Gibberellin signaling: biosynthesis, catabolism, and response pathways

Fine mapping and identification of CqMYB62 as the subgynoecy gene in chieh-qua (Benincasa hispida Cogn. var. Chieh-qua How)

KEY MESSAGE

It was hypothesized that Bch08G003160 (CqMYB62), located in the 51.08 Kb region on chromosome 08, might be an important candidate gene for the subgynoecy trait in chieh-qua, based on BSA-seq and linkage mapping approaches. In cucurbit crops, the use of female lines can greatly increase the yield of a single plant and is especially important for the production of hybrid generation seeds, thus being of great interest to breeders. To identify genes regulating sex differentiation in chieh-qua, genetic analysis of the subgynoecy trait was conducted using a chieh-qua F2 population. Initial localization of the locus was done using BSA-seq, followed by fine mapping with a large F2 population (n = 2,741). The locus was ultimately narrowed down to a 51.08 Kb region on Chr08, revealing a single gene Bch08G003160 (CqMYB62) in this region. Further analysis revealed that the presence of two variant loci (SNP_416 and SNP_317) in the coding region resulted in premature termination of the codon and loss of function of the structural domain of the PLN03212 superfamily. Moreover, our research indicated that the subgynoecy trait mediated by CqMYB62 in chieh-qua is potentially regulated by gibberellic acid (GA). Two efficient dCAPS markers were developed to distinguish subgynoecy. In summary, these findings highlight the critical role of CqMYB62 in subgynoecy trait regulation, offering potential implications for chieh-qua breeding programs.

Plant Signaling Hormones and Transcription Factors: Key Regulators of Plant Responses to Growth, Development, and Stress

Plants constantly encounter a wide range of biotic and abiotic stresses that adversely affect their growth, development, and productivity. Phytohormones such as abscisic acid, jasmonic acid, salicylic acid, and ethylene serve as crucial regulators, integrating internal and external signals to mediate stress responses while also coordinating key developmental processes, including seed germination, root and shoot growth, flowering, and senescence. Transcription factors (TFs) such as WRKY, NAC, MYB, and AP2/ERF play complementary roles by orchestrating complex transcriptional reprogramming, modulating stress-responsive genes, and facilitating physiological adaptations. Recent advances have deepened our understanding of hormonal networks and transcription factor families, revealing their intricate crosstalk in shaping plant resilience and development. Additionally, the synthesis, transport, and signaling of these molecules, along with their interactions with stress-responsive pathways, have emerged as critical areas of study. The integration of cutting-edge biotechnological tools, such as CRISPR-mediated gene editing and omics approaches, provides new opportunities to fine-tune these regulatory networks for enhanced crop resilience. By leveraging insights into transcriptional regulation and hormone signaling, these advancements provide a foundation for developing stress-tolerant, high-yielding crop varieties tailored to the challenges of climate change.

Unraveling the Hormonal and Molecular Mechanisms Shaping Fruit Morphology in Plants

The importance of fruit shape studies extends beyond fundamental plant biology, as it holds significant implications for breeding. Understanding the genetic and hormonal regulation of fruit morphology can facilitate targeted breeding strategies to enhance yield, quality, and stress resistance, ultimately contributing to sustainable farming and nutrition security. The diversity in fruit shapes is the result of complex hormone regulation and molecular pathways that affect key traits, including carpel number, fruit length, and weight. Fruit shape is a quality attribute that directly influences consumer preference, marketability and the ease of post-harvest processing. This article focuses on investigations carried out on molecular, genetic and hormonal regulation mechanisms of fruit shape, color, maturation in fruit plants and key genetic pathways such as CLV-WUS and OVATE, as well as their roles in shaping non-climacteric fruits such as strawberries, grapes and raspberries. Plant hormones, especially abscisic acid (ABA) and indole-3-acetic acid (IAA), play a crucial role in enhancing desirable traits such as color and taste, while regulating anthocyanin synthesis and growth time. In addition, the dynamic interactions between auxin, gibberellin, and ethylene are crucial for the ripening process. Jasmonate enhances stress response, brassinosteroids promote ripening and cytokinins promote early fruit development. In addition, this review also studied the fruit morphology of species such as tomatoes and cucumbers, emphasizing the importance of the CLV-WUS pathway, which regulates the number of carpels through genes such as WUSCHEL (WUS), FRUITFULL1 (FUL1), and auxin response factor 14 (ARF14). The weight of fresh fruit is affected by microRNAs such as miRNA156, which emphasizes the importance of post transcriptional regulation. The involvement of transcription factors such as SISHN1, CaOvate, and CISUN25-26-27a further emphasizes the complexity of hormone regulation. Understanding these regulatory mechanisms can enhance our understanding of fruit development and have a profound impact on agricultural practices and crop improvement strategies aimed at meeting the growing global demand for high-quality agricultural products.

Molecular genetic regulation of the vegetative-generative transition in wheat from an environmental perspective

The key to the wide geographical distribution of wheat is its high adaptability. One of the most commonly used methods for studying adaptation is investigation of the transition between the vegetative-generative phase and the subsequent intensive stem elongation process. These processes are determined largely by changes in ambient temperature, the diurnal and annual periodicity of daylength, and the composition of the light spectrum. Many genes are involved in the perception of external environmental signals, forming a complex network of interconnections that are then integrated by a few integrator genes. This hierarchical cascade system ensures the precise occurrence of the developmental stages that enable maximum productivity. This review presents the interrelationship of molecular-genetic pathways (Earliness per se, circadian/photoperiod length, vernalization - cold requirement, phytohormonal - gibberellic acid, light perception, ambient temperature perception and ageing - miRNA) responsible for environmental adaptation in wheat. Detailed molecular genetic mapping of wheat adaptability will allow breeders to incorporate new alleles that will create varieties best adapted to local environmental conditions.

Reciprocal grafting reveals the role of gibberellins in tomato root-shoot communication

Gibberellins (GAs) serve a multitude of functions in the regulation of processes associated with plant growth and development. The GA demand of an organ can be met through long-range transport from the site of synthesis. To examine the impact of altered GA biosynthesis on metabolism and growth, we performed reciprocal grafts of wild-type (WT; Solanum lycopersicum L.) and mutants exhibiting varying degrees of GA-deficiency (gib lines). The relative growth rate, based on plant height and specific leaf area, of the gib scions demonstrated partial recovery upon grafting to a WT rootstock. In contrast, the WT scion demonstrated recovery of root biomass and the root/shoot ratio in plants with gib rootstocks. Although the majority of free amino acids accumulated and negatively affected root growth of the WT rootstock, while the levels of organic acids and sugars were reduced. Increased levels of sugars and decreased levels of branched-chain amino acids in the roots of gib rootstock suggested that were the main carbon source to sustain the root growth. The multivariate analysis demonstrated growth and metabolism adjustments of the WT rootstock to supply the higher GA demand of the gib scions. In contrast, the WT scion displayed relatively minor metabolic alterations to support high rates of root growth and a reduced GA demand by the gib rootstocks. In this context, the strategic use of grafting between WT plants and GA-deficient mutants offers a viable approach to boosting agricultural productivity and strengthening plant resilience against abiotic stresses, providing an innovative alternative for sustainable crop management under challenging environmental conditions.

Genome-Wide Characterization of Gibberellin Oxidase Genes (GbGAoxs) and Illustration of Their Molecular Responses to Exogenous GA3 in Gossypium barbadense

As key enzymes in the gibberellin (GA) biosynthesis pathway, GAoxs function as regulators of bioactive GA levels and plant architecture, yet little is understood about GAoxs in Gossypium. In this study, 78 GAox genes identified in four cotton species were divided into three subgroups: GA2ox, GA3ox, and GA20ox. Syntenic relationships of GAoxs in Gossypium suggested that divergencies in gene function may be attributed to whole-genome duplication during evolution. Cis-acting element analysis suggested that the GbGAox genes might participate in plant growth, development, and hormone responses. Moreover, transcriptome analysis was performed to characterize the molecular response of the exogenous GA3 application. It was found that DEGs (differentially expressed genes) are widely involved in cell division and cell wall modification, in which the most XTH (xyloglucan endotransglucosylase/hydrolase) and GAox genes responded actively to the exogenous GA3 treatment. Some transcription factors and protein kinases cooperated with those GbGAoxs in response to GA3. These findings underlie the biological function of GAox genes and their responses to GA3 in regulating plant growth in Gossypium barbadense.

