Grass flower development

Comparative case study of evolutionary insights and floral complexity in key early-diverging eudicot Ranunculales models

Famously referred to as "Darwin's abominable mystery," the rapid diversification of angiosperms over the last ~140 million years presents a fascinating enigma. This diversification is underpinned by complex genetic pathways that evolve and rewire to produce diverse and sometimes novel floral forms. Morphological innovations in flowers are shaped not only by genetics but also by evolutionary constraints and ecological dynamics. The importance of model organisms in addressing the long-standing scientific questions related to diverse floral forms cannot be overstated. In plant biology, Arabidopsis thaliana, a core eudicot, has emerged as a premier model system, with its genome being the first plant genome to be fully sequenced. Similarly, model systems derived from crop plants such as Oryza sativa (rice) and Zea mays (maize) have been invaluable, particularly for crop improvement. However, despite their substantial utility, these model systems have limitations, especially when it comes to exploring the evolution of diverse and novel floral forms. The order Ranunculales is the earliest-diverging lineage of eudicots, situated phylogenetically between core eudicots and monocots. This group is characterized by its exceptional floral diversity, showcasing a wide range of floral morphologies and adaptations that offer valuable insights into the evolutionary processes of flowering plants. Over the past two decades, the development of at least five model systems including, Aquilegia, Thalictrum, Nigella, Delphinium and Eschscholzia within the Ranunculales order has significantly advanced our understanding of floral evolution. This review highlights the conservation and divergence of floral organ identity programs observed among these models and discusses their importance in advancing research within the field. The review also delves into elaborate petal morphology observed in Aquilegia, Nigella, and Delphinium genera, and further discusses the contributions, limitations, and future research directions for Ranunculales model systems. Integrating these diverse models from the early-diverging eudicot order has enhanced our understanding of the complex evolutionary pathways that shape floral diversity in angiosperms, bridging the knowledge gaps essential for a comprehensive understanding of floral evolution.

OsMADS6-OsMADS32 and REP1 control palea cellular heterogeneity and morphogenesis in rice

Precise regulation of cell proliferation and differentiation is vital for organ morphology. Rice palea, serving as sepal, comprises two distinct regions: the marginal region (MRP) and body of palea (BOP), housing heterogeneous cell populations, which makes it an ideal system for studying organ morphogenesis. We report that the transcription factor (TF) REP1 promotes epidermal cell proliferation and differentiation in the BOP, resulting in hard silicified protrusion cells, by regulating the cyclin-dependent kinase gene, OsCDKB1;1. Conversely, TFs OsMADS6 and OsMADS32 are expressed exclusively in the MRP, where they limit cell division rates by inhibiting OsCDKB2;1 expression and promote endoreduplication, yielding elongated epidermal cells. Furthermore, reciprocal inhibition between the OsMADS6-OsMADS32 complex and REP1 fine-tunes the balance between cell division and differentiation during palea morphogenesis. We further show the functional conservation of these organ identity genes in heterogeneous cell growth in Arabidopsis, emphasizing a critical framework for controlling cellular heterogeneity in organ morphogenesis.

STAMENLESS1 activates SUPERWOMAN 1 and FLORAL ORGAN NUMBER 1 to control floral organ identities and meristem fate in rice

Floral patterns are unique to rice and contribute significantly to its reproductive success. SL1 encodes a C2H2 transcription factor that plays a critical role in flower development in rice, but the molecular mechanism regulated by it remains poorly understood. Here, we describe interactions of the SL1 with floral homeotic genes, SPW1, and DL in specifying floral organ identities and floral meristem fate. First, the sl1 spw1 double mutant exhibited a stamen-to-pistil transition similar to that of sl1, spw1, suggesting that SL1 and SPW1 may located in the same pathway regulating stamen development. Expression analysis revealed that SL1 is located upstream of SPW1 to maintain its high level of expression and that SPW1, in turn, activates the B-class genes OsMADS2 and OsMADS4 to suppress DL expression indirectly. Secondly, sl1 dl displayed a severe loss of floral meristem determinacy and produced amorphous tissues in the third/fourth whorl. Expression analysis revealed that the meristem identity gene OSH1 was ectopically expressed in sl1 dl in the fourth whorl, suggesting that SL1 and DL synergistically terminate the floral meristem fate. Another meristem identity gene, FON1, was significantly decreased in expression in sl1 background mutants, suggesting that SL1 may directly activate its expression to regulate floral meristem fate. Finally, molecular evidence supported the direct genomic binding of SL1 to SPW1 and FON1 and the subsequent activation of their expression. In conclusion, we present a model to illustrate the roles of SL1, SPW1, and DL in floral organ specification and regulation of floral meristem fate in rice.

Femaleness for improving grain yield potential and hybrid production in barley

This article comments on:

Selva C, Yang X, Shirley NJ, Whitford R, Baumann U, Tucker MR. 2023. HvSL1 and HvMADS16 promote stamen identity to restrict multiple ovary formation in barley. Journal of Experimental Botany 74, 5039–5057.

Identification of candidate genes responsible for chasmogamy in wheat

BACKGROUND

The flowering biology of wheat plants favours self-pollination which causes obstacles in wheat hybrid breeding. Wheat flowers can be divided into two groups, the first one is characterized by flowering and pollination within closed flowers (cleistogamy), while the second one possesses the ability to open flowers during processes mentioned above (chasmogamy). The swelling of lodicules is involved in the flowering of cereals and among others their morphology, calcium and potassium content differentiate between cleistogamic and non-cleistogamous flowers. A better understanding of the chasmogamy mechanism can lead to the development of tools for selection of plants with the desired outcrossing rate. To learn more, the sequencing of transcriptomes (RNA-Seq) and Representational Difference Analysis products (RDA-Seq) were performed to investigate the global transcriptomes of wheat lodicules in two highly chasmogamous (HCH, Piko and Poezja) and two low chasmogamous (LCH, Euforia and KWS Dacanto) varieties at two developmental stages-pre-flowering and early flowering.

