Exploiting DELLA Signaling in Cereals

Molecular mechanisms regulating GROWTH-REGULATING FACTORS activity in plant growth, development, and environmental responses

Plants rely on complex regulatory mechanisms to ensure proper growth and development. As plants are sessile organisms, these mechanisms must be flexible enough to adapt to changes in the environment. GROWTH-REGULATING FACTORS (GRFs) are plant-specific transcription factors that act as a central hub controlling plant growth and development, which offer promising biotechnological applications to enhance plant performance. Here, we analyze the complex molecular mechanisms that regulate GRFs activity, and how their natural and synthetic variants can impact on plant growth and development. We describe the biological roles of the GRFs and examine how they regulate gene expression and contribute to the control of organ growth and plant responses to a changing environment. This review focuses on the premise that unlocking the full biotechnological potential of GRFs requires a thorough understanding of the various regulatory layers governing GRF activity, the functional divergence among GRF family members, and the gene networks that they regulate.

The cotton MYB33 gene is a hub gene regulating the trade-off between plant growth and defense in Verticillium dahliae infection

INTRODUCTION

Sessile plants engage in trade-offs between growth and defense capacity in response to fluctuating environmental cues. MYB is an important transcription factor that plays many important roles in controlling plant growth and defense. However, the mechanism behind how it keeps a balance between these two physiological processes is still largely unknown.

OBJECTIVES

Our work focuses on the dissection of the molecular mechanism by which GhMYB33 regulates plant growth and defense.

METHODS

The CRISPR/Cas9 technique was used to generate mutants for deciphering GhMYB33 functions. Yeast two-hybrid, luciferase complementary imaging, and co-immunoprecipitation assays were used to prove that proteins interact with each other. We used the electrophoretic mobility shift assay, yeast one-hybrid, and luciferase activity assays to analyze GhMYB33 acting as a promoter. A β-glucuronidase fusion reporter and 5' RNA ligase mediated amplification of cDNA ends analysis showed that ghr-miR319c directedly cleaved the GhMYB33 mRNA.

RESULTS

Overexpressing miR319c-resistant GhMYB33 (rGhMYB33) promoted plant growth, accompanied by a significant decline in resistance against Verticillium dahliae. Conversely, its knockout mutant, ghmyb33, demonstrated growth restriction and concomitant augmentation of V. dahliae resistance. GhMYB33 was found to couple with the DELLA protein GhGAI1 and bind to the specific cis-elements of GhSPL9 and GhDFR1 promoters, thereby modulating internode elongation and plant resistance in V. dahliae infection. The ghr-miR319c was discovered to target and suppress GhMYB33 expression. The overexpression of ghr-miR319c led to enhanced plant resistance and a simultaneous reduction in plant height.

CONCLUSION

Our findings demonstrate that GhMYB33 encodes a hub protein and controls the expression of GhSPL9 and GhDFR1, implicating a pivotal role for the miR319c-MYB33 module to regulate the trade-offs between plant growth and defense.

ABA-mediated regulation of rice grain quality and seed dormancy via the NF-YB1-SLRL2-bHLH144 Module

Abscisic acid (ABA) plays a crucial role in promoting plant stress resistance and seed dormancy. However, how ABA regulates rice quality remains unclear. This study identifies a key transcription factor SLR1-like2 (SLRL2), which mediates the ABA-regulated amylose content (AC) of rice. Mechanistically, SLRL2 interacts with NF-YB1 to co-regulate Wx, a determinant of AC and rice quality. In contrast to SLR1, SLRL2 is ABA inducible but insensitive to GA. In addition, SLRL2 exhibits DNA-binding activity and directly regulates the expression of Wx, bHLH144 and MFT2. SLRL2 competes with NF-YC12 for interaction with NF-YB1. NF-YB1 also directly represses SLRL2 transcription. Genetic validation supports that SLRL2 functions downstream of NF-YB1 and bHLH144 in regulating rice AC. Thus, an NF-YB1-SLRL2-bHLH144 regulatory module is successfully revealed. Furthermore, SLRL2 regulates rice dormancy by modulating the expression of MFT2. In conclusion, this study revealed an ABA-responsive regulatory cascade that functions in both rice quality and seed dormancy.

A quantitative gibberellin signaling biosensor reveals a role for gibberellins in internode specification at the shoot apical meristem

Growth at the shoot apical meristem (SAM) is essential for shoot architecture construction. The phytohormones gibberellins (GA) play a pivotal role in coordinating plant growth, but their role in the SAM remains mostly unknown. Here, we developed a ratiometric GA signaling biosensor by engineering one of the DELLA proteins, to suppress its master regulatory function in GA transcriptional responses while preserving its degradation upon GA sensing. We demonstrate that this degradation-based biosensor accurately reports on cellular changes in GA levels and perception during development. We used this biosensor to map GA signaling activity in the SAM. We show that high GA signaling is found primarily in cells located between organ primordia that are the precursors of internodes. By gain- and loss-of-function approaches, we further demonstrate that GAs regulate cell division plane orientation to establish the typical cellular organization of internodes, thus contributing to internode specification in the SAM.

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.

Unraveling the molecular mechanisms governing axillary meristem initiation in plants

MAIN CONCLUSION

Axillary meristems (AMs) located in the leaf axils determine the number of shoots or tillers eventually formed, thus contributing significantly to the plant architecture and crop yields. The study of AM initiation is unavoidable and beneficial for crop productivity. Shoot branching is an undoubted determinant of plant architecture and thus greatly impacts crop yield due to the panicle-bearing traits of tillers. The emergence of the AM is essential for the incipient bud formation, and then the bud is dormant or outgrowth immediately to form a branch or tiller. While numerous reviews have focused on plant branching and tillering development networks, fewer specifically address AM initiation and its regulatory mechanisms. This review synthesizes the significant advancements in the genetic and hormonal factors governing AM initiation, with a primary focus on studies conducted in Arabidopsis (Arabidopsis thaliana L.) and rice (Oryza sativa L.). In particular, by elaborating on critical genes like LATERAL SUPPRESSOR (LAS), which specifically regulates AM initiation and the networks in which they are involved, we attempt to unify the cascades through which they are positioned. We concentrate on clarifying the precise mutual regulation between shoot apical meristem (SAM) and AM-related factors. Additionally, we examine challenges in elucidating AM formation mechanisms alongside opportunities provided by emerging omics approaches to identify AM-specific genes. By expanding our comprehension of the genetic and hormonal regulation of AM development, we can develop strategies to optimize crop production and address global food challenges effectively.

Gibberellic acid promotes single-celled fiber elongation through the activation of two signaling cascades in cotton

The agricultural green revolution spectacularly enhanced crop yield through modification of gibberellin (GA) signaling. However, in cotton, the GA signaling cascades remain elusive, limiting our potential to cultivate new cotton varieties and improve yield and quality. Here, we identified that GA prominently stimulated fiber elongation through the degradation of DELLA protein GhSLR1, thereby disabling GhSLR1's physical interaction with two transcription factors, GhZFP8 and GhBLH1. Subsequently, the resultant free GhBLH1 binds to GhKCS12 promoter and activates its expression to enhance VLCFAs biosynthesis. With a similar mechanism, the free GhZFP8 binds to GhSDCP1 promoter and activates its expression. As a result, GhSDCP1 upregulates the expression of GhPIF3 gene associated with plant cell elongation. Ultimately, the two parallel signaling cascades synergistically promote cotton fiber elongation. Our findings outline the mechanistic framework that translates the GA signal into fiber cell elongation, thereby offering a roadmap to improve cotton fiber quality and yield.