CsIREH1 phosphorylation regulates DELLA protein affecting plant height in cucumber (Cucumis sativus)

Plant height is a critical agronomic trait that affects crop yield, plant architecture, and environmental adaptability. Gibberellins (GAs) regulate plant height, with DELLA proteins acting as key repressors in the GA signaling pathway by inhibiting GA-induced growth. While DELLA phosphorylation is essential for regulating plant height, the precise mechanisms underlying this process remain incompletely understood. In this study, we identified a cucumber mutant with delayed growth, which exhibited reduced sensitivity to GA treatment. Through bulked segregant analysis (BSA-seq) combined with molecular marker linkage analysis, we successfully identified and cloned the gene responsible for the dwarf phenotype, CsIREH1 (INCOMPLETE ROOT HAIR ELONGATION 1), which encodes an AGC protein kinase. Further research revealed that CsIREH1 interacts with and phosphorylates DELLA proteins, specifically targeting CsGAIP and CsGAI2. We propose that IREH1-dependent phosphorylation of DELLA proteins prevents their excessive accumulation, thereby maintaining normal plant growth. Therefore, investigating the role of IREH1-mediated DELLA phosphorylation provides valuable insights and theoretical foundations for understanding how plants regulate growth mechanisms.

Evolutionary analysis of DELLA proteins in sweet potato and related species reveals their roles in development and stress responses

DELLA proteins act as master negative regulators in the gibberellin signaling pathway, which controls numerous aspects of plant growth and development. Despite the pivotal role of DELLA proteins, a comprehensive genome-wide analysis of the DELLA gene family in sweet potato (Ipomoea batatas) and its related species has yet to be conducted. Here, we performed a comparative analysis of this gene family among six Ipomoea species, including Ipomoea batatas, Ipomoea trifida, Ipomoea triloba, Ipomoea nil, Ipomoea cairica, and Ipomoea aquatica. Among the six Ipomoea species, only I. nil contains five DELLA genes, while the remaining species have three DELLA genes each. The DELLA genes were categorized into three distinct subgroups based on the phylogenetic topology in selected Ipomoea species. Comparative analysis of gene structure and protein motifs revealed that members within the same phylogenetic group exhibit comparable exon/intron and motif organization. The cis-regulatory elements of the DELLA gene in selected Ipomoea species contain unique promoter elements, indicating the presence of species-specific regulatory mechanisms. A multitude of shared cis-regulatory elements related to stress responses were identified in the DELLA gene promoters. Furthermore, a syntenic analysis indicates two groups of syntenic DELLA genes have undergone several rearrangements. The results of the duplication analysis indicated that dispersed duplications contribute to the expansion of the DELLA genes. Moreover, the DELLA genes in sweet potato display an expression pattern that tends to control the growth and development of either the aerial or below-ground parts, and they are responsive to a range of hormones and abiotic stresses. Thus, these findings provide insights into the evolutionary history of DELLA genes within the genus Ipomoea and the functions of sweet potato DELLA genes.

Study on the physiological mechanism and transcriptional regulatory network of early fruit development in Gleditsia sinensis Lam. (Fabaceae)

BACKGROUND

Gleditsia sinensis Lam. (Fabaceae) is a medicinal legume characterized by its spines and pods, which are rich in saponins, polysaccharides, and various specialized metabolites with potential medicinal and industrial applications. The low fruit set rate in artificially cultivated economic forests significantly impedes its development and utilization. A comprehensive understanding of the cellular events, physiological and biochemical processes, and molecular regulatory mechanisms underlying fruit initiation and early fruit development is essential for enhancing yield. However, such information for G. sinensis remains largely unexplored.

RESULTS

In this study, we identified that the early fruit development process in G. sinensis can be categorized into three distinct stages: pollination, the critical period of fertilization, and the initial fruit development followed by subsequent growth. The dynamic changes in non-structural carbohydrates and endogenous plant hormones within the ovary were found to play a significant role during fruit set and the early stages of fruit development. Additionally, the high activity of gibberellin, cytokinin, and sucrose-metabolizing enzymes in the ovary was conducive to early fruit development. Furthermore, we generated high-resolution spatiotemporal gene expression profiles in the ovary from the stage of efflorescence to early fruit development. Comparative transcriptomics and weighted gene co-expression network analysis revealed specific genes and gene modules predominant at distinct developmental stages, thereby highlighting unique genetic programming. Overall, we identified the potential regulatory network governing fruit initiation and subsequent development, as well as the sets of candidate genes involved, based on the aforementioned results.

CONCLUSIONS

The results offer a valuable reference and resource for the application of exogenous substances, such as hormones and sugars, during critical fruit development periods, and for the development of molecular tools aimed at improving yield.

Different roles of the phytohormone gibberellin in the wide-spread arbuscular mycorrhiza and in orchid mycorrhiza

Gibberellin (GA) is a classical plant hormone that regulates many physiological processes, such as plant growth, development, and environmental responses. GA inhibits arbuscular mycorrhizal (AM) symbiosis, the most ancient and widespread type of mycorrhizal symbiosis. Knowledge about mycorrhizal symbioses at the molecular level has been obtained mainly in model plants such as legumes and rice. In contrast, molecular mechanisms in non-model plants are still unclear. Recent studies have revealed the novel roles of GA in mycorrhizal symbioses: its positive effect in Paris-type AM symbiosis in Eustoma grandiflorum and its negative effect on both seed germination and mycorrhizal symbiosis in orchids. This review focuses on the recent data on GA function in AM and orchid mycorrhizal symbioses.

The role of gibberellin synthase gene VvGA2ox7 acts as a positive regulator to salt stress in Arabidopsis thaliana

BACKGROUND

Soil salinity is an important environmental component affecting plant growth and yield, but high-salinity soils are a major constraint to the development of the grape industry. Previous studies have provided lines of evidence that gibberellins (GAs) play a significant regulatory role in plant responses to salt stress. However, it remains unclear whether GA2ox, a key enzyme that maintains the balance of bioactive gibberellins and intermediates in plants, is involved in the mechanism of salt stress tolerance in grapes.

RESULTS

In this study, we found that GA2ox7 positively modulates salt stress via its ectopic expression in Arabidopsis thaliana. The GA2ox7 gene cloned from grape was a hydrophilic protein, its CDS length was 1002 bp. Besides, VvGA2ox7 protein contained DIOX_N and 2OG-FeII_Oxy domains and was localized at the nucleus and cytoplasm. Yeast two-hybrid (Y2H) showed VvARCN1, VvB5R, VvRUB2, and VvCAR11 might be potential interaction proteins of VvGA2ox7. Compared with the wild type, overexpression of VvGA2ox7 in Arabidopsis thaliana enhanced antioxidant enzymatic activities and proline, chlorophyll, and ABA contents, and decreased relative electrical conductivity, malondialdehyde, and GA3 contents. Moreover, overexpression of VvGA2ox7 positively regulated the expression of salt stress response genes (KAT1, APX1, LEA, P5CS1, AVP1, CBF1), indicating that the VvGA2ox7 overexpression improved the salt stress tolerance of plants.

CONCLUSIONS

Taken together, this investigation indicates that VvGA2ox7 may act as a positive regulator in response to salt stress and provide novel insights for a deeper understanding of the role of VvGA2ox7 in grapes.

Rice seed storability: From molecular mechanisms to agricultural practices

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

Functional characterisation of BnaA02.TOP1α and BnaC02.TOP1α involved in true leaf biomass accumulation in Brassica napus L

Leaves, as primary photosynthetic organs essential for high crop yield and quality, have attracted significant attention. The functions of DNA topoisomerase 1α (TOP1α) in various biological processes, including leaf development, in Brassica napus remain unknown. Here, four paralogs of BnaTOP1α, namely BnaA01.TOP1α, BnaA02.TOP1α, BnaC01.TOP1α and BnaC02.TOP1α, were identified and cloned in the B. napus inbred line 'K407'. Expression pattern analysis revealed that BnaA02.TOP1α and BnaC02.TOP1α, but not BnaA01.TOP1α and BnaC01.TOP1α, were persistently and highly expressed in B. napus true leaves. Preliminary analysis in Arabidopsis thaliana revealed that BnaA02.TOP1α and BnaC02.TOP1α paralogs, but not BnaA01.TOP1α and BnaC01.TOP1α, performed biological functions. Targeted mutations of four BnaTOP1α paralogs in B. napus using the CRISPR-Cas9 system revealed that BnaA02.TOP1α and BnaC02.TOP1α served as functional paralogs and redundantly promoted true leaf number and size, thereby promoting true leaf biomass accumulation. Moreover, BnaA02.TOP1α modulated the levels of endogenous gibberellins, cytokinins and auxins by indirectly regulating several genes related to their metabolism processes. BnaA02.TOP1α directly activated BnaA03.CCS52A2 and BnaC09.AN3 by facilitating the recruitment of RNA polymerase II and modulating H3K27me3, H3K36me2 and H3K36me3 levels at these loci and indirectly activated the BnaA08.PARL1 expression, thereby positively controlling the true leaf size in B. napus. Additionally, BnaA02.TOP1α indirectly activated the BnaA07.PIN1 expression to positively regulate the true leaf number. These results reveal the important functions of BnaTOP1α and provide insights into the regulatory network controlling true leaf biomass accumulation in B. napus.

