slender rice, a constitutive gibberellin response mutant, is caused by a null mutation of the SLR1 gene, an ortholog of the height-regulating gene GAI/RGA/RHT/D8

The VcGID1-VcDELLA-VcGID2 complex participates in regulating the dormancy release of blueberry flower buds

Bud dormancy is a crucial mechanism that allows perennial woody plants to withstand adverse environmental conditions, and gibberellin (GA) typically promotes the dormancy release of buds. DELLA protein is the core factor in the GA signaling pathway. This study identified 11 VcDELLA genes from the blueberry genome and performed a comprehensive bioinformatics analysis and prediction of the VcDELLA gene family. GA not only inhibits the dormancy entry of blueberry flower buds under low temperature and short-day conditions but also promotes the dormancy release of flower buds. During the dormancy release process, exogenous GA4+7 significantly increased the GA level and VcDELLA2/4/7/10/11 expression, while it significantly decreased VcDELLA3/6/8 expression. It is widely accepted that the GA-GID1-DELLA signaling module plays important roles in regulating the dormancy process of flower buds. In this study, Y2H and BiFC experiments showed that VcDELLA3/6 proteins could interact withVcGID1b/c, VcGID2, and VcSOC1 proteins. Regardless of the presence or absence of GA, VcGID1b/c and VcGID2 proteins could interact with VcDELLA3/6 proteins to form the VcGID1-VcDELLA-VcGID2 complex. In the leaves of VcDELLA3/6-silenced blueberry plants, VcDELLA3/6, VcGA3ox, VcGA20ox, and VcSOC1 expression was significantly decreased. Meanwhile, VcGID1b and VcGID1c expression was significantly increased. The leaf shedding rates of blueberry plants overexpressing VcDELLA3 and VcDELLA6 increased by 25 % and 33.33 %, respectively. In VcDELLA3/6-overexpressing plants, the GA level and VcDELLA3/6, VcGA2ox, VcGA3ox, VcGA20ox, VcGID2, and VcSOC1 expression were significantly increased, whereas VcGID1b/c expression levels were significantly decreased in VcDELLA6-overexpressing plants. Furthermore, exogenous GA effectively alleviated the deciduous phenotype of VcDELLA3/6 overexpressing blueberry plants and downregulated VcGA2ox, VcGA3ox, and VcGA20ox expression. It could be inferred that VcDELLA3/6 could regulate the transition of dormancy states in blueberry flower buds through interactions with GA biosynthesis (VcGA2ox, VcGA3ox, and VcGA20ox), GA signal transduction (VcGID1b/c and VcGID2), and the flowering related protein VcSOC1. Additionally, it is proposed that there might be a pathway with VcDELLA6 as the core to regulate the chilling-mediated dormancy release of blueberry flower buds. The formation of the GA4+7-VcGID1b/c-VcDELLA6-VcGID2 complex could activate VcSOC1 expression, thereby promoting the dormancy release of blueberry flower buds.

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.

Genome-wide analysis of GRAS gene family and functional identification of a putative development and maintenance of axillary meristematic tissue gene PlGRAS22 in Paeonia ludlowii

The GRAS gene family, is instrumental in a myriad of biological processes, including plant growth and development. Our findings revealed that Paeonia ludlowii (Stern & G.Taylor) D.Y.Hong) harbored 45 PlGRAS genes, which are categorized into eight subfamilies. These genes are distributed across chromosomes 1 through 5, with their encoded proteins exhibiting variation in physicochemical properties. The promoter regions of the Paeonia ludlowii GRAS genes are enriched with cis-acting elements associated with growth and development, hormonal responses, and light signaling, among others. Among these genes, we have pinpointed PlGRAS22, which bears the closest resemblance to the AtLAS gene in Arabidopsis. Notably, this gene exhibits heightened expression levels within the LAS subfamily across a range of tissues, and it demonstrates an exceptionally robust response to treatments with exogenous gibberellins and cytokinins. The subdued expression of TRV2-PlGRAS22 within the flower buds of the Paeonia ludlowii has resulted in a diminished development of axillary bud primordia. Intriguingly, overexpression of PlGRAS22 in Arabidopsis led to an increase in the number of branches, highlighting its potential role in developmental processes. Furthermore, through the use of luciferase and yeast one-hybrid assays, we have demonstrated that PlGRAS22 interacts with the SPL transcription factor PlSPL3. The comprehensive analysis presented in this study lays a solid foundation for future investigations into the functional roles of Paeonia ludlowii GRAS genes and elucidates the underlying mechanisms governing growth and development in this species.

SLR1-LPA1 signal regulates sheath blight resistance and lamina joint angle in rice

Previous studies have suggested that Dense and Erect Panicle 1 (DEP1) interacts with Lose Plant Architecture 1 (LPA1) to regulate auxin transport by which DEP1-LPA1 modulates rice sheath blight (ShB) resistance. In this study, we identified that dep1 and lpa1 exhibited semi-dwarfism and dep1/lpa1 was shorter than the single mutant. LPA1 OX displayed higher height, whereas DEP1 OX exhibited similar height with wild-type. The gibberellic acid (GA)-dependent shoot growth was inhibited in dep1 and lpa1 while activated in LPA1 OX, suggesting that LPA1 may play a role in GA signaling transduction. Yeast two-hybrid screening revealed that slender rice 1 (SLR1), a GA signaling negative regulator, interacted with LPA1. Additionally, slr1 was less susceptible to ShB, whereas the GA signaling positive regulator DWARF1 mutant d1 was more susceptible to ShB. This suggested that GA signaling positively regulates rice resistance to ShB. Furthermore, slr1 was similar to LPA1 OX in terms of reduced lamina joint angle, whereas d1 did not show any difference. This implied that SLR1 may regulate LPA1 dependent signaling to control the lamina joint angle via a mechanism that was independent of GA signaling. Transcriptome data indicated that GA signaling and catabolic genes were regulated by LPA1. Transient and ChIP assays suggested that LPA1 bound to the promoter of gibberellin 2-beta-dioxygenase, a GA catabolic gene, to activate its expression. These findings indicated that LPA1 modulated GA homeostasis and SLR1 interacted with and inhibited LPA1 to regulate ShB resistance and lamina joint angle in rice.

Allelism of Uncharacterized Dwarf Mutants in Maize

Gibberellic acid (GA) is a phytohormone that is important for plant growth and development. Mutants in GA biosynthesis, signaling and metabolism have been critical to understanding the role GA plays in plants. GA mutants have also revolutionized global production of staple crops such as rice, wheat, and barley. GA mutants have been isolated in maize and characterization of the underlying genes has helped map the GA biosynthesis and signaling pathways. However, the number of maize dwarf mutants is far less than other species. Here, we identify new dwarf mutants that could benefit our understanding of maize plant height control.

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.

Overexpression of the general transcription factor OsTFIIB5 alters rice development and seed quality

KEY MESSAGE

Overexpression of general transcription factor OsTFIIB5 in rice affects seedling growth, plant height, flowering time, panicle architecture, and seed protein/starch levels and involves modulation of expression of associated genes. TFIIB, a key general transcription factor (GTF), plays a critical role in pre-initiation complex (PIC) formation and facilitates RNA polymerase II-mediated transcription. In humans and yeast, TFIIB is encoded by a single gene; however, in plants it is encoded by a multigene family whose products may perform specialized transcriptional functions. The role of plant TFIIBs, particularly in monocots, remains largely unexplored. This study presents the first functional characterization of the rice TFIIB gene, OsTFIIB5 (LOC_Os09g36440), during development. Expression profiling of OsTFIIB5 revealed differential patterns across various developmental stages, with pronounced transcript accumulation during seed development. Overexpression of OsTFIIB5 impacted multiple stages of plant growth and development, leading to phenotypic changes such as altered seedling growth, reduced plant height, early heading, altered panicle architecture, decreased yield, and changes in seed storage substances. Notably, there were no effects on seed germination, pollen development, and grain size. Reduction in shoot length and plant height was linked to altered expression of genes involved in gibberellin (GA) biosynthesis, signalling, and deactivation. Overexpression of OsTFIIB5 enhanced the expression of genes involved in the photoperiodic flowering pathway, resulting in early panicle emergence. Higher expression levels of OsTFIIB5 also induced the accumulation of seed storage proteins (SSPs), while reducing starch content and altering the proportions of amylose and amylopectin in seeds. These findings suggest that OsTFIIB5 functions as a transcriptional regulator, governing multiple aspects of rice growth and development.