OsNAC120 balances plant growth and drought tolerance by integrating GA and ABA signaling in rice

The crosstalk between gibberellin (GA) and abscisic acid (ABA) signaling is crucial for balancing plant growth and adaption to environmental stress. Nevertheless, the molecular mechanism of their mutual antagonism still remains to be fully clarified. In this study, we found that knockout of the rice NAC (NAM, ATAF1/2, CUC2) transcription factor gene OsNAC120 inhibits plant growth but enhances drought tolerance, whereas OsNAC120 overexpression produces the opposite results. Exogenous GA can rescue the semi-dwarf phenotype of osnac120 mutants, and further study showed that OsNAC120 promotes GA biosynthesis by transcriptionally activating the GA biosynthetic genes OsGA20ox1 and OsGA20ox3. The DELLA protein SLENDER RICE1 (SLR1) interacts with OsNAC120 and impedes its transactivation ability, and GA treatment can remove the inhibition of transactivation activity caused by SLR1. On the other hand, OsNAC120 negatively regulates rice drought tolerance by repressing ABA-induced stomatal closure. Mechanistic investigation revealed that OsNAC120 inhibits ABA biosynthesis via transcriptional repression of the ABA biosynthetic genes OsNCED3 and OsNCED4. Rice OSMOTIC STRESS/ABA-ACTIVATED PROTEIN KINASE 9 (OsSAPK9) physically interacts with OsNAC120 and mediates its phosphorylation, which results in OsNAC120 degradation. ABA treatment accelerates OsNAC120 degradation and reduces its transactivation activity. Together, our findings provide evidence that OsNAC120 plays critical roles in balancing GA-mediated growth and ABA-induced drought tolerance in rice. This research will help us to understand the mechanisms underlying the trade-off between plant growth and stress tolerance and to engineer stress-resistant, high-yielding crops.

Genome-wide identification and expression pattern analysis of the kiwifruit GRAS transcription factor family in response to salt stress

BACKGROUND

GRAS is a family of plant-specific transcription factors (TFs) that play a vital role in plant growth and development and response to adversity stress. However, systematic studies of the GRAS TF family in kiwifruit have not been reported.

RESULTS

In this study, we used a bioinformatics approach to identify eighty-six AcGRAS TFs located on twenty-six chromosomes and phylogenetic analysis classified them into ten subfamilies. It was found that the gene structure is relatively conserved for these genes and that fragmental duplication is the prime force for the evolution of AcGRAS genes. However, the promoter region of the AcGRAS genes mainly contains cis-acting elements related to hormones and environmental stresses, similar to the results of GO and KEGG enrichment analysis, suggesting that hormone signaling pathways of the AcGRAS family play a vital role in regulating plant growth and development and adversity stress. Protein interaction network analysis showed that the AcGRAS51 protein is a relational protein linking DELLA, SCR, and SHR subfamily proteins. The results demonstrated that 81 genes were expressed in kiwifruit AcGRAS under salt stress, including 17 differentially expressed genes, 13 upregulated, and four downregulated. This indicates that the upregulated AcGRAS55, AcGRAS69, AcGRAS86 and other GRAS genes can reduce the salt damage caused by kiwifruit plants by positively regulating salt stress, thus improving the salt tolerance of the plants.

CONCLUSIONS

These results provide a theoretical basis for future exploration of the characteristics and functions of more AcGRAS genes. This study provides a basis for further research on kiwifruit breeding for resistance to salt stress. RT-qPCR analysis showed that the expression of 3 AcGRAS genes was elevated under salt stress, indicating that AcGRAS exhibited a specific expression pattern under salt stress conditions.

Gene editing of ZmGA20ox3 improves plant architecture and drought tolerance in maize

KEY MESSAGE

Editing ZmGA20ox3 can achieve the effect similar to applying Cycocel, which can reduce maize plant height and enhance stress resistance. Drought stress, a major plant abiotic stress, is capable of suppressing crop yield performance severely. However, the trade-off between crop drought tolerance and yield performance turns out to be significantly challenging in drought-resistant crop breeding. Several phytohormones [e.g., gibberellin (GA)] have been reported to play a certain role in plant drought response, which also take on critical significance in plant growth and development. In this study, the loss-of-function mutations of GA biosynthesis enzyme ZmGA20ox3 were produced using the CRISPR-Cas9 system in maize. As indicated by the result of 2-year field trials, the above-mentioned mutants displayed semi-dwarfing phenotype with the decrease of GA1, and almost no yield loss was generated compared with wild-type (WT) plants. Interestingly, as revealed by the transcriptome analysis, differential expressed genes (DEGs) were notably enriched in abiotic stress progresses, and biochemical tests indicated the significantly increased ABA, JA, and DIMBOA levels in mutants, suggesting that ZmGA20ox3 may take on vital significance in stress response in maize. The in-depth analysis suggested that the loss function of ZmGA20ox3 can enhance drought tolerance in maize seedling, reduce Anthesis-Silking Interval (ASI) delay while decreasing the yield loss significantly in the field under drought conditions. The results of this study supported that regulating ZmGA20ox3 can improve plant height while enhancing drought resistance in maize, thus serving as a novel method for drought-resistant genetic improvement in maize.

The Roles of Mepiquate Chloride and Melatonin in the Morpho-Physiological Activity of Cotton under Abiotic Stress

Cotton growth and yield are severely affected by abiotic stress worldwide. Mepiquate chloride (MC) and melatonin (MT) enhance crop growth and yield by reducing the negative effects of abiotic stress on various crops. Numerous studies have shown the pivotal role of MC and MT in regulating agricultural growth and yield. Nevertheless, an in-depth review of the prominent performance of these two hormones in controlling plant morpho-physiological activity and yield in cotton under abiotic stress still needs to be documented. This review highlights the effects of MC and MT on cotton morpho-physiological and biochemical activities; their biosynthetic, signaling, and transduction pathways; and yield under abiotic stress. Furthermore, we also describe some genes whose expressions are affected by these hormones when cotton plants are exposed to abiotic stress. The present review demonstrates that MC and MT alleviate the negative effects of abiotic stress in cotton and increase yield by improving its morpho-physiological and biochemical activities, such as cell enlargement; net photosynthesis activity; cytokinin contents; and the expression of antioxidant enzymes such as catalase, peroxidase, and superoxide dismutase. MT delays the expression of NCED1 and NCED2 genes involved in leaf senescence by decreasing the expression of ABA-biosynthesis genes and increasing the expression of the GhYUC5, GhGA3ox2, and GhIPT2 genes involved in indole-3-acetic acid, gibberellin, and cytokinin biosynthesis. Likewise, MC promotes lateral root formation by activating GA20x genes involved in gibberellin catabolism. Overall, MC and MT improve cotton's physiological activity and antioxidant capacity and, as a result, improve the ability of the plant to resist abiotic stress. The main purpose of this review is to present an in-depth analysis of the performance of MC and MT under abiotic stress, which might help to better understand how these two hormones regulate cotton growth and productivity.

