Hd3a protein is a mobile flowering signal in rice

Florigen-like protein OsFTL1 promotes flowering without essential florigens Hd3a and RFT1 in rice

Flowering time is a critical agronomic trait in rice, directly influencing grain yield and adaptability to specific planting regions and seasons. Florigens, including FLOWERING LOCUS T (FT) proteins Hd3a (OsFTL2) and RFT1 (OsFTL3), play central roles in transmitting flowering signals through rice's photoperiod regulatory network. While Hd3a and RFT1 have been extensively studied, the functions and interactions of other FT-like proteins remain unclear, limiting advancements in breeding strategies for early-maturing rice varieties. Here, we demonstrate that the florigen-like protein OsFTL1 forms a florigen activation complex (FAC) and promotes flowering under both short-day and long-day conditions. OsFTL1 localizes to the nucleus and cytoplasm, with predominant expression in the shoot base, facilitating its mobilization to the shoot apical meristem (SAM) to initiate flowering. Overexpression of OsFTL1 (OsFTL1-OE) in leaves or shoot bases significantly accelerates flowering and alters plant architecture. In the nucleus, OsFTL1 interacts with GF14c and OsFD1 to form an FAC, activating OsMADS14 and OsMADS15 expression to drive flowering. Markedly, OsFTL1-OE plants deficient in Hd3a and RFT1 exhibited earlier flowering compared with wild-type plants, indicating that OsFTL1 can independently promote flowering. Furthermore, haplotype analysis identified OsFTL1-Hap3, a beneficial variant associated with early flowering and comparable grain yields. These findings revealed that OsFTL1 can substitute for Hd3a and RFT1 in FAC formation, promoting flowering across photoperiods, and highlighting its potential application in breeding early-maturing, high-yield rice varieties suitable for diverse environments.

Temporal transcriptome analysis reveals the two-phase action of florigens in rice flowering

Two florigen genes, Hd3a and RFT1, are essential for the floral transition in rice. To elucidate the early steps of the transcriptional dynamics during rice floral induction, we compared a set of temporal transcriptome data of SAM (shoot apical meristem)-region samples between the wild-type and a non-flowering line of the hd3a rft1 double mutant during a short-day (SD) treatment after growing under long-day conditions for 42 days, and identified 6,978 DEGs (differentially expressed genes). As expected, FUL-like MADS-box genes were induced just after 4 days SD treatment; meanwhile, SEP-type and AGL-type MADS-box genes were induced after 9 days of SD treatment. We here newly revealed that majority of rhythmic genes including major circadian clock genes were not affected by the florigen genes, implying normal circadian clock phasing at the SAM regions regardless of floral transitions. We found that around two thousands of genes were repressed by Hd3a and RFT1 genes at the SAM regions before the SD treatments and become derepressed and similar to WT expression levels in the double mutants according to the SD treatments. These clearly imply two distinct actions of florigen genes: one for repression of some developmental key genes during vegetative growth possibly by very low level of florigen expression and the other for floral induction by relatively high florigen expressions upon short-day inductions. This repression by low levels of florigens may serve as a maintenance system for vegetative growth before floral induction, which implies a novel role for florigen genes in rice.

Chemodiversity of sulfur-containing metabolites emphasizing the ecophysiology of Allium plants and the developmental innovations in bulb formation

Sulfur (S) metabolism has played a critical role in the evolution of life, serving as an energy source for early biochemical pathways like dissimilatory S reduction and anoxygenic photosynthesis. Across kingdoms, S metabolism displays remarkable diversity. S-containing metabolites like glucosinolates (GLSs) in Brassicaceae and S-alk(en)ylcysteine sulfoxides in Allium species illustrate the ecological and evolutionary significance of S-containing compounds. These metabolites contribute to defense, homeostasis, and ecological interactions, with mechanisms like enzymatic hydrolysis releasing bioactive molecules such as allicin. Further, advances in transcriptomics and biochemical studies have revealed the genetic underpinnings of S metabolism and specialized pathways in bulb-forming Allium species. The role extends to ecological interactions by modulating S-associated defense pathways. This integrative understanding of S metabolism underscores its evolutionary, physiological, and ecological importance.

Breeding D1-Type Hybrid Japonica Rice in Diverse Upland Rainfed Environments

'Dianheyou615' (DHY615) is an elite Dian (D1)-type hybrid japonica rice variety, renowned for its high yield, exceptional grain quality, and unique adaptability to both irrigated and rainfed conditions in the Yungui Plateau of southwestern China. However, the genetic mechanisms underlying the agronomic performance of the D1-type hybrid japonica rice remain unclear. In this study, a comprehensive analysis of 'DHY615''s agronomic performance, genetic genealogy, and molecular genetic foundation was conducted to dissect its desirable traits for upland rainfed cultivation across diverse ecological environments. The main findings indicate that 'DHY615' possesses 6432 heterozygous SNPs, with 57.48% and 14.43% located in the promoter and coding regions, respectively, potentially affecting key phenotypic traits. High-impact SNPs variants and numerous well-known functional genes were identified, such as OsAAP6, GS3, Sd1, Rf1, BADH2, BPh14, Rymv1, OsFRO1, NRT1.1B, SKC1, OsNCED2, and qUVR-10, which are likely linked to traits including plant architecture, grain yield, grain quality, and resistance to various biotic and abiotic stresses (e.g., disease, cold, drought, salt, high iron, and high UV radiation). Notably, 'Nan615' harbors a greater number of functional allele variants compared to 'H479A', which potentially explaining its superior grain yield and remarkable adaptability. This study offers novel and valuable insights into the molecular genetic foundation of the plateau D1-type hybrid japonica rice, underscoring its potential for sustainable rice production across diverse ecological zones, especially with its unparalleled high-altitude adaptability to rainfed upland planting.

Physiological factors influencing climate-smart agriculture: Daylength-mediated interaction between tillering and flowering in rice

BACKGROUND

Controlling rice tillering and flowering is essential for reducing greenhouse gas emissions from paddy fields, a key objective in climate-smart agriculture. However, the interaction between tillering and flowering remains controversial and poorly understood. In this study, we subjected plants of the rice cultivars 'Saenuri' and 'Odae' to short- and long-day conditions and compared their growth and flowering responses after tiller removal.

RESULTS

The effects of tiller removal differed depending on daylength conditions. Under short days, plants in the tiller-removal group flowered earlier than the controls, whereas the opposite trend was observed under long days. This response was associated with changes in florigen gene expression. Under short days, the expression of Hd3a, which promotes flowering, increased in the tiller-removal group compared with that in the controls. In contrast, under long days, the expression of OsMFT1, a gene that delays flowering and promotes spikelet formation, was significantly upregulated, leading to an increased spikelet number. Notably, spikelets per panicle in the tiller-removal groups increased approximately 3.4-fold in 'Saenuri' and 2.2-fold in 'Odae' under long-day conditions compared with those in their respective controls.

CONCLUSIONS

These findings highlight the daylength-dependent variability in tillering and flowering interactions, providing new insights into their regulatory mechanisms. This study offers a foundation for optimizing rice growth strategies under varying photoperiod conditions, contributing to climate-smart agricultural practices and improved breeding programs.

Overexpressing OsCCT23 Delays Heading Date and Increases Grain Yield by Activating Ghd7 in Rice

Heading date and panicle architecture are pivotal traits that significantly influence rice yield. Here, we identified a gene OsCCT23 encoding a CCT domain-containing protein that delays heading by over 40 days and increases grain yield by 60-104% through overexpressing. Two types transcripts OsCCT23L and OsCCT23S were isolated by 5'RACE, and transgenic events demonstrated that the effect of the predominant transcript OsCCT23S, encoding an 81-aa protein without the B-box domain, is comparable to OsCCT23. OsCCT23 is predominantly expressed in leaves and follows a diurnal expression pattern with a peak at dawn. Overexpressing OsCCT23 upregulated the floral repressor Ghd7 and downregulated the floral inducer RID1, consequently led to the downregulation of Ehd1, Hd3a and RFT1. Additionally, it regulates the expression of certain circadian clock-related genes, including OsGI and OsTOC1. RNA in situ hybridisation analysis confirmed that OsCCT23 activates the expression of Ghd7 in the panicle branch meristem. OsCCT23 suppresses the expression of four OsCKX genes including Gn1a, which associate with cytokinin accumulation in panicles. Natural variation in OsCCT23 promoter identified by eGWAS associates its mRNA abundance and rice heading date. Consequently, OsCCT23 substantially delays heading and significantly increases grain yield, making it highly valuable for rice breeding.

