Expression differences between normal and indeterminate1 maize suggest downstream targets of ID1, a floral transition regulator in maize

Genome-Wide Characterization of the INDETERMINATE DOMAIN (IDD) Zinc Finger Gene Family in Solanum lycopersicum and the Functional Analysis of SlIDD15 in Shoot Gravitropism

The plant-specific IDD transcription factors (TFs) are vital for regulating plant growth and developmental processes. However, the characteristics and biological roles of the IDD gene family in tomato (Solanum lycopersicum) are still largely unexplored. In this study, 17 SlIDD genes were identified in the tomato genome and classified into seven subgroups according to the evolutionary relationships of IDD proteins. Analysis of exon-intron structures and conserved motifs reflected the evolutionary conservation of SlIDDs in tomato. Collinearity analysis revealed that segmental duplication promoted the expansion of the SlIDD family. Ka/Ks analysis indicated that SlIDD gene orthologs experienced predominantly purifying selection throughout evolution. The analysis of cis-acting elements revealed that the promoters of SlIDD genes contain numerous elements associated with light, plant hormones, and abiotic stresses. The RNA-seq data and qRT-PCR experimental results showed that the SlIDD genes exhibited tissue-specific expression. Additionally, Group A members from Arabidopsis thaliana and rice are known to play a role in regulating plant shoot gravitropism. QRT-PCR analysis confirmed that the expression level of SlIDD15 in Group A was high in the hypocotyls and stems. Subcellular localization demonstrated that the SlIDD15 protein was localized in the nucleus. Surprisingly, the loss-of-function of SlIDD15 by CRISPR/Cas9 gene editing technology did not display obvious gravitropic response defects, implying the existence of functional redundant factors within SlIDD15. Taken together, this study offers foundational insights into the tomato IDD gene family and serves as a valuable guide for exploring their molecular mechanisms in greater detail.

INDETERMINATE1 autonomously regulates phosphate homeostasis upstream of the miR399-ZmPHO2 signaling module in maize

The macronutrient phosphorus is essential for plant growth and development. Plants have evolved multiple strategies to increase the efficiency of phosphate (Pi) acquisition to protect themselves from Pi starvation. However, the crosstalk between Pi homeostasis and plant development remains to be explored. Here, we report that overexpressing microRNA399 (miR399) in maize (Zea mays) is associated with premature senescence after pollination. Knockout of ZmPHO2 (Phosphate 2), a miR399 target, resulted in a similar premature senescence phenotype. Strikingly, we discovered that INDETERMINATE1 (ID1), a floral transition regulator, inhibits the transcription of ZmMIR399 genes by directly binding to their promoters, alleviating the repression of ZmPHO2 by miR399 and ultimately contributing to the maintenance of Pi homeostasis in maize. Unlike ZmMIR399 genes, whose expression is induced by Pi deficiency, ID1 expression was independent of the external inorganic orthophosphate status, indicating that ID1 is an autonomous regulator of Pi homeostasis. Furthermore, we show that ZmPHO2 was under selection during maize domestication and cultivation, resulting in a more sensitive response to Pi starvation in temperate maize than in tropical maize. Our study reveals a direct functional link between Pi-deprivation sensing by the miR399-ZmPHO2 regulatory module and plant developmental regulation by ID1.

Two interacting basic helix-loop-helix transcription factors control flowering time in rice

Flowering time is one of the most important agronomic traits affecting the adaptation and yield of rice (Oryza sativa). Heading date 1 (Hd1) is a key factor in the photoperiodic control of flowering time. In this study, two basic helix-loop-helix (bHLH) transcription factors, Hd1 Binding Protein 1 (HBP1) and Partner of HBP1 (POH1) were identified as transcriptional regulators of Hd1. We generated knockout mutants of HBP1 and ectopically expressed transgenic lines of the two bHLH transcription factors and used these lines to investigate the roles of these two factors in regulating flowering time. HBP1 physically associated with POH1 forming homo- or heterodimers to perform their functions. Both HBP1 and POH1 bound directly to the cis-acting elements located in the promoter of Hd1 to activate its expression. CRISPR/Cas9-generated knockout mutations of HBP1, but not POH1 mutations, promoted earlier flowering time; conversely, HBP1 and POH1 overexpression delayed flowering time in rice under long-day and short-day conditions by activating the expression of Hd1 and suppressing the expression of Early heading date 1 (Ehd1), Heading date 3a (Hd3a), and Rice Flowering locus T 1 (RFT1), thus controlling flowering time in rice. Our findings revealed a mechanism for flowering time control through transcriptional regulation of Hd1 and laid theoretical and practical foundations for improving the growth period, adaptation, and yield of rice.

Comprehensive Analysis of the INDETERMINATE DOMAIN (IDD) Gene Family and Their Response to Abiotic Stress in Zea mays

Transcription factors (TFs) are important regulators of numerous gene expressions due to their ability to recognize and combine cis-elements in the promoters of target genes. The INDETERMINATE DOMAIN (IDD) gene family belongs to a subfamily of C2H2 zinc finger proteins and has been identified only in terrestrial plants. Nevertheless, little study has been reported concerning the genome-wide analysis of the IDD gene family in maize. In total, 22 ZmIDD genes were identified, which can be distributed on 8 chromosomes in maize. On the basis of evolutionary relationships and conserved motif analysis, ZmIDDs were categorized into three clades (1, 2, and 3), each owning 4, 6, and 12 genes, respectively. We analyzed the characteristics of gene structure and found that 3 of the 22 ZmIDD genes do not contain an intron. Cis-element analysis of the ZmIDD promoter showed that most ZmIDD genes possessed at least one ABRE or MBS cis-element, and some ZmIDD genes owned the AuxRR-core, TCA-element, TC-rich repeats, and LTR cis-element. The Ka:Ks ratio of eight segmentally duplicated gene pairs demonstrated that the ZmIDD gene families had undergone a purifying selection. Then, the transcription levels of ZmIDDs were analyzed, and they showed great differences in diverse tissues as well as abiotic stresses. Furthermore, regulatory networks were constructed through the prediction of ZmIDD-targeted genes and miRNAs, which can inhibit the transcription of ZmIDDs. In total, 6 ZmIDDs and 22 miRNAs were discovered, which can target 180 genes and depress the expression of 9 ZmIDDs, respectively. Taken together, the results give us valuable information for studying the function of ZmIDDs involved in plant development and climate resilience in maize.