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.

Phosphorylation Promotes DELLA Activity by Enhancing Its Binding to Histone H2A at Target Chromatin in Arabidopsis

DELLA proteins are conserved master growth regulators that play a central role in controlling plant development in response to internal and environmental cues. DELLAs function as transcription regulators, which are recruited to target promoters by binding to transcription factors (TFs) and histone H2A via its GRAS domain. Recent studies showed that DELLA stability is regulated post-translationally via two mechanisms, phytohormone gibberellin-induced polyubiquitination for its rapid degradation, and Small Ubiquitin-like Modifier (SUMO)- conjugation to alter its accumulation. Moreover, DELLA activity is dynamically modulated by two distinct glycosylations: DELLA-TF interactions are enhanced by O -fucosylation, but inhibited by O -linked N -acetylglucosamine ( O -GlcNAc) modification. However, the role of DELLA phosphorylation remains unclear. Here, we identified phosphorylation sites in REPRESSOR OF ga1-3 (RGA, an AtDELLA) purified from Arabidopsis by tandem mass spectrometry analysis, and showed that phosphorylation of the RGA LKS-peptide in the poly- S/T region enhances RGA-H2A interaction and RGA association with target promoters. Interestingly, phosphorylation does not affect RGA-TF interactions. Our study has uncovered that phosphorylation is a new regulatory mechanism of DELLA activity.

Interaction of VvDELLA2 and VvCEB1 Mediates Expression of Expansion-Related Gene during GA-Induced Enlargement of Grape Fruit

Exogenous gibberellin treatment can promote early growth of grape fruit, but the underlying regulatory mechanisms are not well understood. Here, we show that VvDELLA2 directly regulates the activity of the VvCEB1 transcription factor, a key regulator in the control of cell expansion in grape fruit. Our results show that VvCEB1 binds directly to the promoters of cell expansion-related genes in grape fruit and acts as a transcriptional activator, while VvDELLA2 blocks VvCEB1 function by binding to its activating structural domain. The exogenous gibberellin treatment relieved this inhibition by promoting the degradation of VvDELLA2 protein, thus, allowing VvCEB1 to transcriptionally activate the expression of cell expansion-related genes. In conclusion, we conclude that exogenous GA3 treatment regulates early fruit expansion by affecting the VvDELLA-VvCEB1 interaction in grape fruit development.

High-resolution genetic linkage map and height-related QTLs in an oil palm (Elaeis guineensis) family planted across multiple sites

A refined SNP array containing 92,459 probes was developed and applied for chromosome scanning, construction of a high-density genetic linkage map and QTL analysis in a selfed Nigerian oil palm family (T128). Genotyping of the T128 mapping family generated 76,447 good quality SNPs for detailed scanning of aberration and homozygosity in the individual pseudo-chromosomes. Of them, 25,364 polymorphic SNPs were used for linkage analysis resulting in an 84.4% mapping rate. A total of 21,413 SNPs were mapped into 16 linkage groups (LGs), covering a total map length of 1364.5 cM. This genetic map is 16X denser than the previous version used to establish pseudo-chromosomes of the oil palm reference genome published in 2013. The QTLs associated with height, height increment and rachis length were identified in LGs TT05, 06, 08, 15 and 16. The present QTLs as well as those published previously were tagged to the reference genome to determine their chromosomal locations. Almost all the QTLs identified in this study were either close to or co-located with those reported in other populations. Determining the QTL position on chromosomes was also helpful in mining for the underlying candidate genes. In total, 55 putative genes and transcription factors involved in the biosynthesis, conjugation and signalling of the major phytohormones, especially for gibberellins and cell wall morphogenesis were found to be present in the identified genomic QTL regions, and their potential roles in plant dwarfism are discussed.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01360-2.

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.

Primary and Secondary Metabolites in Lotus japonicus

Lotus japonicus is a leguminous model plant used to gain insight into plant physiology, stress response, and especially symbiotic plant-microbe interactions, such as root nodule symbiosis or arbuscular mycorrhiza. Responses to changing environmental conditions, stress, microbes, or insect pests are generally accompanied by changes in primary and secondary metabolism to account for physiological needs or to produce defensive or signaling compounds. Here we provide an overview of the primary and secondary metabolites identified in L. japonicus to date. Identification of the metabolites is mainly based on mass spectral tags (MSTs) obtained by gas chromatography linked with tandem mass spectrometry (GC-MS/MS) or liquid chromatography-MS/MS (LC-MS/MS). These MSTs contain retention index and mass spectral information, which are compared to databases with MSTs of authentic standards. More than 600 metabolites are grouped into compound classes such as polyphenols, carbohydrates, organic acids and phosphates, lipids, amino acids, nitrogenous compounds, phytohormones, and additional defense compounds. Their physiological effects are briefly discussed, and the detection methods are explained. This review of the exisiting literature on L. japonicus metabolites provides a valuable basis for future metabolomics studies.

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.

Comparative transcriptome profiling reveals the multiple levels of crosstalk in phytohormone networks in Brassica napus

Plant hormones are the intrinsic factors that control plant development. The integration of different phytohormone pathways in a complex network of synergistic, antagonistic and additive interactions has been elucidated in model plants. However, the systemic level of transcriptional responses to hormone crosstalk in Brassica napus is largely unknown. Here, we present an in-depth temporal-resolution study of the transcriptomes of the seven hormones in B. napus seedlings. Differentially expressed gene analysis revealed few common target genes that co-regulated (up- and down-regulated) by seven hormones; instead, different hormones appear to regulate distinct members of protein families. We then constructed the regulatory networks between the seven hormones side by side, which allowed us to identify key genes and transcription factors that regulate the hormone crosstalk in B. napus. Using this dataset, we uncovered a novel crosstalk between gibberellin and cytokinin in which cytokinin homeostasis was mediated by RGA-related CKXs expression. Moreover, the modulation of gibberellin metabolism by the identified key transcription factors was confirmed in B. napus. Furthermore, all data were available online from http://yanglab.hzau.edu.cn/BnTIR/hormone. Our study reveals an integrated hormone crosstalk network in Brassica napus, which also provides a versatile resource for future hormone studies in plant species.