Functional Characterization of the Gibberellin (GA) Receptor ScGID1 in Sugarcane

Sugarcane smut caused by Sporisorium scitamineum represents the most destructive disease in the sugarcane industry, causing host hormone disruption and producing a black whip-like sorus in the apex of the stalk. In this study, the gibberellin metabolic pathway was found to respond to S. scitamineum infection, and the contents of bioactive gibberellins were significantly reduced in the leaves of diseased plants. The gibberellin receptor gene ScGID1 was identified and significantly downregulated. ScGID1 localized in both the nucleus and cytoplasm and had the highest expression level in the leaves. Eight proteins that interact with ScGID1 were screened out using a yeast two-hybrid assay. Novel DELLA proteins named ScGAI1a and ScGA20ox2, key enzymes in GA biosynthesis, were both found to interact with ScGID1 in a gibberellin-independent manner. Transcription factor trapping with a yeast one-hybrid system identified 50 proteins that interacted with the promoter of ScGID1, among which ScS1FA and ScPLATZ inhibited ScGID1 transcription, while ScGDSL promoted transcription. Overexpression of ScGID1 in transgenic Nicotiana benthamiana plants could increase plant height and promote flowering. These results not only contribute to improving our understanding of the metabolic regulatory network of sugarcane gibberellin but also expand our knowledge of the interaction between sugarcane and pathogens.

How chromatin senses plant hormones

Plant hormones activate receptors, initiating intracellular signaling pathways. Eventually, hormone-specific transcription factors become active in the nucleus, facilitating hormone-induced transcriptional regulation. Chromatin plays a fundamental role in the regulation of transcription, the process by which genetic information encoded in DNA is converted into RNA. The structure of chromatin, a complex of DNA and proteins, directly influences the accessibility of genes to the transcriptional machinery. The different signaling pathways and transcription factors involved in the transmission of information from the receptors to the nucleus have been readily explored, but not so much for the specific mechanisms employed by the cell to ultimately instruct the chromatin changes necessary for a fast and robust transcription activation, specifically for plant hormone responses. In this review, we will focus on the advancements in understanding how chromatin receives plant hormones, facilitating the changes necessary for fast, robust, and specific transcriptional regulation.

ZmGDIα-hel counters the RBSDV-induced reduction of active gibberellins to alleviate maize rough dwarf virus disease

Maize rough dwarf disease (MRDD) threatens maize production globally. The P7-1 effector of the rice black-streaked dwarf virus (RBSDV) targets maize Rab GDP dissociation inhibitor alpha (ZmGDIα) to cause MRDD. However, P7-1 has difficulty recruiting a ZmGDIα variant with an alternative helitron-derived exon 10 (ZmGDIα-hel), resulting in recessive resistance. Here, we demonstrate that P7-1 can recruit another maize protein, gibberellin 2-oxidase 13 (ZmGA2ox7.3), which also exhibits tighter binding affinity for ZmGDIα than ZmGDIα-hel. The oligomerization of ZmGA2ox7.3 is vital for its function in converting bioactive gibberellins into inactive forms. Moreover, the enzymatic activity of ZmGA2ox7.3 oligomers increases when forming hetero-oligomers with P7-1/ZmGDIα, but decreases when ZmGDIα-hel replaces ZmGDIα. Viral infection significantly promotes ZmGA2ox7.3 expression and oligomerization in ZmGDIα-containing susceptible maize, resulting in reduced bioactive GA1/GA4 levels. This causes an auxin/cytokinin imbalance and ultimately manifests as MRDD syndrome. Conversely, in resistant maize, ZmGDIα-hel counters these virus-induced changes, thereby mitigating MRDD severity.

Gamma-aminobutyric acid interactions with phytohormones and its role in modulating abiotic and biotic stress in plants

Gamma-aminobutyric acid (GABA), a ubiquitous non-protein 4-carbon amino acid present in both prokaryotic and eukaryotic organisms. It is conventionally recognized as a neurotransmitter in mammals and plays a crucial role in plants. The context of this review centers on the impact of GABA in mitigating abiotic stresses induced by climate change, such as drought, salinity, heat, and heavy metal exposure. Beyond its neurotransmitter role, GABA emerges as a key player in diverse metabolic processes, safeguarding plants against multifaceted abiotic as well as biotic challenges. This comprehensive exploration delves into the GABA biosynthetic pathway, its transport mechanisms, and its intricate interplay with various abiotic stresses. The discussion extends to the nuanced relationship between GABA and phytohormones during abiotic stress acclimation, offering insights into the strategic development of mitigation strategies against these stresses. The delineation of GABA's crosstalk with phytohormones underscores its pivotal role in formulating crucial strategies for abiotic stress alleviation in plants.

Genome-Wide Analysis of the Gibberellin-Oxidases Family Members in Four Prunus Species and a Functional Analysis of PmGA2ox8 in Plant Height

Gibberellins (GAs), enzymes that play a significant role in plant growth and development, and their levels in plants could be regulated by gibberellin-oxidases (GAoxs). As important fruit trees and ornamental plants, the study of the mechanism of plant architecture formation of the Prunus genus is crucial. Here, 85 GAox genes were identified from P. mume, P. armeniaca, P. salicina, and P. persica, and they were classified into six subgroups. Conserved motif and gene structure analysis showed that GAoxs were conserved in the four Prunus species. Collinearity analysis revealed two fragment replication events of PmGAoxs in the P. mume genome. Promoter cis-elements analysis revealed 24 PmGAoxs contained hormone-responsive elements and development regulatory elements. The expression profile indicated that PmGAoxs have tissue expression specificity, and GA levels during the dormancy stage of flower buds were controlled by certain PmGAoxs. After being treated with IAA or GA3, the transcription level of PmGA2ox8 in stems was significantly increased and showed a differential expression level between upright and weeping stems. GUS activity driven by PmGA2ox8 promoter was detected in roots, stems, leaves, and flower organs of Arabidopsis. PmGA2ox8 overexpression in Arabidopsis leads to dwarfing phenotype, increased number of rosette leaves but decreased leaf area, and delayed flowering. Our results showed that GAoxs were conserved in Prunus species, and PmGA2ox8 played an essential role in regulating plant height.

The MdNAC72-MdABI5 module acts as an interface integrating jasmonic acid and gibberellin signals and undergoes ubiquitination-dependent degradation regulated by MdSINA2 in apple

Jasmonic acid (JA) and gibberellin (GA) coordinately regulate plant developmental programs and environmental cue responses. However, the fine regulatory network of the cross-interaction between JA and GA remains largely elusive. In this study, we demonstrate that MdNAC72 together with MdABI5 positively regulates anthocyanin biosynthesis through an exquisite MdNAC72-MdABI5-MdbHLH3 transcriptional cascade in apple. MdNAC72 interacts with MdABI5 to promote the transcriptional activation of MdABI5 on its target gene MdbHLH3 and directly activates the transcription of MdABI5. The MdNAC72-MdABI5 module regulates the integration of JA and GA signals in anthocyanin biosynthesis by combining with JA repressor MdJAZ2 and GA repressor MdRGL2a. MdJAZ2 disrupts the MdNAC72-MdABI5 interaction and attenuates the transcriptional activation of MdABI5 by MdNAC72. MdRGL2a sequesters MdJAZ2 from the MdJAZ2-MdNAC72 protein complex, leading to the release of MdNAC72. The E3 ubiquitin ligase MdSINA2 is responsive to JA and GA signals and promotes ubiquitination-dependent degradation of MdNAC72. The MdNAC72-MdABI5 interface fine-regulates the integration of JA and GA signals at the transcriptional and posttranslational levels by combining MdJAZ2, MdRGL2a, and MdSINA2. In summary, our findings elucidate the fine regulatory network connecting JA and GA signals with MdNAC72-MdABI5 as the core in apple.