Expression of coffee florigen CaFT1 reveals a sustained floral induction window associated with asynchronous flowering in tropical perennials

The behavior of florigen(s) and environment-influenced regulatory pathways that control floral initiation in tropical perennials species with complex phenological cycles is poorly understood. Understanding the mechanisms underlying this process is important for food production in the face of climate change, thus, we used Coffea sp. L. (Rubiaceae) as a model to explore this issue. Homologs of FLOWERING LOCUS T (CaFT1) and environment-related regulators CONSTANS (CaCO), PHYTOCHROME INTERACTING FACTOR 4 (CaPIF4) and FLOWERING LOCUS C (CaFLC) were retrieved from coffee genomes and identified through phylogenetic analysis. Overexpression of CaFT1 in Arabidopsis caused early-flowering phenotype and yeast two hybrid studies indicated CaFT1 binding to bZIP floral regulator FD, which suggests that CaFT1 is a coffee florigen. Expression of CaFT1 and other floral regulators, together with carbohydrate analysis, were evaluated over one year using three contrasting genotypes, two C. arabica cultivars and C. canephora. All genotypes showed active and variable CaFT1 transcription from February until October, indicating the potential window for floral induction that reached a maximum in the cold period of June. CaCO expression, as expected, varied over a 24-hour day period and monthly with day length, whereas expression of temperature-responsive homologs, CaFLC and CaPIF4, did not correlate with temperature changes nor CaFT1 expression, suggesting alternative FT regulatory pathways in coffee. Based on our results, we suggest a continuum of floral induction that allows different starting points for floral activation, which explains developmental asynchronicity and prolonged anthesis events in tropical perennial species.

The Arabidopsis IDD14 transcription factor interacts with bZIP-type ABFs/AREBs and cooperatively regulates ABA-mediated drought tolerance

The INDETERMINATE DOMAIN (IDD) transcription factors mediate various aspects of plant growth and development. We previously reported that an Arabidopsis IDD subfamily regulates spatial auxin accumulation, and thus organ morphogenesis and gravitropic responses. However, its functions in stress responses are not well defined. Here, we use a combination of physiological, biochemical, molecular, and genetic approaches to provide evidence that the IDD14 cooperates with basic leucine zipper-type binding factors/ABA-responsive element (ABRE)-binding proteins (ABRE-binding factors (ABFs)/AREBs) in ABA-mediated drought tolerance. idd14-1D, a gain-of-function mutant of IDD14, exhibits decreased leaf water loss and improved drought tolerance, whereas inactivation of IDD14 in idd14-1 results in increased transpiration and reduced drought tolerance. Altered IDD14 expression affects ABA sensitivity and ABA-mediated stomatal closure. IDD14 can physically interact with ABF1-4 and subsequently promote their transcriptional activities. Moreover, ectopic expression and mutation of ABFs could, respectively, suppress and enhance plant sensitivity to drought stress in the idd14-1 mutant. Our results demonstrate that IDD14 forms a functional complex with ABFs and positively regulates drought-stress responses, thus revealing a previously unidentified role of IDD14 in ABA signaling and drought responses.

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.

Transcriptome Analysis to Identify Genes Related to Flowering Reversion in Tomato

Flowering reversion is a common phenomenon in plant development in which differentiated floral organs switch from reproductive growth to vegetative growth and ultimately form abnormal floral organs or vegetative organs. This greatly reduces tomato yield and quality. Research on this phenomenon has recently increased, but there is a lack of research at the molecular and gene expression levels. Here, transcriptomic analyses of the inflorescence meristem were performed in two kinds of materials at different developmental stages, and a total of 3223 differentially expressed genes (DEGs) were screened according to the different developmental stages and trajectories of the two materials. The analysis of database annotations showed that these DEGs were closely related to starch and sucrose metabolism, DNA replication and modification, plant hormone synthesis and signal transduction. It was further speculated that tomato flowering reversion may be related to various biological processes, such as cell signal transduction, energy metabolism and protein post-transcriptional regulation. Combined with the results of previous studies, our work showed that the gene expression levels of CLE9, FA, PUCHI, UF, CLV3, LOB30, SFT, S-WOX9 and SVP were significantly different in the two materials. Endogenous hormone analysis and exogenous hormone treatment revealed a variety of plant hormones involved in flowering reversion in tomato. Thus, tomato flowering reversion was studied comprehensively by transcriptome analysis for the first time, providing new insights for the study of flower development regulation in tomato and other plants.

MicroRNA-resistant alleles of HOMEOBOX DOMAIN-2 modify inflorescence branching and increase grain protein content of wheat

Plant and inflorescence architecture determine the yield potential of crops. Breeders have harnessed natural diversity for inflorescence architecture to improve yields, and induced genetic variation could provide further gains. Wheat is a vital source of protein and calories; however, little is known about the genes that regulate the development of its inflorescence. Here, we report the identification of semidominant alleles for a class III homeodomain-leucine zipper transcription factor, HOMEOBOX DOMAIN-2 (HB-2), on wheat A and D subgenomes, which generate more flower-bearing spikelets and enhance grain protein content. These alleles increase HB-2 expression by disrupting a microRNA 165/166 complementary site with conserved roles in plants; higher HB-2 expression is associated with modified leaf and vascular development and increased amino acid supply to the inflorescence during grain development. These findings enhance our understanding of genes that control wheat inflorescence development and introduce an approach to improve the nutritional quality of grain.

GmIDD Is Induced by Short Days in Soybean and May Accelerate Flowering When Overexpressed in Arabidopsis via Inhibiting AGAMOUS-LIKE 18

Photoperiod is one of the main climatic factors that determine flowering time and yield. Some members of the INDETERMINATE DOMAIN (IDD) transcription factor family have been reported to be involved in regulation of flowering time in Arabidopsis, maize, and rice. In this study, the domain analysis showed that GmIDD had a typical ID domain and was a member of the soybean IDD transcription factor family. Quantitative real-time PCR analysis showed that GmIDD was induced by short day conditions in leaves and regulated by circadian clock. Under long day conditions, transgenic Arabidopsis overexpressing GmIDD flowered earlier than wild-type, and idd mutants flowered later, while the overexpression of GmIDD rescued the late-flowering phenotype of idd mutants. Chromatin immunoprecipitation sequencing assays of GmIDD binding sites in GmIDD-overexpression (GmIDD-ox) Arabidopsis further identified potential direct targets, including a transcription factor, AGAMOUS-like 18 (AGL18). GmIDD might inhibit the transcriptional activity of flower repressor AGL18 by binding to the TTTTGGTCC motif of AGL18 promoter. Furthermore, the results also showed that GmIDD overexpression increased the transcription levels of flowering time-related genes FLOWERING LOCUS T (FT), SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1), LEAFY (LFY) and APETALA1 (AP1) in Arabidopsis. Taken together, GmIDD appeared to inhibit the transcriptional activity of AGL18 and induced the expression of FT gene to promote Arabidopsis flowering.

