Multiple Gibberellin Receptors Contribute to Phenotypic Stability under Changing Environments

Functional identification of mango MiGID1A and MiGID1B genes confers early flowering and stress tolerance

The GIBBERELLIN INSENSITIVE DWARF1 (GID1) gene encodes a receptor integral to Gibberellic acid (GA) signaling, which is pivotal for plant growth, development, and stress responses. Until now, GID1 genes have not been documented in mango. In this research, the mango (Mangifera indica) genome yielded four GID1 homologous genes, and this study focuses on the research of MiGID1A and MiGID1B genes. Expression analysis indicated that MiGID1A is mainly expressed in leaves, while MiGID1B is predominantly found in flowers and buds. Both genes exhibited a significant upsurge in expression under salt and drought stress conditions. Moreover, the overexpression of these genes significantly advanced early flowering under long-day conditions. MiGID1A and MiGID1B transgenic plants showed significantly higher root length and survival rate than WT plants under drought and salt stress treatment. In addition, under drought and salt stress treatment, the contents of malonaldehyde (MAD) and hydrogen peroxide (H2O2) decreased significantly, and the levels of proline (Pro) and superoxide dismutase (SOD) notably increased in the MiGID1A-OE and MiGID1B-OE transgenic plants. GA3 treatment significantly improved germination rates, root elongation, and early flowering in both MiGID1A-OE and MiGID1B-OE lines. At the same time, ABA treatment alleviated the inhibition of seed germination, root growth, and flowering in transgenic Arabidopsis. Moreover, yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays demonstrated that MiGID1A and MiGID1B were capable of interacting with DELLA family proteins. Existing reports have demonstrated that GID1 participates in various regulatory processes by promoting the degradation of DELLA proteins. SQUAMOSA promoter binding protein-like (SPL3a/b) and WRKY12a/b. The findings imply a significant regulatory function for the MiGID1A and MiGID1B genes in the processes of flowering, stress management, and gibberellin response. KEY MESSAGE: MiGID1 as a GA receptor plays a critical role in the function of hormones, stress response, and promoting plant flowering.

Induction of α-amylase and endosperm-imposed seed dormancy: two pioneering papers in gibberellin research

MAIN CONCLUSION

Two papers with quite different objectives established protocols that proved pivotal for future work on the role of gibberellins in seed germination. In their paper published in 1967, Russell Jones and Joseph Varner (Planta 72: 155-161) developed a bioassay based on induction of α-amylase activity in barley embryo-less half-seeds that was specific for bioactive gibberellins. The induction of α-amylase in the aleurone of barley and other cereals was to become the experimental system of choice to study gibberellin signalling. However, despite much progress in identifying the molecular events linking gibberellin action and α-amylase gene expression, in many cases their role in the process is still unclear. In 1987, Steven Groot and Cees Karssen (Planta 171:525-531) showed that germination of tomato seeds was limited by the ability of the radicle to penetrate the surrounding layers, with the endosperm forming the major barrier. They used a modified needle attached to a tensiometer to measure the force required to break through the endosperm. While in wild-type seeds, a factor from the embryo, assumed to be gibberellin, promoted breakdown of the endosperm, gibberellin-deficient seeds required an external supply of the hormone to weaken the endosperm or for it to be mechanically disrupted for germination to occur. The paradigm of seed germination being physically restricted by surrounding layers and the role of gibberellin in weakening these tissues has been confirmed in many eudicot species. Gibberellin signalling induces the production of cell-wall loosening enzymes in the micropylar endosperm adjacent to the radicle, but it is unclear whether or not this is a direct response. In both eudicot and monocot systems, there is still much to learn about the role of gibberellin signalling in germination.

Dressed Up to the Nines: The Interplay of Phytohormones Signaling and Redox Metabolism During Plant Response to Drought

Plants must effectively respond to various environmental stimuli to achieve optimal growth. This is especially relevant in the context of climate change, where drought emerges as a major factor globally impacting crops and limiting overall yield potential. Throughout evolution, plants have developed adaptative strategies for environmental stimuli, with plant hormones and reactive oxygen species (ROS) playing essential roles in their development. Hormonal signaling and the maintenance of ROS homeostasis are interconnected, playing indispensable roles in growth, development, and stress responses and orchestrating diverse molecular responses during environmental adversities. Nine principal classes of phytohormones have been categorized: auxins, brassinosteroids, cytokinins, and gibberellins primarily oversee developmental growth regulation, while abscisic acid, ethylene, jasmonic acid, salicylic acid, and strigolactones are the main orchestrators of environmental stress responses. Coordination between phytohormones and transcriptional regulation is crucial for effective plant responses, especially in drought stress. Understanding the interplay of ROS and phytohormones is pivotal for elucidating the molecular mechanisms involved in plant stress responses. This review provides an overview of the intricate relationship between ROS, redox metabolism, and the nine different phytohormones signaling in plants, shedding light on potential strategies for enhancing drought tolerance for sustainable crop production.

Gibberellin regulates the synthesis of stone cells in 'Nanguo' pear via the PuMYB91-PuERF023 module

Stone cells are one of the limiting factors affecting pear fruit quality and commodity value. The formation of stone cell is highly correlated with lignin deposition. However, the molecular mechanism of stone cell formation and regulation is still unclear. Here, we observed that exogenous application of GA significantly inhibited the formation of stone cells and also decreased the content of lignin in 'Nanguo' (Pyrus ussuriensis) pear fruits. The key gene PuPRX73 involved in the lignin synthesis pathway was further identified using RT-PCR, and GA-treatment significantly inhibited the expression of PuPRX73. Overexpression or silencing of PuPRX73 in pear fruits significantly increases or decreases the content of stone cells and lignin. We identified the transcription factors PuMYB91 and PuERF023 using mRNA-seq and their expression was significantly decreased after GA-treatment. Transient overexpression of PuMYB91 and PuERF023 promotes lignin and stone cells content in pear fruits, while silencing of PuMYB91 and PuERF023 led to the opposite results and inhibited the expression of PuPRX73. Yeast one-hybrid (Y1H) and GUS activity analysis revealed that PuMYB91 and PuERF023 directly bind and activate the PuPRX73 promoter, and co-transfection of PuMYB91 and PuERF023 in Nicotiana benthamiana leaves further promoted the promoter activity of PuPRX73. Furthermore, we found that PuMYB91 interacted with PuERF023 in vitro by using Yeast two-hybrid assays (Y2H). In conclusion, our results revealed that exogenous GA-treatment inhibits stone cell production by suppressing the expression of PuMYB91 and PuERF023 in pear fruits.

