolerance to ABA and mannitol stresses during seed germination and root growth. At the mature stage, overexpression of CePP2C19 resulted in a higher tolerance to drought stress in transgenic Arabidopsis, as confirmed by a visible phenotype and several physiological parameters. Noticeably, the silencing of CePP2C19 by virus-induced gene silencing (VIGS) showed obvious reduction in drought tolerance in tiger nut plants.

CONCLUSIONS

The CePP2C19 emerges as a pivotal gene involved in the ABA signaling pathway, which likely reduce ABA sensitivity and thus enhances drought tolerance in Cyperus esculentus.

Genome-wide identification and expression analysis of PYL family genes and functional characterization of GhPYL8D2 under drought stress in Gossypium hirsutum

Cotton is a crucial economic crop, serving as a natural fiber source for the textile industry. However, drought stress poses a significant threat to cotton fiber quality and productivity worldwide. Pyrabactin Resistance 1-Like (PYL) proteins, as abscisic acid (ABA) receptors, play a crucial role in adverse stress responses, but knowledge about the PYLs in cotton remains limited. In our study, we identified 40 GhPYL genes in Gossypium hirsutum through a genome-wide analysis of the cotton genome database. Our analysis revealed that the PYL family formed three distinct subfamilies with typical family characteristics in G. hirsutum. Additionally, through quantitative expression analysis, including transcriptome dataset and qRT-PCR, we found that all GhPYLs were expressed in all tissues of G. hirsutum, and all GhPYLs were differentially expressed under drought stress. Among them, GhPYL4A1, GhPY5D1, GhPY8D2, and a member of the type 2C protein phosphatases clade A family in Gossypium hirsutum (GhPP2CA), GhHAI2D, showed significant differences in expression levels within 12 h after stress treatment. Our protein interaction analysis and BiFC demonstrated the complex regulatory network between GhPYL family proteins and GhPP2CA proteins. We also found that there is an interaction between GhPYL8D2 and GhHAI2D, and through drought treatment of transgenic cotton, we found that GhPYL8D2 played a vital role in the response of G. hirsutum to drought through stomatal control via co-regulation with GhHAI2D. Our findings provide useful insights into the regulation of GhPYL family genes that occur in response to abiotic stresses in cotton.

A metabolome and transcriptome survey to tap the dynamics of fruit prolonged shelf-life and improved quality within Greek tomato germplasm

Introduction

Tomato is a high economic value crop worldwide with recognized nutritional properties and diverse postharvest potential. Nowadays, there is an emerging awareness about the exploitation and utilization of underutilized traditional germplasm in modern breeding programs. In this context, the existing diversity among Greek accessions in terms of their postharvest life and nutritional value remains largely unexplored.

Methods

Herein, a detailed evaluation of 130 tomato Greek accessions for postharvest and nutritional characteristics was performed, using metabolomics and transcriptomics, leading to the selection of accessions with these interesting traits.

Results

The results showed remarkable differences among tomato Greek accessions for overall ripening parameters (color, firmness) and weight loss. On the basis of their postharvest performance, a balance between short shelf life (SSL) and long shelf life (LSL) accessions was revealed. Metabolome analysis performed on 14 selected accessions with contrasting shelf-life potential identified a total of 206 phytonutrients and volatile compounds. In turn, transcriptome analysis in fruits from the best SSL and the best LSL accessions revealed remarkable differences in the expression profiles of transcripts involved in key metabolic pathways related to fruit quality and postharvest potential.

Discussion

The pathways towards cell wall synthesis, polyamine synthesis, ABA catabolism, and steroidal alkaloids synthesis were mostly induced in the LSL accession, whereas those related to ethylene biosynthesis, cell wall degradation, isoprenoids, phenylpropanoids, ascorbic acid and aroma (TomloxC) were stimulated in the SSL accession. Overall, these data would provide valuable insights into the molecular mechanism towards enhancing shelf-life and improving flavor and aroma of modern tomato cultivars.

Biostimulant activity of Galaxaura rugosa seaweed extracts against water deficit stress in tomato seedlings involves activation of ABA signaling

Water scarcity is a serious constraint for agriculture, and global warming and climate change can exacerbate it in many areas. Therefore, sustainable approaches must be implemented to deal with current and future water scarcity scenarios. Genetic and chemical approaches are being applied to manage this limitation and maintain crop yields. In particular, biostimulants obtained from natural sources such as marine algae are promising aids for coping with water deficit stress in agriculture. Here we present a bioprospection study of extracts of the macroalgae Bonnemaisonia hamifera, Galaxaura rugosa, Dasycladus vermicularis, Ulva clathrata, Cystoseira foeniculacea, Cystoseira humilis, Lobophora dagamae, Colpomenia sinuosa and Halopteris scoparia from the north coast of Tenerife, in the Canary Islands. The aqueous extracts of Bonnemaisonia hamifera, Galaxaura rugosa, Dasycladus vermicularis and Cystoseira humilis show biostimulant activity against water deficit stress in tomato seedlings under controlled conditions, providing higher tolerance than the mock-treated control. The Galaxaura rugosa extract showed the highest biostimulant activity against water deficit stress. We demonstrate that this positive effect involves the activation of the abscisic acid (ABA) pathway in Arabidopsis thaliana (arabidopsis) and Solanum lycopersicum (tomato). Application of G. rugosa extract to the root system by drenching tomato seedlings subjected to water deficit leads to improved CO2 assimilation and water use efficiency (WUEp), compared to mock-treated plants. These results highlight a new potential seaweed source of substances with osmoprotectant properties, useful for biostimulant development. Future studies may provide further insight into which components of the seaweed extract induce activation of the ABA pathway.

PYL Family Genes from Liriodendron chinense Positively Respond to Multiple Stresses

The phytohormone abscisic acid (ABA) plays important roles in response to abiotic and biotic stresses in plants. Pyrabactin resistance 1-like (PYR/PYL) proteins are well-known as ABA receptors, which are responsible for ABA signal transduction. Nevertheless, the characteristics of PYL genes from Liriodendron chinense, an endangered timber tree, remain unclear in coping with various stresses. In this study, five PYLs were identified from the genome of Liriodendron chinense by sequence alignment and conserved motif analysis, which revealed that these LcPYLs contain a conserved gate and latch motif for ABA binding. The LcPYL promoters possess a series of cis-acting elements involved in response to various hormone and abiotic stresses. Moreover, the transcriptome data of Liriodendron hybrid leaves reveal that LcPYL genes specifically transcript under different abiotic stresses; Lchi11622 transcription was induced by drought and cold treatment, and Lchi01385 and Lchi16997 transcription was upregulated under cold and hot stress, respectively. Meanwhile, the LcPYLs with high expression levels shown in the transcriptomes were also found to be upregulated in whole plants treated with the same stresses tested by qPCR. Moreover, under biotic stress caused by scale insect and whitefly, Liriodendron hybrid leaves exhibited a distinct phenotype including disease spots that are dark green in the middle and yellow on the margin; the qPCR results showed that the relative expression levels of Lchi13641 and Lchi11622 in infected leaves were upregulated by 1.76 and 3.75 folds relative to normal leaves, respectively. The subcellular localizations of these stress-responsive LcPYLs were also identified in protoplasts of Liriodendron hybrid. These results provide a foundation to elucidate the function of PYLs from this elite tree species and assist in understanding the molecular mechanism of Liriodendron hybrid in dealing with abiotic and biotic stresses. In future research, the detailed biological function of LcPYLs and the genetic redundancy between LcPYLs can be explored by gene overexpression and knockout based on this study.