Light and temperature signals are integrated through a phytochrome B-dependent gene regulatory network in rice

Angiosperms are the most dominant land plant flora and have colonized most of the terrestrial habitats, thriving in different environmental conditions, among which light and temperature play a crucial role. In the eudicot Arabidopsis thaliana, light and temperature are integrated into a phytochrome B (phyB)-dependent signalling network that regulates development. However, whether this signal integration controls the development in other angiosperm lineages and whether phyB is a conserved hub of this integratory network in angiosperms is unclear. We used a combination of phylogenetic, phenotypic, and transcriptomic analyses to understand the phyB-dependent light and temperature integratory network in the monocot Oryza sativa and infer its conservation in angiosperms. Here, we showed that light and temperature co-regulate rice growth through a phyB-dependent regulatory network that shares conserved features between O. sativa and A. thaliana. Despite the conservation of the components of this regulatory network, the transcriptional regulation between the components has changed qualitatively since monocots and eudicots diverged (~192-145 million years ago). The evolutionary flexibility of this integratory network might underlie the successful adaptation of plants to diverse ecological niches. Furthermore, our findings provide promising candidate genes whose activity and expression can be fine-tuned to improve plant growth and productivity in a warming planet.

The LCG1-OsBP5/OsEBP89-Wx module regulates the grain chalkiness and taste quality in rice

It is well known that the overall quality of japonica/geng rice is superior to that of indica/xian rice varieties. However, the molecular mechanisms underlying the quality disparities between these two subspecies of rice are still largely unknown. In this study, we have pinpointed a gene homologous to SLR1, termed LCG1, exhibiting significant expression during early caryopsis development and playing a specific role in regulating rice chalkiness and taste by affecting the accumulation of grain storage components, starch granule structure and chain length distribution of amylopectin. LCG1 physically interacts with OsBP5 and indirectly influences the expression of the amylose synthesis gene Waxy (Wx) by hindering the transcriptional activity of the OsBP5/OsEBP89 complex. Notably, sequence variations in the promoter region of LCG1 result in enhanced transcription in japonica rice accessions. This leads to elevated LCG1 expression in CSSL-LCG1Nip, thereby enhancing rice quality. Our research elucidates the molecular mechanism underlying the impact of the LCG1-OsBP5/OsEBP89-Wx regulatory pathway on rice chalkiness and taste quality, offering new genetic resources for improving the indica rice quality.

The DENSE AND ERECT PANICLE1-GRAIN NUMBER ASSOCIATED module enhances rice yield by repressing CYTOKININ OXIDASE 2 expression

The phytohormone cytokinin (CK) positively regulates the activity of the inflorescence meristem (IM). Cytokinin oxidase 2/Grain number 1a (OsCKX2/Gn1a)-mediated degradation of CK in rice (Oryza sativa L.) negatively regulates panicle grain number, whereas DENSE AND ERECT PANICLE 1 (DEP1) positively regulates grain number per panicle (GNP). However, the detailed regulatory mechanism between DEP1 and OsCKX2 remains elusive. Here, we report the GRAS (GIBBERELLIN ACID INSENSITIVE, REPRESSOR OF GA1, and SCARECROW) transcription factor GRAIN NUMBER ASSOCIATED (GNA), previously thought to be involved in the Brassinosteroids (BRs) signaling pathway, directly inhibits OsCKX2 expression in the IM through a DEP1-GNA regulatory module. Overexpressing GNA leads to increased CK levels and consequently higher branch number, GNP, and yield. Both DEP1 and dep1 enhance the inhibitory effect of GNA on OsCKX2 expression through interacting with GNA. GNA promotes the translocation of DEP1 to the nucleus, while the gain-of-function mutant dep1 translocates into the nucleus in the absence of GNA. Our findings provide insight into the regulatory mechanism underlying OsCKX2 and a strategy to improve rice yield.

Development and optimization of base editors and its application in crops

Genome editing technologies hold significant potential for targeted mutagenesis in crop development, aligning with evolving agricultural needs. Point mutations, or single nucleotide polymorphisms (SNPs), define key agronomic traits in various crop species and play a pivotal role. The implementation of single nucleotide variations through genome editing-based base editing offers substantial promise in expediting crop improvement by inducing advantageous trait variations. Among many genome editing techniques, base editing stands out as an advanced next-generation technology, evolved from the CRISPR/Cas9 system.Base editing, a recent advancement in genome editing, enables precise DNA modification without the risks associated with double-strand breaks. Base editors, designed as precise genome editing tools, enable the direct and irreversible conversion of specific target bases. Base editors consist of catalytically active CRISPR-Cas9 domains, including Cas9 variants, fused with domains like cytidine deaminase, adenine deaminase, or reverse transcriptase. These fusion proteins enable the introduction of specific point mutations in target genomic regions. Currently developed are cytidine base editors (CBEs), mutating C to T; adenine base editors (ABEs), changing A to G; and prime editors (PEs), enabling arbitrary base conversions, precise insertions, and deletions. In this review, the research, development, and progress of various base editing systems, along with their potential applications in crop improvement, were intended to be summarized. The limitations of this technology will also be discussed. Finally, an outlook on the future of base editors will be provided.

Overexpression of two DELLA subfamily genes MiSLR1 and MiSLR2 from mango promotes early flowering and enhances abiotic stress tolerance in Arabidopsis

Gibberellic acids (GAs) are a group of endogenous phytohormones that play important roles in plant growth and development. SLENDER RICE (SLR) serves as a vital component of the DELLA gene family, which plays an irreplaceable role in regulating plant flowering and height, as well as stress responses. SLR gene has not been reported in mango, and its function is unknown. In present study, two DELLA subfamily genes MiSLR1 and MiSLR2 were identified from mango. MiSLR1 and MiSLR2 were highly expressed in the stems of the juvenile stage, but were expressed at a low level in flower buds and flowers. Gibberellin treatment could up-regulate the expression of MiSLR1 and MiSLR2 genes, but gibberellin biosynthesis inhibitor prohexadione-calcium (Pro-Ca) and paclobutrazol (PAC) treatments significantly down-regulated the expression of MiSLR1, while MiSLR2 was up-regulated. The expression levels of MiSLR1 and MiSLR2 were up-regulated under both salt and drought treatments. Overexpression of MiSLR1 and MiSLR2 genes significantly resulted early flowering in transgenic Arabidopsis and significantly up-regulated the expression levels of endogenous flower-related genes, such as SUPPRESSOR OF CONSTANS1 (SOC1), APETALA1 (AP1), and FRUITFULL (FUL). Interestingly, MiSLR1 significantly reduced the height of transgenic plants, while MiSLR2 gene increased. Overexpression of MiSLR1 and MiSLR2 increased seed germination rate, root length and survival rate of transgenic plants under salt and drought stress. Physiological and biochemical detection showed that the contents of proline (Pro) and superoxide dismutase (SOD) were significantly increased, while the contents of malondialdehyde (MDA) and H2O2 were significantly decreased. Additionally, protein interaction analysis revealed that MiSLR1 and MiSLR2 interacted with several flowering-related and GA-related proteins. The interaction between MiSLR with MiGF14 and MiSOC1 proteins was found for the first time. Taken together, the data showed that MiSLR1 and MiSLR2 in transgenic Arabidopsis both regulated the flowering time and plant height, while also acting as positive regulators of abiotic stress responses.