New insight into comprehensive analysis of INDETERMINATE DOMAIN (IDD) gene family in rice

The INDETERMINATE DOMAIN (IDD) transcription factor (TF), as a family of plant-specific zinc-finger proteins, regulates a variety of development processes and abiotic stresses in plants. IDD genes have been identified and characterized in other plants, however, the rice IDD family genes have not been investigated at genome-wide. In this study, 15 OsIDD genes were identified in rice genome and phylogenetically classified into two groups. Conserved motifs and potential interaction protein analysis about OsIDD proteins were carried out. Exon-intron structures, cis-acting elements and expression profiles of OsIDD genes were also examined. Exon-intron structures analysis revealed that overall structures of OsIDD genes were relatively conserved although they contained different numbers of introns. Cis-acting elements analysis suggested that most OsIDD gene transcripts could be induced by various abiotic stresses and phytohormones. The expression patterns of OsIDD genes were detected by qRT-PCR under cold and drought conditions, and by exogenous auxin (2,4-D), gibberellin (GA₃), and abscisic acid (ABA) treatments, respectively. The results showed that the OsIDDs might play essential roles under abiotic stresses and hormone responses. Distinct expression profiles in tissues/organs suggested that OsIDDs might be involved in different development processes in rice. More interestingly, the prediction of protein-protein interactions (PPIs) revealed OsIDDs could cooperate with some histone modifiers. Yeast two-hybrid assays were performed and confirmed it. Collectively, these results provide a foundation for further elucidation on the molecular mechanisms of OsIDD genes and advance our understanding of their biological function in rice.

Knowing When to Silence: Roles of Polycomb-Group Proteins in SAM Maintenance, Root Development, and Developmental Phase Transition

Polycomb repressive complex 1 (PRC1) and PRC2 are the major complexes composed of polycomb-group (PcG) proteins in plants. PRC2 catalyzes trimethylation of lysine 27 on histone 3 to silence target genes. Like Heterochromatin Protein 1/Terminal Flower 2 (LHP1/TFL2) recognizes and binds to H3K27me3 generated by PRC2 activities and enrolls PRC1 complex to further silence the chromatin through depositing monoubiquitylation of lysine 119 on H2A. Mutations in PcG genes display diverse developmental defects during shoot apical meristem (SAM) maintenance and differentiation, seed development and germination, floral transition, and so on so forth. PcG proteins play essential roles in regulating plant development through repressing gene expression. In this review, we are focusing on recent discovery about the regulatory roles of PcG proteins in SAM maintenance, root development, embryo development to seedling phase transition, and vegetative to reproductive phase transition.

Step by step evolution of Indeterminate Domain (IDD) transcriptional regulators: from algae to angiosperms

INTRODUCTION

The Indeterminate Domain (IDD) proteins are a plant-specific subclass of C2H2 Zinc Finger transcription factors. Some of these transcription factors play roles in diverse aspects of plant metabolism and development, but the function of most of IDD genes is unknown and the molecular evolution of the subfamily has not been explored in detail.

METHODS

In this study, we mined available genome sequences of green plants (Viridiplantae) to reconstruct the phylogeny and then described the motifs/expression patterns of IDD genes.

KEY RESULTS

We identified the complete set of IDD genes of 16 Streptophyta genomes. We found that IDD and its sister clade STOP arose by a duplication at the base of Streptophyta. Once on land, the IDD genes duplicated extensively, giving rise to at least ten lineages. Some of these lineages were lost in extant non-vascular plants and gymnosperms, but all of them were retained in angiosperms, duplicating profoundly in dicots and monocots and acquiring, at the same time, surprising heterogeneity in their C-terminal regions and expression patterns.

CONCLUSIONS

IDDs were present in the last common ancestor of Streptophyta. On land, IDDs duplicated extensively, leading to ten lineages. Later, IDDs were recruited by angiosperms where they diversified greatly in number, C-terminal and expression patterns. Interestingly, such diversification occurred during the evolution of novel traits of the plant body. This study provides a solid framework of the orthology relationships of green land plant IDD transcription factors, thus increasing the accuracy of orthologue identification in model and non-model species and facilitating the identification of agronomically important genes related to plant metabolism and development.

Interaction Between Induced and Natural Variation at oil yellow1 Delays Reproductive Maturity in Maize

We previously demonstrated that maize (Zea mays) locus very oil yellow1 (vey1) encodes a putative cis-regulatory expression polymorphism at the magnesium chelatase subunit I gene (aka oil yellow1) that strongly modifies the chlorophyll content of the semi-dominant Oy1-N1989 mutants. The vey1 allele of Mo17 inbred line reduces chlorophyll content in the mutants leading to reduced photosynthetic output. Oy1-N1989 mutants in B73 reached reproductive maturity four days later than wild-type siblings. Enhancement of Oy1-N1989 by the Mo17 allele at the vey1 QTL delayed maturity further, resulting in detection of a flowering time QTL in two bi-parental mapping populations crossed to Oy1-N1989. The near isogenic lines of B73 harboring the vey1 allele from Mo17 delayed flowering of Oy1-N1989 mutants by twelve days. Just as previously observed for chlorophyll content, vey1 had no effect on reproductive maturity in the absence of the Oy1-N1989 allele. Loss of chlorophyll biosynthesis in Oy1-N1989 mutants and enhancement by vey1 reduced CO₂ assimilation. We attempted to separate the effects of photosynthesis on the induction of flowering from a possible impact of chlorophyll metabolites and retrograde signaling by manually reducing leaf area. Removal of leaves, independent of the Oy1-N1989 mutant, delayed flowering but surprisingly reduced chlorophyll contents of emerging leaves. Thus, defoliation did not completely separate the identity of the signal(s) that regulates flowering time from changes in chlorophyll content in the foliage. These findings illustrate the necessity to explore the linkage between metabolism and the mechanisms that connect it to flowering time regulation.