GhPYL9-5D and GhPYR1-3 A positively regulate Arabidopsis and cotton responses to ABA, drought, high salinity and osmotic stress

BACKGROUND

Abscisic acid (ABA) receptor pyrabactin resistance 1/PYR1-like/regulatory components of ABA receptor proteins (PYR/PYL/RCARs) have been demonstrated to play pivotal roles in ABA signaling and in response to diverse environmental stimuli including drought, salinity and osmotic stress in Arabidopsis. However, whether and how GhPYL9-5D and GhPYR1-3A, the homologues of Arabidopsis PYL9 and PYR1 in cotton, function in responding to ABA and abiotic stresses are still unclear.

RESULTS

GhPYL9-5D and GhPYR1-3A were targeted to the cytoplasm and nucleus. Overexpression of GhPYL9-5D and GhPYR1-3A in Arabidopsis wild type and sextuple mutant pyr1pyl1pyl2pyl4pyl5pyl8 plants resulted in ABA hypersensitivity in terms of seed germination, root growth and stomatal closure, as well as seedling tolerance to water deficit, salt and osmotic stress. Moreover, the VIGS (Virus-induced gene silencing) cotton plants, in which GhPYL9-5D or GhPYR1-3A were knocked down, showed clearly reduced tolerance to polyethylene glycol 6000 (PEG)-induced drought, salinity and osmotic stresses compared with the controls. Additionally, transcriptomic data revealed that GhPYL9-5D was highly expressed in the root, and GhPYR1-3A was strongly expressed in the fiber and stem. GhPYL9-5D, GhPYR1-3A and their homologs in cotton were highly expressed after treatment with PEG or NaCl, and the two genes were co-expressed with redox signaling components, transcription factors and auxin signal components. These results suggest that GhPYL9-5D and GhPYR1-3A may serve important roles through interplaying with hormone and other signaling components in cotton adaptation to salt or osmotic stress.

CONCLUSIONS

GhPYL9-5D and GhPYR1-3A positively regulate ABA-mediated seed germination, primary root growth and stomatal closure, as well as tolerance to drought, salt and osmotic stresses likely through affecting the expression of multiple downstream stress-associated genes in Arabidopsis and cotton.

Abscisic acid mimic-fluorine derivative 4 alleviates water deficit stress by regulating ABA-responsive genes, proline accumulation, CO2 assimilation, water use efficiency and better nutrient uptake in tomato plants

Water deficit represents a serious limitation for agriculture and both genetic and chemical approaches are being used to cope with this stress and maintain plant yield. Next-generation agrochemicals that control stomatal aperture are promising for controlling water use efficiency. For example, chemical control of abscisic acid (ABA) signaling through ABA-receptor agonists is a powerful method to activate plant adaptation to water deficit. Such agonists are molecules able to bind and activate ABA receptors and, although their development has experienced significant advances in the last decade, few translational studies have been performed in crops. Here, we describe protection by the ABA mimic-fluorine derivative 4 (AMF4) agonist of the vegetative growth in tomato plants subjected to water restriction. Photosynthesis in mock-treated plants is markedly impaired under water deficit conditions, whereas AMF4 treatment notably improves CO₂ assimilation, the relative plant water content and growth. As expected for an antitranspirant molecule, AMF4 treatment diminishes stomatal conductance and transpiration in the first phase of the experiment; however, when photosynthesis declines in mock-treated plants as stress persists, higher photosynthetic and transpiration parameters are recorded in agonist-treated plants. Additionally, AMF4 increases proline levels over those achieved in mock-treated plants in response to water deficit. Thus water deficit and AMF4 cooperate to upregulate P5CS1 through both ABA-independent and ABA-dependent pathways, and therefore, higher proline levels are produced Finally, analysis of macronutrients reveals higher levels of Ca, K and Mg in AMF4- compared to mock-treated plants subjected to water deficit. Overall, these physiological analyses reveal a protective effect of AMF4 over photosynthesis under water deficit and enhanced water use efficiency after agonist treatment. In summary, AMF4 treatment is a promising approach for farmers to protect the vegetative growth of tomatoes under water deficit stress.

Abscisic Acid Synthesis and Signaling during the Ripening of Raspberry (Rubus idaeus 'Heritage') Fruit

The raspberry (Rubus idaeus L.) fruit is characterized by its richness in functional molecules and high nutritional value, but the high rate of fruit softening limits its quality during postharvest. Raspberry drupelets have a particular ripening regulation, depending partially on the effect of ethylene produced from the receptacle. However, the possible role of abscisic acid (ABA) in the modulation of quality parameters during the ripening of raspberry is unclear. This study characterized the fruit quality-associated parameters and hormonal contents during fruit development in two seasons. The quality parameters showed typical changes during ripening: a drastic loss of firmness, increase in soluble solids content, loss of acidity, and turning to a red color from the large green stage to fully ripe fruit in both seasons. A significant increase in the ABA content was observed during the ripening of drupelets and receptacles, with the higher content in the receptacle of ripe and overripe stages compared to the large green stage. Moreover, identification of ABA biosynthesis-(9-cis-epoxycarotenoid dioxygenase/NCED) and ABA receptor-related genes (PYRs-like receptors) showed three genes encoding RiNCEDs and nine genes for RiPYLs. The expression level of these genes increased from the large green stage to the full-ripe stage, specifically characterized by a higher expression of RiNCED1 in the receptacle tissue. This study reports a consistent concomitant increase in the ABA content and the expression of RiNCED1, RiPYL1, and RiPYL8 during the ripening of the raspberry fruit, thus supporting the role for ABA signaling in drupelets.