Crape myrtle LiGAoxs displaying activities of gibberellin oxidases respond to branching architecture

In the realm of ornamental horticulture, crape myrtle (Lagerstroemia indica) stands out for its aesthetic appeal, attributed largely to its vibrant flowers and distinctive branching architecture. This study embarked on a comprehensive exploration of the gibberellin oxidase (GAox) gene family in crape myrtle, illuminating its pivotal role in regulating GA levels, a key determinant of plant developmental processes. We identified and characterized 36 LiGAox genes, subdivided into GA2ox, GA3ox, GA20ox, and GAox-like subgroups, through genomic analyses. These genes' evolutionary trajectories were delineated, revealing significant gene expansions attributed to segmental duplication events. Functional analyses highlighted the divergent expression patterns of LiGAox genes across different crape myrtle varieties, associating them with variations in flower color and branching architecture. Enzymatic activity assays on selected LiGA2ox enzymes exhibited pronounced GA2 oxidase activity, suggesting a potential regulatory role in GA biosynthesis. Our findings offered a novel insight into the molecular underpinnings of GA-mediated growth and development in L. indica, providing a foundational framework for future genetic enhancements aimed at optimizing ornamental traits.

Inhibition of flowering by gibberellins in the woody plant Jatropha curcas is restored by overexpression of JcFT

Jatropha curcas (J. curcas) is a perennial oil-seed plant with vigorous vegetative growth but relatively poor reproductive growth and low seed yield. Gibberellins (GAs) promotes flowering in most annual plants but inhibits flowering in many woody plants, including J. curcas. However, the underlying mechanisms of GA inhibits flowering in perennial woody plants remain unclear. Here, we found that overexpression of the GA biosynthesis gene JcGA20ox1 inhibits flowering in J. curcas and in J. curcas × J. integerrima hybrids. Consistent with this finding, overexpression of the GA catabolic gene JcGA2ox6 promotes flowering in J. curcas. qRTPCR revealed that inhibits floral transition by overexpressing JcGA20ox1 resulted from a decrease in the expression of JcFT and other flowering-related genes, which was restored by overexpressing JcFT in J. curcas. Overexpression of JcGA20ox1 or JcGA2ox6 reduced seed yield, but overexpression of JcFT significantly increased seed yield. Furthermore, hybridization experiments showed that the reduction in seed yield caused by overexpression of JcGA20ox1 or JcGA2ox6 was partially restored by the overexpression of JcFT. In addition, JcGA20ox1, JcGA2ox6 and JcFT were also found to be involved in the regulation of seed oil content and endosperm development. In conclusion, our study revealed that the inhibitory effect of GA on flowering is mediated through JcFT and demonstrated the effects of JcGA20ox1, JcGA2ox6 and JcFT on agronomic traits in J. curcas. This study also indicates the potential value of GA metabolism genes and JcFT in the breeding of new varieties of woody oil-seed plants.

Overexpression of CsBRC, an F-box gene from Camellia sinensis, increased the plant branching in tobacco and rice

Tea plant (Camellia sinensis [L.]) is one of the most important crops in China, and tea branch is an important agronomic trait that determines the yield of tea plant. In previous work focused on GWAS that detecting GWAS signals related to plant architecture through whole genome re-sequencing of ancient tea plants, a gene locus TEA 029928 significantly related to plant type was found. Sequence alignment results showed that this gene belonged to the F-box family. We named it CsBRC. CsBRC-GFP fusion proteins were mainly localized in the plasma membrane. By comparing the phenotypes of CsBRC transgenic tobacco and WT tobacco, it was found that the number of branches of transgenic tobacco was significantly higher than that of wild-type tobacco. Through RNA-seq analysis, it was found that CsBRC affects the branching development of plants by regulating the expression of genes related to brassinosteroid synthesis pathway in plants. In addition, overexpression of CsBRC in rice could increase tiller number, grain length and width, and 1,000-grain weight.

Transcriptomic Profiling of Sugarcane White Leaf (SCWL) Canes during Maturation Phase

Sugarcane white leaf (SCWL) disease, caused by Candidatus Phytoplasma sacchari, results in the most damage to sugarcane plantations. Some SCWL canes can grow unnoticed through the maturation phase, subsequently resulting in an overall low sugar yield, or they can be used accidentally as seed canes. In this work, 12-month-old SCWL and asymptomatic canes growing in the same field were investigated. An abundance of phytoplasma in SCWL canes affected growth and sugar content as well as alterations of transcriptomic profiles corresponding to several pathways that responded to the infection. Suppression of photosynthesis, porphyrin and chlorophyll metabolism, coupled with an increase in the expression of chlorophyllase, contributed to the reduction in chlorophyll levels and photosynthesis. Blockage of sucrose transport plausibly occurred due to the expression of sugar transporters in leaves but suppression in stalks, resulting in low sugar content in canes. Increased expression of genes associated with MAPK cascades, plant hormone signaling transduction, callose plug formation, the phenylpropanoid pathway, and calcium cascades positively promoted defense mechanisms against phytoplasma colonization by an accumulation of lignin and calcium in response to plant immunity. Significant downregulation of CPK plausibly results in a reduction in antioxidant enzymes and likely facilitates pathogen invasion, while expression of sesquiterpene biosynthesis possibly attracts the insect vectors for transmission, thereby enabling the spread of phytoplasma. Moreover, downregulation of flavonoid biosynthesis potentially intensifies the symptoms of SCWL upon challenge by phytoplasma. These SCWL sugarcane transcriptomic profiles describe the first comprehensive sugarcane-phytoplasma interaction during the harvesting stage. Understanding molecular mechanisms will allow for sustainable management and the prevention of SCWL disease-a crucial benefit to the sugar industry.

Integrated proteomic, transcriptomic, and metabolomic profiling reveals that the gibberellin-abscisic acid hub runs flower development in the Chinese orchid Cymbidium sinense

The seasonal flowering Chinese Cymbidium produce an axillary floral meristem and require a dormancy period during cold conditions for flower development. However, the bud activation mechanism remains elusive. This study evaluates the multi-omics across six stages of flower development, along with functional analysis of core genes to decipher the innate mechanism of floral bud initiation and outgrowth in the Chinese orchid Cymbidium sinense. Transcriptome and proteome analyses identified 10 modules with essential roles in floral bud dormancy and activation. Gene clusters in the early stages of flower development were mainly related to flowering time regulation and meristem determination, while the late stages were correlated with hormone signaling pathways. The metabolome identified 69 potential hormones in which gibberellin (GA) and abscisic acid (ABA) were the main regulatory hubs, and GA4 and GA53 exhibited a reciprocal loop. Extraneous GA application caused rapid elongation of flower buds and promoted the expression of flower development genes. Contrarily, exogenous ABA application extended the dormancy process and ABA inhibitors induced dormancy release. Moreover, CsAPETALA1 (CsAP1) was identified as the potential target of ABA for floral bud activation. Transformation of CsAP1 in Arabidopsis and its transient overexpression in C. sinense protoplasts not only affected flowering time and floral organ morphogenesis in Arabidopsis but also orchestrated the expression of flowering and hormone regulatory genes. The presence of ABA response elements in the CsAP1 promoter, rapid downregulation of CsAP1 after exogenous ABA application, and the activation of the floral bud after ABA inhibitor treatment suggest that ABA can control bud outgrowth through CsAP1.

Characterization, expression pattern, and function analysis of gibberellin oxidases in Salix matsudana

Gibberellin oxidases (GAoxs) identified from many species play indispensable roles in GA biosynthesis and GA signal transduction. However, there has been limited research conducted on the GAox family of Salix matsudana, a tetraploid ornamental tree species. Here, 54 GAox genes were identified from S. matsudana and renamed as SmGA20ox1-22, SmGA2ox1-24, SmGA3ox1-6, and SmGAox-like1/2. Gene structure and conserved motif analysis showed that SmGA3ox members possess the 1 intron and other SmGAoxs contain 2-3 introns, and motif 1/2/7 universally present in all SmGAoxs. A total of 69 gene pairs were identified from SmGAox family members, and the Ka/Ks values indicated the SmGAoxs experience the purifying selection. The intra species collinearity analysis implied S. matsudana, S. purpurea, and Populus trichocarpa have the close genetic relationship. The GO analysis suggested SmGAoxs are dominantly involved in GA metabolic process, ion binding, and oxidoreductase activity. RNA-sequencing demonstrated that some SmGAoxs may play an essential role in salt and submergence stresses. In addition, the SmGA20ox13/21 displayed the dominant vitality of GA20 oxidase, but the SmGA20ox13/21 still possessed low activities of GA2 and GA3 oxidases. This study can contribute to reveal the regulatory mechanism of salt and submergence tolerance in willow.