NADP-malic Enzyme OsNADP-ME2 Modulates Plant Height Involving in Gibberellin Signaling in Rice

Plants NADP-malic enzymes (NADP-MEs) act as a class of oxidative decarboxylase to mediate malic acid metabolism in organisms. Despite NADP-MEs have been demonstrated to play pivotal roles in regulating diverse biological processes, the role of NADP-MEs involving in plant growth and development remains rarely known. Here, we characterized the function of rice cytosolic OsNADP-ME2 in regulating plant height. The results showed that RNAi silencing and knock-out of OsNADP-ME2 in rice results in a dwarf plant structure, associating with significant expression inhibition of genes involving in phytohormone Gibberellin (GA) biosynthesis and signaling transduction, but with up-regulation for the expression of GA signaling suppressor SLR1. The accumulation of major bioactive GA1, GA4 and GA7 are evidently altered in RNAi lines, and exogenous GA treatment compromises the dwarf phenotype of OsNADP-ME2 RNAi lines. RNAi silencing of OsNADP-ME2 also causes the reduction of NADP-ME activity associating with decreased production of pyruvate. Thus, our data revealed a novel function of plant NADP-MEs in modulation of rice plant height through regulating bioactive GAs accumulation and GA signaling, and provided a valuable gene resource for rice plant architecture improvement.

Identification of Apple Flower Development-Related Gene Families and Analysis of Transcriptional Regulation

Apple (Malus domestica Borkh.) stands out as a globally significant fruit tree with considerable economic importance. Nonetheless, the orchard production of 'Fuji' apples faces significant challenges, including delayed flowering in young trees and inconsistent annual yields in mature trees, ultimately resulting in suboptimal fruit yield due to insufficient flower bud formation. Flower development represents a pivotal process influencing plant adaptation to environmental conditions and is a crucial determinant of successful plant reproduction. The three gene or transcription factor (TF) families, C2H2, DELLA, and FKF1, have emerged as key regulators in plant flowering regulation; however, understanding their roles during apple flowering remains limited. Consequently, this study identified 24 MdC2H2, 6 MdDELLA, and 6 MdFKF1 genes in the apple genome with high confidence. Through phylogenetic analyses, the genes within each family were categorized into three distinct subgroups, with all facets of protein physicochemical properties and conserved motifs contingent upon subgroup classification. Repetitive events between these three gene families within the apple genome were elucidated via collinearity analysis. qRT-PCR analysis was conducted and revealed significant expression differences among MdC2H2-18, MdDELLA1, and MdFKF1-4 during apple bud development. Furthermore, yeast two-hybrid analysis unveiled an interaction between MdC2H2-18 and MdDELLA1. The genome-wide identification of the C2H2, DELLA, and FKF1 gene families in apples has shed light on the molecular mechanisms underlying apple flower bud development.

Rice bundle sheath cell shape is regulated by the timing of light exposure during leaf development

Plant leaves contain multiple cell types which achieve distinct characteristics whilst still coordinating development within the leaf. The bundle sheath possesses larger individual cells and lower chloroplast content than the adjacent mesophyll, but how this morphology is achieved remains unknown. To identify regulatory mechanisms determining bundle sheath cell morphology we tested the effects of perturbing environmental (light) and endogenous signals (hormones) during leaf development of Oryza sativa (rice). Total chloroplast area in bundle sheath cells was found to increase with cell size as in the mesophyll but did not maintain a 'set-point' relationship, with the longest bundle sheath cells demonstrating the lowest chloroplast content. Application of exogenous cytokinin and gibberellin significantly altered the relationship between cell size and chloroplast biosynthesis in the bundle sheath, increasing chloroplast content of the longest cells. Delayed exposure to light reduced the mean length of bundle sheath cells but increased corresponding leaf length, whereas premature light reduced final leaf length but did not affect bundle sheath cells. This suggests that the plant hormones cytokinin and gibberellin are regulators of the bundle sheath cell-chloroplast relationship and that final bundle sheath length may potentially be affected by light-mediated control of exit from the cell cycle.

Research Progress on Mechanical Strength of Rice Stalks

As one of the most important food crops in the world, rice yield is directly related to national food security. Lodging is one of the most important factors restricting rice production, and the cultivation of rice varieties with lodging resistance is of great significance in rice breeding. The lodging resistance of rice is directly related to the mechanical strength of the stalks. In this paper, we reviewed the cell wall structure, its components, and its genetic regulatory mechanism, which improved the regulatory network of rice stalk mechanical strength. Meanwhile, we analyzed the new progress in genetic breeding and put forward some scientific problems that need to be solved in this field in order to provide theoretical support for the improvement and application of rice breeding.

Research Overview and Trends of the Effects of Gibberellins (GAs) on Rice Biological Processes: A Bibliometric Analysis

Rice (Oryza sativa L.) is a vital crop that feeds more than half of the world's population. Gibberellins (GAs), a crucial phytohormone, play a significant role in the growth and development of rice. Since 1985, there has been a notable increase in the number of studies investigating the effects of GA on various biological processes in rice. Nevertheless, conducting scientific and quantitative research on the extensive literature available poses significant challenges, particularly in understanding the development trajectory of the field, examining major contributors, and identifying emerging research trends. The objective of this study is to address these challenges by analyzing global research patterns and trends using bibliometric methods from 1985 to 2024. Through the application of advanced analytical tools, progress in this field is studied in depth and the global research landscape is characterized from multiple dimensions including countries, institutions, authors, and journals. The analysis of 2118 articles extracted and screened from the Web of Science Core dataset shows a steady growth in the number of publications. The research published in China and the USA has significantly advanced the development of the field. In particular, institutions such as the Chinese Academy of Sciences and Nagoya University have shown impressive productivity. Lee In-Jung stands out as the most influential author. The journal Plant Physiology publishes the highest number of articles. The study also provides a thorough examination of current research hotspots, indicating a predominant focus on understanding the role of GAs in the biological processes that regulate diverse rice phenotypes, including plant height, seed dormancy, germination, and stress resistance. By tracing the development characteristics and key points in this area, this study contributes to a quantitative and comprehensive understanding of the impact of GAs on rice.

Transcriptional changes during crown-root development and emergence in barley (Hordeum vulgare L.)

BACKGROUND

Roots play an important role during plant growth and development, ensuring water and nutrient uptake. Understanding the mechanisms regulating their initiation and development opens doors towards root system architecture engineering.

RESULTS

Here, we investigated by RNA-seq analysis the changes in gene expression in the barley stem base of 1 day-after-germination (DAG) and 10DAG seedlings when crown roots are formed. We identified 2,333 genes whose expression was lower in the stem base of 10DAG seedlings compared to 1DAG seedlings. Those genes were mostly related to basal cellular activity such as cell cycle organization, protein biosynthesis, chromatin organization, cytoskeleton organization or nucleotide metabolism. In opposite, 2,932 genes showed up-regulation in the stem base of 10DAG seedlings compared to 1DAG seedlings, and their function was related to phytohormone action, solute transport, redox homeostasis, protein modification, secondary metabolism. Our results highlighted genes that are likely involved in the different steps of crown root formation from initiation to primordia differentiation and emergence, and revealed the activation of different hormonal pathways during this process.

CONCLUSIONS

This whole transcriptomic study is the first study aiming at understanding the molecular mechanisms controlling crown root development in barley. The results shed light on crown root emergence that is likely associated with a strong cell wall modification, death of the cells covering the crown root primordium, and the production of defense molecules that might prevent pathogen infection at the site of root emergence.