OsNF-YA3 regulates plant growth and osmotic stress tolerance by interacting with SLR1 and SAPK9 in rice

The antagonism between gibberellin (GA) and abscisic acid (ABA) signaling pathways is vital to balance plant growth and stress response. Nevertheless, the mechanism by which plants determine the balance remains to be elucidated. Here, we report that rice NUCLEAR FACTOR-Y A3 (OsNF-YA3) modulates GA- and ABA-mediated balance between plant growth and osmotic stress tolerance. OsNF-YA3 loss-of-function mutants exhibit stunted growth, compromised GA biosynthetic gene expression, and decreased GA levels, while its overexpression lines have promoted growth and enhanced GA content. Chromatin immunoprecipitation-quantitative polymerase chain reaction analysis and transient transcriptional regulation assays demonstrate that OsNF-YA3 activates GA biosynthetic gene OsGA20ox1 expression. Furthermore, the DELLA protein SLENDER RICE1 (SLR1) physically interacts with OsNF-YA3 and thus inhibits its transcriptional activity. On the other side, OsNF-YA3 negatively regulates plant osmotic stress tolerance by repressing ABA response. OsNF-YA3 reduces ABA levels by transcriptionally regulating ABA catabolic genes OsABA8ox1 and OsABA8ox3 by binding to their promoters. Furthermore, OSMOTIC STRESS/ABA-ACTIVATED PROTEIN KINASE 9 (SAPK9), the positive component in ABA signaling, interacts with OsNF-YA3 and mediates OsNF-YA3 phosphorylation, resulting in its degradation in plants. Collectively, our findings establish OsNF-YA3 as an important transcription factor that positively modulates GA-regulated plant growth and negatively controls ABA-mediated water-deficit and salt tolerance. These findings shed light on the molecular mechanism underlying the balance between the growth and stress response of the plant.

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.

SCL14 Inhibits the Functions of the NAC043-MYB61 Signaling Cascade to Reduce the Lignin Content in Autotetraploid Populus hopeiensis

Whole-genome duplication often results in a reduction in the lignin content in autopolyploid plants compared with their diploid counterparts. However, the regulatory mechanism underlying variation in the lignin content in autopolyploid plants remains unclear. Here, we characterize the molecular regulatory mechanism underlying variation in the lignin content after the doubling of homologous chromosomes in Populus hopeiensis. The results showed that the lignin content of autotetraploid stems was significantly lower than that of its isogenic diploid progenitor throughout development. Thirty-six differentially expressed genes involved in lignin biosynthesis were identified and characterized by RNA sequencing analysis. The expression of lignin monomer synthase genes, such as PAL, COMT, HCT, and POD, was significantly down-regulated in tetraploids compared with diploids. Moreover, 32 transcription factors, including MYB61, NAC043, and SCL14, were found to be involved in the regulatory network of lignin biosynthesis through weighted gene co-expression network analysis. We inferred that SCL14, a key repressor encoding the DELLA protein GAI in the gibberellin (GA) signaling pathway, might inhibit the NAC043-MYB61 signaling functions cascade in lignin biosynthesis, which results in a reduction in the lignin content. Our findings reveal a conserved mechanism in which GA regulates lignin synthesis after whole-genome duplication; these results have implications for manipulating lignin production.

Harnessing hormone gibberellin knowledge for plant height regulation

Harnessing hormone GA knowledge is a potential means to develop plant height ideotypes. Plant height holds significance for natural beauty and agricultural revolution. The increased grain productivity during the Green Revolution of the 1960s is partly attributed to the reshaping of plant stature, which is conferred by changes in phytohormone gibberellin (GA) metabolism or signaling. GA fine-tunes multiple aspects of biological events and plays a pivotal role in plant height determinant. Harnessing hormone GA knowledge is a potential means to develop ideal plant height to meet the future demand. Here, we present an overview of characterized GA pathway genes for plant height regulation. Novel alleles of Green Revolution genes sd1 and Rht are specially delineated. Through interactome analysis, we uncover GA20ox and GA3ox family members as central hub modulators of GA pathway. Empowered by GA knowledge, we suggest ways towards design breeding of plant height ideotypes through harnessing the alterations of GA cascade. We highlight the utility of genome editing to generate weak alleles to circumvent side effects of GA pathway perturbation.

The genome of Aechmea fasciata provides insights into the evolution of tank epiphytic habits and ethylene-induced flowering

Aechmea fasciata is one of the most popular bromeliads and bears a water-impounding tank with a vase-like rosette. The tank habit is a key innovation that has promoted diversity among bromeliads. To reveal the genomic basis of tank habit formation and ethylene-induced flowering, we sequenced the genome of A. fasciata and assembled 352 Mb of sequences into 24 chromosomes. Comparative genomic analysis showed that the chromosomes experienced at least two fissions and two fusions from the ancestral genome of A. fasciata and Ananas comosus. The gibberellin receptor gene GID1C-like was duplicated by a segmental duplication event. This duplication may affect GA signalling and promote rosette expansion, which may permit water-impounding tank formation. During ethylene-induced flowering, AfFTL2 expression is induced and targets the EIN3 binding site ‘ATGTAC’ by AfEIL1-like. The data provided here will serve as an important resource for studying the evolution and mechanisms underlying flowering time regulation in bromeliads.

The genome of <i>Aechmea fasciata <i > , a common house plant and popular bromelioid provides insights into its evolution.

PavGA2ox-2L inhibits the plant growth and development interacting with PavDWARF in sweet cherry (Prunus avium L.)

Dwarf dense planting is helpful to improve the yield and quality of sweet cherry, which has enormous market demand. GA2oxs (GA oxidases) affect plant height, dormancy release, flower development, and seed germination by participating in the metabolic regulation and signal transduction of GA (Gibberellin). However, the research on GA2ox in sweet cherry is little and worthy of further investigation. Therefore, we identified the PavGA2ox-2L gene from sweet cherry, close to PynGA2ox-2 from Prunus yedoensis var. Nudiflora. The phylogenetic analysis indicated conserved functions with these evolutionarily closer GA2ox subfamily genes. Subcellular localization forecast analysis indicated that PavGA2ox-2L was localized in the nucleus or cytoplasm. The expression levels of PavGA2ox-2L were higher in winter, indicating that PavGA2ox-2L promoted maintained flower bud dormancy. The expression levels of PavGA2ox-2L were significantly increased after GA₄₊₇ treatment while decreased after GR24 (a synthetic analog of SLs (Strigolactones)) or TIS108 (a triazole-type SL-biosynthesis inhibitor) treatments. Over-expression of PavGA2ox-2L resulted in decreased plant height, delayed flowering time, and low seed germination rate in Arabidopsis thaliana. Furthermore, the interaction between PavGA2ox-2L and PavDWARF was verified by Y2H and BiFC assays. In the current investigation, PavGA2ox-2L functions as a GA metabolic gene that promotes dwarf dense planting, delays flowering time, and inhibits seed germination. In addition, it also participates in regulating plant growth and development through the interaction with the critical negative regulator PavDWARF of Gibberellin. These results will help us better explore the molecular mechanism of GA2ox-mediated dwarf and late-maturing varieties for fruit trees.