Phosphorylation regulates the activity of INDETERMINATE-DOMAIN (IDD/BIRD) proteins in response to diverse environmental conditions

INDETERMINATE-DOMAIN proteins (IDDs) belong to a diverse plant-specific family of transcriptional regulators that coordinate distinct functions during plant growth and development. The functions of several of these IDD members are transcriptionally regulated, but so far nothing is known about the regulation at the post-translational level in spite of the fact that post-translational modifications of these proteins have been reported in several large-scale proteomics studies. Recently, we showed that IDD4 is a repressor of basal immunity and its characteristic traits are predominantly determined by the phosphorylation at two distinct phosphorylation sites. This finding prompted us to comprehensively review phosphorylation of the various IDD members from the plethora of phosphoproteomics studies demonstrating the post-translational modification of IDDs at highly conserved sites under various experimental conditions. We reckon that the phosphorylation of IDDs is an underrated mechanistic aspect in their regulation and we postulate their importance in IDD/BIRD functioning.

A Chimeric IDD4 Repressor Constitutively Induces Immunity in Arabidopsis via the Modulation of Salicylic Acid and Jasmonic Acid Homeostasis

INDETERMINATE DOMAIN (IDD)/BIRD proteins belong to a highly conserved plant-specific group of transcription factors with dedicated functions in plant physiology and development. Here, we took advantage of the chimeric repressor gene-silencing technology (CRES-T, SRDX) to widen our view on the role of IDD4/IMPERIAL EAGLE and IDD family members in plant immunity. The hypomorphic idd4SRDX lines are compromised in growth and show a robust autoimmune phenotype. Hormonal measurements revealed the concomitant accumulation of salicylic acid and jasmonic acid suggesting that IDDs are involved in regulating the metabolism of these biotic stress hormones. The analysis of immunity-pathways showed enhanced activation of immune MAP kinase-signaling pathways, the accumulation of hydrogen peroxide and spontaneous programmed cell death. The transcriptome of nonelicited idd4SRDX lines can be aligned to approximately 40% of differentially expressed genes (DEGs) in flg22-treated wild-type plants. The pattern of DEGs implies IDDs as pivotal repressors of flg22-dependent gene induction. Infection experiments showed the increased resistance of idd4SRDX lines to Pseudomonas syringae and Botrytis cinerea implying a function of IDDs in defense adaptation to hemibiotrophs and necrotrophs. Genome-wide IDD4 DNA-binding studies (DAP-SEQ) combined with DEG analysis of idd4SRDX lines identified IDD4-regulated functional gene clusters that contribute to plant growth and development. In summary, we discovered that the expression of idd4SRDX activates a wide range of defense-related traits opening up the possibility to apply idd4SRDX as a powerful tool to stimulate innate immunity in engineered crops.

INDETERMINATE-DOMAIN 4 (IDD4) coordinates immune responses with plant-growth in Arabidopsis thaliana

INDETERMINATE DOMAIN (IDD)/ BIRD proteins are a highly conserved plant-specific family of transcription factors which play multiple roles in plant development and physiology. Here, we show that mutation in IDD4/IMPERIAL EAGLE increases resistance to the hemi-biotrophic pathogen Pseudomonas syringae, indicating that IDD4 may act as a repressor of basal immune response and PAMP-triggered immunity. Furthermore, the idd4 mutant exhibits enhanced plant-growth indicating IDD4 as suppressor of growth and development. Transcriptome comparison of idd4 mutants and IDD4ox lines aligned to genome-wide IDD4 DNA-binding studies revealed major target genes related to defense and developmental-biological processes. IDD4 is a phospho-protein that interacts and becomes phosphorylated on two conserved sites by the MAP kinase MPK6. DNA-binding studies of IDD4 after flg22 treatment and with IDD4 phosphosite mutants show enhanced binding affinity to ID1 motif-containing promoters and its function as a transcriptional regulator. In contrast to the IDD4-phospho-dead mutant, the IDD4 phospho-mimicking mutant shows altered susceptibility to PstDC3000, salicylic acid levels and transcriptome reprogramming. In summary, we found that IDD4 regulates various hormonal pathways thereby coordinating growth and development with basal immunity.

Distinct gene networks modulate floral induction of autonomous maize and photoperiod-dependent teosinte

Temperate maize was domesticated from its tropical ancestor, teosinte. Whereas temperate maize is an autonomous day-neutral plant, teosinte is an obligate short-day plant that requires uninterrupted long nights to induce flowering. Leaf-derived florigenic signals trigger reproductive growth in both teosinte and temperate maize. To study the genetic mechanisms underlying floral inductive pathways in maize and teosinte, mRNA and small RNA genome-wide expression analyses were conducted on leaf tissue from plants that were induced or not induced to flower. Transcriptome profiles reveal common differentially expressed genes during floral induction, but a comparison of candidate flowering time genes indicates that photoperiod and autonomous pathways act independently. Expression differences in teosinte are consistent with the current paradigm for photoperiod-induced flowering, where changes in circadian clock output trigger florigen production. Conversely, differentially expressed genes in temperate maize link carbon partitioning and flowering, but also show altered expression of circadian clock genes that are distinct from those altered upon photoperiodic induction in teosinte. Altered miRNA399 levels in both teosinte and maize suggest a novel common connection between flowering and phosphorus perception. These findings provide insights into the molecular mechanisms underlying a strengthened autonomous pathway that enabled maize growth throughout temperate regions.

Strategies and tools to improve crop productivity by targeting photosynthesis

Crop productivity needs to substantially increase to meet global food and feed demand for a rapidly growing world population. Agricultural technology developers are pursuing a variety of approaches based on both traditional technologies such as genetic improvement, pest control and mechanization as well as new technologies such as genomics, gene manipulation and environmental modelling to develop crops that are capable of meeting growing demand. Photosynthesis is a key biochemical process that, many suggest, is not yet optimized for industrial agriculture or the modern global environment. We are interested in identifying control points in maize photoassimilation that are amenable to gene manipulation to improve overall productivity. Our approach encompasses: developing and using novel gene discovery techniques, translating our discoveries into traits and evaluating each trait in a stepwise manner that reflects a modern production environment. Our aim is to provide step change advancement in overall crop productivity and deliver this new technology into the hands of growers.This article is part of the themed issue 'Enhancing photosynthesis in crop plants: targets for improvement'.

Making Roots, Shoots, and Seeds: IDD Gene Family Diversification in Plants

The INDETERMINATE DOMAIN (IDD) family of transcriptional regulators controls a diversity of processes in a variety of plant tissues and organs and at different stages of plant development. Several recent reports describe the genetic characterization of IDD family members, including those that are likely to regulate C₄ kranz anatomy, with implications for the engineering of C₄ traits into C₃ crops. In this review we summarize the reported functions of IDD members in the regulation of metabolic sensing and leaf, root, seed, and inflorescence development. We also provide an IDD phylogeny for the grasses and suggest future directions and strategies to define the function of IDDs in C₄ photosynthesis and other developmental processes.