Overexpression of Calcineurin B-like Interacting Protein Kinase 31 Promotes Lodging and Sheath Blight Resistance in Rice

A breakthrough "Green Revolution" in rice enhanced lodging resistance by using gibberellin-deficient semi-dwarf varieties. However, the gibberellic acid (GA) signaling regulation on rice disease resistance remains unclear. The resistance test showed that a positive GA signaling regulator DWARF1 mutant d1 was more susceptible while a negative GA signaling regulator Slender rice 1 (SLR1) mutant was less susceptible to sheath blight (ShB), one of the major rice diseases, suggesting that GA signaling positively regulates ShB resistance. To isolate the regulator, which simultaneously regulates rice lodging and ShB resistance, SLR1 interactors were isolated. Yeast two-hybrid (Y2H), bimolecular fluorescence complementation (BiFC), and Co-IP assay results indicate that SLR1 interacts with Calcineurin B-like-interacting protein kinase 31 (CIPK31). cipk31 mutants exhibited normal plant height, but CIPK31 OXs showed semi-dwarfism. In addition, the SLR1 level was much higher in CIPK31 OXs than in the wild-type, suggesting that CIPK31 OX might accumulate SLR1 to inhibit GA signaling and thus regulate its semi-dwarfism. Recently, we demonstrated that CIPK31 interacts and inhibits Catalase C (CatC) to accumulate ROS, which promotes rice disease resistance. Interestingly, CIPK31 interacts with Vascular Plant One Zinc Finger 2 (VOZ2) in the nucleus, and expression of CIPK31 accumulated VOZ2. Inoculation of Rhizoctonia solani AG1-IA revealed that the voz2 mutant was more susceptible to ShB. Thus, these data prove that CIPK31 promotes lodging and ShB resistance by regulating GA signaling and VOZ2 in rice. This study provides a valuable reference for rice ShB-resistant breeding.

Transcription factor OsSHR2 regulates rice architecture and yield per plant in response to nitrogen

MAIN CONCLUSION

Mutation of OsSHR2 adversely impacted root and shoot growth and impaired plant response to N conditions, further reducing the yield per plant. Nitrogen (N) is a crucial factor that regulates the plant architecture. There is still a lack of research on it. In our study, it was observed that the knockout of the SHORTROOT 2 (OsSHR2) which was induced by N deficiency, can significantly affect the regulation of plant architecture response to N in rice. Under N deficiency, the mutation of OsSHR2 significantly reduced root growth, and impaired the sensitivity of the root meristem length to N deficiency. The mutants were found to have approximately a 15% reduction in plant height compared to wild type. But mutants showed a significant increase in tillering at post-heading stage, approximately 26% more than the wild type, particularly in high N conditions. In addition, due to reduced seed setting rate and 1000-grain weight, mutant yield was significantly decreased by approximately 33% under low N fertilizer supply. The mutation also changed the distribution of N between the vegetative and reproductive organs. Our findings suggest that the transcription factor OsSHR2 plays a regulatory role in the response of plant architecture and yield per plant to N in rice.

Highlights in gibberellin research: A tale of the dwarf and the slender

It has been almost a century since biologically active gibberellin (GA) was isolated. Here, we give a historical overview of the early efforts in establishing the GA biosynthesis and catabolism pathway, characterizing the enzymes for GA metabolism, and elucidating their corresponding genes. We then highlight more recent studies that have identified the GA receptors and early GA signaling components (DELLA repressors and F-box activators), determined the molecular mechanism of DELLA-mediated transcription reprograming, and revealed how DELLAs integrate multiple signaling pathways to regulate plant vegetative and reproductive development in response to internal and external cues. Finally, we discuss the GA transporters and their roles in GA-mediated plant development.

Synergizing biotechnology and natural farming: pioneering agricultural sustainability through innovative interventions

The world has undergone a remarkable transformation from the era of famines to an age of global food production that caters to an exponentially growing population. This transformation has been made possible by significant agricultural revolutions, marked by the intensification of agriculture through the infusion of mechanical, industrial, and economic inputs. However, this rapid advancement in agriculture has also brought about the proliferation of agricultural inputs such as pesticides, fertilizers, and irrigation, which have given rise to long-term environmental crises. Over the past two decades, we have witnessed a concerning plateau in crop production, the loss of arable land, and dramatic shifts in climatic conditions. These challenges have underscored the urgent need to protect our global commons, particularly the environment, through a participatory approach that involves countries worldwide, regardless of their developmental status. To achieve the goal of sustainability in agriculture, it is imperative to adopt multidisciplinary approaches that integrate fields such as biology, engineering, chemistry, economics, and community development. One noteworthy initiative in this regard is Zero Budget Natural Farming, which highlights the significance of leveraging the synergistic effects of both plant and animal products to enhance crop establishment, build soil fertility, and promote the proliferation of beneficial microorganisms. The ultimate aim is to create self-sustainable agro-ecosystems. This review advocates for the incorporation of biotechnological tools in natural farming to expedite the dynamism of such systems in an eco-friendly manner. By harnessing the power of biotechnology, we can increase the productivity of agro-ecology and generate abundant supplies of food, feed, fiber, and nutraceuticals to meet the needs of our ever-expanding global population.

OsCSN2 orchestrates Oryza sativa L. growth and development through modulation of the GA and BR pathways

The COP9 signalosome (CSN) is a conserved protein complex found in higher eukaryotes, consisting of eight subunits, and it plays a crucial role in regulating various processes of plant growth and development. Among these subunits, CSN2 is one of the most conserved components within the COP9 signalosome complex. Despite its prior identification in other species, its specific function in Oryza sativa L. (Rice) has remained poorly understood. In this study, we investigated the role of CSN2 in rice using gene editing CRISPR/Cas9 technology and overexpression techniques. We created two types of mutants: the oscsn2 mutant and the OsCSN2-OE mutant, both in the background of rice, and also generated point mutants of OsCSN2 (OsCSN2K64E, OsCSN2K67E, OsCSN2K71E and OsCSN2K104E) to further explore the regulatory function of OsCSN2. Phenotypic observation and gene expression analysis were conducted on plants from the generated mutants, tracking their growth from the seedling to the heading stages. The results showed that the loss and modification of OsCSN2 had limited effects on plant growth and development during the early stages of both the wild-type and mutant plants. However, as the plants grew to 60 days, significant differences emerged. The OsCSN2 point mutants exhibited increased tillering compared to the OsCSN2-OE mutant plants, which were already at the tillering stage. On the other hand, the OsCSN2 point mutant had already progressed to the heading and flowering stages, with the shorter plants. These results, along with functional predictions of the OsCSN2 protein, indicated that changes in the 64th, 67th, 71st, and 104th amino acids of OsCSN2 affected its ubiquitination site, influencing the ubiquitination function of CSN and consequently impacting the degradation of the DELLA protein SLR1. Taken together, it can be speculated that OsCSN2 plays a key role in GA and BR pathways by influencing the functional regulation of the transcription factor SLR1 in CSN, thereby affecting the growth and development of rice and the number of tillers.

The PGPR Bacillus aryabhattai promotes soybean growth via nutrient and chlorophyll maintenance and the production of butanoic acid

Plant growth-promoting rhizobacteria (PGPR) colonize plant roots, establish a mutualistic relationship with the plants and help them grow better. This study reports novel findings on the plant growth-promoting effects of the PGPR Bacillus aryabhattai. Soil was collected from a soybean field, PGPR were isolated, identified, and characterized for their ability to promote plant growth and development. The bacterium was isolated from the soybean rhizosphere and identified as B. aryabhattai strain SRB02 via 16s rRNA sequencing. As shown by SEM, the bacterium successfully colonized rice and soybean roots within 2 days and significantly promoted the growth of the GA-deficient rice cultivar Waito-C within 10 days, as well as the growth of soybean plants with at least six times longer shoots, roots, higher chlorophyll content, fresh, and dry weight after 10 days of inoculation. ICP analysis showed up to a 100% increase in the quantity of 18 different amino acids in the SRB02-treated soybean plants. Furthermore, the 2-DE gel assay indicated the presence of several differentially expressed proteins in soybean leaves after 24 hrs of SRB02 application. MALDI-TOF-MS identified β-conglycinin and glycinin along with several other proteins that were traced back to their respective genes. Analysis of bacterial culture filtrates via GCMS recorded significantly higher quantities of butanoic acid which was approximately 42% of all the metabolites found in the filtrates. The application of 100 ppm butanoic acid had significantly positive effects on plant growth via chlorophyll maintenance. These results establish the suitability of B. aryabhattai as a promising PGPR for field application in various crops.

