Binding of GID1 to DELLAs promotes dissociation of GAF1 from DELLA in GA dependent manner

Integrated physiological and transcriptomic analyses reveal that cell wall biosynthesis and expansion play an important role in the regulation of plant height in alfalfa. BMC PLANT BIOLOGY 2025;25:267. [PMID: 40021950 PMCID: PMC11869670 DOI: 10.1186/s12870-025-06172-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

BACKGROUND

Alfalfa (Medicago sativa L.) is a high-quality, high-protein forage, and the improvement and breeding of key traits are important for enhancing the productivity of alfalfa. Plant height is an important trait that affects crop yield, and its regulatory network mechanism has been widely reported in model plants, however, there are fewer studies on the developmental regulatory of plant height in alfalfa.

RESULTS

In this study, we screened tall (WL525HQ) and short (WL343HQ) alfalfa materials through field experiments and analyzed the regulatory mechanism of plant height based on the multidimensional joint analysis of phenotype, cell, physiology, and molecular biology. The results showed that internode length was an important factor determining plant height in alfalfa, and cell size affected the internode elongation to a certain extent, whereas cell size was limited by cell wall. Moreover, changes in cell wall components play an important role in cell wall expansion, especially lignin synthesis. Transcriptome analysis showed that the high expression of hydrolase activity in T1 (initiation growth period) facilitates the expansion of the cell wall, the significant enrichment of the cellular modification process in T3 (rapid growth period) increases the cell size, and the synthesis of cell wall structural constituents and plant-type cell wall organization in T5 (growth stabilization) further improves and modifies the cell wall structure. Differential genes involved in cell wall biosynthesis and expansion were mainly enriched in cellulose synthesis, pectin cleavage, lignin formation, expansion protein (EXP), and xyloglucan endotransglycosidase (XTH).

CONCLUSIONS

These findings elucidated the plant height regulation mechanisms throughout the alfalfa plant and provided a theoretical basis for the generation of ideal alfalfa plant height germplasm.

The MADS-domain transcription factor DAL10 is a direct target of putative DAL1-mediated age pathway in conifers

The optimal timing of the transition from vegetative growth to reproductive growth is critical for plant reproductive success, and the underlying regulatory mechanisms have been well studied in angiosperm model species, but relatively little in gymnosperms. DAL1, a MADS domain transcription factor (TF) that shows a conserved age-related expression profile in conifers, may be an age timer. However, how DAL1 mediates the onset of reproductive growth remains poorly understood. Here, we showed that PtDAL1 directly regulates PtDAL10 transcription by binding to its promoter region in vitro. Both in vitro and in Nicotiana benthamiana PtDAL1 forms ternary complexes with PtDAL10 and PtMADS11, two potential candidate regulators of the vegetative to reproductive transition in Chinese pine (Pinus tabuliformis). In new shoots PtDAL10 was progressively induced with age and was also expressed in male and female cones. Overexpression of PtDAL10 rescued the flowering of ft-10 and soc1-1-2 mutants in Arabidopsis. We provide insights into the molecular components associated with PtDAL1, which integrates the vegetative to reproductive phase transition into age-mediated progressive development of the whole plant in conifers.

Interactions between Brassinosteroids and Strigolactones in Alleviating Salt Stress in Maize