Maize susceptibility to Ustilago maydis is influenced by genetic and chemical perturbation of carbohydrate allocation

The ability of biotrophic fungi to metabolically adapt to the host environment is a critical factor in fungal diseases of crop plants. In this study, we analysed the transcriptome of maize tumours induced by Ustilago maydis to identify key features underlying metabolic shifts during disease. Among other metabolic changes, this analysis highlighted modifications during infection in the transcriptional regulation of carbohydrate allocation and starch metabolism. We confirmed the relevance of these changes by establishing that symptom development was altered in an id1 (indeterminate1) mutant that showed increased accumulation of sucrose as well as being defective in the vegetative to reproductive transition. We further established the relevance of specific metabolic functions related to carbohydrate allocation by assaying disease in su1 (sugary1) mutant plants with altered starch metabolism and in plants treated with glucose, sucrose and silver nitrate during infection. We propose that specific regulatory and metabolic changes influence the balance between susceptibility and resistance by altering carbon allocation to promote fungal growth or to influence plant defence. Taken together, these studies reveal key aspects of metabolism that are critical for biotrophic adaptation during the maize-U. maydis interaction.

Starch as a source, starch as a sink: the bifunctional role of starch in carbon allocation

Starch commands a central role in the carbon budget of the majority of plants on earth, and its biological role changes during development and in response to the environment. Throughout the life of a plant, starch plays a dual role in carbon allocation, acting as both a source, releasing carbon reserves in leaves for growth and development, and as a sink, either as a dedicated starch store in its own right (in seeds and tubers), or as a temporary reserve of carbon contributing to sink strength, in organs such as flowers, fruits, and developing non-starchy seeds. The presence of starch in tissues and organs thus has a profound impact on the physiology of the growing plant as its synthesis and degradation governs the availability of free sugars, which in turn control various growth and developmental processes. This review attempts to summarize the large body of information currently available on starch metabolism and its relationship to wider aspects of carbon metabolism and plant nutrition. It highlights gaps in our knowledge and points to research areas that show promise for bioengineering and manipulation of starch metabolism in order to achieve more desirable phenotypes such as increased yield or plant biomass.

Suppressor of rid1 (SID1) shares common targets with RID1 on florigen genes to initiate floral transition in rice

The transition from vegetative to reproductive growth is a critical process in the life cycle of higher plants. Previously, we cloned Rice Indeterminate 1 (RID1), which acts as the master switch for the transition from the vegetative to reproductive phase in rice. Although the photoperiod pathway of RID1 inducing expression of the florigen genes Hd3a and RFT1 via Ehd1 has been established, the alternative pathways for the essential flowering transition need to be further examined. Here, we identified a Suppressor of rid1 (SID1), which rescues the never-flowering phenotype of rid1. SID1 encodes an INDETERMINATE DOMAIN (IDD) transcription factor. Mutation in SID1 showed the delayed flowering phenotype. Gain-of-function of SID1, OsIDD1, or OsIDD6 could restore the rid1 to flowering. Further analyses showed SID1 and RID1 directly target the promoter regions of Hd3a and RFT1, two florigen genes in rice. Taken together, our results reveal an autonomous flowering pathway might be mediated by RID1, thereby controlling the phase transition from vegetative to reproductive development in rice.

Transition from vegetative to reproductive phase is a critical developmental switch in the life cycle of higher plants. In rice, our previous work suggested Rice Indeterminate 1 (RID1) acts as the master switch for the transition to flowering. Mutation in RID1 results in a never-flowering phenotype. In order to uncover the molecular network regulated by RID1, a Suppressor of rid1 (SID1) was identified in this study. Both SID1 and RID1 encode a plant-specific INDETERMINATE DOMAIN (IDD) transcription factor. Overexpression of SID1, OsIDD1, or OsIDD6 could rescue the never-flowering phenotype of rid1. Molecular data indicate both SID1 and RID1 physically bind the promoters of the florigen genes Hd3a and RFT1 in rice. Thus, we propose that the transition to flowering could be regulated by RID1 through the autonomous pathway, in addition to the photoperiod pathway.

Genetic Architecture of Flowering Phenology in Cereals and Opportunities for Crop Improvement

Cereal crop species including bread wheat (Triticum aestivum L.), barley (Hordeum vulgare L.), rice (Oryza sativa L.), and maize (Zea mays L.) provide the bulk of human nutrition and agricultural products for industrial use. These four cereals are central to meet future demands of food supply for an increasing world population under a changing climate. A prerequisite for cereal crop production is the transition from vegetative to reproductive and grain-filling phases starting with flower initiation, a key developmental switch tightly regulated in all flowering plants. Although studies in the dicotyledonous model plant Arabidopsis thaliana build the foundations of our current understanding of plant phenology genes and regulation, the availability of genome assemblies with high-confidence sequences for rice, maize, and more recently bread wheat and barley, now allow the identification of phenology-associated gene orthologs in monocots. Together with recent advances in next-generation sequencing technologies, QTL analysis, mutagenesis, complementation analysis, and RNA interference, many phenology genes have been functionally characterized in cereal crops and conserved as well as functionally divergent genes involved in flowering were found. Epigenetic and other molecular regulatory mechanisms that respond to environmental and endogenous triggers create an enormous plasticity in flowering behavior among cereal crops to ensure flowering is only induced under optimal conditions. In this review, we provide a summary of recent discoveries of flowering time regulators with an emphasis on four cereal crop species (bread wheat, barley, rice, and maize), in particular, crop-specific regulatory mechanisms and genes. In addition, pleiotropic effects on agronomically important traits such as grain yield, impact on adaptation to new growing environments and conditions, genetic sequence-based selection and targeted manipulation of phenology genes, as well as crop growth simulation models for predictive crop breeding, are discussed.