Potential of rice tillering for sustainable food production

Tillering, also known as shoot branching, is a fundamental trait for cereal crops such as rice to produce sufficient panicle numbers. Effective tillering that guarantees successful panicle production is essential for achieving high crop yields. Recent advances in molecular biology have revealed the mechanisms underlying rice tillering; however, in rice breeding and cultivation, there remain limited genes or alleles suitable for effective tillering and high yields. A recently identified quantitative trait locus (QTL) called MORE PANICLES 3 (MP3) has been cloned as a single gene and shown to promote tillering and to moderately increase panicle number. This gene is an ortholog of the maize domestication gene TB1, and it has the potential to increase grain yield under ongoing climate change and in nutrient-poor environments. This review reconsiders the potential and importance of tillering for sustainable food production. Thus, I provide an overview of rice tiller development and the currently understood molecular mechanisms that underly it, focusing primarily on the biosynthesis and signaling of strigolactones, effective QTLs, and the importance of MP3 (TB1). The possible future benefits in using promising QTLs such as MP3 to explore agronomic solutions under ongoing climate change and in nutrient-poor environments are also highlighted.

GRAS gene family in rye (Secale cereale L.): genome-wide identification, phylogeny, evolutionary expansion and expression analyses

BACKGROUND

The GRAS transcription factor family plays a crucial role in various biological processes in different plants, such as tissue development, fruit maturation, and environmental stress. However, the GRAS family in rye has not been systematically analyzed yet.

RESULTS

In this study, 67 GRAS genes in S. cereale were identified and named based on the chromosomal location. The gene structures, conserved motifs, cis-acting elements, gene replications, and expression patterns were further analyzed. These 67 ScGRAS members are divided into 13 subfamilies. All members include the LHR I, VHIID, LHR II, PFYRE, and SAW domains, and some nonpolar hydrophobic amino acid residues may undergo cross-substitution in the VHIID region. Interested, tandem duplications may have a more important contribution, which distinguishes them from other monocotyledonous plants. To further investigate the evolutionary relationship of the GRAS family, we constructed six comparative genomic maps of homologous genes between rye and different representative monocotyledonous and dicotyledonous plants. The response characteristics of 19 ScGRAS members from different subfamilies to different tissues, grains at filling stages, and different abiotic stresses of rye were systematically analyzed. Paclobutrazol, a triazole-based plant growth regulator, controls plant tissue and grain development by inhibiting gibberellic acid (GA) biosynthesis through the regulation of DELLA proteins. Exogenous spraying of paclobutrazol significantly reduced the plant height but was beneficial for increasing the weight of 1000 grains of rye. Treatment with paclobutrazol, significantly reduced gibberellin levels in grain in the filling period, caused significant alteration in the expression of the DELLA subfamily gene members. Furthermore, our findings with respect to genes, ScGRAS46 and ScGRAS60, suggest that these two family members could be further used for functional characterization studies in basic research and in breeding programmes for crop improvement.

CONCLUSIONS

We identified 67 ScGRAS genes in rye and further analysed the evolution and expression patterns of the encoded proteins. This study will be helpful for further analysing the functional characteristics of ScGRAS genes.

MKK3 Cascade Regulates Seed Dormancy Through a Negative Feedback Loop Modulating ABA Signal in Rice

BACKGROUND

With the increasing frequency of climatic anomalies, high temperatures and long-term rain often occur during the rice-harvesting period, especially for early rice crops in tropical and subtropical regions. Seed dormancy directly affects the resistance to pre-harvest sprouting (PHS). Therefore, in order to increase rice production, it is critical to enhance seed dormancy and avoid yield losses to PHS. The elucidation and utilization of the seed dormancy regulation mechanism is of great significance to rice production. Preliminary results indicated that the OsMKKK62-OsMKK3-OsMPK7/14 module might regulate ABA sensitivity and then control seed dormancy. The detailed mechanism is still unclear.

RESULTS

The overexpression of OsMKK3 resulted in serious PHS. The expression levels of OsMKK3 and OsMPK7 were upregulated by ABA and GA at germination stage. OsMKK3 and OsMPK7 are both located in the nucleus and cytoplasm. The dormancy level of double knockout mutant mkk3/mft2 was lower than that of mkk3, indicating that OsMFT2 functions in the downstream of MKK3 cascade in regulating rice seeds germination. Biochemical results showed that OsMPK7 interacted with multiple core ABA signaling components according to yeast two-hybrid screening and luciferase complementation experiments, suggesting that MKK3 cascade regulates ABA signaling by modulating the core ABA signaling components. Moreover, the ABA response and ABA responsive genes of mpk7/14 were significantly higher than those of wild-type ZH11 when subjected to ABA treatment.

CONCLUSION

MKK3 cascade mediates the negative feedback loop of ABA signal through the interaction between OsMPK7 and core ABA signaling components in rice.

Seed Longevity and Ageing: A Review on Physiological and Genetic Factors with an Emphasis on Hormonal Regulation

Upon storage, seeds inevitably age and lose their viability over time, which determines their longevity. Longevity correlates with successful seed germination and enhancing this trait is of fundamental importance for long-term seed storage (germplasm conservation) and crop improvement. Seed longevity is governed by a complex interplay between genetic factors and environmental conditions experienced during seed development and after-ripening that will shape seed physiology. Several factors have been associated with seed ageing such as oxidative stress responses, DNA repair enzymes, and composition of seed layers. Phytohormones, mainly abscisic acid, auxins, and gibberellins, have also emerged as prominent endogenous regulators of seed longevity, and their study has provided new regulators of longevity. Gaining a thorough understanding of how hormonal signalling genes and pathways are integrated with downstream mechanisms related to seed longevity is essential for formulating strategies aimed at preserving seed quality and viability. A relevant aspect related to research in seed longevity is the existence of significant differences between results depending on the seed equilibrium relative humidity conditions used to study seed ageing. Hence, this review delves into the genetic, environmental and experimental factors affecting seed ageing and longevity, with a particular focus on their hormonal regulation. We also provide gene network models underlying hormone signalling aimed to help visualize their integration into seed longevity and ageing. We believe that the format used to present the information bolsters its value as a resource to support seed longevity research for seed conservation and crop improvement.

DWARF AND LOW-TILLERING 2 functions in brassinosteroid signaling and controls plant architecture and grain size in rice

Brassinosteroids (BRs) are a class of steroid phytohormones that control various aspects of plant growth and development. Several transcriptional factors (TFs) have been suggested to play roles in BR signaling. However, their possible relationship remains largely unknown. Here, we identified a rice mutant dwarf and low-tillering 2 (dlt2) with altered plant architecture, increased grain width, and reduced BR sensitivity. DLT2 encodes a GIBBERELLIN INSENSITIVE (GAI)-REPRESSOR OF GAI (RGA)-SCARECROW (GRAS) TF that is mainly localized in the nucleus and has weak transcriptional activity. Our further genetic and biochemical analyses indicate that DLT2 interacts with two BR-signaling-related TFs, DLT and BRASSINAZOLE-RESISTANT 1, and probably modulates their transcriptional activity. These findings imply that DLT2 is implicated in a potentially transcriptional complex that mediates BR signaling and rice development and suggests that DLT2 could be a potential target for improving rice architecture and grain morphology. This work also sheds light on the role of rice GRAS members in regulating numerous developmental processes.

A genome-wide analysis of the GRAS gene family in upland cotton and a functional study of the role of the GhGRAS55 gene in regulating early maturity in cotton

The members of the GRAS gene family play important roles in regulating plant growth and development, but their functions in regulating early plant maturity traits are still unknown. In this study, we used a series of bioinformatics tools to identify GRAS gene family members and investigate the function of the gene family (GhGRAS55) using a genome-wide database of upland cotton samples. A total of 58 members of the GRAS gene family were identified and screened, which were distributed on 21 chromosomes within the whole cotton genome. The results of the phylogenetic analysis showed that the genes of upland cotton, island cotton, African cotton, Raymond cotton, and Arabidopsis were distributed in subfamilies I-VIII, although subfamily II did not contain any upland cotton or Arabidopsis GRAS family members. The structures and other characteristics of the genes in this family were clarified using bioinformatics technology. The transcriptomic sequencing results for early and late maturing cotton species showed that the expression of most GRAS family genes, such as GhGRAS10, GhGRAS5511, and GhGRAS55, was lower in early maturing species than late maturing species. We also found that cotton plants with GhGRAS55 genes that were silenced by virus-induced gene silencing (VIGS) technology showed early bud emergence phenotypes, so it could be speculated that the GhGRAS55 gene has the function of regulating early maturity in cotton.