An F-box Kelch repeat protein, PmFBK2, from Persicaria minor interacts with GID1b to modulate gibberellin signalling

The F-box protein (FBP) family plays diverse functions in the plant kingdom, with the function of many members still unrevealed. In this study, a specific FBP called PmFBK2, containing Kelch repeats from Persicaria minor, was functionally investigated. Employing the yeast two-hybrid (Y2H) assay, PmFBK2 was found to interact with Skp1-like proteins from P. minor, suggesting its potential to form an E3 ubiquitin ligase, known as the SCF complex. Y2H and co-immunoprecipitation tests revealed that PmFBK2 interacts with full-length PmGID1b. The interaction marks the first documented binding between these two protein types, which have never been reported in other plants before, and they exhibited a negative effect on gibberellin (GA) signal transduction. The overexpression of PmFBK2 in the kmd3 mutant, a homolog from Arabidopsis, demonstrated the ability of PmFBK2 to restore the function of the mutated KMD3 gene. The function restoration was supported by morphophysiological and gene expression analyses, which exhibited patterns similar to the wild type (WT) compared to the kmd3 mutant. Interestingly, the overexpression of PmFBK2 or PmGID1b in Arabidopsis had opposite effects on rosette diameter, seed weight, and plant height. This study provides new insights into the complex GA signalling. It highlights the crucial roles of the interaction between FBP and the GA receptor (GID1b) in regulating GA responses. These findings have implications for developing strategies to enhance plant growth and yield by modulating GA signalling in crops.

Cloning and functional mechanism of the dwarf gene gba affecting stem elongation and cellulose biosynthesis in jute (Corchorus olitorius)

Plant height (PH) is an important factor affecting bast fiber yield in jute. Here, we report the mechanism of dwarfism in the 'Guangbaai' (gba) of jute. The mutant gba had shorter internode length and cell length compared to the standard cultivar 'TaiZi 4' (TZ4). Exogenous GA3 treatment indicated that gba is a GA-insensitive dwarf mutant. Quantitative trait locus (QTL) analysis of three PH-related traits via a high-density genetic linkage map according to re-seq showed that a total of 25 QTLs were identified, including 13 QTLs for PH, with phenotypic variation explained ranging from 2.42 to 74.16%. Notably, the functional mechanism of the candidate gene CoGID1a, the gibberellic acid receptor, of the major locus qPHIL5 was evaluated by transgenic analysis and virus-induced gene silencing. A dwarf phenotype-related single nucleotide mutation in CoGID1a was identified in gba, which was also unique to the dwarf phenotype of gba among 57 cultivars. Cogid1a was unable to interact with the growth-repressor DELLA even in the presence of highly accumulated gibberellins in gba. Differentially expressed genes between transcriptomes of gba and TZ4 after GA3 treatment indicated up-regulation of genes involved in gibberellin and cellulose synthesis in gba. Interestingly, it was found that up-regulation of CoMYB46, a key transcription factor in the secondary cell wall, by the highly accumulated gibberellins in gba promoted the expression of cellulose synthase genes CoCesA4 and CoCesA7. These findings provide valuable insights into fiber development affected by endogenous gibberellin accumulation in plants.

A tomato NAC transcription factor, SlNAP1, directly regulates gibberellin-dependent fruit ripening

In tomato (Solanum lycopersicum), the ripening of fruit is regulated by the selective expression of ripening-related genes, and this procedure is controlled by transcription factors (TFs). In the various plant-specific TF families, the no apical meristem (NAM), Arabidopsis thaliana activating factor 1/2 (ATAF1/2), and cup-shaped cotyledon 2 (CUC2; NAC) TF family stands out and plays a significant function in plant physiological activities, such as fruit ripening (FR). Despite the numerous genes of NAC found in the tomato genome, limited information is available on the effects of NAC members on FR, and there is also a lack of studies on their target genes. In this research, we focus on SlNAP1, which is a NAC TF that positively influences the FR of tomato. By employing CRISPR/Cas9 technology, compared with the wild type (WT), we generated slnap1 mutants and observed a delay in the ethylene production and color change of fruits. We employed the yeast one-hybrid (Y1H) and dual-luciferase reporter (DLR) assays to confirm that SlNAP1 directly binds to the promoters of two crucial genes involved in gibberellin (GA) degradation, namely SlGA2ox1 and SlGA2ox5, thus activating their expression. Furthermore, through a yeast two-hybrid (Y2H), bimolecular fluorescence complementation (BIFC) and luciferase (LUC) assays, we established an interaction between SlNAP1 and SlGID1. Hence, our findings suggest that SlNAP1 regulates FR positively by activating the GA degradation genes directly. Additionally, the interaction between SlNAP1 and SlGID1 may play a role in SlNAP1-induced FR. Overall, our study provides important insights into the molecular mechanisms through which NAC TFs regulate tomato FR via the GA pathway.

The tomato EAR-motif repressor, SlERF36, accelerates growth transitions and reduces plant life cycle by regulating GA levels and responses

Faster vegetative growth and early maturity/harvest reduce plant life cycle time and are important agricultural traits facilitating early crop rotation. GA is a key hormone governing developmental transitions that determine growth speed in plants. An EAR-motif repressor, SlERF36 that regulates various growth transitions, partly through regulation of the GA pathway and GA levels, was identified in tomato. Suppression of SlERF36 delayed germination, slowed down organ growth and delayed the onset of flowering time, fruit harvest and whole-plant senescence by 10-15 days. Its over-expression promoted faster growth by accelerating all these transitions besides increasing organ expansion and plant height substantially. The plant life cycle and fruit harvest were completed 20-30 days earlier than control without affecting yield, in glasshouse as well as net-house conditions, across seasons and generations. These changes in life cycle were associated with reciprocal changes in expression of GA pathway genes and basal GA levels between suppression and over-expression lines. SlERF36 interacted with the promoters of two GA2 oxidase genes, SlGA2ox3 and SlGA2ox4, and the DELLA gene, SlDELLA, reducing their transcription and causing a 3-5-fold increase in basal GA3/GA4 levels. Its suppression increased SlGA2ox3/4 transcript levels and reduced GA3/GA4 levels by 30%-50%. SlERF36 is conserved across families making it an important candidate in agricultural and horticultural crops for manipulation of plant growth and developmental transitions to reduce life cycles for faster harvest.