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

The Physiological Basis of Alfalfa Plant Height Establishment

Plant height plays an important role in crop yield, product quality, and cultivation management. However, the physiological mechanisms that regulate the establishment of plant height in alfalfa plants remain unclear. Herein, we measured plant height traits, leaf characteristics, photosynthetic physiology, cell wall composition, and endogenous hormone contents of tall- and short-stalked alfalfa materials at different reproductive periods. We analyzed the physiology responsible for differences in plant height. The results demonstrated that the number of internodes in tall- and short-stalked alfalfa materials tended to converge with the advancement of the fertility period. Meanwhile, the average internode length (IL) of tall-stalked materials was significantly higher than that of short-stalked materials at different fertility periods, with internode length identified as the main trait determining the differences in alfalfa plant height. Leaf characteristics, which are closely related to photosynthetic capacity, are crucial energy sources supporting the expression of plant height traits, and we found that an increase in the number of leaves contributed to a proportional increase in plant height. Additionally, a significant positive correlation was observed between plant height and leaf dry weight per plant during the branching and early flowering stages of alfalfa. The leaves of alfalfa affect plant height through photosynthesis, with the budding stage identified as the key period for efficient light energy utilization. Plant height at the budding stage showed a significant positive correlation with soluble sugar (SS) content and a significant negative correlation with intercellular CO2 concentration. Moreover, we found that alfalfa plant height was significantly correlated with the contents of indole-3-acetic acid in stem tips (SIAA), gibberellin A3 in leaves (LGA3), zeatin in stem tips (SZT), and abscisic acid in leaves (LABA). Further investigation revealed that SS, SIAA, and LGA3 contents were important physiological indicators affecting alfalfa plant height. This study provides a theoretical basis for understanding the formation of alfalfa plant height traits and for genetic improvement studies.

Morphological, transcriptomic and metabolomic analyses of Sophora davidii mutants for plant height

Sophora davidii is an important plant resource in the karst region of Southwest China, but S. davidii plant-height mutants are rarely reported. Therefore, we performed phenotypic, anatomic structural, transcriptomic and metabolomic analyses to study the mechanisms responsible for S. davidii plant-height mutants. Phenotypic and anatomical observations showed that compared to the wild type, the dwarf mutant displayed a significant decrease in plant height, while the tall mutant displayed a significant increase in plant height. The dwarf mutant cells were smaller and more densely arranged, while those of the wild type and the tall mutant were larger and loosely arranged. Transcriptomic analysis revealed that differentially expressed genes (DEGs) involved in cell wall biosynthesis, expansion, phytohormone biosynthesis, signal transduction pathways, flavonoid biosynthesis and phenylpropanoid biosynthesis were significantly enriched in the S. davidii plant-height mutants. Metabolomic analysis revealed 57 significantly differential metabolites screened from both the dwarf and tall mutants. A total of 8 significantly different flavonoid compounds were annotated to LIPID MAPS, and three metabolites (chlorogenic acid, kaempferol and scopoletin) were involved in phenylpropanoid biosynthesis and flavonoid biosynthesis. These results shed light on the molecular mechanisms of plant height in S. davidii mutants and provide insight for further molecular breeding programs.

Interactions of Gibberellins with Phytohormones and Their Role in Stress Responses

Gibberellins are amongst the main plant growth regulators. Discovered over a century ago, the interest in gibberellins research is growing due to their current and potential applications in crop production and their role in the responses to environmental stresses. In the present review, the current knowledge on gibberellins’ homeostasis and modes of action is outlined. Besides this, the complex interrelations between gibberellins and other plant growth regulators are also described, providing an intricate network of interactions that ultimately drives towards precise and specific gene expression. Thus, genes and proteins identified as being involved in gibberellin responses in model and non-model species are highlighted. Furthermore, the molecular mechanisms governing the gibberellins’ relation to stress responses are also depicted. This review aims to provide a comprehensive picture of the state-of-the-art of the current perceptions of the interactions of gibberellins with other phytohormones, and their responses to plant stresses, thus allowing for the identification of the specific mechanisms involved. This knowledge will help us to improve our understanding of gibberellins’ biology, and might help increase the biotechnological toolbox needed to refine plant resilience, particularly under a climate change scenario.

Masks Start to Drop: Suppressor of MAX2 1-Like Proteins Reveal Their Many Faces

Although the main players of the strigolactone (SL) signaling pathway have been characterized genetically, how they regulate plant development is still poorly understood. Of central importance are the SUPPRESSOR OF MAX2 1-LIKE (SMXL) proteins that belong to a family of eight members in Arabidopsis thaliana, of which one subclade is involved in SL signaling and another one in the pathway of the chemically related karrikins. Through proteasomal degradation of these SMXLs, triggered by either DWARF14 (D14) or KARRIKIN INSENSITIVE2 (KAI2), several physiological processes are controlled, such as, among others, shoot and root architecture, seed germination, and seedling photomorphogenesis. Yet another clade has been shown to be involved in vascular development, independently of the D14 and KAI2 actions and not relying on proteasomal degradation. Despite their role in several aspects of plant development, the exact molecular mechanisms by which SMXLs regulate them are not completely unraveled. To fill the major knowledge gap in understanding D14 and KAI2 signaling, SMXLs are intensively studied, making it challenging to combine all the insights into a coherent characterization of these important proteins. To this end, this review provides an in-depth exploration of the recent data regarding their physiological function, evolution, structure, and molecular mechanism. In addition, we propose a selection of future perspectives, focusing on the apparent localization of SMXLs in subnuclear speckles, as observed in transient expression assays, which we couple to recent advances in the field of biomolecular condensates and liquid-liquid phase separation.