Multiple indeterminate domain (IDD)-DELLA1 complexes participate in gibberellin feedback regulation in peach

Peach encodes 14 INDETERMINATE DOMAIN (IDD) transcription factors. PpIDD4, -12 and -13 mediated PpDELLA1 binding to the PpGA20ox1 promoter. Each of these three PpIDD-DELLA1 complexes activated transcription of PpGA20ox1. PpTPR1 and -4 interrupted the interaction of PpIDDs with PpDELLA1. The plant growth regulator gibberellin (GA) plays an important role in the rapid growth of annual shoots in peach. Our previous study showed that the peach cultivar 'FenHuaShouXingTao' (FHSXT), a gibberellic acid receptor (gid1) mutant, accumulates active GAs in annual shoot tips. This mutant enhances GA feedback regulation in peach. The results of this study suggested that the PpIDD-DELLA1 complex is the underlying mechanism of GA feedback regulation in peach. Fourteen IDD genes were identified in peach, and three PpIDDs (PpIDD4, -12 and -13, all from group IV) interacted with PpDELLA1, an important component in GA signaling pathway. Truncation, segmentation and site mutation of the promoter of PpGA20ox1 (a GA biosynthesis gene) showed that all three PpIDD proteins recognized the core motif TTGTC. PpIDD4 and -13 mainly bind to site 3, while PpIDD12 binds to site 5 of the PpGA20ox1 promoter. All three PpIDD-DELLA1 complexes activated the PpGA20ox1 promoter-LUC fusion. These data suggested that PpIDDs bridge PpDELLA1 and the promoter of PpGA20ox1, which then activated the transcription of PpGA20ox1. In addition, PpTPR1 and -4 disrupted the interaction of PpIDDs with PpDELLA1. Our research will be helpful for understanding and possibly modifying the regulation of annual shoot growth and GA biosynthesis.

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.

The O2-ZmGRAS11 transcriptional regulatory network orchestrates the coordination of endosperm cell expansion and grain filling in maize

Maize (Zea mays) endosperm filling is coordinated with cell expansion to enlarge the grain size, but the mechanism coupling the two processes is poorly understood. Starchy endosperm cells basically contain no visible vacuoles for cell expansion. During grain filling, efficient synthesis of storage compounds leads to reduced cytoplasm and thus lowered cell turgor pressure. Although bioactive gibberellins (GAs) are essential for cell expansion, they accumulate at a low level at this stage. In this study, we identified an endosperm-specific GRAS domain-containing protein (ZmGRAS11) that lacks the DELLA domain and promotes cell expansion in the filling endosperm. The zmgras11 loss-of-function mutants showed normal grain filling but delayed cell expansion, thereby resulting in reduced kernel size and weight. Overexpression of ZmGRAS11 led to larger endosperm cells and therefore increased kernel size and weight. Consistent with this, ZmGRAS11 positively regulates the expression of ZmEXPB12, which is essential for cell expansion, at the endosperm filling stage. Moreover, we found that Opaque2 (O2), a central transcription factor that regulates endosperm filling, could directly bind to the promoter of ZmGRAS11 and activate its expression. Taken together, these results suggest that endosperm cell expansion is coupled with endosperm filling, which is orchestrated by the O2-ZmGRAS11-centered transcriptional regulatory network. Our findings also provide potential targets for maize yield improvement by increasing the storage capacity of endosperm cells.

The GA-DELLA-OsMS188 module controls male reproductive development in rice

Pollen protects male sperm and allows flowering plants to adapt to diverse terrestrial environments, thereby leading to the rapid expansion of plants into new regions. The process of anther/pollen development is coordinately regulated by internal and external factors including hormones. Currently, the molecular mechanisms underlying gibberellin (GA)-mediated male reproductive development in plants remain unknown. We show here that rice DELLA/SLR1, which encodes the central negative regulator of GA signaling, is essential for rice anther development. The slr1-5 mutant exhibits premature programmed cell death of the tapetum, lacks Ubisch bodies, and has no exine and no mature pollen. SLR1 is mainly expressed in tapetal cells and tetrads, and is required for the appropriate expression of genes encoding key factors of pollen development, which are suggested to be OsMS188-targeted genes. OsMS188 is the main component in the essential genetic program of tapetum and pollen development. Further, we demonstrate that SLR1 interacts with OsMS188 to cooperatively activate the expression of the sporopollenin biosynthesis and transport-related genes CYP703A3, DPW, ABCG15 and PKS1 for rapid formation of pollen walls. Overall, the results of this study suggest that the GA hormonal signal is integrated into the anther genetic program and regulates rice anther development through the GA-DELLA-OsMS188 module.

A genome‐wide analysis suggests pleiotropic effects of Green Revolution genes on shade avoidance in wheat

A classic example of phenotypic plasticity in plants is the suit of phenotypic responses induced by a change in the ratio of red to far-red light (R∶FR) as a result of shading, also known as the shade avoidance syndrome (SAS). While the adaptive consequences of this syndrome have been extensively discussed in natural ecosystems, how SAS varies within crop populations and how SAS evolved during crop domestication and breeding remain poorly known. In this study, we grew a panel of 180 durum wheat (Triticum turgidum ssp. durum) genotypes spanning diversity from wild, early domesticated, and elite genetic compartments under two light treatments: low R:FR light (shaded treatment) and high R:FR light (unshaded treatment). We first quantified the genetic variability of SAS, here measured as a change in plant height at the seedling stage. We then dissected the genetic basis of this variation through genome-wide association mapping. Genotypes grown in shaded conditions were taller than those grown under unshaded conditions. Interaction between light quality and genotype did not affect plant height. We found six QTLs affecting plant height. Three significantly interacted with light quality among which the well-known Rht1 gene introgressed in elite germplasm during the Green Revolution. Interestingly at three loci, short genotypes systematically expressed reduced SAS, suggesting a positive genetic correlation between plant height and plant height plasticity. Overall, our study sheds light on the evolutionary history of crops and illustrates the relevance of genetic approaches to tackle agricultural challenges.

Modification of tomato breeding traits and plant hormone signaling by target-AID, the genome-editing system inducing efficient nucleotide substitution

Target activation-induced cytidine deaminase (Target-AID), a novel CRISPR/Cas9-based genome-editing tool, confers the base-editing capability on the Cas9 genome-editing system. It involves the fusion of cytidine deaminase (CDA), which catalyzes cytidine (C) to uridine (U) substitutions, to the mutated nickase-type nCas9 or deactivated-type dCas9. To confirm and extend the applicability of the Target-AID genome-editing system in tomatoes (Solanum lycopersicum L.), we transformed the model tomato cultivar "Micro-Tom" and commercial tomato cultivars using this system by targeting SlDELLA, which encodes a negative regulator of the plant phytohormone gibberellic acid (GA) signaling pathway. We confirmed that the nucleotide substitutions were induced by the Target-AID system, and we isolated mutants showing high GA sensitivity in both "Micro-Tom" and the commercial cultivars. Moreover, by successfully applying this system to ETHYLENE RECEPTOR 1 (SlETR1) with single sgRNA targeting, double sgRNA targeting, as well as dual-targeting of both SlETR1 and SlETR2 with a single sgRNA, we demonstrated that the Target-AID genome-editing system is a promising tool for molecular breeding in tomato crops. This study highlights an important aspect of the scientific and agricultural potential of the combinatorial use of the Target-AID and other base-editing systems.