Identification of Pyrabactin resistance 1-like (PYL) genes in Brachypodium distachyon and functional characterization of BdPYL5

Abscisic acid (ABA) is an endogenous phytohormone that plays an important role in regulating plant growth, development, and stress response. Pyrabactin resistance 1-like (PYR/PYL) proteins are ABA receptors and core components of ABA signalling in plants. This study identified nine PYL genes in the Brachypodium distachyon genome and they distribute on three chromosomes. Phylogenetical BdPYLs were classified into three clades. 81 protein-protein interactions between 9 BdPYLs and 9 BdPP2C proteins were predicted and 66 pairs were verified by yeast two-hybrid assay previously. Relatively, BdPYL genes are expressed in leaves at high level, and ABA and drought regulate their expression. A homologue of Arabidopsis PYL9, BdPYL5 was selected to overexpress in Arabidopsis to characterize its function. In general, overexpression of BdPYL5 enhanced ABA sensitivity and drought tolerance, implying its conserved function. Our study lays the foundation for further functional elucidation of BdPYL genes.

Structure-guided engineering of a receptor-agonist pair for inducible activation of the ABA adaptive response to drought

Strategies to activate abscisic acid (ABA) receptors and boost ABA signaling by small molecules that act as ABA receptor agonists are promising biotechnological tools to enhance plant drought tolerance. Protein structures of crop ABA receptors might require modifications to improve recognition of chemical ligands, which in turn can be optimized by structural information. Through structure-based targeted design, we have combined chemical and genetic approaches to generate an ABA receptor agonist molecule (iSB09) and engineer a CsPYL1 ABA receptor, named CsPYL1^5m, which efficiently binds iSB09. This optimized receptor-agonist pair leads to activation of ABA signaling and marked drought tolerance. No constitutive activation of ABA signaling and hence growth penalty was observed in transformed Arabidopsis thaliana plants. Therefore, conditional and efficient activation of ABA signaling was achieved through a chemical-genetic orthogonal approach based on iterative cycles of ligand and receptor optimization driven by the structure of ternary receptor-ligand-phosphatase complexes.

Traces of Introgression from cAus into Tropical Japonica Observed in African Upland Rice Varieties

BACKGROUND

Asian rice Oryza sativa, first domesticated in East Asia, has considerable success in African fields. When and where this introduction occurred is unclear. Rice varieties of Asian origin may have evolved locally during and after migration to Africa, resulting in unique adaptations, particularly in relation to upland cultivation as frequently practiced in Africa.

METHODS

We investigated the genetic differentiation between Asian and African varieties using the 3000 Rice Genomes SNP dataset. African upland cultivars were first characterized using principal component analysis among 292 tropical Japonica accessions from Africa and Asia. The particularities of African accessions were then explored using two inference techniques, PCA-KDE for supervised classification and chromosome painting, and ELAI for individual allelic dosage monitoring.

KEY RESULTS

Ambiguities of local differentiation between Japonica and other groups pointed at genomic segments that potentially resulted from genetic exchange. Those specific to West African upland accessions were concentrated on chromosome 6 and featured several cAus introgression signals, including a large one between 17.9 and 21.7 Mb. We found iHS statistics in support of positive selection in this region and we provide a list of candidate genes enriched in GO terms that have regulatory functions involved in stress responses that could have facilitated adaptation to harsh upland growing conditions.

Jasmonic acid enhances osmotic stress responses by MYC2-mediated inhibition of protein phosphatase 2C1 and response regulators 26 transcription factor in tomato

The jasmonic acid (JA) signaling pathway is involved in the plant response to drought stress. JA and other hormones synergistically regulate the drought response in plants. However, the molecular mechanism underlying this synergism remains poorly defined. In the present study, transcriptome analyses of guard cells and quantitative PCR experiments revealed that MYC2 negatively regulated the negative regulator of ABA signaling, SlPP2C1, and the type-B response regulator in the cytokinin pathway, SlRR26, and this negative regulation was direct. SlRR26 overexpression reduced drought tolerance in transgenic tomatoes, whereas slrr26^cr lines were more tolerant to drought. SlRR26 negatively modulated reactive oxygen species levels in stomata and stomatal closure through RobhB. Moreover, SlRR26 overexpression counteracted JA-mediated stomatal closure, suggesting that SlRR26 played a negative role in the JA-mediated drought response. These findings suggest that MYC2 plays a key role in JA-regulated stomatal closure under drought stress by inhibiting SlPP2C1 and SlRR26.

How Changes in ABA Accumulation and Signaling Influence Tomato Drought Responses and Reproductive Development

Water deficit conditions trigger the production of a chemical signal, the phytohormone abscisic acid (ABA), which coordinates multiple responses at different temporal and spatial scales. Despite the complexity of natural drought conditions, the modulation of ABA signaling could be harnessed to ameliorate the drought performances of crops in the face of increasingly challenging climate conditions. Based on recent studies, increasing ABA sensitivity can lead to genotypes with improved drought resistance traits, with sustained biomass production in water-limiting environments and little or no costs with respect to biomass production under optimal conditions. However, variations in ABA production and sensitivity lead to changes in various aspects of reproductive development, including flowering time. Here we provide an updated summary of the literature on ABA-related genes in tomato and discuss how their manipulation can impact water-deficit-related responses and/or other developmental traits. We suggest that a better understanding of specific ABA components’ function or their expression may offer novel tools to specifically engineer drought resistance without affecting developmental traits.

PePYL4 enhances drought tolerance by modulating water-use efficiency and ROS scavenging in Populus

Drought is one of the major limiting factors in the growth of terrestrial plants. Abscisic acid (ABA) and pyrabactin resistance 1/prabactin resistance-1 like/regulatory components of ABA receptors (PYR/PYL/RCARs) play a key role in response to drought stress. However, the underlying mechanisms of this control remain largely elusive in trees. In this study, PePYL4, a potential ortholog of the PYR/PYL/RCARs gene, was cloned from Populus euphratica. It was localized in the cytoplasm and nucleus, induced by ABA, osmotic and dehydration treatments. To study the potential biological functions of PePYL4, transgenic triploid white poplars (Populus tomentosa 'YiXianCiZhu B38') overexpressing PePYL4 were generated. PePYL4 overexpression significantly increased ABA sensitivity and reduced stomatal aperture. Compared with wild-type plants, transgenic plants had higher water-use efficiency (WUE) and lower transpiration. When exposed to drought stress, PePYL4 overexpression plants maintained higher photosynthetic activity and accumulated more biomass. Moreover, overexpression of PePYL4 improved antioxidant enzyme activity and ascorbate content to accelerate reactive oxygen species scavenging. Meanwhile, upregulation expression of the stress-related genes also contributed to improving the drought tolerance of transgenic plants. In conclusion, our data suggest that PePYL4 is a promising gene target for regulating WUE and drought tolerance in Populus.