New Advances in the Study of Regulation of Tomato Flowering-Related Genes Using Biotechnological Approaches

The tomato is a convenient object for studying reproductive processes, which has become a classic. Such complex processes as flowering and fruit setting require an understanding of the fundamental principles of molecular interaction, the structures of genes and proteins, the construction of signaling pathways for transcription regulation, including the synchronous actions of cis-regulatory elements (promoter and enhancer), trans-regulatory elements (transcription factors and regulatory RNAs), and transposable elements and epigenetic regulators (DNA methylation and acetylation, chromatin structure). Here, we discuss the current state of research on tomatoes (2017-2023) devoted to studying the function of genes that regulate flowering and signal regulation systems using genome-editing technologies, RNA interference gene silencing, and gene overexpression, including heterologous expression. Although the central candidate genes for these regulatory components have been identified, a complete picture of their relationship has yet to be formed. Therefore, this review summarizes the latest achievements related to studying the processes of flowering and fruit set. This work attempts to display the gene interaction scheme to better understand the events under consideration.

Cucumber mosaic virus-induced gene and microRNA silencing in water dropwort (Oenanthe javanica (Blume) DC)

Water dropwort (Oenanthe javanica (Blume) DC), an aquatic perennial plant from the Apiaceae family, rich in dietary fibert, vitamins, and minerals. It usually grows in wet soils and water. Despite accumulating the transcriptomic data, gene function research on water dropwort is still far behind than that of the other crops. The cucumber mosaic virus (CMV) induced gene silencing was established to study the functions of gene and microRNA (miRNA) in the water dropwort. CMV Fast New York strain (CMV-Fny) genomic RNAs 1, 2, and 3 were individually cloned into pCB301 vectors. We deleted part of the ORF 2b region and introduced recognition sites. A CMV-induced gene silencing vector was employed to suppress the expression of endogenous genes, including phytoene desaturase (PDS). In order to assess the efficacy of gene silencing, we also cloned conserved sequence of gibberellin insensitive dwarf (GID1) cDNA sequences into the vector and inoculated the water dropwort. The height of CMV-GID1-infected plants was marginally reduced as a result of GID1 gene silencing, and their leaves were noticeably longer and thinner. Additionally, we also used a CMV-induced silencing vector to analyze the roles of endogenous miRNAs. We used a short tandem target mimic approach to clone miR319 and miR396 from water dropwort into the CMV vector. Plants with CMV-miRNA infection were driven to exhibit the distinctive phenotypes. We anticipate that functional genomic research on water dropwort will be facilitated by the CMV-induced gene silencing technique.

Recent Advances in Studying the Regulation of Fruit Ripening in Tomato Using Genetic Engineering Approaches

Tomato (Solanum lycopersicum L.) is one of the most commercially essential vegetable crops cultivated worldwide. In addition to the nutritional value, tomato is an excellent model for studying climacteric fruits' ripening processes. Despite this, the available natural pool of genes that allows expanding phenotypic diversity is limited, and the difficulties of crossing using classical selection methods when stacking traits increase proportionally with each additional feature. Modern methods of the genetic engineering of tomatoes have extensive potential applications, such as enhancing the expression of existing gene(s), integrating artificial and heterologous gene(s), pointing changes in target gene sequences while keeping allelic combinations characteristic of successful commercial varieties, and many others. However, it is necessary to understand the fundamental principles of the gene molecular regulation involved in tomato fruit ripening for its successful use in creating new varieties. Although the candidate genes mediate ripening have been identified, a complete picture of their relationship has yet to be formed. This review summarizes the latest (2017-2023) achievements related to studying the ripening processes of tomato fruits. This work attempts to systematize the results of various research articles and display the interaction pattern of genes regulating the process of tomato fruit ripening.

LTP2 hypomorphs show genotype-by-environment interaction in early seedling traits in Arabidopsis thaliana

Isogenic individuals can display seemingly stochastic phenotypic differences, limiting the accuracy of genotype-to-phenotype predictions. The extent of this phenotypic variation depends in part on genetic background, raising questions about the genes involved in controlling stochastic phenotypic variation. Focusing on early seedling traits in Arabidopsis thaliana, we found that hypomorphs of the cuticle-related gene LIPID TRANSFER PROTEIN 2 (LTP2) greatly increased variation in seedling phenotypes, including hypocotyl length, gravitropism and cuticle permeability. Many ltp2 hypocotyls were significantly shorter than wild-type hypocotyls while others resembled the wild-type. Differences in epidermal properties and gene expression between ltp2 seedlings with long and short hypocotyls suggest a loss of cuticle integrity as the primary determinant of the observed phenotypic variation. We identified environmental conditions that reveal or mask the increased variation in ltp2 hypomorphs and found that increased expression of its closest paralog LTP1 is necessary for ltp2 phenotypes. Our results illustrate how decreased expression of a single gene can generate starkly increased phenotypic variation in isogenic individuals in response to an environmental challenge.

Characteristics of CXE family of Salvia miltiorrhiza and identification of interactions between SmGID1s and SmDELLAs

Carboxylesterase (CXE) is a class of hydrolases that contain an α/β folding domain, which plays critical roles in plant growth, development, and stress responses. Based on the genomic and transcriptomic data of Salvia miltiorrhiza, the SmCXE family was systematically analyzed using bioinformatics. The results revealed 34 SmCXE family members in S. miltiorrhiza, and the SmCXE family could be divided into five groups (Group I, Group II, Group III, Group IV, and Group V). Cis-regulatory elements indicated that the SmCXE promoter region contained tissue-specific and development-related, hormone-related, stress-related, and photoresponsive elements. Transcriptome analysis revealed that the expression levels of SmCXE2 were highest in roots and flowers (SmCXE8 was highest in stems and SmCXE19 was highest in leaves). Further, two GA receptors SmCXE1 (SmGID1A) and SmCXE2 (SmGID1B) were isolated from the SmCXE family, which are homologous to other plants. SmGID1A and SmGID1B have conserved HGGSF motifs and active amino acid sites (Ser-Asp-Val/IIe), which are required to maintain their GA-binding activities. SmGID1A and SmGID1B were significantly responsive to gibberellic acid (GA3) and methyl jasmonate (MeJA) treatment. A subcellular assay revealed that SmCXE1 and SmCXE2 resided within the nucleus. SmGID1B can interact with SmDELLAs regardless of whether GA3 exists, whereas SmGID1A can only interact with SmDELLAs in the presence of GA3. A Further assay showed that the GRAS domain mediated the interactions between SmGID1s and SmDELLAs. This study lays a foundation for further elucidating the role of SmCXE in the growth and development of S. miltiorrhiza.