Manipulation of Barley Development and Flowering Time by Exogenous Application of Plant Growth Regulators

Matching flowering time to the optimal flowering period in Mediterranean cropping zones is pivotal to maximize yield. Aside from variety selection and sowing date, growers have limited options to alter development in season. Plant hormones and growth regulators are used in perennial horticultural systems to manipulate development and floral initiation. In this study, a range of plant hormonal products were tested to analyze their effects on barley (Hordeum vulgare L) development by exogenous spray applications. Plants were grown in controlled conditions under long and short photoperiods with different vernalization treatments. The gibberellin (GA) products demonstrated the greatest potential for altering development. The GA inhibitor trinexapac-ethyl was able to delay the time to flowering in genetically divergent barley cultivars by up to 200 degree days under controlled conditions. A similar delay in flowering could be achieved via application at both early (GS13) and late (GS33) stages, with higher rates delaying flowering further. Notably, trinexapac-ethyl was able to extend the duration of pre-anthesis phases of development. By contrast, GA3 was unable to accelerate development under extreme short (8 h) or long (16 h) day lengths. There was also little evidence that GA3 could reproducibly accelerate development under intermediate 10-12 h day lengths. In addition, sprays of the cytokinin 6-benzyladenine (6-BA) were unable to reduce the vernalization requirement of the winter genotype Urambie. The present study provides baseline data for plant growth regulator treatments that delay cereal development. These treatments might be extended in field studies to align flowering of early sown crops to the optimal flowering period.

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

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

Nitrate signaling promotes plant growth by upregulating gibberellin biosynthesis and destabilization of DELLA proteins

Nitrate, one of the main nitrogen (N) sources for crops, acts as a nutrient and key signaling molecule coordinating gene expression, metabolism, and various growth processes throughout the plant life cycle. It is widely accepted that nitrate-triggered developmental programs cooperate with hormone synthesis and transport to finely adapt plant architecture to N availability. Here, we report that nitrate, acting through its signaling pathway, promotes growth in Arabidopsis and wheat, in part by modulating the accumulation of gibberellin (GA)-regulated DELLA growth repressors. We show that nitrate reduces the abundance of DELLAs by increasing GA contents through activation of GA metabolism gene expression. Consistently, the growth restraint conferred by nitrate deficiency is partially rescued in global-DELLA mutant that lacks all DELLAs. At the cellular level, we show that nitrate enhances both cell proliferation and elongation in a DELLA-dependent and -independent manner, respectively. Our findings establish a connection between nitrate and GA signaling pathways that allow plants to adapt their growth to nitrate availability.

Gibberellins orchestrate panicle architecture mediated by DELLA-KNOX signalling in rice

Panicle architecture is a key determinant of grain yield in cereals, but the mechanisms governing panicle morphogenesis and organ development remain elusive. Here, we have identified a quantitative trait locus (qPA1) associated with panicle architecture using chromosome segment substitution lines from parents Nipponbare and 9311. The panicle length, branch number and grain number of Nipponbare were significantly higher than CSSL-9. Through map-based cloning and complementation tests, we confirmed that qPA1 was identical to SD1 (Semi Dwarf1), which encodes a gibberellin 20-oxidase enzyme participating in gibberellic acid (GA) biosynthesis. Transcript analysis revealed that SD1 was widely expressed during early panicle development. Analysis of sd1/osga20ox2 and gnp1/ osga20ox1 single and double mutants revealed that the two paralogous enzymes have non-redundant functions during panicle development, likely due to differences in spatiotemporal expression; GNP1 expression under control of the SD1 promoter could rescue the sd1 phenotype. The DELLA protein SLR1, a component of the GA signalling pathway, accumulated more highly in sd1 plants. We have demonstrated that SLR1 physically interacts with the meristem identity class I KNOTTED1-LIKE HOMEOBOX (KNOX) protein OSH1 to repress OSH1-mediated activation of downstream genes related to panicle development, providing a mechanistic link between gibberellin and panicle architecture morphogenesis.

DELLA proteins BnaA6.RGA and BnaC7.RGA negatively regulate fatty acid biosynthesis by interacting with BnaLEC1s in Brassica napus

Seed oil content (SOC) and fatty acid (FA) composition determine the quality and economic value of rapeseed (Brassica napus). Little is known about the role of gibberellic acid (GA) in regulating FA biosynthesis in B. napus. Here, we discovered that four BnaRGAs (B. napus REPRESSOR OF GA), encoding negative regulators of GA signalling, were suppressed during seed development. Compared to the wild type, SOC was reduced in gain-of-function mutants bnaa6.rga-D and ds-3, which also showed reduced oleic acid and increased linoleic acid contents. By contrast, the loss-of-function quadruple mutant bnarga displayed higher SOC during early seed development than the wild type, with increased oleic acid and reduced linoleic acid contents. Notably, only BnaA6.RGA and BnaC7.RGA physically interacted with two BnaLEC1s, which function as essential transcription factors in FA biosynthesis. The FA composition did not significantly differ between bnarga bnalec1 sextuple mutants and bnalec1, suggesting that BnaLEC1s are epistatic to BnaRGAs in the regulation of FA composition. Furthermore, BnaLEC1-induced activation of BnaABI3 expression was repressed by BnaA6.RGA, indicating that GA triggers the degradation of BnaRGAs to relieve their repression of BnaLEC1s, thus promoting the transcription of downstream genes to facilitate oil biosynthesis. Therefore, we uncovered a developmental stage-specific role of GA in regulating oil biosynthesis via the GA-BnaRGA-BnaLEC1 signalling cascade, providing a novel mechanistic understanding of how phytohormones regulate FA biosynthesis in seeds. BnaRGAs represent promising targets for oil crop improvement.

New insights into gibberellin signaling in regulating plant growth-metabolic coordination

The Green Revolution of the 1960s boosted cereal crop yields in part through widespread adoption of semi-dwarf plant varieties, many of which were later found to have mutations in either gibberellins (GAs) homeostasis or DELLA proteins. GA is essential for plant growth and developmental regulation and plays an important role in improving crop plant architecture for enhanced grain yield under high nitrogen conditions. A complex regulatory network governs the spatially and temporally controlled genes expression through integrative GA signaling in response to multiple endogenous and environmental cues. In this review, we summarize current advances in understanding the molecular mechanisms of DELLA-dependent and DELLA-independent GA signaling pathways and their contributions to plant developmental and metabolic adaptations to changes in nitrogen availability. The progress in molecular understanding of the plant growth-metabolic coordination will facilitate breeding strategies for future sustainable agriculture and a new Green Revolution.

Will Plant Genome Editing Play a Decisive Role in "Quantum-Leap" Improvements in Crop Yield to Feed an Increasing Global Human Population?