Repressor for hire! The vital roles of TOPLESS-mediated transcriptional repression in plants

Transcriptional corepressors play important roles in establishing the appropriate levels of gene expression during growth and development. The TOPLESS (TPL) family of corepressors are critical for all plant life. TPLs are involved in numerous developmental processes and in the response to extrinsic challenges. As such these proteins have been the focus of intense study since Long and colleagues first described the TPL corepressor in 2006. In this review we will explore the evolutionary history of these essential plant-specific proteins, their mechanism of action based on recent structural analyses, and the myriad of pathways in which they function. We speculate how relatively minor changes in the peptide sequence of transcriptional regulators allowed them to recruit TPL into new processes, driving innovation and resulting in TPL becoming vital for plant development.

Genome-wide analysis and functional characterization of the DELLA gene family associated with stress tolerance in B. napus

BACKGROUND

Brassica napus is an essential crop for oil and livestock feed. Eventually, this crop's economic interest is at the most risk due to anthropogenic climate change. DELLA proteins constitute a significant repressor of plant growth to facilitate survival under constant stress conditions. DELLA proteins lack DNA binding domain but can interact with various transcription factors or transcription regulators of different hormonal families. Significant progress has been made on Arabidopsis and cereal plants. However, no comprehensive study regarding DELLA proteins has been delineated in rapeseed.

RESULTS

In our study, we have identified 10 BnaDELLA genes. All of the BnaDELLA genes are closely related to five AtDELLA genes, suggesting a relative function and structure. Gene duplication and synteny relationship among Brassica. napus, Arabidopsis. thaliana, Brassica rapa, Brassica oleracea, and Brassica nigra genomes were also predicted to provide valuable insights into the BnaDELLA gene family evolutionary characteristics. Chromosomal mapping revealed the uneven distribution of BnaDELLA genes on eight chromosomes, and site-specific selection assessment proposes BnaDELLA genes purifying selection. The motifs composition in all BnaDELLA genes is inconsistent; however, every BnaDELLA gene contains 12 highly conserved motifs, encoding DELLA and GRAS domains. The two known miRNAs (bna-miR6029 and bna-miR603) targets BnaC07RGA and BnaA09GAI, were also predicted. Furthermore, quantitative real-time PCR (qRT-PCR) analysis has exhibited the BnaDELLA genes diverse expression patterns in the root, mature-silique, leaf, flower, flower-bud, stem, shoot-apex, and seed. Additionally, cis-acting element prediction shows that all BnaDELLA genes contain light, stress, and hormone-responsive elements on their promoters. The gene ontology (GO) enrichment report indicated that the BnaDELLA gene family might regulate stress responses. Combine with transcriptomic data used in this study, we detected the distinct expression patterns of BnaDELLA genes under biotic and abiotic stresses.

CONCLUSION

In this study, we investigate evolution feature, genomic structure, miRNAs targets, and expression pattern of the BnaDELLA gene family in B. napus, which enrich our understanding of BnaDELLA genes in B. napus and suggests modulating individual BnaDELLA expression is a promising way to intensify rapeseed stress tolerance and harvest index.

