RID1 sets rice heading date by balancing its binding with SLR1 and SDG722

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.

A Series of Novel Alleles of Ehd2 Modulating Heading and Salt Tolerance in Rice

Rice (Oryza sativa L.) is a staple crop for nearly half of the global population and one of China's most extensively cultivated cereals. Heading date, a critical agronomic trait, determines the regional and seasonal adaptability of rice varieties. In this study, a series of mutants (elh5 to elh12) exhibiting extremely late heading under both long-day (LD) and short-day (SD) conditions were identified from an ethyl methanesulfonate (EMS) mutant library. Using MutMap and map-based cloning, the causative gene was identified as a novel allele of Ehd2/OsID1/RID1/Ghd10. Functional validation through CRISPR/Cas9 knockout and complementation assays confirmed its role in regulating heading. The elh6 mutation was found to cause intron retention due to alternative splicing. Ehd2 encodes a Cys-2/His-2-type zinc finger transcription factor with an IDD domain and transcriptional activity in yeast. Its expression peaks in developing leaves before heading and spikes during reproductive conversion. In elh6 mutants, delayed heading resulted from downregulating the Ehd1-Hd3a pathway genes. Salinity stress significantly hampers rice growth and productivity. Transcriptomic analysis of elh10 and ZH8015 seedlings exposed to salt stress for 24 h identified 5150 differentially expressed genes (DEGs) at the seedling stage, predominantly linked to stress response pathways. Ehd2 was revealed as a modulator of salt tolerance, likely through the regulation of ion transport, enzyme activity, and antioxidant systems. This study establishes Ehd2 as a pivotal factor in promoting heading while negatively regulating salt tolerance in rice.

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.

INDETERMINATE DOMAIN Transcription Factors in Crops: Plant Architecture, Disease Resistance, Stress Response, Flowering, and More

INDETERMINATE DOMAIN (IDD) genes encode plant-specific transcription factors containing a conserved IDD domain with four zinc finger motifs. Previous studies on Arabidopsis IDDs (AtIDDs) have demonstrated that these genes play roles in diverse physiological and developmental processes, including plant architecture, seed and root development, flowering, stress responses, and hormone signaling. Recent studies have revealed important functions of IDDs from rice and maize, especially in regulating leaf differentiation, which is related to the evolution of C4 leaves from C3 leaves. Moreover, IDDs in crops are involved in the regulation of agriculturally important traits, including disease and stress resistance, seed development, and flowering. Thus, IDDs are valuable targets for breeding manipulation. This review explores the role of IDDs in plant development, environmental responses, and evolution, which provides idea for agricultural application.

Research Progress on Photoperiod Gene Regulation of Heading Date in Rice

Heading date is a critical physiological process in rice that is influenced by both genetic and environmental factors. The photoperiodic pathway is a primary regulatory mechanism for rice heading, with key florigen genes Hd3a (Heading date 3a) and RFT1 (RICE FLOWERING LOCUS T1) playing central roles. Upstream regulatory pathways, including Hd1 and Ehd1, also significantly impact this process. This review aims to provide a comprehensive examination of the localization, cloning, and functional roles of photoperiodic pathway-related genes in rice, and to explore the interactions among these genes as well as their pleiotropic effects on heading date. We systematically review recent advancements in the identification and functional analysis of genes involved in the photoperiodic pathway. We also discuss the molecular mechanisms underlying rice heading date variation and highlight the intricate interactions between key regulatory genes. Significant progress has been made in understanding the molecular mechanisms of heading date regulation through the cloning and functional analysis of photoperiod-regulating genes. However, the regulation of heading date remains complex, and many underlying mechanisms are not yet fully elucidated. This review consolidates current knowledge on the photoperiodic regulation of heading date in rice, emphasizing novel findings and gaps in the research. It highlights the need for further exploration of the interactions among flowering-related genes and their response to environmental signals. Despite advances, the full regulatory network of heading date remains unclear. Further research is needed to elucidate the intricate gene interactions, transcriptional and post-transcriptional regulatory mechanisms, and the role of epigenetic factors such as histone methylation in flowering time regulation. This review provides a detailed overview of the current understanding of photoperiodic pathway genes in rice, setting the stage for future research to address existing gaps and improve our knowledge of rice flowering regulation.

Sorghum bicolor INDETERMINATE1 is a conserved primary regulator of flowering

Introduction

A fundamental developmental switch for plants is transition from vegetative to floral growth, which integrates external and internal signals. INDETERMINATE1 (Id1) family proteins are zinc finger transcription factors that activate flowering in grasses regardless of photoperiod. Mutations in maize Id1 and rice Id1 (RID1) cause very late flowering. RID1 promotes expression of the flowering activator genes Early Heading Date1 (Ehd1) and Heading date 1 (Hd1), a rice homolog of CONSTANS (CO).