Amino acid motifs for the identification of novel protein interactants

Biological systems consist of multiple components of different physical and chemical properties that require complex and dynamic regulatory loops to function efficiently. The discovery of ever more novel interacting sites in complex proteins suggests that we are only beginning to understand how cellular and biological functions are integrated and tuned at the molecular and systems levels. Here we review recently discovered interacting sites which have been identified through rationally designed amino acid motifs diagnostic for specific molecular functions, including enzymatic activities and ligand-binding properties. We specifically discuss the nature of the latter using as examples, novel hormone recognition and gas sensing sites that occur in moonlighting protein complexes. Drawing evidence from the current literature, we discuss the potential implications at the cellular, tissue, and/or organismal levels of such non-catalytic interacting sites and provide several promising avenues for the expansion of amino acid motif searches to discover hitherto unknown protein interactants and interaction networks. We believe this knowledge will unearth unexpected functions in both new and well-characterized proteins, thus filling existing conceptual gaps or opening new avenues for applications either as drug targets or tools in pharmacology, cell biology and bio-catalysis. Beyond this, motif searches may also support the design of novel, effective and sustainable approaches to crop improvements and the development of new therapeutics.

Modifications of Phytohormone Metabolism Aimed at Stimulation of Plant Growth, Improving Their Productivity and Tolerance to Abiotic and Biotic Stress Factors

Due to the growing human population, the increase in crop yield is an important challenge for modern agriculture. As abiotic and biotic stresses cause severe losses in agriculture, it is also crucial to obtain varieties that are more tolerant to these factors. In the past, traditional breeding methods were used to obtain new varieties displaying demanded traits. Nowadays, genetic engineering is another available tool. An important direction of the research on genetically modified plants concerns the modification of phytohormone metabolism. This review summarizes the state-of-the-art research concerning the modulation of phytohormone content aimed at the stimulation of plant growth and the improvement of stress tolerance. It aims to provide a useful basis for developing new strategies for crop yield improvement by genetic engineering of phytohormone metabolism.

Transcriptome analysis of response strategy in Hemerocallis fulva under drought stress

BACKGROUND

Hemerocallis fulva is an important ground cover plant widely used in urban greening. The analysis of the molecular mechanism underlying the drought response of H. fulva can lay a foundation for improving its adaptability and expanding its planting area.

OBJECTIVE

To reveal the drought response mechanisms of H. fulva, identify candidate unigenes associated with drought response, and lay a foundation for further unigenes functional study and drought resistance improvement of H. fulva via genetic engineering.

METHODS

RNA was isolated from H. fulva under different experimental conditions. De novo transcriptomic analysis of the samples was performed to screen drought response unigenes. The transcriptional changes of candidate drought response unigenes were verified by quantitative real-time PCR.

RESULTS

The differentially expressed unigenes and their functions were analyzed after H. fulva treated by PEG-simulated drought stress and rewatering. The candidate unigenes, associated with H. fulva drought response, were identified after transcriptome analysis. Then, the transcription level of drought response unigenes of H. fulva under different conditions was further verified. Abscisic acid, protein phosphorylation, sterol biosynthesis and ion transport were involved in drought response with quick restore in H. fulva. The response unigenes, involved in hormone (ABA, JA, CK and GA) signaling pathways, defense response, high light response, karrikin response and leaf shaping, can maintain at changed expression levels even after stress withdraw.

CONCLUSION

Hemerocallis fulva has unique drought response mechanism. Negative regulation mechanism may play more important roles in drought response of H. fulva. The analysis of candidate unigenes, associated with drought response, lays a foundation for further drought resistance improvement of H. fulva.

TaPYL4, an ABA receptor gene of wheat, positively regulates plant drought adaptation through modulating the osmotic stress-associated processes

BACKGROUND

Abscisic acid receptors (ABR) involve transduction of the ABA signaling in plants, impacting largely on stress-defensive physiological processes and plant osmotic stress response. In this study, we characterized TaPYL4, a gene of ABR family in T. aestivum, in mediating plant drought tolerance given scarcity of functional characterization on wheat ABR members thus far.

RESULTS

TaPYL4 harbors nine conserved domains shared by its PYL counterparts, targeting onto plasma membrane and nucleus after endoplasmic reticulum assortment. TaPYL4 interacts with TaPP2C2 whereas the latter with TaSnRK2.1, which establish a core module of the ABA signaling pathway. TaPYL4 expression was upregulated in root and aerial tissues upon drought stress. Overexpressing TaPYL4 conferred plants improved growth traits whereas knockdown expression of target gene alleviated growth feature compared with wild type under drought treatment. The TaPYL4-enhanced drought adaptation associates gene function in positively regulating stomata movement, osmolyte biosynthesis, and root system architecture (RSA) establishment. Expression analysis on the P5CS family genes involving proline biosynthesis indicated that TaP5CS1 exerts critical roles in promoting osmolytes accumulation in drought-challenged TaPYL4 lines. TaPIN9, a PIN-FORMED gene modulating cellular auxin translocation, was validated to function as a crucial mediator in defining RSA establishment underlying TaPYL4 regulation. Transcriptome analysis revealed that TaPYL4 controls transcription of numerous genes, which impact on physiological processes associated with 'biological process', 'molecular component', and 'cellular process'. Moreover, the differentially expressed genes mediated by TaPYL4 were closely related to stress defensive pathways.

CONCLUSIONS

Our investigation suggested that TaPYL4 acts as a positive regulator in plant drought tolerance and a valuable target for engineering drought-tolerant cultivars in T. aestivum.

Structure-Based Modulation of the Ligand Sensitivity of a Tomato Dimeric Abscisic Acid Receptor Through a Glu to Asp Mutation in the Latch Loop

The binding of the plant phytohormone Abscisic acid (ABA) to the family of ABA receptors (PYR/PYL/RCAR) triggers plant responses to abiotic stress. Thus, the implementation of genetic or chemical strategies to modulate PYR/PYL activity might be biotechnologically relevant. We have employed the available structural information on the PYR/PYL receptors to design SlPYL1, a tomato receptor, harboring a single point mutation that displays enhanced ABA dependent and independent activity. Interestingly, crystallographic studies show that this mutation is not directly involved in ABA recognition or in the downstream phosphatase (PP2C) inhibitory interaction, rather, molecular dynamic based ensemble refinement restrained by crystallographic data indicates that it enhances the conformational variability required for receptor activation and it is involved in the stabilization of an active form of the receptor. Moreover, structural studies on this receptor have led to the identification of niacin as an ABA antagonist molecule in vivo. We have found that niacin blocks the ABA binding site by mimicking ABA receptor interactions, and the niacin interaction inhibits the biochemical activity of the receptor.