Mutations in HEADING DATE 1 affect transcription and cell wall composition in rice

Plants utilize environmental information to modify their developmental trajectories for optimal survival and reproduction. Over a century ago, day length (photoperiod) was identified as a major factor influencing developmental transitions, particularly the shift from vegetative to reproductive growth. In rice (Oryza sativa), exposure to day lengths shorter than a critical threshold accelerates flowering, while longer days inhibit this process. This response is mediated by HEADING DATE 1 (Hd1), a zinc finger transcription factor that is central in the photoperiodic flowering network. Hd1 acts as a repressor of flowering under long days but functions as a promoter of flowering under short days. However, how global transcription of genes downstream of Hd1 changes in response to the photoperiod is still not fully understood. Furthermore, it is unclear whether Hd1 target genes are solely involved in flowering time control or mediate additional functions. In this study, we utilized RNA-Seq to analyze the transcriptome of hd1 mutants under both long and short day conditions. We identified genes involved in the phenylpropanoid pathway that are deregulated under long days in the mutant. Quantitative profiling of cell wall components and abiotic stress assays suggested that Hd1 is involved in processes considered unrelated to flowering control. This indicates that day length perception and responses are intertwined with physiological processes beyond flowering.

Genome-wide identification, phylogeny, and expression analysis of PEBP gene family in Castanea mollissima

The phosphatidylethanolamine binding protein (PEBP) family plays an important part in growth and development of plants. Castanea mollissima is an economic plant with significant financial value and has become an important food source in the Northern Hemisphere. However, the PEBP genes in C. mollissima have not been studied yet. In this study, six PEBP genes (CmPEBP1 ∼ CmPEBP6) were identified in C. mollissima and comprehensively analyzed in terms of physicochemical properties, phylogeny, gene structures, cis-regulatory elements (CREs), transcription factor interaction, and expression profiles. The six CmPEBP genes were categorized into three subfamilies according to the phylogeny analysis, and all of them share extremely similar gene and protein structures. A total of 136 CREs were identified in the promoter regions of the CmPEBP genes, mainly related to growth and development, environmental stress, hormone response, and light response. Comparative genomic analysis indicated that the expansion of the CmPEBP genes was mainly driven by dispersed duplication, and the CmPEBP3/CmPEBP5 derived from eudicot common hexaploidization (ECH) events retained orthologous genes in all species studied. A total of 259 transcription factors (TFs) belonging to 39 families were predicted to be regulators of CmPEBP genes, and CmPEBP4 was predicted to interact with the most TFs. The RNA-seq data analysis indicated the potential roles of CmPEBP genes in the ovule, bud, and flower development of C. mollissima, as well as in the response to temperature stress, drought stress, and the gall wasp Dryocosmus kuriphilus (GWDK) infestation. Additionally, the expression of CmPEBP genes in C. mollissima seed kernel development and their response to temperature stress were confirmed by RT-qPCR assays. This study gives references and directions for future in-depth studies of PEBP genes.

TaFT-D1 positively regulates grain weight by acting as a coactivator of TaFDL2 in wheat

FLOWERING LOCUS T (FT), a multifunctional regulator in crops, modulates multiple key agronomic traits such as flowering time or heading date and plant height; however, its role in grain development regulation is unclear. Herein, through genome-wide association studies (GWAS), we identified TaFT-D1, which encodes a phosphatidylethanolamine-binding protein (PEBP), as a candidate gene for grain weight in wheat. A one-bp insertion/deletion (InDel) (G/-) in the third exon of TaFT-D1, resulting in different protein lengths, was significantly associated with grain weight. TaFT-D1 knockout via the CRISPR-Cas9 system reduced grain size and weight, and TaFT-D1 increased grain size by promoting cell proliferation and starch synthesis. Transcriptome analysis revealed a significant decrease in the expression of cell cycle- and starch synthesis-related genes, including TaNAC019-3A, TaSWEET15-like-7B, TaCYCD4;1 and TaCYCD3;2, in the taft-d1 knockout line. TaFT-D1 interacted with the bZIP transcription factor TaFDL2, and the tafdl2 mutant presented relatively small grains, suggesting that TaFDL2 is a positive regulator of grain size. Moreover, TaFDL2 bound to the promoters of downstream cell cycle- and starch synthesis-related genes, activating their expression, whereas TaFT-D1 increased this activation via TaFDL2. Interaction assays demonstrated that TaFT-D1, Ta14-3-3A and TaFDL2 formed a regulatory complex. Furthermore, the TaFT-D1(G) allele was significantly correlated with greater thousand-grain weight and earlier heading. This favourable allele has undergone strong positive selection during wheat breeding in China. Our findings provide novel insights into how TaFT-D1 regulates grain weight and highlight its potential application for yield improvement in wheat.

CRISPR/Cas9-mediated GhFT-targeted mutagenesis prolongs indeterminate growth and alters plant architecture in cotton

The shift from vegetative to reproductive growth is an important developmental transition that affects flowering and maturation, architecture, and ecological adaptability in plants. The florigen-antiflorigen system universally controls flowering and plant architecture, and changes to the ratio of these components alter this transition and disrupt growth. The genes FT (FLOWERING LOCUS T), encoding the florigen protein FT, and CETS [CENTRORADIALIS (CEN)/TERMINAL FLOWER1 (TFL1)/SELF-PRUNING (SP)], encoding antiflorigen proteins, have opposing roles. Upland cotton (Gossypium hirsutum) is one of the world's most widely cultivated cotton varieties, and its complex allotetraploid genome contains only one homoeologous pair of FT genes (GhFT-A and GhFT-D). The functionally conserved gene GhFT promotes flowering and plays a role in plant architecture, although the molecular regulation of flowering and plant architecture in cotton remains unclear. In this study, CRISPR/Cas9 technology was used to induce mutations in the first and second exons of GhFT, respectively. G. hirsutum cv. YZ-1 was transformed with a CRISPR/Cas9-GhFT vector using Agrobacterium tumefaciens, and a diverse set of mutations was identified at the editing site. Compared with the wild type, mutant plants could not transition between vegetative and reproductive growth, and significant alterations to plant architecture were observed. Quantitative RT-PCR revealed downregulation of the homologous floral meristem identity genes APETALA1 (GhAP1) and OVEREXPRESSION OF CONSTANS 1 (GhSOC1) and upregulation of the TFL1 homologs GhTFL1-1 and GhTFL1-2. These results suggested that GhFT played a significant role in flowering time and plant architecture and that the ratio of florigen-antiflorigen components was critical to producing improved cotton varieties. This study provided a basis for future investigations of molecular breeding in cotton and guidance for the agricultural production of this crop.

More than flowering: CONSTANS plays multifaceted roles in plant development and stress responses

Plants have evolved a remarkable ability to sense and respond to changes in photoperiod, allowing adjustments to their growth and development based on seasonal and environmental cues. The floral transition is a pivotal stage in plant growth and development, signifying a shift from vegetative to reproductive growth. CONSTANS (CO), a central photoperiodic response factor conserved in various plants, mediates day-length signals to control the floral transition, although its mechanisms of action vary among plants with different day-length requirements. In addition, recent studies have uncovered roles for CO in organ development and stress responses. These pleiotropic roles in model plants and crops make CO a potentially fruitful target for molecular breeding aimed at modifying crop agronomic traits. This review systematically traces research on CO, from its discovery and functional studies to the exploration of its regulatory mechanisms and newly discovered functions, providing important insight into the roles of CO and laying a foundation for future research.

Isolation of OsMetAP10, a Peptidase_M24 Superfamily Gene, Regulating Heading Date in Rice

The heading date is one of the important traits in rice, which greatly affects grain yield and regional adaptability. Although the flowering pathways in rice have been extensively investigated, the genes involved in flowering remain largely unknown. Here, we report a rice lhd mutant, which showed late flowering under both long-day (LD) and short-day (SD) conditions. Through MutMap+ and linkage analysis, a deletion mutation in OsMetAP10 was inferred as the most likely candidate for lhd late flowering. OsMetAP10 encodes a methionine aminopeptidase that belongs to the peptidase_M24 subfamily III. The OsMetAP10 gene is constitutively expressed in rice and is induced by light, with a rhythmic expression pattern. OsMetAP10 knockout lines displayed late heading as the lhd mutation, while no alternations in morphology and heading were observed on OsMetAP10 overexpression lines, further confirming the mutation of OsMetAP10 as responsible for the late heading of lhd. Through RT-qPCR and transcriptome analysis, we revealed that the upregulated expression of the FT-like gene OsFLT4, a negatively flowering regulator, and the downregulation of flower development-related genes, OsMADS14, OsMADS15, and OsMADS34, played critical roles in determining the late flowering of the OsMetAP10 mutation. This study reports a new gene affecting flowering and provides a new insight into the role of OsMetAP10 in regulating rice heading.