Integrative Metabolomic and Transcriptomic Analysis Elucidates That the Mechanism of Phytohormones Regulates Floral Bud Development in Alfalfa

Floral bud growth influences seed yield and quality; however, the molecular mechanism underlying the development of floral buds in alfalfa (Medicago sativa) is still unclear. Here, we comprehensively analyzed the transcriptome and targeted metabolome across the early, mid, and late bud developmental stages (D1, D2, and D3) in alfalfa. The metabolomic results revealed that gibberellin (GA), auxin (IAA), cytokinin (CK), and jasmonic acid (JA) might play an essential role in the developmental stages of floral bud in alfalfa. Moreover, we identified some key genes associated with GA, IAA, CK, and JA biosynthesis, including CPS, KS, GA20ox, GA3ox, GA2ox, YUCCA6, amid, ALDH, IPT, CYP735A, LOX, AOC, OPR, MFP2, and JMT. Additionally, many candidate genes were detected in the GA, IAA, CK, and JA signaling pathways, including GID1, DELLA, TF, AUX1, AUX/IAA, ARF, GH3, SAUR, AHP, B-ARR, A-ARR, JAR1, JAZ, and MYC2. Furthermore, some TFs related to flower growth were screened in three groups, such as AP2/ERF-ERF, MYB, MADS-M-type, bHLH, NAC, WRKY, HSF, and LFY. The findings of this study revealed the potential mechanism of floral bud differentiation and development in alfalfa and established a theoretical foundation for improving the seed yield of alfalfa.

The transcription factor PtoMYB142 enhances drought tolerance in Populus tomentosa by regulating gibberellin catabolism

Drought stress caused by global warming has resulted in significant tree mortality, driving the evolution of water conservation strategies in trees. Although phytohormones have been implicated in morphological adaptations to water deficits, the molecular mechanisms underlying these processes in woody plants remain unclear. Here, we report that overexpression of PtoMYB142 in Populus tomentosa results in a dwarfism phenotype with reduced leaf cell size, vessel lumen area, and vessel density in the stem xylem, leading to significantly enhanced drought resistance. We found that PtoMYB142 modulates gibberellin catabolism in response to drought stress by binding directly to the promoter of PtoGA2ox4, a GA2-oxidase gene induced under drought stress. Conversely, knockout of PtoMYB142 by the CRISPR/Cas9 system reduced drought resistance. Our results show that the reduced leaf size and vessel area, as well as the increased vessel density, improve leaf relative water content and stem water potential under drought stress. Furthermore, exogenous GA3 application rescued GA-deficient phenotypes in PtoMYB142-overexpressing plants and reversed their drought resistance. By suppressing the expression of PtoGA2ox4, the manifestation of GA-deficient characteristics, as well as the conferred resistance to drought in PtoMYB142-overexpressing poplars, was impeded. Our study provides insights into the molecular mechanisms underlying tree drought resistance, potentially offering novel transgenic strategies to enhance tree resistance to drought.

Genome-wide identification of GA2ox genes family and analysis of PbrGA2ox1-mediated enhanced chlorophyll accumulation by promoting chloroplast development in pear

BACKGROUND

Chlorophyll (Chl) is an agronomic trait associated with photosynthesis and yield. Gibberellin 2-oxidases (GA2oxs) have previously been shown to be involved in Chl accumulation. However, whether and how the PbrGA2ox proteins (PbrGA2oxs) mediate Chl accumulation in pear (Pyrus spp.) is scarce.

RESULTS

Here, we aimed to elucidate the role of the pear GA2ox gene family in Chl accumulation and the related underlying mechanisms. We isolated 13 PbrGA2ox genes (PbrGA2oxs) from the pear database and identified PbrGA2ox1 as a potential regulator of Chl accumulation. We found that transiently overexpressing PbrGA2ox1 in chlorotic pear leaves led to Chl accumulation, and PbrGA2ox1 silencing in normal pear leaves led to Chl degradation, as evident by the regreening and chlorosis phenomenon, respectively. Meanwhile, PbrGA2ox1-overexpressing (OE) tobacco plants discernably exhibited Chl built-up, as evidenced by significantly higher Pn and Fv/Fm. In addition, RNA sequencing (RNA-seq), physiological and biochemical investigations revealed an increase in abscisic acid (ABA), methyl jasmonate (MeJA), and salicylic acid (SA) concentrations and signaling pathways; a marked elevation in reducing and soluble sugar contents; and a marginal decline in the starch and sucrose levels in OE plants. Interestingly, PbrGA2ox1 overexpression did not prominently affect Chl synthesis. However, it indeed facilitated chloroplast development by increasing chloroplast number per cell and compacting the thylakoid granum stacks. These findings might jointly contribute to Chl accumulation in OE plants.

CONCLUSION

Overall, our results suggested that GA2oxs accelerate Chl accumulation by stimulating chloroplast development and proved the potential of PbrGA2ox1 as a candidate gene for genetically breeding biofortified pear plants with a higher yield.

The SIAMESE family of cell-cycle inhibitors in the response of plants to environmental stresses

Environmental abiotic constraints are known to reduce plant growth. This effect is largely due to the inhibition of cell division in the leaf and root meristems caused by perturbations of the cell cycle machinery. Progression of the cell cycle is regulated by CDK kinases whose phosphorylation activities are dependent on cyclin proteins. Recent results have emphasized the role of inhibitors of the cyclin-CDK complexes in the impairment of the cell cycle and the resulting growth inhibition under environmental constraints. Those cyclin-CDK inhibitors (CKIs) include the KRP and SIAMESE families of proteins. This review presents the current knowledge on how CKIs respond to environmental changes and on the role played by one subclass of CKIs, the SIAMESE RELATED proteins (SMRs), in the tolerance of plants to abiotic stresses. The SMRs could play a central role in adjusting the balance between growth and stress defenses in plants exposed to environmental stresses.

Arabidopsis retromer subunit AtVPS29 is involved in SLY1-mediated gibberellin signaling

KEY MESSAGE

Retromer protein AtVPS29 upregulates the SLY1 protein and downregulates the RGA protein, positively stimulating the development of the root meristematic zone, which indicates an important role of AtVPS29 in gibberellin signaling. In plants, the large retromer complex is known to play roles in multiple development processes, including cell polarity, programmed cell death, and root hair growth in Arabidopsis. However, many of its roles in plant development remain unknown. Here, we show that Arabidopsis trimeric retromer protein AtVPS29 (vacuolar protein sorting 29) modulates gibberellin signaling. The SLEEPY1 (SLY1) protein, known as a positive regulator of gibberellic acid (GA) signaling, exhibited lower abundance in vps29-3 mutants compared to wild-type (WT) plants. Conversely, the DELLA repressor protein, targeted by the E3 ubiquitin ligase SCF (Skp, Cullin, F-box) complex and acting as a negative regulator of GA signaling, showed increased abundance in vps29-3 mutants compared to WT. The vps29-3 mutants exhibited decreased sensitivity to exogenous GA supply in contrast to WT, despite an upregulation in the expression of GA receptor genes within the vps29-3 mutants. In addition, the expression of the GA synthesis genes was downregulated in vps29-3 mutants, implying that the loss of AtVPS29 causes the downregulation of GA synthesis and signaling. Furthermore, vps29-3 mutants exhibited a reduced meristematic zone accompanied by a decreased cell number. Together, these data indicate that AtVPS29 positively regulates SLY1-mediated GA signaling and plant growth.

Integration of Physiological, Transcriptomic, and Metabolomic Analyses Reveal Molecular Mechanisms of Salt Stress in Maclura tricuspidata

Salt stress is a universal abiotic stress that severely affects plant growth and development. Understanding the mechanisms of Maclura tricuspidate's adaptation to salt stress is crucial for developing salt-tolerant plant varieties. This article discusses the integration of physiology, transcriptome, and metabolome to investigate the mechanism of salt adaptation in M. tricuspidata under salt stress conditions. Overall, the antioxidant enzyme system (SOD and POD) of M. tricuspidata exhibited higher activities compared with the control, while the content of soluble sugar and concentrations of chlorophyll a and b were maintained during salt stress. KEGG analysis revealed that deferentially expressed genes were primarily involved in plant hormone signal transduction, phenylpropanoid and flavonoid biosynthesis, alkaloids, and MAPK signaling pathways. Differential metabolites were enriched in amino acid metabolism, the biosynthesis of plant hormones, butanoate, and 2-oxocarboxylic acid metabolism. Interestingly, glycine, serine, and threonine metabolism were found to be important both in the metabolome and transcriptome-metabolome correlation analyses, suggesting their essential role in enhancing the salt tolerance of M. tricuspidata. Collectively, our study not only revealed the molecular mechanism of salt tolerance in M. tricuspidata, but also provided a new perspective for future salt-tolerant breeding and improvement in salt land for this species.