Growing scientific evidence demonstrates unprecedented planetary-scale human impacts on the Earth's system with a predicted threat to the existence of the terrestrial biosphere due to population increase, resource depletion, and pollution. Food systems account for 21-34% of global carbon dioxide (CO2) emissions. Over the past half-century, water and land-use changes have significantly impacted ecosystems, biogeochemical cycles, biodiversity, and climate. At the same time, food production is falling behind consumption, and global grain reserves are shrinking. Some predictions suggest that crop yields must approximately double by 2050 to adequately feed an increasing global population without a large expansion of crop area. To achieve this, "quantum-leap" improvements in crop cultivar productivity are needed within very narrow planetary boundaries of permissible environmental perturbations. Strategies for such a "quantum-leap" include mutation breeding and genetic engineering of known crop genome sequences. Synthetic biology makes it possible to synthesize DNA fragments of any desired sequence, and modern bioinformatics tools may hopefully provide an efficient way to identify targets for directed modification of selected genes responsible for known important agronomic traits. CRISPR/Cas9 is a new technology for incorporating seamless directed modifications into genomes; it is being widely investigated for its potential to enhance the efficiency of crop production. We consider the optimism associated with the new genetic technologies in terms of the complexity of most agronomic traits, especially crop yield potential (Yp) limits. We also discuss the possible directions of overcoming these limits and alternative ways of providing humanity with food without transgressing planetary boundaries. In conclusion, we support the long-debated idea that new technologies are unlikely to provide a rapidly growing population with significantly increased crop yield. Instead, we suggest that delicately balanced humane measures to limit its growth and the amount of food consumed per capita are highly desirable for the foreseeable future.

MiR396-GRF module associates with switchgrass biomass yield and feedstock quality

Improving plant biomass yield and/or feedstock quality for highly efficient lignocellulose conversion has been the main research focus in genetic modification of switchgrass (Panicum virgatum L.), a dedicated model plant for biofuel production. Here, we proved that overexpression of miR396 (OE-miR396) leads to reduced plant height and lignin content mainly by reducing G-lignin monomer content. We identified nineteen PvGRFs in switchgrass and proved thirteen of them were cleaved by miR396. MiR396-targeted PvGRF1, PvGRF9 and PvGRF3 showed significantly higher expression in stem. By separately overexpressing rPvGRF1, 3 and 9, in which synonymous mutations abolished the miR396 target sites, and suppression of PvGRF1/3/9 activity via PvGRF1/3/9-SRDX overexpression in switchgrass, we confirmed PvGRF1 and PvGRF9 played positive roles in improving plant height and G-lignin content. Overexpression of PvGRF9 was sufficient to complement the defective phenotype of OE-miR396 plants. MiR396-PvGRF9 modulates these traits partly by interfering GA and auxin biosynthesis and signalling transduction and cell wall lignin, glucose and xylan biosynthesis pathways. Moreover, by enzymatic hydrolysis analyses, we found that overexpression of rPvGRF9 significantly enhanced per plant sugar yield. Our results suggest that PvGRF9 can be utilized as a candidate molecular tool in modifying plant biomass yield and feedstock quality.

Barley plants carrying the altered function Sln1d allele display modified responses to low phosphorus supply: implications for phosphorus utilisation efficiency

The module GA-GID1-DELLA (Gibberellin-Gibberellin Receptor-DELLA proteins) provides a point for the integration of signals potentially relevant in determining nutrient utilisation and acquisition efficiencies. In this study, we explored the role of components of this module during the acclimation of barley plants (Hordeum vulgare L.) to different phosphorus (P) supplies by using two related genotypes, harbouring either the WT or the Sln1d alleles of the DELLA-coding gene Sln1. Dwarf Sln1d plants exhibited reduced shoot P utilisation efficiency (PUtE) and better performance at low levels of P supply. The superior PUtE displayed by WT plants disappeared when corrected by internal P concentration, indicating that multiple analyses are necessary to fully understand the meaning of PUtE estimates. Over a wide range of external supplies of P, Sln1d plants displayed enhanced P concentration, which was associated with low relative growth rate, high biomass partitioning to roots and high P-uptake-rate, thus suggesting that the effect of the Sln1d allele on P dynamics is not simply a consequence of slow growth habit. An enhanced P concentration was also found in a mutant with defective GAs-synthesis. Our results suggest that components of the GA-GID1-DELLAs module contribute to set the acclimation response of barley plants to low P supply through both P-dynamics dependent and P-dynamics independent mechanisms.

Genome Identification and Expression Analysis of GRAS Family Related to Development, Hormone and Pathogen Stress in Brachypodium distachyon

GRAS transcription factors are widely present in the plant kingdom and play important roles in regulating multiple plant physiological processes. Brachypodium distachyon is a model for grasses for researching plant-pathogen interactions. However, little is known about the BdGRAS family genes involved in plant response to biotic stress. In this study, we identified 63 genes of the GRAS family in B. distachyon. The phylogenetic analysis showed that BdGRAS genes were divided into ten subfamilies and unevenly distributed on five chromosomes. qRT-PCR results showed that the BdGRAS family genes were involved in the growth and development of B. distachyon. Moreover, the expression of the HAM subfamily genes of BdGRAS changed during the interaction between B. distachyon and Magnaporthe oryzae. Interestingly, BdGRAS31 in the HAM subfamily was regulated by miR171 after inoculation with M. oryzae. These results provide insight into the potential functions of the BdGRAS family in disease resistance.

Interaction between the MtDELLA-MtGAF1 Complex and MtARF3 Mediates Transcriptional Control of MtGA3ox1 to Elaborate Leaf Margin Formation in Medicago truncatula

The molecular mechanisms underlying the diversity of leaf shapes have been of great interest to researchers. Leaf shape depends on the pattern of serrations and the degree of indentation of leaf margins. Multiple transcription factors and hormone signaling pathways are involved in this process. In this study, we characterized the developmental roles of SMALL AND SERRATED LEAF (SSL) by analyzing a recessive mutant in the model legume Medicago truncatula. An ortholog of Arabidopsis thaliana GA3-oxidase 1 (GA3ox1), MtGA3ox1/SSL, is required for GA biosynthesis. Loss of function in MtGA3ox1 results in the small plant and lateral organs. The prominent phenotype of the mtga3ox1 mutant is a more pronounced leaf margin, indicating the critical role of GA level in leaf margin formation. Moreover, 35S:MtDELLA2ΔDELLA and 35S:MtARF3 transgenic plants display leaves with a deeply wavy margin, which resembles those of mtga3ox1. Further investigations show that MtGA3ox1 is under the control of MtDELLA1/2/3-MtGAF1 complex-dependent feedback regulation. Further, MtARF3 behaves as a competitive inhibitor of MtDELLA2/3-MtGAF1 complexes to repress the expression of MtGA3ox1 indirectly. These findings suggest that GA feedback regulatory circuits play a fundamental role in leaf margin formation, in which the posttranslational interaction between transcription factors functions as an additional feature.