GhCOL2 Positively Regulates Flowering by Activating the Transcription of GhHD3A in Upland Cotton (Gossypium hirsutum L.)

Plants have evolved sophisticated signaling networks to adjust flowering time, ensuring successful reproduction. Two crucial flowering regulators, FLOWERING LOCUS T (FT) and CONSTANS (CO), play pivotal roles in regulating flowering across various species. Previous studies have indicated that suppressing Gossypium hirsutum CONSTANS-LIKE 2 (GhCOL2), a homolog of Arabidopsis CO, leads to delayed flowering in cultivated cotton. However, the underlying regulatory mechanisms remain unknown. In this study, a yeast one-hybrid and dual-LUC expression assays were used to elucidate the molecular mechanism through which GhCOL2 regulates the transcription of GhHD3A. RT-qPCR was used to examine the expression of GhCOL2 and GhHD3A. Our findings reveal that GhCOL2 directly binds to CCACA cis-elements and atypical CORE (TGTGTATG) cis-elements in the promoter regions of HEADING DATE 3 A (HD3A), thereby activating GhHD3A transcription. Notably, GhCOL2 and GhHD3A exhibited high expression levels in the adult stage and low levels in the juvenile stage. Interestingly, the expression of GhCOL2 and GhHD3A varied significant between the two cotton varieties (Tx2094 and Maxxa). In summary, our study enhances the understanding of the molecular mechanism by which cotton GhCOL2-GhHD3A regulates flowering at the molecular level. Furthermore, it contributes to a broader comprehension of the GhCOL2-GhHD3A model in G. hirsutum.

OsbZIP23 delays flowering by repressing OsMADS14 expression in rice

Flowering time is a fundamental factor determining the global distribution and final yield of rice (Oryza sativa L.). The initiation of the floral transition process signifies the beginning of the reproductive phase. The florigens Heading Date 3a (Hd3a) and Rice Flowering Locus T 1 (RFT1) combine with GF14 proteins and OsFD-like basic leucine zipper (bZIP) transcription factors to form florigen activation/repressor complexes (FACs/FRCs) that regulate the transition to flowering. We herein report that a bZIP transcription factor (OsbZIP23) functions as a flowering repressor. Transgenic plants overexpressing OsbZIP23 exhibited delayed flowering, which was in contrast to the slightly early flowering of the osbzip23 mutants, under natural short-day and long-day conditions. Molecular and biochemical analyses indicated that OsbZIP23 can bind to the 5' untranslated region of OsMADS14 and suppress expression. Moreover, it delays the floral transition probably by interacting with OsFTL1/Hd3a/RFT1 and 14-3-3 proteins to form FRCs. Our findings have further elucidated the molecular mechanisms regulating the flowering time in rice.

OsMAINTENANCE OF MERISTEM LIKE 1 controls style number at high temperatures in rice

OsMAIL1 encodes for a rice protein of the Plant Mobile Domain (PMD) family and is strongly upregulated during floral induction in response to the presence of the florigens Heading date 3a (Hd3a) and RICE FLOWERING LOCUS T1 (RFT1). Although OsMAIL1 expression depends on the florigens, osmail1 null mutants do not show delay in flowering time, rather OsMAIL1 participates in ensuring successful reproduction. Indeed, when day temperatures reach 35 °C (7 °C higher than standard greenhouse conditions), osmail1 mutants show increased sterility due to abnormal pistil development with about half of the plants developing three styles topped by stigmas. OsMAIL1 expression correlates with that of carpel identity genes and RNA-seq of osmail1-1 mutant compared to the wt during inflorescence development showed that OsMAIL1 is required to activate carpel identity genes expression when floral meristems are about to be initiated. OsMAIL1 is a newly characterized rice gene that specifically controls carpel development under heat stress, ensuring plant female fertility in these conditions.

New insights into rice phenology: discovering the effect of insolation on heading response

Precise growth management is required for climate-smart and sustainable crop production in response to climate change, with the heading stage being the most important. Research on the control of heading in rice (Oryza sativa) has mainly focused on day length and temperature; however, research on the effects of insolation is limited. Therefore, this study analyzed the differences in rice growth and heading responses under different light intensity and temperature conditions. Five early-maturing and seven medium-late-maturing rice varieties were used for each japonica heading ecology type. Our results showed that leaf age development, an indirect measure of rice phenological development, was inhibited under low light intensity and low-temperature conditions. Accordingly, the heading date was also delayed by approximately 18 days at low temperatures and 21 days at low light intensity, with no difference among ecotypes. We also found an interaction between temperature and light intensity, with the light intensity-mediated delay in heading date being affected more by high temperatures. This study demonstrated that light intensity and temperature have a major effect on heading date variation, suggesting that the impact of insolation must be considered for the accurate prediction of heading stage variation. These results could shed new light on rice phenology research and contribute to the implementation of precision agriculture.

The role of sugar transporter BrSWEET11 in promoting plant early flowering and preliminary exploration of its molecular mechanism

KEY MESSAGE

BrSWEET11 accelerated Arabidopsis thaliana flowering, while silencing Brsweet11 in Brassica rapa delayed flowering relative to controls. BrSWEET11 is involved in sucrose transport after being induced by long-day conditions. SWEETs (Sugars Will Eventually Be Exported Transporters) are sugar outflow transporters that may participate in the regulation of plant flowering. In this study, the open reading frame of Brassica rapa ssp. pekinensis SWEET11 (BrSWEET11) was cloned and found to be 858 bp in length and encode 285 amino acids, which is typical of SWEET family proteins. The BrSWEET11 gene was strongly expressed in reproductive growth organs, particularly flowers, according to tissue expression analyses and GUS histochemical staining. BrSWEET11 promotes early flowering in Arabidopsis thaliana by 3-4 days, whereas Brsweet11 silencing in Brassica rapa delays flowering by 8-12 days relative to controls. BrSWEET11 promoted early flowering in A. thaliana, and compared with that in control plants, flowering was delayed in Brsweet11-silenced Brassica rapa. Transcriptome analysis of BrSWEET11-overexpressing A. thaliana and wild-type (WT) plants was performed and the results showed that eight key flowering genes jointly regulated flowering time, which was also validated in the Brsweet11-silenced plants. In addition, through photoperiod treatments and sugar content measurements, it was found that the expression of BrSWEET11 is induced by long-day conditions and is involved in sucrose transport. Further investigation using yeast library screening, yeast two-hybrid, and bimolecular fluorescence complementation assay techniques revealed that the BrSWEET11 protein interacts with the sugar transporter 4a (BrSUT4a) protein. Therefore, BrSWEET11 was induced by long-day conditions, and may promote early flowering in Brassica rapa through sucrose transport. This study provides a theoretical basis for elucidating the molecular mechanism through which SWEET genes are involved in flowering time regulation in Brassica rapa.

Genome-Wide Identification and Expression Analysis of FD Gene Family in Bamboos

The regulation of flowering time is a highly coordinative process that involves the interplay of multiple genes. The FLOWERING LOCUS D (FD) gene is one of those important players. In this study, we identified and characterized FD genes in bamboo, a plant with the unique monocarpy flowering phenomenon. An angiosperm-wide FD gene family analysis demonstrated that unlike the most recent common ancestor (MRCA) of angiosperms, which had only one FD gene, five FD copies were present in the MRCA of Poaceae, and the same gene copy number was retained in the MRCA of the Bambusoideae subfamily. Further analysis of the Poaceae FD gene family revealed five distinctive clades resulted from four duplication events, with two of these events being specific to the Bambusoideae subfamily. High levels of conservation were observed in the gene structure and amino acid composition of structural domain among the FD genes across bamboos and their close relatives, indicating functional conservation. Furthermore, gene expression profiling indicated that FD gene expression in bamboo closely resemble the expression patterns of their homologs in rice. Additionally, overexpression of two bamboo genes (Phy.ed_05093.t1 and Phy.ed_14669.t1) in Arabidopsis resulted in an early flowering phenotype, demonstrating their involvement in the regulation of the flowering process in plants. Our findings provide a comprehensive resource for understanding the evolution, structure, expression, and function of FD genes in Poaceae and Bambusoideae.