Molecular, hormonal, and metabolic mechanisms of fruit set, the ovary-to-fruit transition, in horticultural crops

Fruit set is the process by which the ovary develops into a fruit and is an important factor in determining fruit yield. Fruit set is induced by two hormones, auxin and gibberellin, and the activation of their signaling pathways, partly by suppressing various negative regulators. Many studies have investigated the structural changes and gene networks in the ovary during fruit set, revealing the cytological and molecular mechanisms. In tomato (Solanum lycopersicum), SlIAA9 and SlDELLA/PROCERA act as auxin and gibberellin signaling repressors, respectively, and are important regulators of the activity of transcription factors and downstream gene expression involved in fruit set. Upon pollination, SlIAA9 and SlDELLA are degraded, which subsequently activates downstream cascades and mainly contributes to active cell division and cell elongation, respectively, in ovaries during fruit setting. According to current knowledge, the gibberellin pathway functions as the most downstream signal in fruit set induction, and therefore its role in fruit set has been extensively explored. Furthermore, multi-omics analysis has revealed the detailed dynamics of gene expression and metabolites downstream of gibberellins, highlighting the rapid activation of central carbon metabolism. This review will outline the relevant mechanisms at the molecular and metabolic levels during fruit set, particularly focusing on tomato.

LTP2 hypomorphs show genotype-by-environment interaction in early seedling traits in Arabidopsis thaliana

Isogenic individuals can display seemingly stochastic phenotypic differences, limiting the accuracy of genotype-to-phenotype predictions. The extent of this phenotypic variation depends in part on genetic background, raising questions about the genes involved in controlling stochastic phenotypic variation. Focusing on early seedling traits in Arabidopsis thaliana, we found that hypomorphs of the cuticle-related gene LTP2 greatly increased variation in seedling phenotypes, including hypocotyl length, gravitropism and cuticle permeability. Many ltp2 hypocotyls were significantly shorter than wild-type hypocotyls while others resembled the wild type. Differences in epidermal properties and gene expression between ltp2 seedlings with long and short hypocotyls suggest a loss of cuticle integrity as the primary determinant of the observed phenotypic variation. We identified environmental conditions that reveal or mask the increased variation in ltp2 hypomorphs, and found that increased expression of its closest paralog LTP1 is necessary for ltp2 phenotypes. Our results illustrate how decreased expression of a single gene can generate starkly increased phenotypic variation in isogenic individuals in response to an environmental challenge.

Tomato ABA-IMPORTING TRANSPORTER 1.1 inhibits seed germination under high salinity conditions

The plant hormone abscisic acid (ABA) plays a central role in the regulation of seed maturation and dormancy. ABA also restrains germination under abiotic-stress conditions. Here, we show in tomato (Solanum lycopersicum) that the ABA importer ABA-IMPORTING TRANSPORTER 1.1 (AIT1.1/NPF4.6) has a role in radicle emergence under salinity conditions. AIT1.1 expression was upregulated following seed imbibition, and CRISPR/Cas9-derived ait1.1 mutants exhibited faster radicle emergence, increased germination and partial resistance to ABA. AIT1.1 was highly expressed in the endosperm, but not in the embryo, and ait1.1 isolated embryos did not show resistance to ABA. On the other hand, loss of AIT1.1 activity promoted the expression of endosperm-weakening-related genes, and seed-coat scarification eliminated the promoting effect of ait1.1 on radicle emergence. Therefore, we propose that imbibition-induced AIT1.1 expression in the micropylar endosperm mediates ABA-uptake into micropylar cells to restrain endosperm weakening. While salinity conditions strongly inhibited wild-type M82 seed germination, high salinity had a much weaker effect on ait1.1 germination. We suggest that AIT1.1 evolved to inhibit germination under unfavorable conditions, such as salinity. Unlike other ABA mutants, ait1.1 exhibited normal seed longevity, and therefore, the ait1.1 allele may be exploited to improve seed germination in crops.

Gene Editing for Plant Resistance to Abiotic Factors: A Systematic Review

Agricultural crops are exposed to various abiotic stresses, such as salinity, water deficits, temperature extremes, floods, radiation, and metal toxicity. To overcome these challenges, breeding programs seek to improve methods and techniques. Gene editing by Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR/Cas-is a versatile tool for editing in all layers of the central dogma with focus on the development of cultivars of plants resistant or tolerant to multiple biotic or abiotic stresses. This systematic review (SR) brings new contributions to the study of the use of CRISPR/Cas in gene editing for tolerance to abiotic stress in plants. Articles deposited in different electronic databases, using a search string and predefined inclusion and exclusion criteria, were evaluated. This SR demonstrates that the CRISPR/Cas system has been applied to several plant species to promote tolerance to the main abiotic stresses. Among the most studied crops are rice and Arabidopsis thaliana, an important staple food for the population, and a model plant in genetics/biotechnology, respectively, and more recently tomato, whose number of studies has increased since 2021. Most studies were conducted in Asia, specifically in China. The Cas9 enzyme is used in most articles, and only Cas12a is used as an additional gene editing tool in plants. Ribonucleoproteins (RNPs) have emerged as a DNA-free strategy for genome editing without exogenous DNA. This SR also identifies several genes edited by CRISPR/Cas, and it also shows that plant responses to stress factors are mediated by many complex-signaling pathways. In addition, the quality of the articles included in this SR was validated by a risk of bias analysis. The information gathered in this SR helps to understand the current state of CRISPR/Cas in the editing of genes and noncoding sequences, which plays a key role in the regulation of various biological processes and the tolerance to multiple abiotic stresses, with potential for use in plant genetic improvement programs.