Comparative transcript abundance of gibberellin oxidases genes in two barley (Hordeum vulgare) genotypes with contrasting lodging resistance under different regimes of water deficit

Barley (Hordeum vulgare ) is the world's fourth most important cereal crop, and is particularly well adapted to harsh environments. However, lodging is a major productivity constraint causing 13-65% yield losses. Gibberellic acid (GA) homeostatic genes such as HvGA20ox, HvGA3ox and HvGA2ox are responsible for changes in plant phenotype for height and internodal length that contribute towards lodging resistance. This study explored the expression of different HvGAox transcripts in two contrasting barley genotypes (5-GSBON-18, lodging resistant; and 5-GSBON-70, lodging sensitive), which were sown both under controlled (hydroponic, completely randomised factorial design) and field conditions (split-plot, completely randomised block design) with two irrigation treatments (normal with three irrigation events; and water deficit with one irrigation event). In the hydroponic experiment, expression analysis was performed on seedlings at 0, ¾, 1½, 3 and 6h after application of treatment. In the field experiment, leaf, shoot nodes and internodes were sampled. Downregulation of HvGA20ox.1 transcript and 2-fold upregulation of HvGA2ox.2 transcript were observed in 5-GSBON-18 under water deficit conditions. This genotype also showed a significant reduction in plant height (18-20%), lodging (<10%), and increased grain yield (15-18%) under stress. Utilisation of these transcripts in barley breeding has the potential to reduce plant height, lodging and increased grain yield.

Chemical screening of inhibitors specific for MdDOX-Co that cause an apple columnar tree-shape

MdDOX-Co, the ectopic expression of which is considered to cause the apple columnar tree shape, belongs to the 2-oxoglutarate-dependent dioxygenase (2ODD) family. It adds a hydroxyl group to position 12 of gibberellins (GAs). However, the 2ODD enzymes related to GA biosynthesis and catabolism are phylogenetically distinct from MdDOX-Co. Thus, it is possible that substrates other than GAs exist in MdDOX-Co. To identify the previously unidentified substrate(s) of MdDOX-Co, we searched for MdDOX-Co-specific inhibitors. Chemical screening using gas chromatography-mass spectrometry was performed to investigate the effects of 2400 compounds that inhibited the catalytic reaction of MdDOX-Co, but not the catabolic reaction of GA 2-oxidase, an enzyme involved in GA catabolism. By applying two positive compounds in Arabidopsis, a chemical 3-((2-chloro-6-fluorobenzyl)thio)-5,7-dimethyl-5H-pyrazolo[3,4-e][1,4,2]dithiazine-1,1-dioxide designated as TPDD that did not inhibit GA biosynthesis was selected. The structure-activity relationships among the TPDD analogs were also obtained.

Growth Hormones in Broad Bean (Vicia faba L.) and Radish (Raphanus raphanistrum subsp. sativus L.) Are Associated with Accumulated Concentrations of Perfluoroalkyl Substances

In this study, we grew radish (Raphanus raphanistrum subsp. sativus L.) and broad beans (Vicia faba L.) in a greenhouse on soils spiked with a mixture of 15 per- and polyfluoroalkyl substances (PFASs) and investigated the association between accumulated ∑PFAS concentrations, growth, and hormone levels. Short-chained PFASs dominated aboveground tissues, whereas long-chained PFASs were most abundant in the plant roots. Our results showed that the presence or absence of exodermal Casparian strips, as well as the hydrophobicity and anion exchange capacities of PFASs, could explain the translocation of PFASs within plants. Significant associations found between accumulated PFAS concentrations and levels of gibberellins (GA1 and GA15), methionine, and indole-3-acetic acid (IAA) imply potential effects of PFASs on plant development and growth. This study provides the first evidence of associations between PFAS accumulation in plants and growth hormone levels, possibly leading to growth reduction of the apical dome and effects on the cell cycle in pericycle cells and methionine metabolism in plants.

AtHSPR functions in gibberellin-mediated primary root growth by interacting with KNAT5 and OFP1 in Arabidopsis

KEY MESSAGE

AtHSPR forms a complex with KNAT5 and OFP1 to regulate primary root growth through GA-mediated root meristem activity. KNAT5-OFP1 functions as a negative regulator of AtHSPR in response to GA. Plant root growth is modulated by gibberellic acid (GA) signaling and depends on root meristem maintenance. ARABIDOPSIS THALIANA HEAT SHOCK PROTEIN-RELATED (AtHSPR) is a vital regulator of flowering time and salt stress tolerance. However, little is known about the role of AtHSPR in the regulation of primary root growth. Here, we report that athspr mutant exhibits a shorter primary root compared to wild type and that AtHSPR interacts with KNOTTED1-LIKE HOMEOBOX GENE 5 (KNAT5) and OVATE FAMILY PROTEIN 1 (OFP1). Genetic analysis showed that overexpression of KNAT5 or OFP1 caused a defect in primary root growth similar to that of the athspr mutant, but knockout of KNAT5 or OFP1 rescued the short root phenotype in the athspr mutant by altering root meristem activity. Further investigation revealed that KNAT5 interacts with OFP1 and that AtHSPR weakens the inhibition of GIBBERELLIN 20-OXIDASE 1 (GA20ox1) expression by the KNAT5-OFP1 complex. Moreover, root meristem cell proliferation and root elongation in 35S::KNAT5athspr and 35S::OFP1athspr seedlings were hypersensitive to GA3 treatment compared to the athspr mutant. Together, our results demonstrate that the AtHSPR-KNAT5-OFP1 module regulates root growth and development by impacting the expression of GA biosynthetic gene GA20ox1, which could be a way for plants to achieve plasticity in response to the environment.

Vegetative phase change causes age-dependent changes in phenotypic plasticity

Phenotypic plasticity allows organisms to optimize traits for their environment. As organisms age, they experience diverse environments that benefit from varying degrees of phenotypic plasticity. Developmental transitions can control these age-dependent changes in plasticity, and as such, the timing of these transitions can determine when plasticity changes in an organism. Here, we investigate how the transition from juvenile-to adult-vegetative development known as vegetative phase change (VPC) contributes to age-dependent changes in phenotypic plasticity and how the timing of this transition responds to environment using both natural accessions and mutant lines in the model plant Arabidopsis thaliana. We found that the adult phase of vegetative development has greater plasticity in leaf morphology than the juvenile phase and confirmed that this difference in plasticity is caused by VPC using mutant lines. Furthermore, we found that the timing of VPC, and therefore the time when increased plasticity is acquired, varies significantly across genotypes and environments. The consistent age-dependent changes in plasticity caused by VPC suggest that VPC may be adaptive. This genetic and environmental variation in the timing of VPC indicates the potential for population-level adaptive evolution of VPC.

Application of an Improved 2-Dimensional High-Throughput Soybean Root Phenotyping Platform to Identify Novel Genetic Variants Regulating Root Architecture Traits

Nutrient-efficient root system architecture (RSA) is becoming an important breeding objective for generating crop varieties with improved nutrient and water acquisition efficiency. Genetic variants shaping soybean RSA is key in improving nutrient and water acquisition. Here, we report on the use of an improved 2-dimensional high-throughput root phenotyping platform that minimizes background noise by imaging pouch-grown root systems submerged in water. We also developed a background image cleaning Python pipeline that computationally removes images of small pieces of debris and filter paper fibers, which can be erroneously quantified as root tips. This platform was used to phenotype root traits in 286 soybean lines genotyped with 5.4 million single-nucleotide polymorphisms. There was a substantially higher correlation in manually counted number of root tips with computationally quantified root tips (95% correlation), when the background was cleaned of nonroot materials compared to root images without the background corrected (79%). Improvements in our RSA phenotyping pipeline significantly reduced overestimation of the root traits influenced by the number of root tips. Genome-wide association studies conducted on the root phenotypic data and quantitative gene expression analysis of candidate genes resulted in the identification of 3 putative positive regulators of root system depth, total root length and surface area, and root system volume and surface area of thicker roots (DOF1-like zinc finger transcription factor, protein of unknown function, and C2H2 zinc finger protein). We also identified a putative negative regulator (gibberellin 20 oxidase 3) of the total number of lateral roots.