Gibberellin signaling regulates lignin biosynthesis to modulate rice seed shattering

The elimination of seed shattering was a key step in rice (Oryza sativa) domestication. In this paper, we show that increasing the gibberellic acid (GA) content or response in the abscission region enhanced seed shattering in rice. We demonstrate that SLENDER RICE1 (SLR1), the key repressor of GA signaling, could physically interact with the rice seed shattering-related transcription factors quantitative trait locus of seed shattering on chromosome 1 (qSH1), O. sativa HOMEOBOX 15 (OSH15), and SUPERNUMERARY BRACT (SNB). Importantly, these physical interactions interfered with the direct binding of these three regulators to the lignin biosynthesis gene 4-COUMARATE: COENZYME A LIGASE 3 (4CL3), thereby derepressing its expression. Derepression of 4CL3 led to increased lignin deposition in the abscission region, causing reduced rice seed shattering. Importantly, we also show that modulating GA content could alter the degree of seed shattering to increase harvest efficiency. Our results reveal that the "Green Revolution" phytohormone GA is important for regulating rice seed shattering, and we provide an applicable breeding strategy for high-efficiency rice harvesting.

SMALL PLANT AND ORGAN 1 (SPO1) Encoding a Cellulose Synthase-like Protein D4 (OsCSLD4) Is an Important Regulator for Plant Architecture and Organ Size in Rice

Plant architecture and organ size are considered as important traits in crop breeding and germplasm improvement. Although several factors affecting plant architecture and organ size have been identified in rice, the genetic and regulatory mechanisms remain to be elucidated. Here, we identified and characterized the small plant and organ 1 (spo1) mutant in rice (Oryza sativa), which exhibits narrow and rolled leaf, reductions in plant height, root length, and grain width, and other morphological defects. Map-based cloning revealed that SPO1 is allelic with OsCSLD4, a gene encoding the cellulose synthase-like protein D4, and is highly expressed in the roots at the seedling and tillering stages. Microscopic observation revealed the spo1 mutant had reduced number and width in leaf veins, smaller size of leaf bulliform cells, reduced cell length and cell area in the culm, and decreased width of epidermal cells in the outer glume of the grain. These results indicate the role of SPO1 in modulating cell division and cell expansion, which modulates plant architecture and organ size. It is showed that the contents of endogenous hormones including auxin, abscisic acid, gibberellin, and zeatin tested in the spo1 mutant were significantly altered, compared to the wild type. Furthermore, the transcriptome analysis revealed that the differentially expressed genes (DEGs) are significantly enriched in the pathways associated with plant hormone signal transduction, cell cycle progression, and cell wall formation. These results indicated that the loss of SPO1/OsCSLD4 function disrupted cell wall cellulose synthase and hormones homeostasis and signaling, thus leading to smaller plant and organ size in spo1. Taken together, we suggest the functional role of SPO1/OsCSLD4 in the control of rice plant and organ size by modulating cell division and expansion, likely through the effects of multiple hormonal pathways on cell wall formation.

DELLA-mediated gene repression is maintained by chromatin modification in rice

DELLA proteins are master regulators of gibberellic acid (GA) signaling through their effects on gene expression. Enhanced DELLA accumulation in rice and wheat varieties has greatly contributed to grain yield increases during the green revolution. However, the molecular basis of DELLA-mediated gene repression remains elusive. In this work, we show that the rice DELLA protein SLENDER RICE1 (SLR1) forms a tripartite complex with Polycomb-repressive complex 2 (PRC2) and the histone deacetylase HDA702 to repress downstream genes by establishing a silent chromatin state. The slr1 mutation and GA signaling resulted in dissociation of PRC2 and HDA702 from GA-inducible genes. Loss-of-function or downregulation of the chromatin regulators impaired SLR1-dependent histone modification and gene repression. Time-resolved analysis of GA signaling revealed that GA-induced transcriptional activation was associated with a rapid increase of H3K9ac followed by H3K27me3 removal. Collectively, these results establish a general epigenetic mechanism for DELLA-mediated gene repression and reveal details of the chromatin dynamics during transcriptional activation stimulated by GA signaling.

Genome-wide identification and characterization of GRAS gene family in pigeonpea (Cajanus cajan (L.) Millspaugh)

The GRAS proteins are plant-specific transcription factors (TFs) that play a crucial role in various plant physiological processes, including tissue development and stress responses. To date, GRAS family has been comprehensively characterized in Arabidopsis, soybean, rice, chickpea and other plant species. To understand the structural and functional aspects of pigeonpea (C. cajan), we identified 60 putative GRAS (CcGRAS) genes from pigeonpea genome and further analysed their physicochemical properties, subcellular locations, evolutionary classification, exon-intron structures, conserved domains, gene duplication events and cis-promoter regions. Based on the sequence similarity, CcGRAS family was clustered into 9 subfamilies and the genes with a similar structure and motif distribution were clustered in the same group. The gene duplication studies revealed that these genes were derived from tandem and dispersed duplication events. The cis-promoter regulatory analysis of CcGRAS genes indicated the presence of three types of cis-acting elements including light-responsive, hormone-responsive and plant growth and development related. The expression profiling of CcGRAS genes revealed their tissue-specific functions and differential nature. Collectively, this study highlights relevant functional and regulatory elements of GRAS family in pigeonpea creating a significant resource for future functional studies.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03782-x.

Gibberellin metabolism and signaling

Gibberellins (GAs) are plant hormones with a tetracyclic diterpenoid structure that are involved in various important developmental processes. Two GA-deficient mutants were isolated: a semidwarf mutant "sd1", which was found to have a defective GA20ox2 gene and was introduced to the world in a green revolution cultivar, and a severe dwarf allele of "d18", with a defective GA3ox2 gene. Based on the phenotypic similarity of d18, rice dwarf mutants were screened, further classifying them into GA-sensitive and GA-insensitive by applying exogenous GA3. Finally, GA-deficient rice mutants at 6 different loci and 3 GA signaling mutants (gid1, gid2, and slr1) were isolated. The GID1 gene encodes a GA nuclear receptor, and the GID1-DELLA (SLR1) system for GA perception is widely used in vascular plants. The structural characteristics of GID1 and GA metabolic enzymes have also been reviewed.

Cytokinin-inducible response regulator SlRR6 controls plant height through gibberellin and auxin pathways in tomato

Plant height is a key agronomic trait regulated by several phytohormones such as gibberellins (GAs) and auxin. However, little is known about how cytokinin (CK) participates in this process. Here, we report that SlRR6, a type-A response regulator in the CK signaling pathway, positively regulates plant height in tomato. SlRR6 was induced by exogenous kinetin and GA3, but inhibited by indole-3-acetic acid (IAA). Knock out of SlRR6 reduced tomato plant height through shortening internode length, while overexpression of SlRR6 caused taller plants due to increased internode number. Cytological observation of longitudinal stems showed that both knock out and overexpression of SlRR6 generated larger cells, but significantly reduced cell numbers in each internode. Further studies demonstrated that overexpression of SlRR6 enhanced GA accumulation and lowered IAA content, along with expression changes in GA- and IAA-related genes. Exogenous paclobutrazol and IAA treatments restored the increased plant height phenotype in SlRR6-overexpressing lines. Yeast two-hybrid, bimolecular fluorescence complementation, and co-immunoprecipitation assays showed that SlRR6 interacts with a small auxin up RNA protein, SlSAUR58. Moreover, SlSAUR58-overexpressing plants were dwarf with decreased internode length. Overall, our findings establish SlRR6 as a vital component in the CK signaling, GA, and IAA regulatory network that controls plant height.