Methods and results

Mapping of two recessive late flowering mutants from a pedigreed sorghum EMS mutant library identified two distinct mutations in the Sorghum bicolor Id1 (SbId1) homolog, mutant alleles named sbid1-1 and sbid1-2. The weaker sbid1-1 allele caused a 35 day delay in reaching boot stage in the field, but its effect was limited to 6 days under greenhouse conditions. The strong sbid1-2 allele delayed boot stage by more than 60 days in the field and under greenhouse conditions. When sbid1-1 and sbid1-2 were combined, the delayed flowering phenotype remained and resembled that of sbid1-2, confirming late flowering was due to loss of SbId1 function. Evaluation of major flowering time regulatory gene expression in sbid1-2 showed that SbId1 is needed for expression of floral activators, like SbCO and SbCN8, and repressors, like SbPRR37 and SbGhd7.

Discussion

These results demonstrate a conserved role for SbId1 in promotion of flowering in sorghum, where it appears to be critical to allow expression of most major flowering regulatory genes.

Unlocking Nature's Clock: CRISPR Technology in Flowering Time Engineering

Flowering is a crucial process in the life cycle of most plants as it is essential for the reproductive success and genetic diversity of the species. There are situations in which breeders want to expedite, delay, or prevent flowering, for example, to shorten or prolong vegetative growth, to prevent unwanted pollination, to reduce the risk of diseases or pests, or to modify the plant's phenotypes. This review aims to provide an overview of the current state of knowledge to use CRISPR/Cas9, a powerful genome-editing technology to modify specific DNA sequences related to flowering induction. We discuss the underlying molecular mechanisms governing the regulation of the photoperiod, autonomous, vernalization, hormonal, sugar, aging, and temperature signal pathways regulating the flowering time. In addition, we are investigating the most effective strategies for nominating target genes. Furthermore, we have collected a dataset showing successful applications of CRISPR technology to accelerate flowering in several plant species from 2015 up to date. Finally, we explore the opportunities and challenges of using the potential of CRISPR technology in flowering time engineering.

INDETERMINATE1-mediated expression of FT family genes is required for proper timing of flowering in Brachypodium distachyon

The transition to flowering is a major developmental switch in plants. In many temperate grasses, perception of indicators of seasonal change, such as changing day-length and temperature, leads to expression of FLOWERING LOCUS T1 (FT1) and FT-Like (FTL) genes that are essential for promoting the transition to flowering. However, little is known about the upstream regulators of FT1 and FTL genes in temperate grasses. Here, we characterize the monocot-specific gene INDETERMINATE1 (BdID1) in Brachypodium distachyon and demonstrate that BdID1 is a regulator of FT family genes. Mutations in ID1 impact the ability of the short-day (SD) vernalization, cold vernalization, and long-day (LD) photoperiod pathways to induce certain FTL genes. BdID1 is required for upregulation of FTL9 (FT-LIKE9) expression by the SD vernalization pathway, and overexpression of FTL9 in an id1 background can partially restore the delayed flowering phenotype of id1. We show that BdID1 binds in vitro to the promoter region of FTL genes suggesting that ID1 directly activates FTL expression. Transcriptome analysis shows that BdID1 is required for FT1, FT2, FTL12, and FTL13 expression under inductive LD photoperiods, indicating that BdID1 is a regulator of the FT gene family. Moreover, overexpression of FT1 in the id1 background results in rapid flowering similar to overexpressing FT1 in the wild type, demonstrating that BdID1 is upstream of FT family genes. Interestingly, ID1 negatively regulates a previously uncharacterized FTL gene, FTL4, and we show that FTL4 is a repressor of flowering. Thus, BdID1 is critical for proper timing of flowering in temperate grasses.

Properties of INDETERMINATE DOMAIN Proteins from Physcomitrium patens: DNA-Binding, Interaction with GRAS Proteins, and Transcriptional Activity