A mutant allele of the flowering promoting factor 1 gene at the tomato BRACHYTIC locus reduces plant height with high quality fruit

Reduced plant height due to shortened stems is beneficial for improving crop yield potential, better resilience to biotic/abiotic stresses, and rapid crop producer adoption of the agronomic and management practices. Breeding tomato plants with a reduced height, however, poses a particular challenge because this trait is often associated with a significant fruit size (weight) reduction. The tomato BRACHYTIC (BR) locus controls plant height. Genetic mapping and genome assembly revealed three flowering promoting factor 1 (FPF1) genes located within the BR mapping interval, and a complete coding sequence deletion of the telomere proximal FPF1 (Solyc01g066980) was found in the br allele but not in BR. The knock-out of Solyc01g066980 in BR large-fruited fresh-market tomato reduced the height and fruit yield, but the ability to produce large size fruits was retained. However, concurrent yield evaluation of a pair of sister lines with or without the br allele revealed that artificial selection contributes to commercially acceptable yield potential in br tomatoes. A network analysis of gene-expression patterns across genotypes, tissues, and the gibberellic acid (GA) treatment revealed that member(s) of the FPF1 family may play a role in the suppression of the GA biosynthesis in roots and provided a framework for identifying the responsible molecular signaling pathways in br-mediated phenotypic changes. Lastly, mutations of br homologs also resulted in reduced height. These results shed light on the genetic and physiological mechanisms by which the br allele alters tomato architecture.

A Modified Yeast Two-Hybrid Platform Enables Dynamic Control of Expression Intensities to Unmask Properties of Protein-Protein Interactions

The yeast two-hybrid (Y2H) assay is widely used for protein-protein interaction characterization due to its simplicity and accessibility. However, it may mask changes in affinity caused by mutations or ligand activation due to signal saturation. To overcome this drawback, we modified the Y2H system to have tunable protein expression by introducing a fluorescent reporter and a pair of synthetic inducible transcription factors to regulate the expression of interacting components. We found that the application of inducers allowed us to adjust the concentrations of interacting proteins to avoid saturation and observe interactions otherwise masked in the canonical Y2H assay, such as the abscisic acid-mediated increase in affinity of monomeric abscisic acid receptors to the coreceptor. When applied in future studies, our modified system may provide a more accurate characterization of protein-protein interactions.

Genome-Wide Analysis of Genes Involved in the GA Signal Transduction Pathway in 'duli' Pear (Pyrus betulifolia Bunge)

Gibberellic acid (GA) is an important phytohormone that regulates every aspect of plant growth and development. While elements involved in GA signaling have been identified and, hence, their functions have been well studied in model plants, such as Arabidopsis and rice, very little is known in pear. We, therefore, analyzed the genes related to GA signaling from the recently sequenced genome of the wildtype 'duli' pear (Pyrus betulifolia Bunge), a widely used rootstock for grafting in pear cultivation in China due to its vigorous growth and resistance to abiotic and biotic stress. In total, 15 genes were identified, including five GA receptors PbGID1s (GA-INSENSTIVE DWARF 1), six GA negative regulators, PbDELLAs, and four GA positive regulators, PbSLYs. Exogenous application of GA could promote the expression of PbGID1s but inhibit that of PbDELLAs and PbSLYs in tissue culture 'duli' pear seedlings. The expression profiles of these genes in field-grown trees under normal growth conditions, as well as in tissue-cultured seedlings treated with auxin (IAA), GA, paclobutrazol (PAC), abscisic acid (ABA), and sodium chloride (NaCl), were also studied, providing further evidence of the involvement of these genes in GA signaling in 'duli' pear plants. The preliminary results obtained in this report lay a good foundation for future research into GA signaling pathways in pear. Importantly, the identification and preliminary functional verification of these genes could guide molecular breeding in order to obtain the highly desired dwarf pear rootstocks for high-density plantation to aid easy orchard management and high yielding of pear fruits.

Steroidal alkaloids defence metabolism and plant growth are modulated by the joint action of gibberellin and jasmonate signalling

Steroidal glycoalkaloids (SGAs) are protective metabolites constitutively produced by Solanaceae species. Genes and enzymes generating the vast structural diversity of SGAs have been largely identified. Yet, mechanisms of hormone pathways coordinating defence (jasmonate; JA) and growth (gibberellin; GA) controlling SGAs metabolism remain unclear. We used tomato to decipher the hormonal regulation of SGAs metabolism during growth vs defence tradeoff. This was performed by genetic and biochemical characterisation of different JA and GA pathways components, coupled with in vitro experiments to elucidate the crosstalk between these hormone pathways mediating SGAs metabolism. We discovered that reduced active JA results in decreased SGA production, while low levels of GA or its receptor led to elevated SGA accumulation. We showed that MYC1 and MYC2 transcription factors mediate the JA/GA crosstalk by transcriptional activation of SGA biosynthesis and GA catabolism genes. Furthermore, MYC1 and MYC2 transcriptionally regulate the GA signalling suppressor DELLA that by itself interferes in JA-mediated SGA control by modulating MYC activity through protein-protein interaction. Chemical and fungal pathogen treatments reinforced the concept of JA/GA crosstalk during SGA metabolism. These findings revealed the mechanism of JA/GA interplay in SGA biosynthesis to balance the cost of chemical defence with growth.