A translational regulator MHZ9 modulates ethylene signaling in rice

Ethylene plays essential roles in rice growth, development and stress adaptation. Translational control of ethylene signaling remains unclear in rice. Here, through analysis of an ethylene-response mutant mhz9, we identified a glycine-tyrosine-phenylalanine (GYF) domain protein MHZ9, which positively regulates ethylene signaling at translational level in rice. MHZ9 is localized in RNA processing bodies. The C-terminal domain of MHZ9 interacts with OsEIN2, a central regulator of rice ethylene signaling, and the N-terminal domain directly binds to the OsEBF1/2 mRNAs for translational inhibition, allowing accumulation of transcription factor OsEIL1 to activate the downstream signaling. RNA-IP seq and CLIP-seq analyses reveal that MHZ9 associates with hundreds of RNAs. Ribo-seq analysis indicates that MHZ9 is required for the regulation of ~ 90% of genes translationally affected by ethylene. Our study identifies a translational regulator MHZ9, which mediates translational regulation of genes in response to ethylene, facilitating stress adaptation and trait improvement in rice.

Role of BraRGL1 in regulation of Brassica rapa bolting and flowering

Gibberellin (GA) plays a major role in controlling Brassica rapa stalk development. As an essential negative regulator of GA signal transduction, DELLA proteins may exert significant effects on stalk development. However, the regulatory mechanisms underlying this regulation remain unclear. In this study, we report highly efficient and inheritable mutagenesis using the CRISPR/Cas9 gene editing system in BraPDS (phytoene desaturase) and BraRGL1 (key DELLA protein) genes. We observed a loss-of-function mutation in BraRGL1 due to two amino acids in GRAS domain. The flower bud differentiation and bolting time of BraRGL1 mutants were significantly advanced. The expression of GA-regulatory protein (BraGASA6), flowering related genes (BraSOC1, BraLFY), expansion protein (BraEXPA11) and xyloglucan endotransferase (BraXTH3) genes was also significantly upregulated in these mutants. BraRGL1-overexpressing plants displayed the contrasting phenotypes. BraRGL1 mutants were more sensitive to GA signaling. BraRGL1 interacted with BraSOC1, and the interaction intensity decreased after GA3 treatment. In addition, BraRGL1 inhibited the transcription-activation ability of BraSOC1 for BraXTH3 and BraLFY genes, but the presence of GA3 enhanced the activation ability of BraSOC1, suggesting that the BraRGL1-BraSOC1 module regulates bolting and flowering of B. rapa through GA signal transduction. Thus, we hypothesized that BraRGL1 is degraded, and BraSOC1 is released in the presence of GA3, which promotes the expression of BraXTH3 and BraLFY, thereby inducing stalk development in B. rapa. Further, the BraRGL1-M mutant promoted the flower bud differentiation without affecting the stalk quality. Thus, BraRGL1 can serve as a valuable target for the molecular breeding of early maturing varieties.

The master growth regulator DELLA binding to histone H2A is essential for DELLA-mediated global transcription regulation

The DELLA genes, also known as 'Green Revolution' genes, encode conserved master growth regulators that control plant development in response to internal and environmental cues. Functioning as nuclear-localized transcription regulators, DELLAs modulate expression of target genes via direct protein-protein interaction of their carboxy-terminal GRAS domain with hundreds of transcription factors (TFs) and epigenetic regulators. However, the molecular mechanism of DELLA-mediated transcription reprogramming remains unclear. Here by characterizing new missense alleles of an Arabidopsis DELLA, repressor of ga1-3 (RGA), and co-immunoprecipitation assays, we show that RGA binds histone H2A via the PFYRE subdomain within its GRAS domain to form a TF-RGA-H2A complex at the target chromatin. Chromatin immunoprecipitation followed by sequencing analysis further shows that this activity is essential for RGA association with its target chromatin globally. Our results indicate that, although DELLAs are recruited to target promoters by binding to TFs via the LHR1 subdomain, DELLA-H2A interaction via the PFYRE subdomain is necessary to stabilize the TF-DELLA-H2A complex at the target chromatin. This study provides insights into the two distinct key modular functions in DELLA for its genome-wide transcription regulation in plants.

Effects of Hard Water Boiling on Chalky Rice in Terms of Texture Improvement and Ca Fortification

In the present paper, we investigated the characteristics of chalky rice grains generated by ripening under high temperature and compared them with whole grains. We evaluated 14 unpolished Japonica rice grains harvested in Japan in 2021, and these samples (original grains) were divided into two groups (a whole grain group and a chalky grain one). We found that not only activities of endogenous amylase and proteinase, but also cell wall-degrading enzymes, such as xylanase and cellulase, changed markedly between chalky grains and whole grains. Using rice grains blended with 30% of chalky grains as the material, we compared the sugar and mineral contents and textural properties of the rice grains soaked and boiled in either ordinary water or hard water, such as Evian or Contrex. It was shown that xylanase, in addition to amylase and proteinase, may play an important role in changing the texture of the boiled chalky rice grains. For the sake of preventing the above-mentioned deterioration in the texture of boiled grains of chalky rice, we tried to use hard water, such as Evian or Contrex, to soak and cook the chalky rice grains. It was shown that the hard water was useful for the prevention of texture deterioration of the boiled rice grains due to inhibition of the activities of endogenous hydrolytic enzymes, such as α-amylase, β-amylase, proteinase, and xylanase. Furthermore, we found that the hard water was useful in increasing the calcium absorption through the meal by 2.6 to 16.5 times.

Restructuring plant types for developing tailor-made crops

Plants have adapted to different environmental niches by fine-tuning the developmental factors working together to regulate traits. Variations in the developmental factors result in a wide range of quantitative variations in these traits that helped plants survive better. The major developmental pathways affecting plant architecture are also under the control of such pathways. Most notable are the CLAVATA-WUSCHEL pathway regulating shoot apical meristem fate, GID1-DELLA module influencing plant height and tillering, LAZY1-TAC1 module controlling branch/tiller angle and the TFL1-FT determining the floral fate in plants. Allelic variants of these key regulators selected during domestication shaped the crops the way we know them today. There is immense yield potential in the 'ideal plant architecture' of a crop. With the available genome-editing techniques, possibilities are not restricted to naturally occurring variations. Using a transient reprogramming system, one can screen the effect of several developmental gene expressions in novel ecosystems to identify the best targets. We can use the plant's fine-tuning mechanism for customizing crops to specific environments. The process of crop domestication can be accelerated with a proper understanding of these developmental pathways. It is time to step forward towards the next-generation molecular breeding for restructuring plant types in crops ensuring yield stability.

The E3 ubiquitin ligases SINA1 and SINA2 integrate with the protein kinase CIPK20 to regulate the stability of RGL2a, a positive regulator of anthocyanin biosynthesis

Although DELLA protein destabilization mediated by post-translational modifications is essential for gibberellin (GA) signal transduction and GA-regulated anthocyanin biosynthesis, the related mechanisms remain largely unknown. In this study, we report the ubiquitination and phosphorylation of an apple DELLA protein MdRGL2a in response to GA signaling and its regulatory role in anthocyanin biosynthesis. MdRGL2a could interact with MdWRKY75 to enhance the MdWRKY75-activated transcription of anthocyanin activator MdMYB1 and interfere with the interaction between anthocyanin repressor MdMYB308 and MdbHLH3 or MdbHLH33, thereby promoting anthocyanin accumulation. A protein kinase MdCIPK20 was found to phosphorylate and protect MdRGL2a from degradation, and it was essential for MdRGL2a-promoting anthocyanin accumulation. However, MdRGL2a and MdCIPK20 were ubiquitinated and degraded by E3 ubiquitin ligases MdSINA1 and MdSINA2, respectively, both of which were activated in the presence of GA. Our results display the integration of SINA1/2 with CIPK20 to dynamically regulate GA signaling and will be helpful toward understanding the mechanism of GA signal transduction and GA-inhibited anthocyanin biosynthesis. The discovery of extensive interactions between DELLA and SINA and CIPK proteins in apple will provide reference for the study of ubiquitination and phosphorylation of DELLA proteins in other species.