A genome-wide association study using Myanmar indica diversity panel reveals a significant genomic region associated with heading date in rice

Heading date is a key agronomic trait for adapting rice varieties to different growing areas and crop seasons. The genetic mechanism of heading date in Myanmar rice accessions was investigated using a genome-wide association study (GWAS) in a 250-variety indica diversity panel collected from different geographical regions. Using the days to heading data collected in 2019 and 2020, a major genomic region associated with the heading date, designated as MTA3, was found on chromosome 3. The linkage disequilibrium block of the MTA3 contained the coding sequence (CDS) of the phytochrome gene PhyC but not in its promoter region. Haplotype analysis of the 2-kb promoter and gene regions of PhyC revealed the six haplotypes, PHYCHapA, B, C, D, E, and F. The most prominent haplotypes, PHYCHapA and PHYCHapC, had different CDS and were associated with late heading and early heading phenotypes in MIDP, respectively. The difference in CDS effects between the PHYCHapB, which has identical CDS to PHYCHapA, and PHYCHapC was validated by QTL analysis using an F2 population. The distribution of PHYCHapA in the southern coastal and delta regions and of PHYCHapC in the northern highlands appears to ensure heading at the appropriate time in each area under the local day-length conditions in Myanmar. The natural variation in PhyC would be a major determinant of heading date in Myanmar accessions.

The increasing authorship trend in neuroscience: A scientometric analysis across 11 countries

Previous studies have demonstrated an increasing trend of the number of authors across various fields over the years. This trend has been attributed to the necessity for larger collaborations and, at times, to ethical issues regarding authorship attribution. Our study focuses on the evolution of authorship trends in the field of Neuroscience. We conducted our analysis based on a dataset containing 580,782 neuroscience publications produced from 2000 to 2022, focusing on the publications within the Group of ten (G10) countries. Using a matrix-based methodology, we extracted and analyzed the average number of authors per country. Our findings reveal a consistent rise in authorship across all G10 countries over the past two decades. Italy emerged with the highest average number of authors, while France stood out for experiencing the most significant increase, particularly in the last decade. The countries with the lowest number of authors per publication were the USA, UK and Canada. Differences between countries could result from variations in the size of collaboration between researchers in different countries. Additionally, these differences may depend on utilitarian considerations aimed at receiving higher scores in the individual evaluation of their own work. We propose that a normalization procedure for the number of authors should be implemented to ensure a fair evaluation of researchers.

A single-base deletion in exon 2 of Hd1 delineates monogenic recessive photoperiod insensitivity in aromatic Joha rice: a novel allele for seasonal adaptability

BACKGROUND

Assam's aromatic Joha rice is a unique rice class famous for its aroma, taste, and nutritional benefits, which fetch high market prices in domestic and international markets. Joha landraces are inherently poor yielders due to their strong aroma and predominantly photoperiod sensitivity. Hybridization involving non-aromatic HYVs improves yield with concomitant loss of quality. In this context, mutation breeding, a sustainable approach where genetic mutations are induced to create desirable traits, often provides useful allelic variation in specific morpho-agronomic traits. The present study delves into the genetic characterization of a photoperiod-insensitive mutant. As part of our mutation breeding programme, this mutant was isolated from a gamma ray-induced M2 population of a Joha rice landrace, Kon Joha.

RESULTS

The mutant was unique, and a single recessive gene conditions the induced photoperiod insensitivity. Mutant gene tagging involved 402 SSR and InDel markers, and later polymorphic markers were used for bulk segregant analysis (BSA) in the F2 population of 'mutant × Kalijeera (distant parent)'. BSA revealed an association between the SSR marker RM527 and this mutant trait. This marker is present on chromosome 6 of the rice genome. Using chromosome 6-specific SSR markers in polymorphic screening and BSA revealed another associated marker, RM19725, for the mutant trait. The genomic interval between RM527 and RM19725 harbors a photoperiod-insensitive gene, Hd1, on chromosome 6. Cloning and sequencing of Hd1 genomic fragments from the parents and mutants revealed a single-base deletion in exon 2, leading to a frameshift mutation in the Hd1 protein. This mutation in exon 2 leads to severe structural abnormalities in the CCT domain of the Hd1 protein that is critical for the interaction of the repressing complex with conserved response elements in the florigen gene under long-day conditions, thereby causing photoperiod insensitivity.

CONCLUSIONS

The mutant's pleasant aroma and other quality characteristics, comparable to those of the parent cultivar, hold significant promise. They expand its potential use in a structured breeding programme aimed at developing high-value aromatic Joha rice. This rice, resilient to winter- and summer-growing environments and with broad seasonal adaptability, could revolutionize the rice market. The practical value of our research is underscored by this exciting possibility.

Genome-wide characterization of PEBP genes in Mung bean (Vigna radiata L.) with functional analysis of VrFT1 in relation to photoperiod

Mung bean (Vigna radiata L.), a widely cultivated legume, belongs to the Fabaceae family's Papilionoideae subfamily. Although Phosphatidylethanolamine-binding protein (PEBP) genes have been identified in several plant species, their presence and function in mung bean remain largely unexplored. In this study, we identified seven VrPEBP genes from mung bean and classified them into four clades: FT, MFT, TFL and FT-like. Cis-regulatory element analysis revealed that VrPEBP genes may play a role in light, hormone, and stress responses. Quantitative real-time PCR (qRT-PCR) analysis indicated that VrPEBPs were constitutively expressed in various tissues. However, tissue-specific expression patterns were observed among VrPEBP genes. Under short-day (SD) conditions, VrFT1 and VrMFT1 exhibited significantly higher expression levels than under long-day (LD) conditions at 8 and 4 h, respectively. Conversely, VrTFL2 and VrTFL3 showed significantly higher expression levels under LD conditions compared to SD conditions at 8 and 12 h, respectively. The varied expression patterns of these genes under different photoperiod suggest their potential involvement in the photoperiodic regulation of flowering in mung bean. Additionally, phenotypic analysis of transgenic Arabidopsis plants overexpressing VrFT1 revealed higher expression levels under SD conditions and predicted its role in promoting flowering. These results provide valuable insights into the evolution and function of PEBP genes in mung bean and lay the foundation for further research on their regulatory mechanisms and potential applications in mung bean improvement.

Knockout of OsWOX13 moderately delays flowering in rice under natural long-day conditions

Plants are sensitive to photoperiods and are also equipped with systems to adjust their flowering time in response to various changes in the environment and developmental hormones. In the present study, previously generated rice OsWOX13 overexpression and newly generated OsWOX13 knockout lines constructed via CRISPR/Cas9 technology flowered 10 days earlier and 4-6 days later than the wild type, respectively. Quantitative real-time  polymerase chain reaction analyses revealed that OsWOX13 might be involved in drought escape responses through the b-ZIP TRANSCRIPTION FACTOR 23 signaling pathway during rice flowering via photoperiod signaling genes such as Grain number, plant height and heading date 7, Early heading date 1, RICE FLOWERING LOCUS T1, Heading date 3a, and MADS14. Future investigations of OsWOX13 may provide insight into how plants adjust their flowering under stress conditions and how OsWOX13 could be precisely controlled to achieve maximum productivity in rice breeding.

A QTL GN1.1, encoding FT-L1, regulates grain number and yield by modulating polar auxin transport in rice

Rice grain number is a crucial agronomic trait impacting yield. In this study, we characterized a quantitative trait locus (QTL), GRAIN NUMBER 1.1 (GN1.1), which encodes a Flowering Locus T-like1 (FT-L1) protein and acts as a negative regulator of grain number in rice. The elite allele GN1.1B, derived from the Oryza indica variety, BF3-104, exhibits a 14.6% increase in grain yield compared with the O. japonica variety, Nipponbare, based on plot yield tests. We demonstrated that GN1.1 interacted with and enhanced the stability of ADP-ribosylation factor (Arf)-GTPase-activating protein (Gap), OsZAC. Loss of function of OsZAC results in increased grain number. Based on our data, we propose that GN1.1B facilitates the elevation of auxin content in young rice panicles by affecting polar auxin transport (PAT) through interaction with OsZAC. Our study unveils the pivotal role of the GN1.1 locus in rice panicle development and presents a novel, promising allele for enhancing rice grain yield through genetic improvement.