QTL Analysis of Five Morpho-Physiological Traits in Bread Wheat Using Two Mapping Populations Derived from Common Parents

Traits such as plant height (PH), juvenile growth habit (GH), heading date (HD), and tiller number are important for both increasing yield potential and improving crop adaptation to climate change. In the present study, these traits were investigated by using the same bi-parental population at early (F₂ and F₂-derived F₃ families) and late (F₆ and F₇, recombinant inbred lines, RILs) generations to detect quantitative trait loci (QTLs) and search for candidate genes. A total of 176 and 178 lines were genotyped by the wheat Illumina 25K Infinium SNP array. The two genetic maps spanned 2486.97 cM and 3732.84 cM in length, for the F₂ and RILs, respectively. QTLs explaining the highest phenotypic variation were found on chromosomes 2B, 2D, 5A, and 7D for HD and GH, whereas those for PH were found on chromosomes 4B and 4D. Several QTL detected in the early generations (i.e., PH and tiller number) were not detected in the late generations as they were due to dominance effects. Some of the identified QTLs co-mapped to well-known adaptive genes (i.e., Ppd-1, Vrn-1, and Rht-1). Other putative candidate genes were identified for each trait, of which PINE1 and PIF4 may be considered new for GH and TTN in wheat. The use of a large F₂ mapping population combined with NGS-based genotyping techniques could improve map resolution and allow closer QTL tagging.

N-terminal truncated RHT-1 proteins generated by translational reinitiation cause semi-dwarfing of wheat Green Revolution alleles

The unprecedented wheat yield increases during the Green Revolution were achieved through the introduction of the Reduced height (Rht)-B1b and Rht-D1b semi-dwarfing alleles. These Rht-1 alleles encode growth-repressing DELLA genes containing a stop codon within their open reading frame that confers gibberellin (GA)-insensitive semi-dwarfism. In this study, we successfully took the hurdle of detecting wild-type RHT-1 proteins in different wheat organs and confirmed their degradation in response to GAs. We further demonstrated that Rht-B1b and Rht-D1b produce N-terminal truncated proteins through translational reinitiation. Expression of these N-terminal truncated proteins in transgenic lines and in Rht-D1c, an allele containing multiple Rht-D1b copies, demonstrated their ability to cause strong dwarfism, resulting from their insensitivity to GA-mediated degradation. N-terminal truncated proteins were detected in spikes and nodes, but not in the aleurone layers. Since Rht-B1b and Rht-D1b alleles cause dwarfism but have wild-type dormancy, this finding suggests that tissue-specific differences in translational reinitiation may explain why the Rht-1 alleles reduce plant height without affecting dormancy. Taken together, our findings not only reveal the molecular mechanism underlying the Green Revolution but also demonstrate that translational reinitiation in the main open reading frame occurs in plants.

Genome resequencing reveals DNA polymorphisms associated with seed size/weight determination in chickpea

Crop productivity in legumes is determined by number and size/weight of seeds. To understand the genetic basis of seed size/weight in chickpea, we performed genome resequencing of 13 small- and 5 large-seeded genotypes using Illumina platform. Single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) differentiating small- and large-seeded genotypes were identified. A total of 17,902 SNPs and 2594 InDels located in promoter and/or coding regions that may contribute to seed size/weight were detected. Of these, 266 SNPs showed significant association with seed size/weight trait. Twenty-three genes including those involved in cell growth/division, encoding transcription factors and located within QTLs associated with seed size/weight harbored SNPs within transcription factor binding motif(s) and/or coding region. The non-synonymous SNPs were found to affect the mutational sensitivity and stability of the encoded proteins. Overall, we provided a high-quality SNP map for large-scale genotyping applications and identified candidate genes that determine seed size/weight in chickpea.

Characterization of the GRAS gene family reveals their contribution to the high adaptability of wheat

GRAS transcription factors play important roles in many processes of plant development as well as abiotic and biotic stress responses. However, little is known about this gene family in bread wheat (Triticum aestivum), one of the most important crops worldwide. The completion of a quality draft genome allows genome-wide detection and evolutionary analysis of the GRAS gene family in wheat. In this study, 188 TaGRAS genes were detected and divided into 12 subfamilies based on phylogenetic analyses: DELLA, DLT, HAM, LISCL, SCL3, SCL4/7, SCR, SHR, PAT1, Os19, Os4 and LAS. Tandem and segmental duplications are the main contributors to the expansion of TaGRAS, which may contribute to the adaptation of wheat to various environmental conditions. A high rate of homoeolog retention during hexaploidization was detected, suggesting the nonredundancy and biological importance of TaGRAS homoeologs. Systematic analyses of TaGRAS indicated the conserved expression pattern and function of the same subfamily during evolution. In addition, we detected five genes belonging to the LISCL subfamily induced by both biotic and abiotic stresses and they may be potential targets for further research through gene editing. Using degradome and ChIP-seq data, we identified the targets of miR171 and histone modifications and further analyzed the contribution of epigenetic modification to the subfunctionalization of TaGRAS. This study laid a foundation for further functional elucidation of TaGRAS genes.

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.

The semi-dwarfing gene Rht-dp from dwarf polish wheat (Triticum polonicum L.) is the "Green Revolution" gene Rht-B1b

Background

The wheat dwarfing gene increases lodging resistance, the grain number per spike and harvest index. Dwarf Polish wheat (Triticum polonicum L., 2n = 4x = 28, AABB, DPW), initially collected from Tulufan, Xinjiang, China, carries a semi-dwarfing gene Rht-dp on chromosome 4BS. However, Rht-dp and its dwarfing mechanism are unknown.

Results

Homologous cloning and mapping revealed that Rht-dp is the ‘Green Revolution’ gene Rht-B1b. A haplotype analysis in 59 tetraploid wheat accessions showed that Rht-B1b was only present in T. polonicum. Transcriptomic analysis of two pairs of near-isogenic lines (NILs) of DPW × Tall Polish wheat (Triticum polonicum L., 2n = 4x = 28, AABB, TPW) revealed 41 differentially expressed genes (DEGs) as potential dwarfism-related genes. Among them, 28 functionally annotated DEGs were classed into five sub-groups: hormone-related signalling transduction genes, transcription factor genes, cell wall structure-related genes, reactive oxygen-related genes, and nitrogen regulation-related genes.

Conclusions

These results indicated that Rht-dp is Rht-B1b, which regulates pathways related to hormones, reactive oxygen species, and nitrogen assimilation to modify the cell wall structure, and then limits cell wall loosening and inhibits cell elongation, thereby causing dwarfism in DPW.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07367-x.

Evolution of DELLA function and signaling in land plants

DELLA proteins are master growth regulators that repress responses to a group of plant growth hormones called gibberellins (GAs). Manipulation of DELLA function and signaling was instrumental in the development of high‐yielding crop varieties that saved millions from starvation during the “Green Revolution.” Despite decades of extensive research, it is still unclear how DELLA function and signaling mechanisms evolved within the land plant lineage. Here, we review current knowledge on DELLA protein function with reference to structure, posttranslational modifications, downstream transcriptional targets, and protein–protein interactions. Furthermore, we discuss older and recent findings regarding the evolution of DELLA signaling within the land plant lineage, with an emphasis on bryophytes, and identify future avenues of research that would enable us to shed more light on the evolution of DELLA signaling. Unraveling how DELLA function and signaling mechanisms have evolved could enable us to engineer better crops in an attempt to contribute to mitigating the effects of global warming and achieving global food security.

DELLA genes first appeared in the common ancestor of land plants and underwent two major duplications during land plant evolution.

DELLAs repress gibberellin responses in vascular plants but their function in nonvascular plants remains elusive.