An insight into the sensitivity of maize to photoperiod changes under controlled conditions

Response of maize to photoperiods affects adaption of this crop to environments. We characterize the phenotypes of four temperate-adapted maize foundation parents, Huangzao 4, Chang 7-2, Ye 478 and Zheng 58, and two tropically adapted maize foundation parents, M9 and Shuang M9 throughout the growth stage under three constant photoperiod regimes in a daily cycle of 24 h at 28 °C, and analysed expression of 48 photoperiod response-associated genes. Consequently, long photoperiod (LP) repressed development of the tassels of photoperiod-sensitive maize lines at V9 stage, and caused subsequent failure in flowering; failure of photoperiod-sensitive maize lines in flowering under LP was associated with lower expression of flowering-related genes; photoperiod changes could make a marked impact on spatial layout of maize inflorescence. The larger oscillation amplitude of expression of photoperiod-responsive genes occurred in LP-sensitive maize lines. In conclusion, failure in development of tassels at V9 stage under LP is an early indicator for judging photoperiod sensitivity. The adaptation of temperate-adapted maize lines to LP is due to the better coordination of expression among photoperiod-sensing genes instead of the loss of the genes. High photoperiod sensitivity of maize is due to high expression of circadian rhythm-responding genes improperly early in the light.

Cracking the Kranz enigma with systems biology

Leaves with Kranz anatomy exhibit a highly characteristic arrangement of closely spaced veins surrounded by concentric wreaths of bundle sheath and mesophyll cells. This anatomical framework is vital for effective C4 photosynthesis in nearly all known land plant lineages and has evolved independently on over 60 occasions. Over the last 3 years, technological advances, particularly in high-throughput DNA sequencing, have allowed the development of Kranz anatomy to be interrogated at unprecedented depth. This review highlights the recent advances in our understanding that have been facilitated by systems biology approaches, and proposes a testable model for the regulation of Kranz development.

Using evolution as a guide to engineer kranz-type c4 photosynthesis

Kranz-type C4 photosynthesis has independently and rapidly evolved over 60 times to dramatically increase radiation use efficiency in both monocots and eudicots. Indeed, it is one of the most exceptional examples of convergent evolution in the history of life. The repeated and rapid evolution of Kranz-type C4 suggests that it may be a derivative of a conserved developmental pathway that is present in all angiosperms. Here, I argue that the Kranz-type C4 photosynthetic system is an extension of the endodermis/starch sheath, that is normally only found in the roots and stems, into photosynthetic structures such as leaves. Support for this hypothesis was recently provided by a study that showed that the same genetic pathway that gives rise to the endodermis in roots, the SCARECROW/SHORT-ROOT radial patterning system, also regulates the development of Kranz anatomy and C4 physiology in leaves. This new hypothesis for the evolution of Kranz-type C4 photosynthesis has opened new opportunities to explore the underlying genetic networks that regulate the development and physiology of C4 and provides new potential avenues for the engineering of the mechanism into C3 crops.

Heavy traffic in the fast lane: long-distance signalling by macromolecules

The two major vascular conduits in plants, the xylem and phloem, theoretically provide opportunities for the long-distance translocation of almost any type of water-borne molecule. This review focuses on the signalling functions conveyed by the movement of macromolecules. Here, a signal is defined as the communication of information from source to destination, where it modifies development, physiology or defence through altered gene expression or by direct influences on other cellular processes. Xylem and phloem sap both contain diverse classes of proteins; in addition, phloem contains many full-length and small RNA species. Only a few of these mobile molecules have proven functions in signalling. The transduction of signals typically depends on connection to appropriate signalling pathways. Incoming protein signals require specific detection systems, generally via receptors. Mobile RNAs require either the translation or presence of a homologous target. Given that phloem sieve elements are enucleate and lack translation machinery, RNA function requires subsequent unloading at least into adjacent companion cells. The binding of RNA by proteins in ribonucleoprotein complexes enables the translocation of some signals, with evidence for both sequence-specific and size-specific binding. Several examples of long-distance macromolecular signalling are highlighted, including the FT protein signal which regulates flowering time and other developmental switches.

Genome-wide expression profiling of maize in response to individual and combined water and nitrogen stresses

BACKGROUND

Water and nitrogen are two of the most critical inputs required to achieve the high yield potential of modern corn varieties. Under most agricultural settings however they are often scarce and costly. Fortunately, tremendous progress has been made in the past decades in terms of modeling to assist growers in the decision making process and many tools are now available to achieve more sustainable practices both environmentally and economically. Nevertheless large gaps remain between our empirical knowledge of the physiological changes observed in the field in response to nitrogen and water stresses, and our limited understanding of the molecular processes leading to those changes.

RESULTS

This work examines in particular the impact of simultaneous stresses on the transcriptome. In a greenhouse setting, corn plants were grown under tightly controlled nitrogen and water conditions, allowing sampling of various tissues and stress combinations. A microarray profiling experiment was performed using this material and showed that the concomitant presence of nitrogen and water limitation affects gene expression to an extent much larger than anticipated. A clustering analysis also revealed how the interaction between the two stresses shapes the patterns of gene expression over various levels of water stresses and recovery.

CONCLUSIONS

Overall, this study suggests that the molecular signature of a specific combination of stresses on the transcriptome might be as unique as the impact of individual stresses, and hence underlines the difficulty to extrapolate conclusions obtained from the study of individual stress responses to more complex settings.

Florigenic and antiflorigenic signaling in plants

The evidence that FLOWERING LOCUS T (FT) protein, and its paralog TWIN SISTER OF FT, act as the long-distance floral stimulus, or at least that they are part of it in diverse plant species, has attracted much attention in recent years. Studies to understand the physiological and molecular apparatuses that integrate spatial and temporal signals to regulate developmental transitions in plants have occupied countless scientists and have resulted in an unmanageably large amount of research data. Analysis of these data has helped to identify multiple systemic florigenic and antiflorigenic regulators. This study gives an overview of the recent research on gene products, phytohormones and other metabolites that have been demonstrated to have florigenic or antiflorigenic functions in plants.

Transcript and metabolite signature of maize source leaves suggests a link between transitory starch to sucrose balance and the autonomous floral transition

Little is known about the nature of floral inductive cues in day-neutral plants that are insensitive to photoperiod variations and, therefore, rely on endogenous signals to initiate reproductive growth. The INDETERMINATE1 (ID1) transcription factor is a key regulator of the transition to flowering in day-neutral maize. The ID1 gene is expressed exclusively in developing leaves, where it controls the production or transmission of leaf-derived florigenic signals. Florigen-producing source leaves were compared with mature leaves of late-flowering id1 plants, and metabolite and gene expression differences associated with the floral transition in maize were observed. While id1 mutants have a similar capacity for photosynthesis to wild-type siblings, id1 source leaves show quantitative differences in carbohydrate allocation prior to the floral transition stage, with a marked increase in sucrose and other soluble sugars, accompanied by a decrease in tricarboxylic acid (TCA) cycle organic acids. Importantly, source leaves of autonomous-flowering maize are typified by a higher transitory starch to sucrose ratio and a transcript profile enriched for sucrose synthesis and starch metabolism-related gene function. Finally, similar changes in transitory starch and sucrose are not observed in teosinte, the tropical progenitor of maize that requires short-day photoperiods to induce flowering. Together, these data define a transcript and metabolite signature associated with the autonomous floral transition in temperate maize leaves.