SCARECROW-LIKE3 regulates the transcription of gibberellin-related genes by acting as a transcriptional co-repressor of GAI-ASSOCIATED FACTOR1

SCL3 inhibits transcriptional activity of IDD-DELLA complex by acting as a co-repressor and repression activity is enhanced in the presence of GAF1 in a TOPLESS-independent manner. GRAS [GIBBERELLIN-INSENSITIVE (GAI), REPRESSOR OF ga1-3 (RGA) and SCARECROW (SCR)] proteins are a family of plant-specific transcriptional regulators that play diverse roles in development and signaling. GRAS family DELLA proteins act as growth repressors by inhibiting gibberellin (GA) signaling in response to developmental and environmental cues. DELLAs also act as co-activators of transcription factor GAI-ASSOCIATED FACTOR1 (GAF1)/INDETERMINATE DOMAIN2 (IDD2), the GAF1-DELLA complex activating transcription of GAF1 target genes. GAF1 also interacts with TOPLESS (TPL), a transcriptional co-repressor, in the absence of DELLA, the GAF1-TPL complex repressing transcription of the target genes. SCARECROW-LIKE3 (SCL3), another member of the GRAS family, is thought to inhibit transcriptional activity of the IDD-DELLA complex through competitive interaction with IDD. Here, we also revealed that SCL3 inhibits transcriptional activation by the GAF1-DELLA complex via repression activity rather than via competitive inhibition of the GAF1-DELLA interaction. Moreover, the repression activity of SCL3 was enhanced by GAF1 in a TPL-independent manner. While the GRAS domain of DELLA has transcriptional activation activity, that of SCL3 has repression activity. SCL3 also inhibited transcriptional activity of GAF1-RGA fusion proteins. Results from the co-immunoprecipitation assays and the yeast three-hybrid assay suggested the possibility that SCL3 forms a ternary complex with GAF1 and DELLA. These findings provide important information on DELLA-regulated GA signaling and new insight into the transcriptional repression mechanism.

Endodormancy Release Can Be Modulated by the GA4-GID1c-DELLA2 Module in Peach Leaf Buds

Gibberellin (GA) plays a key role in the release of bud dormancy and the GA receptor GID1 (GIBBERELLIN INSENSITIVE DWARF1) and DELLA protein are the GA signaling parts, but the molecular mechanism of GA-GID1-DELLA module regulating leaf bud dormancy in peach (Prunus persica) is still not very clear. In this study, we isolated and characterized the GID1 gene PpGID1c from the peach cultivar "Zhong you No.4." Overexpressing PpGID1c in Arabidopsis promoted seed germination, which indicated that PpGID1c has an important function in dormancy. The expression level of PpGID1c in peach leaf buds during endodormancy release was higher than that during ecodormancy and was positively correlated with GA₄ levels. Our study also found that GA₄ had the most obvious effect on promoting the bud break, indicating that GA₄ may be the key gibberellin to promoting peach leaf bud endodormancy release. Moreover, a quantitative real-time PCR (qRT-PCR) found that GA₄ could increase the expression of the gibberellin signaling gene PpDELLA2. A yeast two-hybrid (Y2H) assay suggested that the PpGID1c interaction with the PpDELLA1 protein was not dependent on gibberellin, while the PpGID1c interaction with PpDELLA2 required GA₄ or another gibberellin. These findings suggested that the GA₄-GID1c-DELLA2 module regulates peach leaf bud endodormancy release, with this finding significantly enhancing our comprehensive understanding of bud endodormancy release and revealing a new mechanism for regulating leaf bud endodormancy release in peach.

Positive and negative regulation of seed germination by the Arabidopsis GA hormone receptors, GID1a, b, and c