Comprehensive Effects of Flowering Locus T-Mediated Stem Growth in Tobacco

In flowering plants, Flowering locus T (FT) encodes a major florigen. It is a key flowering hormone in controlling flowering time and has a wide range of effects on plant development. Although the mechanism by which FT promotes flowering is currently clearly understood, comprehensive effects of the FT gene on plant growth have not been evaluated. Therefore, the effects of FT on vegetative growth need to be explored for a complete understanding of the molecular functions of the FT gene. In this study, the Jatropha curcas L. FT gene was overexpressed in tobacco (JcFT^OE) in order to discover multiple aspects and related mechanisms of how the FT gene affects plant development. In JcFT^OE plants, root, stem, and leaf development was strongly affected. Stem tissues were selected for further transcriptome analysis. In JcFT^OE plants, stem growth was affected because of changes in the nucleus, cytoplasm, and cell wall. In the nucleus of JcFT^OE plants, the primary effect was to weaken all aspects of DNA replication, which ultimately affected the cell cycle and cell division. The number of stem cells decreased significantly in JcFT^OE plants, which decreased the thickness and height of tobacco stems. In the cell wall of JcFT^OE plants, hemicellulose and cellulose contents increased, with the increase in hemicellulose associated with up-regulation of xylan synthase-related genes expression. In the cytoplasm of JcFT^OE plants, the primary effects were on biogenesis of ribonucleoprotein complexes, photosynthesis, carbohydrate biosynthesis, and the cytoskeleton. In addition, in the cytoplasm of JcFT^OE plants, there were changes in certain factors of the core oscillator, expression of many light-harvesting chlorophyll a/b binding proteins was down-regulated, and expression of fructose 1,6-bisphosphatase genes was up-regulated to increase starch content in tobacco stems. Changes in the xylem and phloem of JcFT^OE plants were also identified, and in particular, xylem development was affected by significant increases in expression of irregular xylem genes.

Role of gibberellin and its three GID1 receptors in Jasminum sambac stem elongation and flowering

Taken together, our results establish a reciprocal relationship between vine elongation and flowering, and reveal that GA is a positive signal for stem elogation but a negative regulator of flowering in this species. Vines or climbing plants exhibit vigorous vegetative shoot extension. GA have long been recognized as an important signal for seasonal stem elongation and flowering in many woody perennials. However, less is explored as how GA pathway is involved in the regulation of shoot extension in woody vines. Here, we investigated the role of GA and its signaling components in shoot elongation in Jasminum sambac. We found high accumulation of GA₄ in the elongating internode, in contrast to a depletion of GAs in the floral differentiating shoot, which in turn featured a higher zeatin content, and a lower IAA and JA concentrations. This GA accumulation was coincident with the strong expression of JsGA20ox1 and JsGAS1 in the leaves, as well as of the JsGA2ox3 in the internode. Treatment of GA biosynthesis inhibitor reduced elongation while stimulated the terminal flowering. Remarkably, three B-type GA-receptor genes were abundantly expressed in both internodes and leaves of the extending shoots, which could enhance GA responsiveness in heterologous transgenic Arabidopsis. Furthermore, these JsGID1s showed distinct GA-dependent interaction with the JsDELLA in a yeast-two-hybrid assay. Taken together, our results establish a reciprocal relationship between vine elongation and flowering, and reveal that GA is a positive signal for stem elogation but a negative regulator of flowering in this species.

Ancient rapid functional differentiation and fixation of the duplicated members in rice Dof genes after whole genome duplication

Whole genome duplication (WGD) in plants is typically followed by genomic downsizing, where large portions of the new genome are lost. Whether this downsizing is accompanied by increased or decreased evolutionary rates of the remaining genes is poorly known, not least because homeolog pairings are often obscured by chromosomal rearrangement. Here, we use the newly published genome from a sedge, namely Kobresia littledalei, and CRISPR/Cas-9 editing to investigate how the Rho WGD event 70 million years ago (MYA) affected transcription factor evolutionary rates, fates, and function in rice (Oryza sativa) and sorghum (Sorghum bicolor). We focus on the 30-member DNA-binding with one zinc finger (Dof) transcription factor family in both crops due to their agronomic importance. Using the known speciation dates of rice from Kobresia (97 MYA) and sorghum (50 MYA), we find that rates of amino acid substitution in the critical Dof domain region were over twofold higher during the 20-million-year period following the WGD than before or afterward. Through comparison of synteny blocks, we report that at least 11% of Dof genes were purged from 70 to 50 MYA, while only 6% have been lost in the most recent 50-million-year interval. CRISPR/Cas9 editing revealed widespread fitness-related defects in flowering and lack of redundancy of paired members, as well as significant differences in expression between gene pairs. Together these findings demonstrate the strength of Dof genes as a model for deep evolutionary study and offer one of the most detailed portraits yet of the Rho WGD impact on a gene lineage.

Gibberellin in tomato: metabolism, signaling and role in drought responses

The growth-promoting hormone gibberellin (GA) regulates numerous developmental processes throughout the plant life cycle. It also affects plant response to biotic and abiotic stresses. GA metabolism and signaling in tomato (Solanum lycopersicum) have been studied in the last three decades and major components of the pathways were characterized. These include major biosynthesis and catabolism enzymes and signaling components, such as the three GA receptors GIBBERELLIN INSENSITIVE DWARF 1 (GID1) and DELLA protein PROCERA (PRO), the central response suppressor. The role of these components in tomato plant development and response to the environment have been investigated. Cultivated tomato, similar to many other crop plants, are susceptible to water deficiency. Numerous studies on tomato response to drought have been conducted, including the possible role of GA in tomato drought resistance. Most studies showed that reduced levels or activity of GA improves drought tolerance and drought avoidance. This review aims to provide an overview on GA biosynthesis and signaling in tomato, how drought affects these pathways and how changes in GA activity affect tomato plant response to water deficiency. It also presents the potential of using the GA pathway to generate drought-tolerant tomato plants with improved performance under both irrigation and water-limited conditions.

Meristem transitions and plant architecture-learning from domestication for crop breeding

Genetic networks that regulate meristem transitions were recurrent targets of selection during crop domestication and allow fine-tuning of plant architecture for improved crop productivity.

Comparisons within the Rice GA 2-Oxidase Gene Family Revealed Three Dominant Paralogs and a Functional Attenuated Gene that Led to the Identification of Four Amino Acid Variants Associated with GA Deactivation Capability

BACKGROUND

GA 2-oxidases (GA2oxs) are involved in regulating GA homeostasis in plants by inactivating bioactive GAs through 2β-hydroxylation. Rice GA2oxs are encoded by a family of 10 genes; some of them have been characterized, but no comprehensive comparisons for all these genes have been conducted.