THYLAKOID FORMATION 1 interacts with FLOWERING LOCUS T and modulates temperature-responsive flowering in Arabidopsis

The intracellular localization of the florigen FLOWERING LOCUS T (FT) is important for its long-distance transport toward the shoot apical meristem. However, the mechanisms regulating the FT localization remain poorly understood. Here, we discovered that in Arabidopsis thaliana, the chloroplast-localized protein THYLAKOID FORMATION 1 (THF1) physically interacts with FT, sequestering FT in the outer chloroplast envelope. Loss of THF1 function led to temperature-insensitive flowering, resulting in early flowering, especially under low ambient temperatures. THF1 mainly acts in the leaf vasculature and shoot apex to prevent flowering. Mutation of CONSTANS or FT completely suppressed the early flowering of thf1-1 mutants. FT and THF1 interact via their anion binding pocket and coiled-coil domain (CCD), respectively. Deletion of the CCD in THF1 by gene editing caused temperature-insensitive early flowering similar to that observed in the thf1-1 mutant. FT levels in the outer chloroplast envelope decreased in the thf1-1 mutant, suggesting that THF1 is important for sequestering FT. Furthermore, THF1 protein levels decreased in seedlings grown at high ambient temperature, suggesting an explanation for its role in plant responses to ambient temperature. A thf1-1 phosphatidylglycerolphosphate synthase 1 (pgp1) double mutant exhibited additive acceleration of flowering at 23 and 16°C, compared to the single mutants, indicating that THF1 and phosphatidylglycerol (PG) act as independent but synergistic regulators of temperature-responsive flowering. Collectively, our results provide an understanding of the genetic pathway involving THF1 and its role in temperature-responsive flowering and reveal a previously unappreciated additive interplay between THF1 and PG in temperature-responsive flowering.

ZmARF16 Regulates ZCN12 to Promote the Accumulation of Florigen and Accelerate Flowering

Auxin response factors(ARFs) are a class of transcription factors that regulate the expression of auxin response genes and play a crucial role in plant growth and development. Florigen plays a crucial role in the process of flowering. However, the process by which auxin regulates the accumulation of florigen remains largely unclear. This study found that the expression of ZmARF16 in maize increases during flowering, and the genetic transformation of ZmARF16 accelerates the flowering process in Arabidopsis and maize. Furthermore, ZmARF16 was found to be positively correlated with the transcription of the ZCN12 gene. Similarly, the FT-like gene ZCN12 in maize rescues the late flowering phenotype of the FT mutation in Arabidopsis. Moreover, ZCN12 actively participates in the accumulation of florigen and the flowering process. Further research revealed that ZmARF16 positively responds to the auxin signal, and that the interaction between ZmARF16 and the ZCN12 promoter, as well as the subsequent promotion of ZCN12 gene expression, leads to early flowering. This was confirmed through a yeast one-hybrid and dual-luciferase assay. Therefore, the study provides evidence that the ZmARF16-ZCN12 module plays a crucial role in regulating the flowering process of maize.

The phosphatidylethanolamine-binding proteins OsMFT1 and OsMFT2 regulate seed dormancy in rice

Seed dormancy is crucial for optimal plant life-cycle timing. However, domestication has largely diminished seed dormancy in modern cereal cultivars, leading to challenges such as preharvest sprouting (PHS) and subsequent declines in yield and quality. Therefore, it is imperative to unravel the molecular mechanisms governing seed dormancy for the development of PHS-resistant varieties. In this study, we screened a mutant of BASIC HELIX-LOOP-HELIX TRANSCRIPTION FACTOR4 (OsbHLH004) with decreased seed dormancy and revealed that OsbHLH004 directly regulates the expression of 9-CIS-EPOXYCAROTENOID DIOXYGENASE3 (OsNCED3) and GIBBERELLIN 2-OXIDASE6 (OsGA2ox6) in rice (Oryza sativa). Additionally, we determined that two phosphatidylethanolamine-binding proteins, MOTHER OF FT AND TFL1 and 2 (OsMFT1 and OsMFT2; hereafter OsMFT1/2) interact with OsbHLH004 and Ideal Plant Architecture 1 (IPA1) to regulate their binding capacities on OsNCED3 and OsGA2ox6, thereby promoting seed dormancy. Intriguingly, FT-INTERACTING PROTEIN1 (OsFTIP1) interacts with OsMFT1/2 and affects their nucleocytoplasmic translocation into the nucleus, where OsMFT1/2-OsbHLH004 and OsMFT1/2-IPA1 antagonistically modulate the expression of OsNCED3 and OsGA2ox6. Our findings reveal that OsFTIP1-mediated inhibition of nuclear translocation of OsMFT1/2 and the dynamic transcriptional modulation of OsNCED3 and OsGA2ox6 by OsMFT1/2-OsbHLH004 and OsMFT1/2-IPA1 complexes in seed dormancy in rice.

The receptor kinase OsANX limits precocious flowering and inflorescence over-branching and maintains pollen tube integrity in rice

CrRLK1L subfamily members are involved in diverse growth- and development-related processes in Arabidopsis. However, the functions of their counterparts in rice are unknown. Here, OsANX expression was detected in developing inflorescences, mature pollen grains, and growing pollen tubes, and it was localized to the plasma membrane in pollen grains and tobacco epidermal cells. Homozygous osanx progeny could not be segregated from the CRISPR/Cas9-edited mutants osanx-c1+/- and osanx-c2+/-, and such progeny were segregated only occasionally from osanx-c3+/-. Further, all three alleles showed osanx male but not female gamete transmission defects, in line with premature pollen tube rupture in osanx-c3. Additionally, osanx-c3 exhibited precocious flowering, excessively branched inflorescences, and an extremely low seed setting rate of 1.4 %, while osanx-c2+/- and osanx-c3+/- had no obvious defects in inflorescence development or the seed setting rate compared to wild-type Nipponbare (Nip). Consistent with this, the complemented line pPS1:OsANX-GFP/osanx-c2 (PSC), in which the lack of OsANX expression was inflorescence-specific, showed slightly earlier flowering and overly-branched panicles. Multiple inflorescence meristem transition-related and inflorescence architecture-related genes were expressed at higher levels in osanx-c3 than in Nip; thus, they may partially account for the aforementioned mutant phenotypes. Our findings broaden our understanding of the biological functions of OsANX in rice.

PHOSPHATE1-mediated phosphate translocation from roots to shoots regulates floral transition in plants

Phosphorus nutrition has been known for a long time to influence floral transition in plants, but the underlying mechanism is unclear. Arabidopsis phosphate transporter PHOSPHATE1 (PHO1) plays a critical role in phosphate translocation from roots to shoots, but whether and how it regulates floral transition is unknown. Here, we show that knockout mutation of PHO1 delays flowering under both long- and short-day conditions. The late flowering of pho1 mutants can be partially rescued by Pi supplementation in rosettes or shoot apices. Grafting assay indicates that the late flowering of pho1 mutants is a result of impaired phosphate translocation from roots to shoots. Knockout mutation of SPX1 and SPX2, two negative regulators of the phosphate starvation response, partially rescues the late flowering of pho1 mutants. PHO1 is epistatic to PHO2, a negative regulator of PHO1, in flowering time regulation. Loss of PHO1 represses the expression of some floral activators, including FT encoding florigen, and induces the expression of some floral repressors in shoots. Genetic analyses indicate that at least jasmonic acid signaling is partially responsible for the late flowering of pho1 mutants. In addition, we find that rice PHO1;2, the homolog of PHO1, plays a similar role in floral transition. These results suggest that PHO1 integrates phosphorus nutrition and flowering time, and could be used as a potential target in modulating phosphorus nutrition-mediated flowering time in plants.