Characterization of the transcriptional responses of Armillaria gallica 012m to GA3

Gastrodia elata needs to establish a symbiotic relationship with Armillaria strains to obtain nutrients and energy. However, the signaling cross talk between G. elata and Armillaria strains is still unclear. During our experiment, we found that the vegetative mycelium of Armillaria gallica 012m grew significantly better in the media containing gibberellic acid (GA3) than the blank control group (BK). To explore the response mechanism, we performed an RNA-sequencing experiment to profile the transcriptome changes of A. gallica 012m cultured in the medium with exogenous GA3. The transcriptome-guided differential expression genes (DEGs) analysis of GA3 and BK showed that a total of 1309 genes were differentially expressed, including 361 upregulated genes and 948 downregulated genes. Some of those DEGs correlated with the biological process, including positive regulation of chromosome segregation, mitotic metaphase/anaphase transition, attachment of mitotic spindle microtubules to kinetochore, mitotic cytokinesis, and nuclear division. These analyses explained that GA3 actively promoted the growth of A. gallica to some extent. Further analysis of protein domain features showed that the deduced polypeptide contained 41 candidate genes of GA receptor, and 27 of them were expressed in our samples. We speculate that GA receptors exist in A. gallica 012m. Comparative studies of proteins showed that the postulated GA receptor domains of A. gallica 012m have a higher homologous correlation with fungi than others based on cluster analysis.

GA20ox Family Genes Mediate Gibberellin and Auxin Crosstalk in Moso bamboo (Phyllostachys edulis)

Moso bamboo (Phyllostachys edulis) is one of the fastest growing plants. Gibberellin (GA) is a key phytohormone regulating growth, but there are few studies on the growth of Moso bamboo regulated by GA. The gibberellin 20 oxidase (GA20ox) gene family was targeted in this study. Chromosomal distribution and collinearity analysis identified 10 GA20ox genes evenly distributed on chromosomes, and the family genes were relatively conservative in evolution. The genetic relationship of GA20ox genes had been confirmed to be closest in different genera of plants in a phylogenetic and selective pressure analysis between Moso bamboo and rice. About 1/3 GA20ox genes experienced positive selective pressure with segmental duplication being the main driver of gene family expansion. Analysis of expression patterns revealed that only six PheGA20ox genes were expressed in different organs of shoot development and flowers, that there was redundancy in gene function. Underground organs were not the main site of GA synthesis in Moso bamboo, and floral organs are involved in the GA biosynthesis process. The auxin signaling factor PheARF47 was located upstream of PheGA20ox3 and PheGA20ox6 genes, where PheARF47 regulated PheGA20ox3 through cis-P box elements and cis-AuxRR elements, based on the result that promoter analysis combined with yeast one-hybrid and dual luciferase detection analysis identified. Overall, we identified the evolutionary pattern of PheGA20ox genes in Moso bamboo and the possible major synthesis sites of GA, screened for key genes in the crosstalk between auxin and GA, and laid the foundation for further exploration of the synergistic regulation of growth by GA and auxin in Moso bamboo.

Comparative Transcriptomic Analysis of the Metabolism of Betalains and Flavonoids in Red Amaranth Hypocotyl under Blue Light and Dark Conditions

Amaranth plants contain abundant betalains and flavonoids. Anthocyanins are important flavonoids; however, they cannot coexist in the same plant with betalains. Blue light influences metabolite synthesis and hypocotyl elongation; accordingly, analyses of its effects on betalain and flavonoid biosynthesis in Amaranthus tricolor may provide insight into the distribution of these plant pigments. We analyzed the betalain and flavonoid content and transcriptome profiles in amaranth hypocotyls under blue light and dark conditions. Furthermore, we analyzed the expression patterns of key genes related to betalains and flavonoids. Amaranth hypocotyls were shorter and redder and showed higher betalain and flavonoid content under blue light than in dark conditions. Key genes involved in the synthesis of betalains and flavonoids were upregulated under blue light. The gene encoding DELLA was also upregulated. These results suggest that blue light favors the synthesis of both betalains and flavonoids via the suppression of bioactive gibberellin and the promotion of DELLA protein accumulation, which also suppresses hypocotyl elongation. The metabolite profiles differed between plants under blue light and dark conditions. These findings improve our understanding of the environmental cues and molecular mechanisms underlying pigment variation in Amaranthus.

Overexpression of 9-cis-Epoxycarotenoid Dioxygenase Gene, IbNCED1, Negatively Regulates Plant Height in Transgenic Sweet Potato

Plant height is one of the key agronomic traits for improving the yield of sweet potato. Phytohormones, especially gibberellins (GAs), are crucial to regulate plant height. The enzyme 9-cis-epoxycarotenoid dioxygenase (NCED) is the key enzyme for abscisic acid (ABA) biosynthesis signalling in higher plants. However, its role in regulating plant height has not been reported to date. Here, we cloned a new NCED gene, IbNCED1, from the sweet potato cultivar Jishu26. This gene encoded the 587-amino acid polypeptide containing an NCED superfamily domain. The expression level of IbNCED1 was highest in the stem and the old tissues in the in vitro-grown and field-grown Jishu26, respectively. The expression of IbNCED1 was induced by ABA and GA3. Overexpression of IbNCED1 promoted the accumulation of ABA and inhibited the content of active GA3 and plant height and affected the expression levels of genes involved in the GA metabolic pathway. Exogenous application of GA3 could rescue the dwarf phenotype. In conclusion, we suggest that IbNCED1 regulates plant height and development by controlling the ABA and GA signalling pathways in transgenic sweet potato.

ZmCIPK32 positively regulates germination of stressed seeds via gibberellin signal

Calcineurin B-like proteins (CBLs) as specific calcium sensors that interact with CBL-interacting protein kinases (CIPKs) play a key role in the regulation of plant development and abiotic stress tolerance. In this study, we isolated and characterized the CIPK32 gene from Zea mays. ZmCIPK32 showed that it comprised 440 amino acids and a conserved NAF motif responsible for the interaction with CBLs localized in the cytoplasm and cell membrane. The interaction of ZmCIPK32 with ZmCBL1 and ZmCBL9 demonstrated using yeast two-hybrid system and bimolecular fluorescence complementation assay required the presence of the NAF domain. Overexpression of ZmCIPK32 promoted early germination in transgenic Arabidopsis seeds relative to that observed in wild-type (WT) plants under mannitol treatment. In addition, ZmCIPK32-overexpressing plants were insensitive to treatments with exogenous abscisic acid and paclobutrazol (PBZ) at seed germination and early seedling stages. Expression levels of the key genes GA20ox and GA3ox involved in the synthesis of gibberellin (GA) were increased, whereas expression levels of genes involved in the conversion of active GA to inactive forms and GA signaling were reduced in ZmCIPK32-overexpressing plants relative to those in WT plants under mannitol and PBZ treatments. Furthermore, overexpression of ZmCIPK32 increased GA level but decreased abscisic acid level in transgenic lines compared to the respective levels in WT plants under PBZ or mannitol treatments. Our results suggest that ZmCIPK32 positively regulates seed germination under stressed conditions by modulating GA signals.

Seed dormancy loss from dry after-ripening is associated with increasing gibberellin hormone levels in Arabidopsis thaliana

Introduction

The seeds of many plants are dormant and unable to germinate at maturity, but gain the ability to germinate through after-ripening during dry storage. The hormone abscisic acid (ABA) stimulates seed dormancy, whereas gibberellin A (GA) stimulates dormancy loss and germination.

Methods

To determine whether dry after-ripening alters the potential to accumulate ABA and GA, hormone levels were measured during an after-ripening time course in dry and imbibing ungerminated seeds of wildtype Landsberg erecta (Ler) and of the highly dormant GA-insensitive mutant sleepy1-2 (sly1-2).

Results

The elevated sly1-2 dormancy was associated with lower rather than higher ABA levels. Ler germination increased with 2-4 weeks of after-ripening whereas sly1-2 required 21 months to after-ripen. Increasing germination capacity with after-ripening was associated with increasing GA₄ levels in imbibing sly1-2 and wild-type Ler seeds. During the same 12 hr imbibition period, after-ripening also resulted in increased ABA levels.

Discussion

The decreased ABA levels with after-ripening in other studies occurred later in imbibition, just before germination. This suggests a model where GA acts first, stimulating germination before ABA levels decline, and ABA acts as the final checkpoint preventing germination until processes essential to survival, like DNA repair and activation of respiration, are completed. Overexpression of the GA receptor GID1b (GA INSENSITIVE DWARF1b) was associated with increased germination of sly1-2 but decreased germination of wildtype Ler. This reduction of Ler germination was not associated with increased ABA levels. Apparently, GID1b is a positive regulator of germination in one context, but a negative regulator in the other.