Co-silencing of ABA receptors (SlRCAR) reveals interactions between ABA and ethylene signaling during tomato fruit ripening

The ripening of fleshy fruits is highly dependent on the regulation of endogenous hormones, including ethylene, abscisic acid (ABA) and other phytohormones. However, the regulatory mechanism of ABA signaling and its interaction with ethylene signaling in fruit ripening are still unclear. In this study, multi-gene interference (RNAi) was applied to silence the ABA receptor genes in tomato for screening the specific receptors that mediate ABA signaling during fruit ripening. The results indicated that the ABA receptors, including SlRCAR9, SlRCAR12, SlRCAR11, and SlRCAR13, participate in the regulation of tomato fruit ripening. Comparative analysis showed that SlRCAR11 and SlRCAR13 play more important roles in mediating ABA signaling during tomato fruit ripening. Co-silencing of the four genes encoding these receptors could weaken the ethylene biosynthesis and signaling pathway at the early stage of tomato fruit ripening, leading to delayed fruit ripening. Meanwhile, co-silencing enhanced fruit firmness, and altered the shelf-life and susceptibility to Botrytis cinerea of the transgenic fruits. Furthermore, blocking ABA signaling did not affect the ability of ethylene to induce fruit ripening, whereas the block may inhibit the effectiveness of ABA in promoting fruit ripening. These results suggested that ABA signaling may be located upstream of ethylene signaling in regulating fruit ripening. Our findings provide a new insight into the complex regulatory network of phytohormones in regulating fruit ripening in tomato.

The wheat ABA receptor gene TaPYL1-1B contributes to drought tolerance and grain yield by increasing water-use efficiency

The role of abscisic acid (ABA) receptors, PYR1/PYL/RCAR (PYLs), is well established in ABA signalling and plant drought response, but limited research has explored the regulation of wheat PYLs in this process, especially the effects of their allelic variations on drought tolerance or grain yield. Here, we found that the overexpression of a TaABFs-regulated PYL gene, TaPYL1-1B, exhibited higher ABA sensitivity, photosynthetic capacity and water-use efficiency (WUE), all contributed to higher drought tolerance than that of wild-type plants. This heightened water-saving mechanism further increased grain yield and protected productivity during water deficit. Candidate gene association analysis revealed that a favourable allele TaPYL1-1B^In-442 , carrying an MYB recognition site insertion in the promoter, is targeted by TaMYB70 and confers enhanced expression of TaPYL1-1B in drought-tolerant genotypes. More importantly, an increase in frequency of the TaPYL1-1B^In-442 allele over decades among modern Chinese cultivars and its association with high thousand-kernel weight together demonstrated that it was artificially selected during wheat improvement efforts. Taken together, our findings illuminate the role of TaPYL1-1B plays in coordinating drought tolerance and grain yield. In particular, the allelic variant TaPYL1-1B^In-442 substantially contributes to enhanced drought tolerance while maintaining high yield, and thus represents a valuable genetic target for engineering drought-tolerant wheat germplasm.

Brassinosteroid-Insensitive 1-Associated Receptor Kinase 1 Modulates Abscisic Acid Signaling by Inducing PYR1 Monomerization and Association With ABI1 in Arabidopsis

Brassinosteroid-Insensitive 1-Associated Receptor Kinase 1 (BAK1) is a versatile kinase involved in many different plant developmental responses. Previously, we showed that BAK1 interacts with open stomata 1 (OST1), a cytoplasmic kinase, to promote abscisic acid (ABA)-induced stomatal closure. ABA is a plant hormone that primarily regulates stress responses and is recognized by the PYRABACTIN RESISTANCE1 (PYR1)/PYR1-LIKE (PYL)/REGULATORY COMPONENT OF ABA RECEPTORS (RCAR), which activates ABA signaling. Here, we demonstrated that BAK1 interacts with PYR1 and phosphorylates PYR1 in response to ABA in plants. We identified T137 and S142 of PYR1 as the phosphosites targeted by BAK1. Using phosphomimetic (PYR1DD) and phospho-dead (PYR1AA) PYR1 compared with wild-type PYR1, we showed that transgenic plants overexpressing a phosphomimetic PYR1 exhibited hypersensitivity to the inhibition of ABA-induced root growth and seed germination and increased ABA-induced stomatal closure and ABA-inducible gene expression. As underlying reasons for these phenomena, we further demonstrated that phosphorylated PYR1 existed in a monomeric form, in which ABA binding was increased, and the degree of complex formation with ABI1 was also increased. These results suggest that BAK1 positively modulates ABA signaling through interaction with PYR1, in addition to OST1.

Genome-wide identification and comparative analysis of the PYL gene family in eight Rosaceae species and expression analysis of seeds germination in pear

Abscisic acid (ABA) is a phytohormone that plays important roles in the regulation of plant growth, seed germination, and stress responses. The pyrabactin resistance 1-like (PYR/PYL) protein, an ABA receptor, was involved in the initial step in ABA signal transduction. However, the evolutionary history and characteristics of PYL genes expression remain unclear in Chinese white pear (Pyrus bretschneideri) or other Rosaceae species. In this study, 67 PYL genes were identified in eight Rosaceae species, and have been classified into three subgroups based on specific motifs and phylogenetic analysis. Intriguingly, we observed that whole-genome duplication (WGD) and dispersed duplication (DSD) have a major contribution to PYL family expansion. Purifying selection was the major force in PYL genes evolution. Expression analysis finds that PYL genes may function in multiple pear tissues. qRT-PCR validation of 11 PbrPYL genes indicates their roles in seed germination and abiotic stress responses. Our study provides a basis for further elucidation of the function of PYL genes and analysis of their expansion, evolution and expression patterns, which helps to understand the molecular mechanism of pear response to seed germination and seedling abiotic stress.

PYL1- and PYL8-like ABA Receptors of Nicotiana benthamiana Play a Key Role in ABA Response in Seed and Vegetative Tissue

To face the challenges of climate change and sustainable food production, it is essential to develop crop genome editing techniques to pinpoint key genes involved in abiotic stress signaling. The identification of those prevailing abscisic acid (ABA) receptors that mediate plant-environment interactions is quite challenging in polyploid plants because of the high number of genes in the PYR/PYL/RCAR ABA receptor family. Nicotiana benthamiana is a biotechnological crop amenable to genome editing, and given the importance of ABA signaling in coping with drought stress, we initiated the analysis of its 23-member family of ABA receptors through multiplex CRISPR/Cas9-mediated editing. We generated several high-order mutants impaired in NbPYL1-like and NbPYL8-like receptors, which showed certain insensitivity to ABA for inhibition of seedling establishment, growth, and development of shoot and lateral roots as well as reduced sensitivity to the PYL1-agonist cyanabactin (CB). However, in these high-order mutants, regulation of transpiration was not affected and was responsive to ABA treatment. This reveals a robust and redundant control of transpiration in this allotetraploid plant that probably reflects its origin from the extreme habitat of central Australia.