RESULTS

Rice plants with nine functional GA2oxs were demonstrated in the present study, and these genes not only were differentially expressed but also revealed various capabilities for GA deactivation based on their height-reducing effects in transgenic plants. Compared to that of wild-type plants, the relative plant height (RPH) of transgenic plants was scored to estimate their reducing effects, and 8.3% to 59.5% RPH was observed. Phylogenetic analysis of class I GA2ox genes revealed two functionally distinct clades in the Poaceae. The OsGA2ox3, 4, and 8 genes belonging to clade A showed the most severe effect (8.3% to 8.7% RPH) on plant height reduction, whereas the OsGA2ox7 gene belonging to clade B showed the least severe effect (59.5% RPH). The clade A OsGA2ox3 gene contained two conserved C186/C194 amino acids that were crucial for enzymatic activity. In the present study, these amino acids were replaced with OsGA2ox7-conserved arginine (C186R) and proline (C194P), respectively, or simultaneously (C186R/C194P) to demonstrate their importance in planta. Another two amino acids, Q220 and Y274, conserved in OsGA2ox3 were substituted with glutamic acid (E) and phenylalanine (F), respectively, or simultaneously to show their significance in planta. In addition, through sequence divergence, RNA expression profile and GA deactivation capability analyses, we proposed that OsGA2ox1, OsGA2ox3 and OsGA2ox6 function as the predominant paralogs in each of their respective classes.

CONCLUSIONS

This study demonstrates rice has nine functional GA2oxs and the class I GA2ox genes are divided into two functionally distinct clades. Among them, the OsGA2ox7 of clade B is a functional attenuated gene and the OsGA2ox1, OsGA2ox3 and OsGA2ox6 are the three predominant paralogs in the family.

An efficient papaya leaf distortion mosaic potyvirus vector for virus-induced gene silencing in papaya

Papaya (Carica papaya L.) is regarded as an excellent model for genomic studies of tropical trees because of its short generation time and its small genome that has been sequenced. However, functional genomic studies in papaya depend on laborious genetic transformations because no rapid tools exist for this species. Here, we developed a highly efficient virus-induced gene silencing (VIGS) vector for use in papaya by modifying an artificially attenuated infectious clone of papaya leaf distortion mosaic virus (PLDMV; genus: Potyvirus), PLDMV-E, into a stable Nimble Cloning (NC)-based PLDMV vector, pPLDMV-NC, in Escherichia coli. The target fragments for gene silencing can easily be cloned into pPLDMV-NC without multiple digestion and ligation steps. Using this PLDMV VIGS system, we silenced and characterized five endogenous genes in papaya, including two common VIGS marker genes, namely, phytoene desaturase, Mg-chelatase H subunit, putative GIBBERELLIN (GA)-INSENSITIVE DWARF1A and 1B encoding GA receptors; and the cytochrome P450 gene CYP83B1, which encodes a key enzyme involved in benzylglucosinolate biosynthesis. The results demonstrate that our newly developed PLDMV VIGS vector is a rapid and convenient tool for functional genomic studies in papaya.

An ABA-GA bistable switch can account for natural variation in the variability of Arabidopsis seed germination time

Genetically identical plants growing in the same conditions can display heterogeneous phenotypes. Here we use Arabidopsis seed germination time as a model system to examine phenotypic variability and its underlying mechanisms. We show extensive variation in seed germination time variability between Arabidopsis accessions and use a multiparent recombinant inbred population to identify two genetic loci involved in this trait. Both loci include genes implicated in modulating abscisic acid (ABA) sensitivity. Mutually antagonistic regulation between ABA, which represses germination, and gibberellic acid (GA), which promotes germination, underlies the decision to germinate and can act as a bistable switch. A simple stochastic model of the ABA-GA network shows that modulating ABA sensitivity can generate the range of germination time distributions we observe experimentally. We validate the model by testing its predictions on the effects of exogenous hormone addition. Our work provides a foundation for understanding the mechanism and functional role of phenotypic variability in germination time.

Gibberellin Metabolism and Signaling: Targets for Improving Agronomic Performance of Crops

Gibberellins (GAs) are a class of tetracyclic diterpenoid phytohormones that regulate many aspects of plant development, including seed germination, stem elongation, leaf expansion, pollen maturation, and the development of flowers, fruits and seeds. During the past decades, the primary objective of crop breeding programs has been to increase productivity or yields. 'Green Revolution' genes that can produce semidwarf, high-yielding crops were identified as GA synthesis or response genes, confirming the value of research on GAs in improving crop productivity. The manipulation of GA status either by genetic alteration or by exogenous application of GA or GA biosynthesis inhibitors is often used to optimize plant growth and yields. In this review, we summarize the roles of GAs in major aspects of crop growth and development and present the possible targets for the fine-tuning of GA metabolism and signaling as a promising strategy for crop improvement.

Systematic Analysis of Gibberellin Pathway Components in Medicago truncatula Reveals the Potential Application of Gibberellin in Biomass Improvement

Gibberellins (GAs), a class of phytohormones, act as an essential natural regulator of plant growth and development. Many studies have shown that GA is related to rhizobial infection and nodule organogenesis in legume species. However, thus far, GA metabolism and signaling components are largely unknown in the model legume Medicago truncatula. In this study, a genome-wide analysis of GA metabolism and signaling genes was carried out. In total 29 components, including 8 MtGA20ox genes, 2 MtGA3ox genes, 13 MtGA2ox genes, 3 MtGID1 genes, and 3 MtDELLA genes were identified in M. truncatula genome. Expression profiles revealed that most members of MtGAox, MtGID1, and MtDELLA showed tissue-specific expression patterns. In addition, the GA biosynthesis and deactivation genes displayed a feedback regulation on GA treatment, respectively. Yeast two-hybrid assays showed that all the three MtGID1s interacted with MtDELLA1 and MtDELLA2, suggesting that the MtGID1s are functional GA receptors. More importantly, M. truncatula exhibited increased plant height and biomass by ectopic expression of the MtGA20ox1, suggesting that enhanced GA response has the potential for forage improvement.

Genetic dissection of the auxin response network

The expansion of gene families during evolution, which can generate functional overlap or specialization among their members, is a characteristic feature of signalling pathways in complex organisms. For example, families of transcriptional activators and repressors mediate responses to the plant hormone auxin. Although these regulators were identified more than 20 years ago, their overlapping functions and compensating negative feedbacks have hampered their functional analyses. Studies using loss-of-function approaches in basal land plants and gain-of-function approaches in angiosperms have in part overcome these issues but have still left an incomplete understanding. Here, we propose that renewed emphasis on genetic analysis of multiple mutants and species will shed light on the role of gene families in auxin response. Combining loss-of-function mutations in auxin-response activators and repressors can unravel complex outputs enabled by expanded gene families, such as fine-tuned developmental outcomes and robustness. Similar approaches and concepts may help to analyse other regulatory pathways whose components are also encoded by large gene families.