A gene regulatory network model for floral transition of the shoot apex in maize and its dynamic modeling

The transition from the vegetative to reproductive development is a critical event in the plant life cycle. The accurate prediction of flowering time in elite germplasm is important for decisions in maize breeding programs and best agronomic practices. The understanding of the genetic control of flowering time in maize has significantly advanced in the past decade. Through comparative genomics, mutant analysis, genetic analysis and QTL cloning, and transgenic approaches, more than 30 flowering time candidate genes in maize have been revealed and the relationships among these genes have been partially uncovered. Based on the knowledge of the flowering time candidate genes, a conceptual gene regulatory network model for the genetic control of flowering time in maize is proposed. To demonstrate the potential of the proposed gene regulatory network model, a first attempt was made to develop a dynamic gene network model to predict flowering time of maize genotypes varying for specific genes. The dynamic gene network model is composed of four genes and was built on the basis of gene expression dynamics of the two late flowering id1 and dlf1 mutants, the early flowering landrace Gaspe Flint and the temperate inbred B73. The model was evaluated against the phenotypic data of the id1 dlf1 double mutant and the ZMM4 overexpressed transgenic lines. The model provides a working example that leverages knowledge from model organisms for the utilization of maize genomic information to predict a whole plant trait phenotype, flowering time, of maize genotypes.

ZmCCT and the genetic basis of day-length adaptation underlying the postdomestication spread of maize

Teosinte, the progenitor of maize, is restricted to tropical environments in Mexico and Central America. The pre-Columbian spread of maize from its center of origin in tropical Southern Mexico to the higher latitudes of the Americas required postdomestication selection for adaptation to longer day lengths. Flowering time of teosinte and tropical maize is delayed under long day lengths, whereas temperate maize evolved a reduced sensitivity to photoperiod. We measured flowering time of the maize nested association and diverse association mapping panels in the field under both short and long day lengths, and of a maize-teosinte mapping population under long day lengths. Flowering time in maize is a complex trait affected by many genes and the environment. Photoperiod response is one component of flowering time involving a subset of flowering time genes whose effects are strongly influenced by day length. Genome-wide association and targeted high-resolution linkage mapping identified ZmCCT, a homologue of the rice photoperiod response regulator Ghd7, as the most important gene affecting photoperiod response in maize. Under long day lengths ZmCCT alleles from diverse teosintes are consistently expressed at higher levels and confer later flowering than temperate maize alleles. Many maize inbred lines, including some adapted to tropical regions, carry ZmCCT alleles with no sensitivity to day length. Indigenous farmers of the Americas were remarkably successful at selecting on genetic variation at key genes affecting the photoperiod response to create maize varieties adapted to vastly diverse environments despite the hindrance of the geographic axis of the Americas and the complex genetic control of flowering time.

ZCN8 encodes a potential orthologue of Arabidopsis FT florigen that integrates both endogenous and photoperiod flowering signals in maize

Higher plants use multiple perceptive measures to coordinate flowering time with environmental and endogenous cues. Physiological studies show that florigen is a mobile factor that transmits floral inductive signals from the leaf to the shoot apex. Arabidopsis FT protein is widely regarded as the archetype florigen found in diverse plant species, particularly in plants that use inductive photoperiods to flower. Recently, a large family of FT homologues in maize, the Zea CENTRORADIALIS (ZCN) genes, was described, suggesting that maize also contains FT-related proteins that act as a florigen. The product of one member of this large family, ZCN8, has several attributes that make it a good candidate as a maize florigen. Mechanisms underlying the floral transition in maize are less well understood than those of other species, partly because flowering in temperate maize is dependent largely on endogenous signals. The maize indeterminate1 (id1) gene is an important regulator of maize autonomous flowering that acts in leaves to mediate the transmission or production of florigenic signals. This study finds that id1 acts upstream of ZCN8 to control its expression, suggesting a possible new link to flowering in day-neutral maize. Moreover, in teosinte, a tropical progenitor of maize that requires short-day photoperiods to induce flowering, ZCN8 is highly up-regulated in leaves under inductive photoperiods. Finally, vascular-specific expression of ZCN8 in Arabidopsis complements the ft-1 mutation, demonstrating that leaf-specific expression of ZCN8 can induce flowering. These results suggest that ZCN8 may encode a florigen that integrates both endogenous and environmental signals in maize.

Long-distance regulation of flowering time

One of the great mysteries of plant science appears to have been resolved with the discovery that the protein FT can act as a phloem-mobile florigen hormone. The collective evidence from several laboratories, many from studies on photoperiod response, indicates that FT and its homologues are universal signalling molecules for flowering plants. Duplication and divergence of FT-like proteins reveals an increased complexity of function in certain taxonomic groups including grasses and legumes. There are additional components of long-distance flowering time control, such as a role for gibberellins in some species but probably not others. Cytokinins and sugars are further putative signals. Vernalization processes and responses are generally considered to occur in shoot meristems, but systemic responses to cold have been reported several times. Finally, there is increasing evidence that FT does not act purely to switch on flowering, but in addition, has broader roles in seasonal developmental switches such as bud dormancy and tuberization, and in the regulation of meristem determinacy and compound leaf development. This review seeks to highlight recent progress in systemic floral signalling, and to indicate areas in need of further research.

Modulation of sugar metabolism by an INDETERMINATE DOMAIN transcription factor contributes to photoperiodic flowering in Arabidopsis

There has been a long-standing interest in the role played by sugars in flowering. Of particular interest is how sugar-related signals are integrated into flowering genetic pathways. Here, we demonstrate that the INDETERMINATE DOMAIN transcription factor AtIDD8 regulates photoperiodic flowering by modulating sugar transport and metabolism. We found that whereas AtIDD8-deficient idd8 mutants exhibit delayed flowering under long days, AtIDD8-overexpressing plants (35S:IDD8) show early flowering. In addition, the sucrose synthase genes SUS1 and SUS4 were upregulated in 35S:IDD8 plants but downregulated in idd8 mutants, in which endogenous sugar levels were altered. AtIDD8 activates the SUS4 gene by binding directly to its promoter, resulting in promoted flowering in SUS4-overexpressing plants. SUS4 expression also responds to photoperiodic signals. Notably, the AtIDD8 gene is suppressed by sugar deprivation. Therefore, we conclude that AtIDD8 regulation of sugar transport and metabolism is linked to photoperiodic flowering.