A florigen-expressing subpopulation of companion cells expresses other small proteins and reveals a nitrogen-sensitive FT repressor

The precise onset of flowering is crucial to ensure successful plant reproduction. The gene FLOWERING LOCUS T (FT) encodes florigen, a mobile signal produced in leaves that initiates flowering at the shoot apical meristem. In response to seasonal changes, FT is induced in phloem companion cells located in distal leaf regions. Thus far, a detailed molecular characterization of the FT-expressing cells has been lacking. Here, we used bulk nuclei RNA-seq and single nuclei RNA (snRNA)-seq to investigate gene expression in FT-expressing cells and other phloem companion cells. Our bulk nuclei RNA-seq demonstrated that FT-expressing cells in cotyledons and in true leaves differed transcriptionally. Within the true leaves, our snRNA-seq analysis revealed that companion cells with high FT expression form a unique cluster in which many genes involved in ATP biosynthesis are highly upregulated. The cluster also expresses other genes encoding small proteins, including the flowering and stem growth inducer FPF1-LIKE PROTEIN 1 (FLP1) and the anti-florigen BROTHER OF FT AND TFL1 (BFT). In addition, we found that the promoters of FT and the genes co-expressed with FT in the cluster were enriched for the consensus binding motifs of NITRATE-INDUCIBLE GARP-TYPE TRANSCRIPTIONAL REPRESSOR 1 (NIGT1). Overexpression of the paralogous NIGT1.2 and NIGT1.4 repressed FT expression and significantly delayed flowering under nitrogen-rich conditions, consistent with NIGT1s acting as nitrogen-dependent FT repressors. Taken together, our results demonstrate that major FT-expressing cells show a distinct expression profile that suggests that these cells may produce multiple systemic signals to regulate plant growth and development.

Multilayered regulation and implication of flowering time in plants

Initiation of flowering is a key switch for plants to shift from the vegetative growth to the phase of reproductive growth. This critical phase is essential not only for achieving successful reproduction, but also for facilitating environmental adaptation and maximizing yield potential. In the past decades, the environmental factors and genetic pathways that control flowering time have undergone extensive investigation in both model plant Arabidopsis and various crop species. The impact of environmental factors on plant flowering time is well documented. This paper focuses on the multilayered modulation of flowering time. Recent multi-omics approaches, and genetic screens have revealed additional components that modulate flowering time across various levels, encompassing chromatin modification, transcriptional and post-transcriptional control, as well as translational and post-translational regulation. The interplay between these various layers of regulation creates a finely-tuned system that can respond to a wide variety of inputs and allows plants to adjust flowering time in response to changing environmental conditions. In this review, we present a comprehensive overview of the recent progress made in understanding the intricate regulation of flowering time in plants, emphasizing the pivotal molecular components and their intricate interactions. Additionally, we provide an exhaustive list of key genes implicated in the intricate modulation of flowering time and offer a detailed summary of regulators of FLOWERING LOCUS T (FT) and FLOWERING LOCUS (FLC). We also discuss the implications of this knowledge for crop improvement and adaptation to changing environments.

Flowering time genes branching out

Plants are sessile by nature, and as such they have evolved to sense changes in seasonality and their surrounding environment, and adapt to these changes. One prime example of this is the regulation of flowering time in angiosperms, which is precisely timed by the coordinated action of two proteins: FLOWERING LOCUS T (FT) and TERMINAL FLOWER 1 (TFL1). Both of these regulators are members of the PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN (PEBP) family of proteins. These regulatory proteins do not interact with DNA themselves, but instead interact with transcriptional regulators, such as FLOWERING LOCUS D (FD). FT and TFL1 were initially identified as key regulators of flowering time, acting through binding with FD; however, PEBP family members are also involved in shaping plant architecture and development. In addition, PEBPs can interact with TCP transcriptional regulators, such as TEOSINTE BRANCHED 1 (TB1), a well-known regulator of plant architecture, and key domestication-related genes in many crops. Here, we review the role of PEBPs in flowering time, plant architecture, and development. As these are also key yield-related traits, we highlight examples from the model plant Arabidopsis as well as important food and feed crops such as, rice, barley, wheat, tomato, and potato.

Genetic and epigenetic basis of phytohormonal control of floral transition in plants

The timing of the developmental transition from the vegetative to the reproductive stage is critical for angiosperms, and is fine-tuned by the integration of endogenous factors and external environmental cues to ensure successful reproduction. Plants have evolved sophisticated mechanisms to response to diverse environmental or stress signals, and these can be mediated by hormones to coordinate flowering time. Phytohormones such as gibberellin, auxin, cytokinin, jasmonate, abscisic acid, ethylene, and brassinosteroids and the cross-talk among them are critical for the precise regulation of flowering time. Recent studies of the model flowering plant Arabidopsis have revealed that diverse transcription factors and epigenetic regulators play key roles in relation to the phytohormones that regulate floral transition. This review aims to summarize our current knowledge of the genetic and epigenetic mechanisms that underlie the phytohormonal control of floral transition in Arabidopsis, offering insights into how these processes are regulated and their implications for plant biology.

Photoperiod and temperature synergistically regulate heading date and regional adaptation in rice

Plants must accurately integrate external environmental signals with their own development to initiate flowering at the appropriate time for reproductive success. Photoperiod and temperature are key external signals that determine flowering time; both are cyclical and periodic, and they are closely related. In this review, we describe photoperiod-sensitive genes that simultaneously respond to temperature signals in rice (Oryza sativa). We introduce the mechanisms by which photoperiod and temperature synergistically regulate heading date and regional adaptation in rice. We also discuss the prospects for designing different combinations of heading date genes and other cold tolerance or thermo-tolerance genes to help rice better adapt to changes in light and temperature via molecular breeding to enhance yield in the future.

GHCU, a Molecular Chaperone, Regulates Leaf Curling by Modulating the Distribution of KNGH1 in Cotton

Leaf shape is considered to be one of the most significant agronomic traits in crop breeding. However, the molecular basis underlying leaf morphogenesis in cotton is still largely unknown. In this study, through genetic mapping and molecular investigation using a natural cotton mutant cu with leaves curling upward, the causal gene GHCU is successfully identified as the key regulator of leaf flattening. Knockout of GHCU or its homolog in cotton and tobacco using CRISPR results in abnormal leaf shape. It is further discovered that GHCU facilitates the transport of the HD protein KNOTTED1-like (KNGH1) from the adaxial to the abaxial domain. Loss of GHCU function restricts KNGH1 to the adaxial epidermal region, leading to lower auxin response levels in the adaxial boundary compared to the abaxial. This spatial asymmetry in auxin distribution produces the upward-curled leaf phenotype of the cu mutant. By analysis of single-cell RNA sequencing and spatiotemporal transcriptomic data, auxin biosynthesis genes are confirmed to be expressed asymmetrically in the adaxial-abaxial epidermal cells. Overall, these findings suggest that GHCU plays a crucial role in the regulation of leaf flattening through facilitating cell-to-cell trafficking of KNGH1 and hence influencing the auxin response level.

A FLOWERING LOCUS T ortholog is associated with photoperiod-insensitive flowering in hemp (Cannabis sativa L.)

Hemp (Cannabis sativa L.) is an extraordinarily versatile crop, with applications ranging from medicinal compounds to seed oil and fibre products. Cannabis sativa is a short-day plant, and its flowering is highly controlled by photoperiod. However, substantial genetic variation exists for photoperiod sensitivity in C. sativa, and photoperiod-insensitive ("autoflower") cultivars are available. Using a bi-parental mapping population and bulked segregant analysis, we identified Autoflower2, a 0.5 Mbp locus significantly associated with photoperiod-insensitive flowering in hemp. Autoflower2 contains an ortholog of the central flowering time regulator FLOWERING LOCUS T (FT) from Arabidopsis thaliana which we termed CsFT1. We identified extensive sequence divergence between alleles of CsFT1 from photoperiod-sensitive and insensitive cultivars of C. sativa, including a duplication of CsFT1 and sequence differences, especially in introns. Furthermore, we observed higher expression of one of the CsFT1 copies found in the photoperiod-insensitive cultivar. Genotyping of several mapping populations and a diversity panel confirmed a correlation between CsFT1 alleles and photoperiod response, affirming that at least two independent loci involved in the photoperiodic control of flowering, Autoflower1 and Autoflower2, exist in the C. sativa gene pool. This study reveals the multiple independent origins of photoperiod insensitivity in C. sativa, supporting the likelihood of a complex domestication history in this species. By integrating the genetic relaxation of photoperiod sensitivity into novel C. sativa cultivars, expansion to higher latitudes will be permitted, thus allowing the full potential of this versatile crop to be reached.