Mechanisms of Abscisic Acid-Mediated Drought Stress Responses in Plants

Drought is one of the major constraints to rain-fed agricultural production, especially under climate change conditions. Plants evolved an array of adaptive strategies that perceive stress stimuli and respond to these stress signals through specific mechanisms. Abscisic acid (ABA) is a premier signal for plants to respond to drought and plays a critical role in plant growth and development. ABA triggers a variety of physiological processes such as stomatal closure, root system modulation, organizing soil microbial communities, activation of transcriptional and post-transcriptional gene expression, and metabolic alterations. Thus, understanding the mechanisms of ABA-mediated drought responses in plants is critical for ensuring crop yield and global food security. In this review, we highlighted how plants adjust ABA perception, transcriptional levels of ABA- and drought-related genes, and regulation of metabolic pathways to alter drought stress responses at both cellular and the whole plant level. Understanding the synergetic role of drought and ABA will strengthen our knowledge to develop stress-resilient crops through integrated advanced biotechnology approaches. This review will elaborate on ABA-mediated drought responses at genetic, biochemical, and molecular levels in plants, which is critical for advancement in stress biology research.

Genome-wide identification and expression analysis of the cucumber PYL gene family

Abscisic acid (ABA) is a very important hormone in plants. It regulates growth and development of plants and plays an important role in biotic and abiotic stresses. The Pyrabactin resistance 1-like (PYR/PYL) proteins play a central role in ABA signal transduction pathways. The working system of PYL genes in cucumber, an important economical vegetable (Cucumis sativus L.), has not been fully studied yet. Through bioinformatics, a total of 14 individual PYL genes were identified in Chinese long '9930' cucumber. Fourteen PYL genes were distributed on six chromosomes of cucumber, and their encoded proteins predicted to be distributed in cytoplasm and nucleus. Based on the phylogenetic analysis, the PYL genes of cucumber, Arabidopsis, rice, apple, Brachypodium distachyon and soybeancould be classified into three groups. Genetic structures and conserved domains analysis revealed that CsPYL genes in the same group have similar exons and conserved domains. By predicting cis-elements in the promoters, we found that all CsPYL members contained hormone and stress-related elements. Additionally, the expression patterns of CsPYL genes were specific in tissues. Finally, we further examined the expression of 14 CsPYL genes under ABA, PEG, salt stress. The qRT-PCR results showed that most PYL gene expression levels were up-regulated. Furthermore, with different treatments about 3h, the relative expression of PYL8 was up-regulated and more than 20 times higher than 0h. It indicated that this gene may play an important role in abiotic stress.

Abscisic Acid: Role in Fruit Development and Ripening

Abscisic acid (ABA) is a plant growth regulator known for its functions, especially in seed maturation, seed dormancy, adaptive responses to biotic and abiotic stresses, and leaf and bud abscission. ABA activity is governed by multiple regulatory pathways that control ABA biosynthesis, signal transduction, and transport. The transport of the ABA signaling molecule occurs from the shoot (site of synthesis) to the fruit (site of action), where ABA receptors decode information as fruit maturation begins and is significantly promoted. The maximum amount of ABA is exported by the phloem from developing fruits during seed formation and initiation of fruit expansion. In the later stages of fruit ripening, ABA export from the phloem decreases significantly, leading to an accumulation of ABA in ripening fruit. Fruit growth, ripening, and senescence are under the control of ABA, and the mechanisms governing these processes are still unfolding. During the fruit ripening phase, interactions between ABA and ethylene are found in both climacteric and non-climacteric fruits. It is clear that ABA regulates ethylene biosynthesis and signaling during fruit ripening, but the molecular mechanism controlling the interaction between ABA and ethylene has not yet been discovered. The effects of ABA and ethylene on fruit ripening are synergistic, and the interaction of ABA with other plant hormones is an essential determinant of fruit growth and ripening. Reaction and biosynthetic mechanisms, signal transduction, and recognition of ABA receptors in fruits need to be elucidated by a more thorough study to understand the role of ABA in fruit ripening. Genetic modifications of ABA signaling can be used in commercial applications to increase fruit yield and quality. This review discusses the mechanism of ABA biosynthesis, its translocation, and signaling pathways, as well as the recent findings on ABA function in fruit development and ripening.

GhHAI2, GhAHG3, and GhABI2 Negatively Regulate Osmotic Stress Tolerance via ABA-Dependent Pathway in Cotton (Gossypium hirsutum L.)

The type 2C protein phosphatases (PP2Cs) are well known for their vital roles in plant drought stress responses, but their molecular mechanisms in cotton (Gossypium hirsutum L.) remain largely unknown. Here, we investigated the role of three clade A PP2C genes, namely, GhHAI2, GhAHG3, and GhABI2, in regulating the osmotic stress tolerance in cotton. The transcript levels of GhHAI2, GhAHG3, and GhABI2 were rapidly induced by exogenous abscisic acid (ABA) and polyethylene glycol (PEG) treatment. Silencing of GhHAI2, GhAHG3, and GhABI2 via virus-induced gene silencing (VIGS) improved osmotic tolerance in cotton due to decreased water loss, increase in both relative water content (RWC) and photosynthetic gas exchange, higher antioxidant enzyme activity, and lower malondialdehyde (MDA) content. The root analysis further showed that GhHAI2, GhAHG3, and GhABI2-silenced plants were more responsive to osmotic stress. Yeast two-hybrid (Y2H) and luciferase complementation imaging (LCI) assays further substantiated that GhHAI2, GhAHG3, and GhABI2 interact with the core receptors of ABA signaling, GhPYLs. The expression of several ABA-dependent stress-responsive genes was significantly upregulated in GhHAI2-, GhAHG3-, and GhABI2-silenced plants. Our findings suggest that GhHAI2, GhAHG3, and GhABI2 act as negative regulators in the osmotic stress response in cotton through ABA-mediated signaling.

Cloning and expression analyses of a Pyrabactin Resistance 1 (PYR1) gene from Magnolia sieboldii K. Koch

Magnolia sieboldii K. Koch is endemic to China and has high medicinal and ornamental values. However, its seed exhibits morphophysiological dormancy, and the molecular mechanisms of which are not clearly understood. To reveal the regulation mechanism of the ABA signal in seed dormancy, the M. sieboldii ABA receptor Pyrabactin Resistance 1 (PYR1) gene was cloned and analyzed. Analysis of the MsPYR1 sequence analysis showed that the full-length cDNA contained a complete open reading frame of 987 bp and encoded a predicted protein of 204 amino acid residues. The protein had a relative molecular weight of 22.661 kDa and theoretical isoelectric point of 5.01. The transcript levels of MsPYR1 were immediately upregulated at 16 DAI and then decreased at 40 DAI. The highest transcript level of MsPYR1 was found in the dry seeds, indicating that the MsPYR1 gene may play an important role in the regulation of dormancy. The MsPYR1 gene cDNA was successfully expressed in E. coli Rosetta (DE3), and the protein bands were consistent with the prediction. The Anti-MsPYR1antibody could detect the expression of MsPYR1 in M. sieboldii. The results provided a foundation for further study of the function of the MsPYR1 gene.ABBREVIATIONSABA: Abscisic acid; MPD: morphophysiological; PYR1: Pyrabactin Resistance1; PYL: Pyr1-Like; RCAR: Regulatory Components of Aba Receptors; PP2C: protein phosphatases 2C; SnRK2: sucrose non-fermenting1-related protein kinase2; DAI: day after imbibition; NCBI: National Center for Biotechnology Information; BCA: Bicinchoninic acid; CDD: Conserved Domains.