Regulation of flowering in rice: two florigen genes, a complex gene network, and natural variation

Photoperiodic control of flowering time consists of a complicated network that converges into the generation of a mobile flowering signal called florigen. Recent advances identifying the protein FT/Hd3a as the molecular nature responsible for florigen activity have focused current research on florigen genes as the important output of this complex signaling network. Rice is a model system for short-day plants and recent progress in elucidating the flowering network from rice and Arabidopsis, a long-day plant, provides an evolutionarily comparative view of the photoperiodic flowering pathway. This review summarizes photoperiodic flowering control in rice, including the interaction of complex layers of gene networks contributed from evolutionarily unique factors and the regulatory adaptation of conserved factors.

Functional characterization of the HD-ZIP IV transcription factor OCL1 from maize

OCL1 (OUTER CELL LAYER1) encodes a maize HD-ZIP class IV transcription factor (TF) characterized by the presence of a homeo DNA-binding domain (HD), a dimerization leucine zipper domain (ZIP), and a steroidogenic acute regulatory protein (StAR)-related lipid transfer domain (START) involved in lipid transport in animals but the function of which is still unknown in plants. By combining yeast and plant trans-activation assays, the transcriptional activation domain of OCL1 was localized to 85 amino acids in the N-terminal part of the START domain. Full-length OCL1 devoid of this activation domain is unable to trans-activate a reporter gene under the control of a minimal promoter fused to six repeats of the L1 box, a cis-element present in target genes of HD-ZIP IV TFs in Arabidopsis. In addition, ectopic expression of OCL1 leads to pleiotropic phenotypic aberrations in transgenic maize plants, the most conspicuous one being a strong delay in flowering time which is correlated with the misexpression of molecular markers for floral transition such as ZMM4 (Zea Mays MADS-box4) or DLF1 (DELAYED FLOWERING1). As suggested by the interaction in planta between OCL1 and SWI3C1, a bona fide subunit of the SWI/SNF complex, OCL1 may modulate transcriptional activity of its target genes by interaction with a chromatin remodelling complex.

Rice Indeterminate 1 (OsId1) is necessary for the expression of Ehd1 (Early heading date 1) regardless of photoperiod

Indeterminate 1 (Id1), a classical flowering gene first reported in 1946, is one of the earliest genes whose expression in leaf tissues affects the floral transition in the shoot meristem. How Id1 is integrated into the flowering process is largely unknown. In this study, we examined the genetic action of the rice (Oryza sativa) ortholog OsId1. In rice, OsId1 is preferentially expressed in young leaves, but the overall expression pattern is broader than that in maize (Zea mays). OsId1 is able to activate transcription in yeast. RNAi mutants show a delay in flowering under both short-day (SD) and long-day (LD) conditions. OsId1 regulates the expression of Ehd1 (Early heading date 1) and its downstream genes, including Hd3a (a rice ortholog of FT) and RFT1 (Rice Flowering Locus T1), under both SD and LD conditions. In rice, the expression of Ehd1 is also controlled by the photoperiodic flowering genes OsGI (a rice ortholog of GI) and OsMADS51. However, the expression of OsId1 is independent of OsGI, OsMADS51, and OsMADS50 (a rice SOC1 ortholog). This study demonstrates that the activation of Ehd1 by OsId1 is required for the promotion of flowering.

Ehd2, a rice ortholog of the maize INDETERMINATE1 gene, promotes flowering by up-regulating Ehd1

Recent research into the flowering of rice (Oryza sativa) has revealed both unique and conserved genetic pathways in the photoperiodic control of flowering compared with those in Arabidopsis (Arabidopsis thaliana). We discovered an early heading date2 (ehd2) mutant that shows extremely late flowering under both short- and long-day conditions in line with a background deficient in Heading date1 (Hd1), a rice CONSTANS ortholog that belongs to the conserved pathway. This phenotype in the ehd2 mutants suggests that Ehd2 is pivotal for the floral transition in rice. Map-based cloning revealed that Ehd2 encodes a putative transcription factor with zinc finger motifs orthologous to the INDETERMINATE1 (ID1) gene, which promotes flowering in maize (Zea mays). Ehd2 mRNA in rice tissues accumulated most abundantly in developing leaves, but was present at very low levels around the shoot apex and in roots, patterns that are similar to those of ID1. To assign the position of Ehd2 within the flowering pathway of rice, we compared transcript levels of previously isolated flowering-time genes, such as Ehd1, a member of the unique pathway, Hd3a, and Rice FT-like1 (RFT1; rice florigens), between the wild-type plants and the ehd2 mutants. Severely reduced expression of these genes in ehd2 under both short- and long-day conditions suggests that Ehd2 acts as a flowering promoter mainly by up-regulating Ehd1 and by up-regulating the downstream Hd3a and RFT1 genes in the unique genetic network of photoperiodic flowering in rice.

A maize CONSTANS-like gene, conz1, exhibits distinct diurnal expression patterns in varied photoperiods

Maize (Zea mays ssp. mays L.) was domesticated from teosinte (Z. mays L. ssp. parviglumis Iltis & Doebley), a plant requiring short day photoperiods to flower. While photoperiod sensitive landraces of maize exist, post-domestication breeding included efforts to grow maize in a broad range of latitudes. Thus, modern maize is often characterized as day-neutral because time to flower is relatively unaffected by photoperiod. We report the first identification of maize constans of Zea mays1 (conz1), a gene with extensive sequence homology to photoperiod genes CONSTANS (CO) in Arabidopsis (Arabidopsis thaliana (L.) Heynh.) and Heading date1 (Hd1) in rice (Oryza sativa L.). conz1 maps to a syntenous chromosomal location relative to Hd1. Additionally, conz1 and two maize homologs of another photoperiod gene exhibit diurnal expression patterns notably similar to their Arabidopsis and rice homologs. The expression pattern of conz1 in long days is distinct from that observed in short days, suggesting that maize is able to discern variations in photoperiod and respond with differential expression of conz1. We offer models to reconcile the differential expression of conz1 with respect to the photoperiod insensitivity exhibited by temperate inbreds.