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

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

Transcription factor OsWRKY11 induces rice heading at low concentrations but inhibits rice heading at high concentrations

The heading date of rice is a crucial agronomic characteristic that influences its adaptability to different regions and its productivity potential. Despite the involvement of WRKY transcription factors in various biological processes related to development, the precise mechanisms through which these transcription factors regulate the heading date in rice have not been well elucidated. The present study identified OsWRKY11 as a WRKY transcription factor which exhibits a pivotal function in the regulation of the heading date in rice through a comprehensive screening of a clustered regularly interspaced palindromic repeats (CRISPR) ‒ CRISPR-associated nuclease 9 mutant library that specifically targets the WRKY genes in rice. The heading date of oswrky11 mutant plants and OsWRKY11-overexpressing plants was delayed compared with that of the wild-type plants under short-day and long-day conditions. Mechanistic investigation revealed that OsWRKY11 exerts dual effects on transcriptional promotion and suppression through direct and indirect DNA binding, respectively. Under normal conditions, OsWRKY11 facilitates flowering by directly inducing the expression of OsMADS14 and OsMADS15. The presence of elevated levels of OsWRKY11 protein promote formation of a ternary protein complex involving OsWRKY11, Heading date 1 (Hd1), and Days to heading date 8 (DTH8), and this complex then suppresses the expression of Ehd1, which leads to a delay in the heading date. Subsequent investigation revealed that a mild drought condition resulted in a modest increase in OsWRKY11 expression, promoting heading. Conversely, under severe drought conditions, a significant upregulation of OsWRKY11 led to the suppression of Ehd1 expression, ultimately causing a delay in heading date. Our findings uncover a previously unacknowledged mechanism through which the transcription factor OsWRKY11 exerts a dual impact on the heading date by directly and indirectly binding to the promoters of target genes.

The RNA binding protein EHD6 recruits the m6A reader YTH07 and sequesters OsCOL4 mRNA into phase-separated ribonucleoprotein condensates to promote rice flowering

N6-Methyladenosine (m6A) is one of the most abundant modifications of eukaryotic mRNA, but its comprehensive biological functionality remains further exploration. In this study, we identified and characterized a new flowering-promoting gene, EARLY HEADING DATE6 (EHD6), in rice. EHD6 encodes an RNA recognition motif (RRM)-containing RNA binding protein that is localized in the non-membranous cytoplasm ribonucleoprotein (RNP) granules and can bind both m6A-modified RNA and unmodified RNA indiscriminately. We found that EHD6 can physically interact with YTH07, a YTH (YT521-B homology) domain-containing m6A reader. We showed that their interaction enhances the binding of an m6A-modified RNA and triggers relocation of a portion of YTH07 from the cytoplasm into RNP granules through phase-separated condensation. Within these condensates, the mRNA of a rice flowering repressor, CONSTANS-like 4 (OsCOL4), becomes sequestered, leading to a reduction in its protein abundance and thus accelerated flowering through the Early heading date 1 pathway. Taken together, these results not only shed new light on the molecular mechanism of efficient m6A recognition by the collaboration between an RNA binding protein and YTH family m6A reader, but also uncover the potential for m6A-mediated translation regulation through phase-separated ribonucleoprotein condensation in rice.

Insight from expression profiles of FT orthologs in plants: conserved photoperiodic transcriptional regulatory mechanisms

Floral transition from the vegetative to the reproductive stages is precisely regulated by both environmental and endogenous signals. Among these signals, photoperiod is one of the most important environmental factors for onset of flowering. A florigen, FLOWERING LOCUS T (FT) in Arabidopsis, has thought to be a major hub in the photoperiod-dependent flowering time regulation. Expression levels of FT likely correlates with potence of flowering. Under long days (LD), FT is mainly synthesized in leaves, and FT protein moves to shoot apical meristem (SAM) where it functions and in turns induces flowering. Recently, it has been reported that Arabidopsis grown under natural LD condition flowers earlier than that grown under laboratory LD condition, in which a red (R)/far-red (FR) ratio of light sources determines FT expression levels. Additionally, FT expression profile changes in response to combinatorial effects of FR light and photoperiod. FT orthologs exist in most of plants and functions are thought to be conserved. Although molecular mechanisms underlying photoperiodic transcriptional regulation of FT orthologs have been studied in several plants, such as rice, however, dynamics in expression profiles of FT orthologs have been less spotlighted. This review aims to revisit previously reported but overlooked expression information of FT orthologs from various plant species and classify these genes depending on the expression profiles. Plants, in general, could be classified into three groups depending on their photoperiodic flowering responses. Thus, we discuss relationship between photoperiodic responsiveness and expression of FT orthologs. Additionally, we also highlight the expression profiles of FT orthologs depending on their activities in flowering. Comparative analyses of diverse plant species will help to gain insight into molecular mechanisms for flowering in nature, and this can be utilized in the future for crop engineering to improve yield by controlling flowering time.

A data-driven genome annotation approach for cassava

Genome annotation files play a critical role in dictating the quality of downstream analyses by providing essential predictions for gene positions and structures. These files are pivotal in decoding the complex information encoded within DNA sequences. Here, we generated experimental data resolving RNA 5'- and 3'-ends as well as full-length RNAs for cassava TME12 sticklings in ambient temperature and cold. We used these data to generate genome annotation files using the TranscriptomeReconstructoR (TR) tool. A careful comparison to high-quality genome annotations suggests that our new TR genome annotations identified additional genes, resolved the transcript boundaries more accurately and identified additional RNA isoforms. We enhanced existing cassava genome annotation files with the information from TR that maintained the different transcript models as RNA isoforms. The resultant merged annotation was subsequently utilized for comprehensive analysis. To examine the effects of genome annotation files on gene expression studies, we compared the detection of differentially expressed genes during cold using the same RNA-seq data but alternative genome annotation files. We found that our merged genome annotation that included cold-specific TR gene models identified about twice as many cold-induced genes. These data indicate that environmentally induced genes may be missing in off-the-shelf genome annotation files. In conclusion, TR offers the opportunity to enhance crop genome annotations with implications for the discovery of differentially expressed candidate genes during plant-environment interactions.

MsTFL1A delays flowering and regulates shoot architecture and root development in Medicago sativa

KEY MESSAGE

MsTFL1A is an important gene involved in flowering repression in alfalfa (Medicago sativa) which conditions not only above-ground plant shoot architecture but also root development and growth. Delayed flowering is an important trait for forage species, as it allows harvesting of high-quality forage for a longer time before nutritional values decline due to plant architecture changes related to flowering onset. Despite the relevance of delayed flowering, this trait has not yet been thoroughly exploited in alfalfa. This is mainly due to its complex genetics, sensitivity to inbreeding and to the fact that delayed flowering would be only advantageous if it allowed increased forage quality without compromising seed production. To develop new delayed-flowering varieties, we have characterized the three TERMINAL FLOWERING 1 (TFL1) family of genes in alfalfa: MsTFL1A, MsTFL1B and MsTFL1C. Constitutive expression of MsTFL1A in Arabidopsis caused late flowering and changes in inflorescence architecture, indicating that MsTFL1A is the ortholog of Arabidopsis TFL1. Overexpression of MsTFL1A in alfalfa consistently led to delayed flowering in both controlled and natural field conditions, coupled to an increase in leaf/stem ratio, a common indicator of forage quality. Additionally, overexpression of MsTFL1A reduced root development, reinforcing the role of MsTFL1A not only as a flowering repressor but also as a regulator of root development.We conclude that the precise manipulation of MsTFL1A gene expression may represent a powerful tool to improve alfalfa forage quality.

Overexpression of the PtrNF-YA6 gene inhibits secondary cell wall thickening in poplar

The NF-Y gene family in plants plays a crucial role in numerous biological processes, encompassing hormone response, stress response, as well as growth and development. In this study, we first used bioinformatics techniques to identify members of the NF-YA family that may function in wood formation. We then used molecular biology techniques to investigate the role and molecular mechanism of PtrNF-YA6 in secondary cell wall (SCW) formation in Populus trichocarpa. We found that PtrNF-YA6 protein was localized in the nucleus and had no transcriptional activating activity. Overexpression of PtrNF-YA6 had an inhibitory effect on plant growth and development and significantly suppressed hemicellulose synthesis and SCW thickening in transgenic plants. Yeast one-hybrid and ChIP-PCR assays revealed that PtrNF-YA6 directly regulated the expression of hemicellulose synthesis genes (PtrGT47A-1, PtrGT8C, PtrGT8F, PtrGT43B, PtrGT47C, PtrGT8A and PtrGT8B). In conclusion, PtrNF-YA6 can inhibit plant hemicellulose synthesis and SCW thickening by regulating the expression of downstream SCW formation-related target genes.