Peach DELLA Protein PpeDGYLA Is Not Degraded in the Presence of Active GA and Causes Dwarfism When Overexpressed in Poplar and Arabidopsis

Controlling the tree size of fruit species such as peach can reduce the amount of labor and input needed for orchard management. The phytohormone gibberellin (GA) positively regulates tree size by inducing degradation of the GA signaling repressor DELLA. The N-terminal DELLA domain in this protein is critical for its GA-dependent interaction with the GA receptor GID1 and the resulting degradation of the DELLA protein, which allows for growth-promoting GA signaling. In this study, a DELLA family member, PpeDGYLA, contains a DELLA domain but has amino acid changes in three conserved motifs (DELLA into DGYLA, LEQLE into LERLE, and TVHYNP into AVLYNP). In the absence or presence of GA₃, the PpeDGYLA protein did not interact with PpeGID1c and was stable in 35S-PpeDGYLA peach transgenic callus. The overexpression of PpeDGYLA in both polar and Arabidopsis showed an extremely dwarfed phenotype, and these transgenic plants were insensitive to GA₃ treatment. PpeDGYLA could interact with PpeARF6-1 and -2, supposed growth-promoting factors. It is suggested that the changes in the DELLA domain of PpeDGYLA may, to some extent, account for the severe dwarf phenotype of poplar and Arabidopsis transgenic plants. In addition, our study showed that the DELLA family contained three clades (DELLA-like, DELLA, and DGLLA). PpeDGYLA clustered into the DGLLA clade and was expressed in all of the analyzed tissues. These results lay the foundation for the further study of the repression of tree size by PpeDGYLA.

DELLA functions evolved by rewiring of associated transcriptional networks

DELLA proteins are land-plant specific transcriptional regulators that transduce environmental information to multiple processes throughout a plant's life^1-3. The molecular basis for this critical function in angiosperms has been linked to the regulation of DELLA stability by gibberellins and to the capacity of DELLA proteins to interact with hundreds of transcription factors^4,5. Although bryophyte orthologues can partially fulfil functions attributed to angiosperm DELLA^6,7, it is not clear whether the capacity to establish interaction networks is an ancestral property of DELLA proteins or is associated with their role in gibberellin signalling^8-10. Here we show that representative DELLAs from the main plant lineages display a conserved ability to interact with multiple transcription factors. We propose that promiscuity was encoded in the ancestral DELLA protein, and that this property has been largely maintained, whereas the lineage-dependent diversification of DELLA-dependent functions mostly reflects the functional evolution of their interacting partners.

Hormonal control of medial-lateral growth and vein formation in the maize leaf

Parallel veins are characteristic of monocots, including grasses (Poaceae). Therefore, how parallel veins develop as the leaf grows in the medial-lateral (ML) dimension is a key question in grass leaf development. Using fluorescent protein reporters, we mapped auxin, cytokinin (CK), and gibberellic acid (GA) response patterns in maize (Zea mays) leaf primordia. We further defined the roles of these hormones in ML growth and vein formation through combinatorial genetic analyses and measurement of hormone concentrations. We discovered a novel pattern of auxin response in the adaxial protoderm that we hypothesize has important implications for the orderly formation of 3° veins early in leaf development. In addition, we found an auxin transport and response pattern in the margins that correlate with the transition from ML to proximal-distal growth. We present evidence that auxin efflux precedes CK response in procambial strand development. We also determined that GA plays an early role in the shoot apical meristem as well as a later role in the primordium to restrict ML growth. We propose an integrative model whereby auxin regulates ML growth and vein formation in the maize leaf through control of GA and CK.

A rice seed-specific glycine-rich protein OsDOR1 interacts with GID1 to repress GA signaling and regulates seed dormancy

Seed dormancy is an important agronomic trait under the control of complex genetic and environmental interactions, which have not been yet comprehensively understood. From the field screening of rice mutant library generated by a Ds transposable element, we identified a pre-harvest sprouting (PHS) mutant dor1. This mutant has a single insertion of Ds element at the second exon of OsDOR1 (LOC_Os03g20770), which encodes a novel seed-specific glycine-rich protein. This gene successfully complemented the PHS phenotype of dor1 mutant and its ectopic expression enhanced seed dormancy. Here, we demonstrated that OsDOR1 protein binds to the GA receptor protein, OsGID1 in rice protoplasts, and interrupts with the formation OsGID1-OsSLR1 complex in yeast cells. Co-expression of OsDOR1 with OsGID1 in rice protoplasts attenuated the GA-dependent degradation of OsSLR1, the key repressor of GA signaling. We showed the endogenous OsSLR1 protein level in the dor1 mutant seeds is significantly lower than that of wild type. The dor1 mutant featured a hypersensitive GA-response of α-amylase gene expression during seed germination. Based on these findings, we suggest that OsDOR1 is a novel negative player of GA signaling operated in the maintenance of seed dormancy. Our findings provide a novel source of PHS resistance.

Progress in rice sheath blight resistance research

Rice sheath blight (ShB) disease poses a major threat to rice yield throughout the world. However, the defense mechanisms against ShB in rice remain largely unknown. ShB resistance is a typical quantitative trait controlled by multiple genes. With the rapid development of molecular methods, many quantitative trait loci (QTLs) related to agronomic traits, biotic and abiotic stresses, and yield have been identified by genome-wide association studies. The interactions between plants and pathogens are controlled by various plant hormone signaling pathways, and the pathways synergistically or antagonistically interact with each other, regulating plant growth and development as well as the defense response. This review summarizes the regulatory effects of hormones including auxin, ethylene, salicylic acid, jasmonic acid, brassinosteroids, gibberellin, abscisic acid, strigolactone, and cytokinin on ShB and the crosstalk between the various hormones. Furthermore, the effects of sugar and nitrogen on rice ShB resistance, as well as information on genes related to ShB resistance in rice and their effects on ShB are also discussed. In summary, this review is a comprehensive description of the QTLs, hormones, nutrition, and other defense-related genes related to ShB in rice. The prospects of targeting the resistance mechanism as a strategy for controlling ShB in rice are also discussed.

Mechanical Stimulation Decreases Auxin and Gibberellic Acid Synthesis but Does Not Affect Auxin Transport in Axillary Buds; It Also Stimulates Peroxidase Activity in Petunia × atkinsiana

Thigmomorphogenesis (or mechanical stimulation-MS) is a term created by Jaffe and means plant response to natural stimuli such as the blow of the wind, strong rain, or touch, resulting in a decrease in length and an increase of branching as well as an increase in the activity of axillary buds. MS is very well known in plant morphology, but physiological processes controlling plant growth are not well discovered yet. In the current study, we tried to find an answer to the question if MS truly may affect auxin synthesis or transport in the early stage of plant growth, and which physiological factors may be responsible for growth arrest in petunia. According to the results of current research, we noticed that MS affects plant growth but does not block auxin transport from the apical bud. MS arrests IAA and GA3 synthesis in MS-treated plants over the longer term. The main factor responsible for the thickening of cell walls and the same strengthening of vascular tissues and growth arrestment, in this case, is peroxidase (POX) activity, but special attention should be also paid to AGPs as signaling molecules which also are directly involved in growth regulation as well as in cell wall modifications.

Genetic basis controlling rice plant architecture and its modification for breeding

The shoot and root system architectures are fundamental for crop productivity. During the history of artificial selection of domestication and post-domestication breeding, the architecture of rice has significantly changed from its wild ancestor to fulfil requirements in agriculture. We review the recent studies on developmental biology in rice by focusing on components determining rice plant architecture; shoot meristems, leaves, tillers, stems, inflorescences and roots. We also highlight natural variations that affected these structures and were utilized in cultivars. Importantly, many core regulators identified from developmental mutants have been utilized in breeding as weak alleles moderately affecting these architectures. Given a surge of functional genomics and genome editing, the genetic mechanisms underlying the rice plant architecture discussed here will provide a theoretical basis to push breeding further forward not only in rice but also in other crops and their wild relatives.