Analysis of morphological traits and regulatory mechanism of a semi-dwarf, albino, and blue grain wheat line

The plant height and leaf color are important traits in crops since they contribute to the production of grains and biomass. Progress has been made in mapping the genes that regulate plant height and leaf color in wheat (Triticum aestivum L.) and other crops. Wheat line DW-B (dwarfing, white leaves, and blue grains) with semi-dwarfing and albinism at the tillering stage and re-greening at the jointing stage was created using Lango and Indian Blue Grain. Transcriptomic analyses of the three wheat lines at the early jointing stages indicated that the genes of gibberellin (GA) signaling pathway and chlorophyll (Chl) biosynthesis were expressed differently in DW-B and its parents. Furthermore, the response to GA and Chl contents differed between DW-B and its parents. The dwarfing and albinism in DW-B were owing to defects in the GA signaling pathway and abnormal chloroplast development. This study can improve understanding of the regulation of plant height and leaf color.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01379-z.

Gibberellins promote polar auxin transport to regulate stem cell fate decisions in cambium

Vascular cambium contains bifacial stem cells, which produce secondary xylem to one side and secondary phloem to the other. However, how these fate decisions are regulated is unknown. Here we show that the positioning of an auxin signalling maximum within the cambium determines the fate of stem cell daughters. The position is modulated by gibberellin-regulated, PIN1-dependent polar auxin transport. Gibberellin treatment broadens auxin maximum from the xylem side of the cambium towards the phloem. As a result, xylem-side stem cell daughter preferentially differentiates into xylem, while phloem-side daughter retains stem cell identity. Occasionally, this broadening leads to direct specification of both daughters as xylem, and consequently, adjacent phloem-identity cell reverts to being stem cell. Conversely, reduced gibberellin levels favour specification of phloem-side stem cell daughter as phloem. Together, our data provide a mechanism by which gibberellin regulates the ratio of xylem and phloem production.

SlZF3 regulates tomato plant height by directly repressing SlGA20ox4 in the gibberellic acid biosynthesis pathway

Plant height is an important target trait for crop genetic improvement. Our previous work has identified a salt-tolerant C2H2 zinc finger, SlZF3, and its overexpression lines also showed a semi-dwarf phenotype, but the molecular mechanism remains to be elucidated. Here, we characterized the dwarf phenotype in detail. The dwarfism is caused by a decrease in stem internode cell elongation and deficiency of bioactive gibberellic acids (GAs), and can be rescued by exogenous GA3 treatment. Gene expression assays detected reduced expression of genes in the GA biosynthesis pathway of the overexpression lines, including SlGA20ox4. Several protein-DNA interaction methods confirmed that SlZF3 can directly bind to the SlGA20ox4 promoter and inhibit its expression, and the interaction can also occur for SlKS and SlKO. Overexpression of SlGA20ox4 in the SlZF3-overexpressing line can recover the dwarf phenotype. Therefore, SlZF3 regulates plant height by directly repressing genes in the tomato GA biosynthesis pathway.

Comparative analysis of the transcriptome during single-seed formation of Castanea henryi: regulation of starch metabolism and endogenous hormones

BACKGROUND

In seed plants, the ovule is the precursor to the seed. The process of ovule development and differentiation is regulated by multiple factors, including starch metabolism and endogenous hormones. Castanea henryi produces nuts with high nutritional value. However, the high proportion of empty buds restricts the commercial use of the tree. Previous studies have shown that the empty bud phenotype is closely related to ovule abortion. If none of the ovules in the ovary expand rapidly and develop in 7-8 weeks after pollination, an empty bud will form. Therefore, we studied the development and molecular mechanisms underlying single seed formation in C. henryi.

RESULTS

We found that 49 days after pollination (DAP) is a critical period for the formation of fertile and abortive ovules. The morphology and starch distribution of the fertile and abortive ovules differed significantly at 49 DAP. The fertile ovules were smooth and round in appearance, with a large amount of starch. In contrast, abortive ovules were smaller with only a small amount of starch. The embryo sac of the abortive ovule proceeded to develop abnormally, and the entire ovule lacked starch. We identified 37 candidate genes involved in metabolism with potential roles in the regulation of starch levels. Three ADP-glucose pyrophosphorylase (AGPase) genes, one granule-bound starch synthase (GBSS) gene, and two beta-amylase genes could affect starch accumulation. The levels of auxin, cytokinins, gibberellins, and jasmonic acid in fertile ovules were higher than those in abortive ovules. In addition, the levels of endogenous abscisic acid and salicylic acid in abortive ovules were higher than those in fertile ovules of the same age, consistent with the expression patterns of genes related to the synthesis of abscisic and salicylic acid and signal transduction. We identified and mapped the differentially expressed genes associated with hormone synthesis and signal transduction.

CONCLUSIONS

These results improve our general understanding of the molecular mechanisms underlying single seed development in C. henryi and the phenomenon of empty buds, providing directions for future research.

Transcriptome Analysis of the Effects of Grafting Interstocks on Apple Rootstocks and Scions

Apples are a major horticultural crop worldwide. Grafting techniques are widely utilized in apple production to keep the varieties pure. Interstocks are frequently used in Northern China to achieve intensive apple dwarfing cultivation. High-throughput sequencing was used to investigate differentially expressed genes in the phloem tissues of two different xenograft systems, M ('Gala'/'Mac 9'/Malus baccata (L.) Borkh.) and B ('Gala'/Malus baccata (L.) Borkh.). The results showed that dwarfing interstocks could significantly reduce the height and diameters of apple trees while have few effects on the growth of annual branches. The interstocks were found to regulate the expression of genes related to hormone metabolism and tree body control (GH3.9, PIN1, CKI1, ARP1, GA2ox1 and GA20ox1), these effects may attribute the dwarf characters for apple trees with interstocks. Besides, the interstocks reduce photosynthesis-related genes (MADH-ME4 and GAPC), promote carbon (C) metabolism gene expression (AATP1, GDH and PFK3), promote the expression of nitrogen (N)-metabolism-related genes (NRT2.7, NADH and GDH) in rootstocks, and improve the expression of genes related to secondary metabolism in scions (DX5, FPS1, TPS21 and SRG1). We also concluded that the interstocks acquired early blooming traits due to promotion of the expression of flowering genes in the scion (MOF1, FTIP7, AGL12 and AGL24). This study is a valuable resource regarding the molecular mechanisms of dwarf interstocks' influence on various biological processes and transplantation systems in both scions and rootstocks.

Genomic evidence supports the genetic convergence of a supergene controlling the distylous floral syndrome

Heterostyly, a plant sexual polymorphism controlled by the S-locus supergene, has evolved numerous times among angiosperm lineages and represents a classic example of convergent evolution in form and function. Determining whether underlying molecular convergence occurs could provide insights on constraints to floral evolution. Here, we investigated S-locus genes in distylous Gelsemium (Gelsemiaceae) to determine whether there is evidence of molecular convergence with unrelated distylous species. We used several approaches, including anatomical measurements of sex-organ development and transcriptome and whole-genome sequencing, to identify components of the S-locus supergene. We also performed evolutionary analysis with candidate S-locus genes and compared them with those reported in Primula and Turnera. The candidate S-locus supergene of Gelsemium contained four genes, of which three appear to have originated from gene duplication events within Gelsemiaceae. The style-length genes GeCYP in Gelsemium and CYP734A50 in Primula likely arose from duplication of the same gene, CYP734A1. Three out of four S-locus genes in Gelsemium elegans were hemizygous, as previously reported in Primula and Turnera. We provide genomic evidence on the genetic convergence of the supergene underlying distyly among distantly related angiosperm lineages and help to illuminate the genetic architecture involved in the evolution of heterostyly.

OsHLS1 regulates plant height and development by controlling active gibberellin accumulation in rice (Oryza sativa L.)

In this study, we identified a gene related to plant height, leaf, and premature senescence in rice, and named it OsHLS1. Through bioinformatics analysis, it was found that this gene belongs to a new gene family-HLS family, and this gene family exists widely in higher plants. Expression of OsHLS1 was significantly brought about by gibberellin (GA). Subcellular localization showed that OsHLS1 was located in the nucleus. oshls1-3 displayed a GA-deficient phenotype, with dwarf plants. In addition, oshls1-3 also showed premature senescence, shorter and narrower leaves, and pollen abortion. Exogenous GA₃ can restore the plant height of oshls1-3. Histomorphological analysis showed that the gene affected the progress of internode cells in the first and third nodes under the rice panicle. Through the verification of the homologous gene AT4G25690 in Arabidopsis, it was found that the mutant at4g25690 lines also showed plant dwarfing, premature senescence, and shortening and narrowing of leaves and pollen abortion. OsHLS1 affected the expression levels of genes involved in the GA metabolic pathway and affected the content of active GA, thereby regulating plant height development in rice. In conclusion, we suggest that OsHLS1 regulates plant height and development by controlling the accumulation of active gibberellins in rice.