SlGID1a Is a Putative Candidate Gene for qtph1.1, a Major-Effect Quantitative Trait Locus Controlling Tomato Plant Height

Plant height is an important agronomic trait in crops. Several genes underlying tomato (Solanum lycopersicum) plant height mutants have been cloned. However, few quantitative trait genes for plant height have been identified in tomato. In this study, seven quantitative trait loci (QTLs) controlling plant height were identified in tomato. Of which, qtph1.1 (QTL for tomato plant height 1.1), qtph3.1 and qtph12.1 were major QTLs and explained 15, 16, and 12% of phenotypic variation (R²), respectively. The qtph1.1 was further mapped to an 18.9-kb interval on chromosome 1. Based on the annotated tomato genome (version SL2.50, annotation ITAG2.40), Solyc01g098390 encoding GA receptor SlGID1a was the putative candidate gene. The SlGID1a gene underlying the qtph1.1 locus contained a single nucleotide polymorphism (SNP) that resulted in an amino acid alteration in protein sequence. The near-isogenic line containing the qtph1.1 locus (NIL-qtph1.1) exhibited shorter internode length and cell length than the wild type (NIL-WT). The dwarf phenotype of NIL-qtph1.1 could not be rescued by exogenous GA₃ treatment. Transcriptome analysis and real-time quantitative reverse transcription PCR (qPCR) showed that several genes related to biosynthesis and signaling of GA and auxin were differentially expressed in stems between NIL-qtph1.1 and NIL-WT. These findings might pave the road for understanding the molecular regulation mechanism of tomato plant height.

Mutations in the tomato gibberellin receptors suppress xylem proliferation and reduce water loss under water-deficit conditions

Low gibberellin (GA) activity in tomato (Solanum lycopersicum) inhibits leaf expansion and reduces stomatal conductance. This leads to lower transpiration and improved water status under transient drought conditions. Tomato has three GIBBERELLIN-INSENSITIVE DWARF1 (GID1) GA receptors with overlapping activities and high redundancy. We tested whether mutation in a single GID1 reduces transpiration without affecting growth and productivity. CRISPR-Cas9 gid1 mutants were able to maintain higher leaf water content under water-deficit conditions. Moreover, while gid1a exhibited normal growth, it showed reduced whole-plant transpiration and better recovery from dehydration. Mutation in GID1a inhibited xylem vessel proliferation, which led to lower hydraulic conductance. In stronger GA mutants, we also found reduced xylem vessel expansion. These results suggest that low GA activity affects transpiration by multiple mechanisms: it reduces leaf area, promotes stomatal closure, and reduces xylem proliferation and expansion, and as a result, xylem hydraulic conductance. We further examined if gid1a performs better than the control M82 in the field. Under these conditions, the high redundancy of GID1s was lost and gid1a plants were semi-dwarf, but their productivity was not affected. Although gid1a did not perform better under drought conditions in the field, it exhibited a higher harvest index.

Roles of the Brassica napus DELLA Protein BnaA6.RGA, in Modulating Drought Tolerance by Interacting With the ABA Signaling Component BnaA10.ABF2

Drought is a major threat to plant growth and crop productivity. Reduced level of the gibberellin would result in increased drought tolerance, but the underlying mechanism is still unclear. In Brassica napus, there are four BnaRGA genes that code for DELLA proteins, negative regulators of GA signaling. Among them, expression of BnaA6.RGA was greatly induced by drought and abscisic acid (ABA). Previously, we created the gain-of-function mutant of BnaA6.RGA, bnaa6.rga-D, and the loss-of-function quadruple mutant, bnarga by CRISPR/Cas9, respectively. Here we show that bnaa6.rga-D displayed enhanced drought tolerance, and its stomatal closure was hypersensitive to ABA treatment. By contrast, bnarga displayed reduced drought tolerance and was less sensitive to ABA treatment, but there is no difference in drought tolerance between single BnaRGA mutant and WT, suggesting a functional redundancy between the BnaRGA genes in this process. Furthermore, we found that BnaRGAs were able to interact physically with BnaA10.ABF2, an essential transcription factor in ABA signaling. The BnaA10.ABF2-BnaA6.RGA protein complex greatly increased the expression level of the drought responsive gene BnaC9.RAB18. Taken together, this work highlighted the fundamental roles of DELLA proteins in drought tolerance in B. napus, and provide desirable germplasm for further breeding of drought tolerance in rapeseed.

Diverse and dynamic roles of F-box proteins in plant biology

The SCF complex is a widely studied multi-subunit ring E3 ubiquitin ligase that tags targeted proteins with ubiquitin for protein degradation by the ubiquitin 26S-proteasome system (UPS). The UPS is an important system that generally keeps cellular events tightly regulated by purging misfolded or damaged proteins and selectively degrading important regulatory proteins. The specificity of this post-translational regulation is controlled by F-box proteins (FBPs) via selective recognition of a protein-protein interaction motif at the C-terminal domain. Hence, FBPs are pivotal proteins in determining the plant response in multiple scenarios. It is not surprising that the FBP family is one of the largest protein families in the plant kingdom. In this review, the roles of FBPs, specifically in plants, are compiled to provide insights into their involvement in secondary metabolites, plant stresses, phytohormone signalling, plant developmental processes and miRNA biogenesis.

Revolutions in agriculture chart a course for targeted breeding of old and new crops

The dominance of the major crops that feed humans and their livestock arose from agricultural revolutions that increased productivity and adapted plants to large-scale farming practices. Two hormone systems that universally control flowering and plant architecture, florigen and gibberellin, were the source of multiple revolutions that modified reproductive transitions and proportional growth among plant parts. Although step changes based on serendipitous mutations in these hormone systems laid the foundation, genetic and agronomic tuning were required for broad agricultural benefits. We propose that generating targeted genetic variation in core components of both systems would elicit a wider range of phenotypic variation. Incorporating this enhanced diversity into breeding programs of conventional and underutilized crops could help to meet the future needs of the human diet and promote sustainable agriculture.