Evolution of major flowering pathway integrators in Orchidaceae

The Orchidaceae is a mega-diverse plant family with ca. 29,000 species with a large variety of life forms that can colonize transitory habitats. Despite this diversity, little is known about their flowering integrators in response to specific environmental factors. During the reproductive transition in flowering plants a vegetative apical meristem (SAM) transforms into an inflorescence meristem (IM) that forms bracts and flowers. In model grasses, like rice, a flowering genetic regulatory network (FGRN) controlling reproductive transitions has been identified, but little is known in the Orchidaceae. In order to analyze the players of the FRGN in orchids, we performed comprehensive phylogenetic analyses of CONSTANS-like/CONSTANS-like 4 (COL/COL4), FLOWERING LOCUS D (FD), FLOWERING LOCUS C/FRUITFULL (FLC/FUL) and SUPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) gene lineages. In addition to PEBP and AGL24/SVP genes previously analyzed, here we identify an increase of orchid homologs belonging to COL4, and FUL gene lineages in comparison with other monocots, including grasses, due to orchid-specific gene lineage duplications. Contrariwise, local duplications in Orchidaceae are less frequent in the COL, FD and SOC1 gene lineages, which points to a retention of key functions under strong purifying selection in essential signaling factors. We also identified changes in the protein sequences after such duplications, variation in the evolutionary rates of resulting paralogous clades and targeted expression of isolated homologs in different orchids. Interestingly, vernalization-response genes like VERNALIZATION1 (VRN1) and FLOWERING LOCUS C (FLC) are completely lacking in orchids, or alternatively are reduced in number, as is the case of VERNALIZATION2/GHD7 (VRN2). Our findings point to non-canonical factors sensing temperature changes in orchids during reproductive transition. Expression data of key factors gathered from Elleanthus auratiacus, a terrestrial orchid in high Andean mountains allow us to characterize which copies are actually active during flowering. Altogether, our data lays down a comprehensive framework to assess gene function of a restricted number of homologs identified more likely playing key roles during the flowering transition, and the changes of the FGRN in neotropical orchids in comparison with temperate grasses.

CONSTANS, a HUB for all seasons: How photoperiod pervades plant physiology regulatory circuits

How does a plant detect the changing seasons and make important developmental decisions accordingly? How do they incorporate daylength information into their routine physiological processes? Photoperiodism, or the capacity to measure the daylength, is a crucial aspect of plant development that helps plants determine the best time of the year to make vital decisions, such as flowering. The protein CONSTANS (CO) constitutes the central regulator of this sensing mechanism, not only activating florigen production in the leaves but also participating in many physiological aspects in which seasonality is important. Recent discoveries place CO in the center of a gene network that can determine the length of the day and confer seasonal input to aspects of plant development and physiology as important as senescence, seed size, or circadian rhythms. In this review, we discuss the importance of CO protein structure, function, and evolutionary mechanisms that embryophytes have developed to incorporate annual information into their physiology.

Circadian and photoperiodic regulation of the vegetative to reproductive transition in plants

As sessile organisms, plants must respond constantly to ever-changing environments to complete their life cycle; this includes the transition from vegetative growth to reproductive development. This process is mediated by photoperiodic response to sensing the length of night or day through circadian regulation of light-signaling molecules, such as phytochromes, to measure the length of night to initiate flowering. Flowering time is the most important trait to optimize crop performance in adaptive regions. In this review, we focus on interplays between circadian and light signaling pathways that allow plants to optimize timing for flowering and seed production in Arabidopsis, rice, soybean, and cotton. Many crops are polyploids and domesticated under natural selection and breeding. In response to adaptation and polyploidization, circadian and flowering pathway genes are epigenetically reprogrammed. Understanding the genetic and epigenetic bases for photoperiodic flowering will help improve crop yield and resilience in response to climate change.

Unveiling the phenology and associated floral regulatory pathways of Humulus lupulus L. in subtropical conditions

MAIN CONCLUSION

The hop phenological cycle was described in subtropical condition of Brazil showing that flowering can happen at any time of year and this was related to developmental molecular pathways. Hops are traditionally produced in temperate regions, as it was believed that vernalization was necessary for flowering. Nevertheless, recent studies have revealed the potential for hops to flower in tropical and subtropical climates. In this work, we observed that hops in the subtropical climate of Minas Gerais, Brazil grow and flower multiple times throughout the year, independently of the season, contrasting with what happens in temperate regions. This could be due to the photoperiod consistently being inductive, with daylight hours below the described threshold (16.5 h critical). We observed that when the plants reached 7-9 nodes, the leaves began to transition from heart-shaped to trilobed-shaped, which could be indicative of the juvenile to adult transition. This could be related to the fact that the 5th node (in plants with 10 nodes) had the highest expression of miR156, while two miR172s increased in the 20th node (in plants with 25 nodes). Hop flowers appeared later, in the 25th or 28th nodes, and the expression of HlFT3 and HlFT5 was upregulated in plants between 15 and 20 nodes, while the expression of HlTFL3 was upregulated in plants with 20 nodes. These results indicate the role of axillary meristem age in regulating this process and suggest that the florigenic signal should be maintained until the hop plants bloom. In addition, it is possible that the expression of TFL is not sufficient to inhibit flowering in these conditions and promote branching. These findings suggest that the reproductive transition in hop under inductive photoperiodic conditions could occur in plants between 15 and 20 nodes. Our study sheds light on the intricate molecular mechanisms underlying hop floral development, paving the way for potential advancements in hop production on a global scale.

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

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

Floral-promoting GmFT homologs trigger photoperiodic after-effects: An important mechanism for early-maturing soybean varieties to regulate reproductive development and adapt to high latitudes

Soybean (Glycine max) is a typical short-day plant, but has been widely cultivated in high-latitude long-day (LD) regions because of the development of early-maturing genotypes which are photoperiod-insensitive. However, some early-maturing varieties exhibit significant responses to maturity under different daylengths but not for flowering, depicting an evident photoperiodic after-effect, a poorly understood mechanism. In this study, we investigated the postflowering responses of 11 early-maturing soybean varieties to various preflowering photoperiodic treatments. We confirmed that preflowering SD conditions greatly promoted maturity and other postflowering developmental stages. Soybean homologs of FLOWERING LOCUS T (FT), including GmFT2a, GmFT3a, GmFT3b and GmFT5a, were highly accumulated in leaves under preflowering SD treatment. More importantly, they maintained a high expression level after flowering even under LD conditions. E1 RNAi and GmFT2a overexpression lines showed extremely early maturity regardless of preflowering SD and LD treatments due to constitutively high levels of floral-promoting GmFT homolog expression throughout their life cycle. Collectively, our data indicate that high and stable expression of floral-promoting GmFT homologs play key roles in the maintenance of photoperiodic induction to promote postflowering reproductive development, which confers early-maturing varieties with appropriate vegetative growth and shortened reproductive growth periods for adaptation to high latitudes.

Multistage temporal transcriptomic atlas unveils major contributor to reproductive phase in upland cotton

Flowering is a major developmental transition in plants, but asynchronous flowering hinders the utilization of wild cotton relatives in breeding programs. We performed comparative transcriptomic profiling of early- and late-flowering Gossypium hirsutum genotypes to elucidate genetic factors influencing reproductive timing. Shoot apices were sampled from the photoperiod-sensitive landrace G. hirsutum purpurascens (GhP) and early-maturing variety ZhongMianSuo (ZMS) at five time points following the emergence of sympodial nodes. RNA-sequencing revealed extensive transcriptional differences during floral transition. Numerous flowering-associated genes exhibited genotype-specific expression, including FLOWERING LOCUS T (FT) homologs upregulated in ZMS. FT-interacting factors like SOC1 and CO-like also showed higher expression in ZMS, implicating florigen pathways in early flowering. Additionally, circadian clock and light signalling components were misregulated between varieties, suggesting altered photoperiod responses in GhP. Weighted co-expression network analysis specifically linked a module enriched for circadian-related genes to GhP's late flowering. Through an integrated transcriptome analysis, we defined a regulatory landscape of reproductive phase change in cotton. Differentially expressed genes related to photoperiod, circadian clock, and light signalling likely contribute to delayed flowering in wild cottons. Characterization of upstream flowering regulators will enable modifying photoperiod sensitivity and expand germplasm use for cotton improvement. This study provides candidate targets for elucidating interactive mechanisms that control cotton flowering time across diverse genotypes.