Roles of Glutathione in Mediating Abscisic Acid Signaling and Its Regulation of Seed Dormancy and Drought Tolerance

Plant growth and development and interactions with the environment are regulated by phytohormones and other signaling molecules. During their evolution, plants have developed strategies for efficient signal perception and for the activation of signal transduction cascades to maintain proper growth and development, in particular under adverse environmental conditions. Abscisic acid (ABA) is one of the phytohormones known to regulate plant developmental events and tolerance to environmental stresses. The role of ABA is mediated by both its accumulated level, which is regulated by its biosynthesis and catabolism, and signaling, all of which are influenced by complex regulatory mechanisms. Under stress conditions, plants employ enzymatic and non-enzymatic antioxidant strategies to scavenge excess reactive oxygen species (ROS) and mitigate the negative effects of oxidative stress. Glutathione (GSH) is one of the main antioxidant molecules playing a critical role in plant survival under stress conditions through the detoxification of excess ROS, maintaining cellular redox homeostasis and regulating protein functions. GSH has recently emerged as an important signaling molecule regulating ABA signal transduction and associated developmental events, and response to stressors. This review highlights the current knowledge on the interplay between ABA and GSH in regulating seed dormancy, germination, stomatal closure and tolerance to drought.

Overproduction of ABA in rootstocks alleviates salinity stress in tomato shoots

To determine whether root-supplied ABA alleviates saline stress, tomato (Solanum lycopersicum L. cv. Sugar Drop) was grafted onto two independent lines (NCED OE) overexpressing the SlNCED1 gene (9-cis-epoxycarotenoid dioxygenase) and wild type rootstocks. After 200 days of saline irrigation (EC = 3.5 dS m^-1 ), plants with NCED OE rootstocks had 30% higher fruit yield, but decreased root biomass and lateral root development. Although NCED OE rootstocks upregulated ABA-signalling (AREB, ATHB12), ethylene-related (ACCs, ERFs), aquaporin (PIPs) and stress-related (TAS14, KIN, LEA) genes, downregulation of PYL ABA receptors and signalling components (WRKYs), ethylene synthesis (ACOs) and auxin-responsive factors occurred. Elevated SlNCED1 expression enhanced ABA levels in reproductive tissue while ABA catabolites accumulated in leaf and xylem sap suggesting homeostatic mechanisms. NCED OE also reduced xylem cytokinin transport to the shoot and stimulated foliar 2-isopentenyl adenine (iP) accumulation and phloem transport. Moreover, increased xylem GA₃ levels in growing fruit trusses were associated with enhanced reproductive growth. Improved photosynthesis without changes in stomatal conductance was consistent with reduced stress sensitivity and hormone-mediated alteration of leaf growth and mesophyll structure. Combined with increases in leaf nutrients and flavonoids, systemic changes in hormone balance could explain enhanced vigour, reproductive growth and yield under saline stress.

Genome-wide identification of ABA receptor PYL/RCAR gene family and their response to cold stress in Medicago sativa L

Abscisic acid (ABA) is an important phytohormone involved in plant growth, plant development, and the protection of plants against abiotic stresses. PYL/RCAR (pyrabactin resistance/pyr1-like/regulatory components of ABA receptor) is the receptor protein of ABA and the core component of the ABA signal transduction network. The PYL gene family has been identified and analyzed in many species, however, there is no report about the research on the whole genome-wide identification of the alfalfa (Medicago sativa L.) PYL gene family. Therefore, to explore the function of alfalfa PYL genes, 39 MsPYL genes were identified by analyzing the recently published genome of alfalfa. Using bioinformatics methods, we systematically analyzed the chromosome location, protein physicochemical properties, evolutionary relationship, conserved motifs, and response to low-temperature stress of the MsPYL family of alfalfa. The results showed that 39 alfalfa MsPYL genes were distributed on 24 chromosomes, and the analysis of gene duplication events showed that fragment duplication was predominant duplication in alfalfa MsPYL family gene expansion. The phylogenetic tree of MsPYL protein of alfalfa and the phylogenetic tree of PYL genes of 3 species show that the MsPYL gene family can be divided into 3 subfamilies, and the structures of the same subfamilies are relatively similar. The 39 MsPYL gene family members of alfalfa contain 10 Motifs. Motif1, Motif2, Motif3, and Motif5 are the conserved motifs shared by these genes; cis-regulatory elements in promoter regions indicate that regulatory elements related to transcription, cell cycle, development, hormone, and stress response are abundantly present in the MsPYL promoter sequences; Real-time fluorescence quantitative PCR analysis showed that the expression of MsPYL genes can be induced by low-temperature treatment. This study provides a reference for further exploring the structural and functional characterization of the alfalfa PYL gene family.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01066-3.

An Update on Crop ABA Receptors

The hormone abscisic acid (ABA) orchestrates the plant stress response and regulates sophisticated metabolic and physiological mechanisms essential for survival in a changing environment. Plant ABA receptors were described more than 10 years ago, and a considerable amount of information is available for the model plant Arabidopsis thaliana. Unfortunately, this knowledge is still very limited in crops that hold the key to feeding a growing population. In this review, we summarize genomic, genetic and structural data obtained in crop ABA receptors. We also provide an update on ABA perception in major food crops, highlighting specific and common features of crop ABA receptors.

The intricacy of silicon, plant growth regulators and other signaling molecules for abiotic stress tolerance: An entrancing crosstalk between stress alleviators

Unfavorable environmental conditions are the critical inimical to the sustainable agriculture. Among various novel strategies designed to protect plants from abiotic stress threats, use of mineral elements as 'stress mitigators' has emerged as the most crucial and interesting aspect. Silicon (Si) is a quasi-essential nutrient that mediates plant growth and development and interacts with plant growth regulators (PGRs) and signaling molecules to combat abiotic stress induced adversities in plants and increase stress tolerance. PGRs are one of the most important chemical messengers that mediate plant growth and development during stressful conditions. However, the individual roles of Si and PGRs have extensively defined but their exquisite crosstalk with each other to mediate plant stress responses is still indiscernible. The present review is an upfront effort to delineate an intricate crosstalk/interaction between Si and PGRs to reduce abiotic stress adversities. The combined effects of interaction of Si with other signaling molecules such as reactive oxygen species (ROS), nitric oxide (NO) and calcium (Ca²⁺) for the survival of plants under stress and optimal conditions are also discussed.