INDETERMINATE DOMAIN (IDD) proteins are plant-specific transcription factors that interact with GRAS proteins, such as DELLA and SHORT ROOT (SHR), to regulate target genes. The combination of IDD and DELLA proteins regulates genes involved in gibberellic acid (GA) synthesis and GA signaling, whereas the combination of IDD with the complex of SHR and SCARECROW, another GRAS protein, regulates genes involved in root tissue formation. Previous bioinformatic research identified seven IDDs, two DELLA, and two SHR genes in Physcomitrium patens, a model organism for non-vascular plants (bryophytes), which lack a GA signaling pathway and roots. In this study, DNA-binding properties and protein-protein interaction of IDDs from P. patens (PpIDD) were analyzed. Our results showed that the DNA-binding properties of PpIDDs were largely conserved between moss and seed plants. Four PpIDDs showed interaction with Arabidopsis DELLA (AtDELLA) proteins but not with PpDELLAs, and one PpIDD showed interaction with PpSHR but not with AtSHR. Moreover, AtIDD10 (JACKDAW) interacted with PpSHR but not with PpDELLAs. Our results indicate that DELLA proteins have modified their structure to interact with IDD proteins during evolution from moss lineage to seed plants, whereas the interaction of IDD and SHR was already present in moss lineage.

Expression dynamics of phytochrome genes for the shade-avoidance response in densely direct-seeding rice

Because of labor shortages or resource scarcity, direct seeding is the preferred method for rice (Oryza sativa. L) cultivation, and it necessitates direct seeding at the current density. In this study, two density of direct seeding with high and normal density were selected to identify the genes involved in shade-avoidance syndrome. Phenotypic and gene expression analysis showed that densely direct seeding (DDS) causes a set of acclimation responses that either induce shade avoidance or toleration. When compared to normal direct seeding (NDS), plants cultivated by DDS exhibit constitutive shade-avoidance syndrome (SAS), in which the accompanying solar radiation drops rapidly from the middle leaf to the base leaf during flowering. Simulation of shade causes rapid reduction in phytochrome gene expression, changes in the expression of multiple miR156 or miR172 genes and photoperiod-related genes, all of which leads to early flowering and alterations in the plant architecture. Furthermore, DDS causes senescence by downregulating the expression of chloroplast synthesis-related genes throughout almost the entire stage. Our findings revealed that DDS is linked to SAS, which can be employed to breed density-tolerant rice varieties more easily and widely.

Genome-wide binding analysis of transcription factor Rice Indeterminate 1 reveals a complex network controlling rice floral transition

RICE INDETERMINATE 1 (RID1) plays a critical role in controlling floral transition in rice (Oryza sativa). However, the molecular basis for this effect, particularly the target genes and regulatory specificity, remains largely unclear. Here, we performed chromatin immunoprecipitation followed by sequencing (ChIP-seq) in young leaves at the pre-floral-transition stage to identify the target genes of RID1, identifying 2,680 genes associated with RID1 binding sites genome-wide. RID1 binding peaks were highly enriched for TTTGTC, the direct binding motif of the INDETERMINATE DOMAIN protein family that includes RID1. Interestingly, CACGTG and GTGGGCCC, two previously uncharacterized indirect binding motifs, were enriched through the interactions of RID1 with the novel flowering-promoting proteins OsPIL12 and OsTCP11, respectively. Moreover, the ChIP-seq data demonstrated that RID1 bound to numerous rice heading-date genes, such as HEADING DATE 1 (HD1) and FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 (OsFKF1). Notably, transcriptome sequencing (RNA-seq) analysis revealed roles of RID1 in diverse developmental pathways. Genetic analysis combined with genome-wide ChIP-seq and RNA-seq results showed that RID1 directly binds to the promoter of OsERF#136 (a repressor of rice flowering) and negatively regulates its expression. Overall, our findings provide new insights into the molecular and genetic mechanisms underlying rice floral transition and characterize OsERF#136 as a previously unrecognized direct target of RID1.

RNA-seq reveals transcriptional differences in anthocyanin and vitamin biosynthetic pathways between black and white rice

Anthocyanins and vitamins in black rice are the micronutrients vital to human health, both of which predominantly accumulate in the bran fraction. Some studies have demonstrated that black rice contains more vitamins compared with common white rice, indicating potential association between anthocyanin and vitamin accumulation. In this study, transcriptomes of pericarps collected from 27 black rice accessions and 49 white rice accessions at 10 days after flowering (DAF) were sequenced and analyzed. We identified 830 differentially expressed genes (DEGs) including 58 transcription factors (TFs) between black and white rice. Among 58 differentially expressed transcription factors, OsTTG1 was confirmed to be the one and only WD40 repeat protein regulating anthocyanin biosynthesis in the pericarp. Moreover, we identified 53 differentially expressed synthetic-related genes among 42 main synthesis enzymes in the biosynthesis pathway of seven vitamins including β-carotene, vitamin B1, vitamin B2, vitamin B5, vitamin B7, vitamin B9 and vitamin E. Collectively, our results provide valuable insights into the molecular mechanism of biosynthesis of anthocyanins and vitamins and the potential effect of anthocyanin biosynthesis on vitamin biosynthesis in black rice.