Epistasis analysis of gid1 single and double mutants revealed that GID1c is a key positive regulator of seed germination, whereas the GID1b receptor can negatively regulate germination in dormant seeds and in the dark. The GID1 GA receptors were expected to positively regulate germination because the plant hormone gibberellin (GA) is required for seed germination in Arabidopsis thaliana. The three GA hormone receptors, GID1a, GID1b, and GID1c, positively regulate GA responses via GA/GID1-stimulated destruction of DELLA (Asp-Glu-Leu-Leu-Ala) repressors of GA responses. The fact that the gid1abc triple mutant but not gid1 double mutants fail to germinate indicates that all three GA receptors can positively regulate non-dormant seed germination in the light. It was known that the gid1abc triple mutant fails to lose dormancy through the dormancy breaking treatments of cold stratification (moist chilling of seeds) and dry after-ripening (a period of dry storage). Previous work suggested that there may be some specialization of GID1 gene function during germination because GID1b mRNA expression was more highly induced by after-ripening, whereas GID1a and GID1c mRNA levels were more highly induced by cold stratification. In light-germinated dormant seeds, the gid1b mutation can partly rescue the germination efficiency of gid1a but not of gid1c seeds. Thus, GID1b can function as an upstream negative regulator GID1c, a positive regulator of dormant seed germination. Further experiments showed that GID1b can negatively regulate dark germination. Wild-type Arabidopsis seeds do not germinate well in the dark. The gid1b and gid1ab double mutants germinated much more efficiently than wild type, gid1c, or gid1ac mutants in the dark. The observation that the gid1ab double mutant also shows increased dark germination suggests that GID1b, and to some extent GID1a, can act as upstream negative regulators of GID1c. Since the gid1abc triple mutant failed to germinate in the dark, it appears that GID1c is a key downstream positive regulator of dark germination. This genetic analysis indicates that the three GID1 receptors have partially specialized functions in GA signaling.

DELLA-dependent and -independent gibberellin signaling

DELLA proteins act as negative regulators in gibberellin (GA) signal transduction. GA-induced DELLA degradation is a central regulatory system in GA signaling pathway. Intensive studies have revealed the degradation mechanism of DELLA and the functions of DELLA as a transcriptional regulator. Meanwhile, recent studies suggest the existence of a DELLA-independent GA signaling pathway. In this review, we summarized the DELLA-independent GA signaling pathway together with the well-analyzed DELLA-dependent pathway.

The genetic and molecular basis of crop height based on a rice model

This review presents genetic and molecular basis of crop height using a rice crop model. Height is controlled by multiple genes with potential to be manipulated through breeding strategies to improve productivity. Height is an important factor affecting crop architecture, apical dominance, biomass, resistance to lodging, tolerance to crowding and mechanical harvesting. The impressive increase in wheat and rice yield during the 'green revolution' benefited from a combination of breeding for high-yielding dwarf varieties together with advances in agricultural mechanization, irrigation and agrochemical/fertilizer use. To maximize yield under irrigation and high fertilizer use, semi-dwarfing is optimal, whereas extreme dwarfing leads to decreased yield. Rice plant height is controlled by genes that lie in a complex regulatory network, mainly involved in the biosynthesis or signal transduction of phytohormones such as gibberellins, brassinosteroids and strigolactones. Additional dwarfing genes have been discovered that are involved in other pathways, some of which are uncharacterized. This review discusses our current understanding of the regulation of plant height using rice as a well-characterized model and highlights some of the most promising research that could lead to the development of new, high-yielding varieties. This knowledge underpins future work towards the genetic improvement of plant height in rice and other crops.

MYB31/MYB42 Syntelogs Exhibit Divergent Regulation of Phenylpropanoid Genes in Maize, Sorghum and Rice

ZmMYB31 and ZmMYB42 are R2R3-MYB transcription factors implicated in the regulation of phenylpropanoid genes in maize. Here, we tested the hypothesis that the regulatory function of MYB31 and MYB42 is conserved in other monocots, specifically in sorghum and rice. We demonstrate that syntelogs of MYB31 and MYB42 do bind to phenylpropanoid genes that function in all stages of the pathway and in different tissues along the developmental gradient of seedling leaves. We found that caffeic acid O-methyltransferase (COMT1) is a common target of MYB31 and MYB42 in the mature leaf tissues of maize, sorghum and rice, as evidenced by Chromatin immunoprecipitation (ChIP) experiments. In contrast, 4-coumarate-CoA ligase (4CL2), ferulate-5-hydroxylase (F5H), and caffeoyl shikimate esterase (CSE), were targeted by MYB31 or MYB42, but in a more species-specific fashion. Our results revealed MYB31 and MYB42 participation in auto- and cross-regulation in all three species. Apart from a limited conservation of regulatory modules, MYB31 and MYB42 syntelogs appear to have undergone subfunctionalization following gene duplication and divergence of maize, sorghum, and rice. Elucidating the different regulatory roles of these syntelogs in the context of positive transcriptional activators may help guide attempts to alter the flux of intermediates towards lignin production in biofuel grasses.