Expression and processing of polycistronic artificial microRNAs and trans-acting siRNAs from transiently introduced transgenes in Solanum lycopersicum and Nicotiana benthamiana

Targeted gene silencing using small regulatory RNAs is a widely used technique for genetic studies in plants. Artificial microRNAs are one common approach, as they have the advantage of producing just a single functional small RNA, which can be designed for high target specificity and low off-target effects. Simultaneous silencing of multiple targets with artificial microRNAs can be achieved by producing polycistronic microRNA precursors. Alternatively, specialized trans-acting short interfering RNA (tasiRNA) precursors can be designed to produce several specific tasiRNAs at once. Here we tested several artificial microRNA- and tasiRNA-based methods for multiplexed gene silencing in Solanum lycopersicum (tomato) and Nicotiana benthamiana. All analyses used transiently expressed transgenes delivered by infiltration of leaves with Agrobacterium tumefacians. Small RNA sequencing analyses revealed that many previously described approaches resulted in poor small RNA processing. The 5'-most microRNA precursor hairpins on polycistronic artificial microRNA precursors were generally processed more accurately than precursors at the 3'-end. Polycistronic artificial microRNAs where the hairpin precursors were separated by transfer RNAs had the best processing precision. Strikingly, artificial tasiRNA precursors failed to be processed in the expected phased manner in our system. These results highlight the need for further development of multiplexed artificial microRNA and tasiRNA strategies. The importance of small RNA sequencing, as opposed to single-target assays such as RNA blots or real-time polymerase chain reaction, is also discussed.

Integration of mRNA and miRNA analysis reveals the molecular mechanism of potato (Solanum tuberosum L.) response to alkali stress

The continuing increase in the global saline-alkali land area has made saline-alkali stress the principal abiotic stress limiting plant growth. Potato is the most important non-grain crop, and its production is also severely limited by saline-alkali stress. However, few studies have addressed the mechanism of saline-alkali tolerance of potato with a focus on its response to neutral salt NaCl stress, or its response to alkali stress. Recently, miRNA-mRNA analyses have helped advance our understanding of how plants respond to stress. Here, we have characterized the morphological, physiological, and transcriptome changes of tissue culture seedlings of potato variety "Qingshu No. 9" treated with NaHCO₃ (for 0, 2, 6, and 24 h). We found that the leaves of tissue culture seedlings wilted and withered under alkali stress, and the contents of ABA, BRs, trehalose, and lignin in roots increased significantly. The contents of GAs decreased significantly. Subsequently, miRNA-seq analysis results identified 168 differentially expressed miRNAs (DEMIs) under alkali stress, including 21 exist miRNAs and 37 known miRNAs from 47 families and 110 novel miRNAs. The mRNA-seq results identified 5731 differentially expressed mRNAs (DEMs) under alkali stress. By miRNA-mRNA integrated analysis, were obtained 33 miRNA-target gene pairs composed of 20 DEMIs and 33 DEMs. Next, we identified the "phenylpropanoid biosynthesis", "plant hormone signal transduction", and "starch and sucrose metabolism" pathways as necessary for potato to respond to alkali stress. miR4243-x and novel-m064-5p were involved in the response of potato to alkali stress by their negative regulatory effects on shikimate O-hydroxycinnamoyltransferase (HCT) and sucrose-phosphate synthase (SPS) genes, respectively. The expression results of miRNA and mRNA were verified by quantitative real-time PCR (qRT-PCR). Our results clarify the mechanism of potato response to alkali stress at the miRNA level, providing new insights into the molecular mechanisms of potato's response to alkali stress. We report many candidate miRNAs and mRNAs for molecular-assisted screening and salt-alkali resistance breeding.

Signaling in the Tomato Immunity against Fusarium oxysporum

New strategies of control need to be developed with the aim of economic and environmental sustainability in plant and crop protection. Metabolomics is an excellent platform for both understanding the complex plant-pathogen interactions and unraveling new chemical control strategies. GC-MS-based metabolomics, along with a phytohormone analysis of a compatible and incompatible interaction between tomato plants and Fusarium oxysporum f. sp. lycopersici, revealed the specific volatile chemical composition and the plant signals associated with them. The susceptible tomato plants were characterized by the over-emission of methyl- and ethyl-salicylate as well as some fatty acid derivatives, along with an activation of salicylic acid and abscisic acid signaling. In contrast, terpenoids, benzenoids, and 2-ethylhexanoic acid were differentially emitted by plants undergoing an incompatible interaction, together with the activation of the jasmonic acid (JA) pathway. In accordance with this response, a higher expression of several genes participating in the biosynthesis of these volatiles, such as MTS1, TomloxC,TomloxD, and AOS, as well as JAZ7, a JA marker gene, was found to be induced by the fungus in these resistant plants. The characterized metabolome of the immune tomato plants could lead to the development of new resistance inducers against Fusarium wilt treatment.

Identification of ABA-Mediated Genetic and Metabolic Responses to Soil Flooding in Tomato (Solanum lycopersicum L. Mill)

Soil flooding is a compound abiotic stress that alters soil properties and limits atmospheric gas diffusion (O₂ and CO₂) to the roots. The involvement of abscisic acid (ABA) in the regulation of soil flooding-specific genetic and metabolic responses has been scarcely studied despite its key importance as regulator in other abiotic stress conditions. To attain this objective, wild type and ABA-deficient tomatoes were subjected to short-term (24 h) soil waterlogging. After this period, gas exchange parameters were reduced in the wild type but not in ABA-deficient plants that always had higher E and g _s . Transcript and metabolite alterations were more intense in waterlogged tissues, with genotype-specific variations. Waterlogging reduced the ABA levels in the roots while inducing PYR/PYL/RCAR ABA receptors and ABA-dependent transcription factor transcripts, of which induction was less pronounced in the ABA-deficient genotype. Ethylene/O₂-dependent genetic responses (ERFVIIs, plant anoxia survival responses, and genes involved in the N-degron pathway) were induced in hypoxic tissues independently of the genotype. Interestingly, genes encoding a nitrate reductase and a phytoglobin involved in NO biosynthesis and scavenging and ERFVII stability were induced in waterlogged tissues, but to a lower extent in ABA-deficient tomato. At the metabolic level, flooding-induced accumulation of Ala was enhanced in ABA-deficient lines following a differential accumulation of Glu and Asp in both hypoxic and aerated tissues, supporting their involvement as sources of oxalacetate to feed the tricarboxylic acid cycle in waterlogged tissues and constituting a potential advantage upon long periods of soil waterlogging. The promoter analysis of upregulated genes indicated that the production of oxalacetate from Asp via Asp oxidase, energy processes such as acetyl-CoA, ATP, and starch biosynthesis, and the lignification process were likely subjected to ABA regulation. Taken together, these data indicate that ABA depletion in waterlogged tissues acts as a positive signal, inducing several specific genetic and metabolic responses to soil flooding.