RESULTS

The differentially expressed genes were enriched in five, main pathways: "metabolism", "organismal systems", "genetic information processing", "cellular processes" and "environmental information processing", respectively. Important genes with opposite patterns of regulation between the HCH and LCH lines have been associated with the lodicule development i.e. expression levels of MADS16 and MADS58 genes may be responsible for quantitative differences in chasmogamy level in wheat.

CONCLUSIONS

We conclude that the results provide a new insight into lodicules involvement in the wheat flowering process. This study generated important genomic information to support the exploitation of the chasmogamy in wheat hybrid breeding programs.

Evolutionary history of the grass gynoecium

The grass family (Poaceae) includes cereal crops that provide a key food source for the human population. The food industry uses the starch deposited in the cereal grain, which develops directly from the gynoecium. Morphological interpretation of the grass gynoecium remains controversial. We re-examine earlier hypotheses and studies of morphology and development in the context of more recent analyses of grass phylogenetics and developmental genetics. Taken in isolation, data on gynoecium development in bistigmatic grasses do not contradict its interpretation as a solitary ascidiate carpel. Nevertheless, in the context of other data, this interpretation is untenable. Broad comparative analysis in a modern phylogenetic context clearly demonstrates that the grass gynoecium is pseudomonomerous. A bistigmatic grass gynoecium has two sterile carpels, each producing a stigma, and a fertile carpel that lacks a stigma. To date, studies of grass developmental genetics and developmental morphology have failed to fully demonstrate the composite nature of the grass gynoecium be-cause its complex evolutionary history is hidden by extreme organ integration. It is problematic to interpret the gynoecium of grasses in terms of normal angiosperm gynoecium typology. Even the concept of a carpel becomes misleading in grasses; instead, we recommend the term pistil for descriptive purposes.

The Streptochaeta Genome and the Evolution of the Grasses

In this work, we sequenced and annotated the genome of Streptochaeta angustifolia, one of two genera in the grass subfamily Anomochlooideae, a lineage sister to all other grasses. The final assembly size is over 99% of the estimated genome size. We find good collinearity with the rice genome and have captured most of the gene space. Streptochaeta is similar to other grasses in the structure of its fruit (a caryopsis or grain) but has peculiar flowers and inflorescences that are distinct from those in the outgroups and in other grasses. To provide tools for investigations of floral structure, we analyzed two large families of transcription factors, AP2-like and R2R3 MYBs, that are known to control floral and spikelet development in rice and maize among other grasses. Many of these are also regulated by small RNAs. Structure of the gene trees showed that the well documented whole genome duplication at the origin of the grasses (ρ) occurred before the divergence of the Anomochlooideae lineage from the lineage leading to the rest of the grasses (the spikelet clade) and thus that the common ancestor of all grasses probably had two copies of the developmental genes. However, Streptochaeta (and by inference other members of Anomochlooideae) has lost one copy of many genes. The peculiar floral morphology of Streptochaeta may thus have derived from an ancestral plant that was morphologically similar to the spikelet-bearing grasses. We further identify 114 loci producing microRNAs and 89 loci generating phased, secondary siRNAs, classes of small RNAs known to be influential in transcriptional and post-transcriptional regulation of several plant functions.

A Heterozygous Genotype-Dependent Branched-Spike Wheat and the Potential Genetic Mechanism Revealed by Transcriptome Sequencing

Simple Summary

This paper reported a novel type of branched spike wheat from a natural mutation event. The branched spike was controlled by a heterozygous genotype. The genetic patterns showed that gametophytic male sterility probably contributed to the heterozygous genotype responsible for the branched spike trait. Expressional levels and Wheat FRIZZY PANICLE (WFZP) sequencing between the mutant with the branched spike and the wild-type with the normal spike showed that WFZP was not the causal gene for the branched spike. Data from transcriptome sequencing indicated that carbohydrate metabolism might be involved in the formation of the branched spike trait.

Abstract

Wheat (Triticum aestivum L.) spike architecture is an important trait associated with spike development and grain yield. Here, we report a naturally occurring wheat mutant with branched spikelets (BSL) from its wild-type YD-16, which has a normal spike trait and confers a moderate level of resistance to wheat Fusarium head blight (FHB). The lateral meristems positioned at the basal parts of the rachis node of the BSL mutant develop into ramified spikelets characterized as multiple spikelets. The BSL mutant shows three to four-day longer growth period but less 1000-grain weight than the wild type, and it becomes highly susceptible to FHB infection, indicating that the locus controlling the BSL trait may have undergone an intensively artificial and/or natural selection in modern breeding process. The self-pollinated descendants of the lines with the BSL trait consistently segregated with an equal ratio of branched and normal spikelets (NSL) wheat, and homozygotes with the BSL trait could not be achieved even after nine cycles of self-pollination. Distinct segregation patterns both from the self-pollinated progenies of the BSL plants and from the reciprocal crosses between the BSL plants with their sister NSL plants suggested that gametophytic male sterility was probably associated with the heterozygosity for the BSL trait. Transcriptome sequencing of the RNA bulks contrasting in the two types of spike trait at the heading stage indicated that the genes on chromosome 2D_S may be critical for the BSL trait formation since 329 out of 2540 differentially expressed genes (DEGs) were located on that chromosome, and most of them were down-regulated. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that carbohydrate metabolism may be involved in the BSL trait expression. This work provides valuable clues into understanding development and domestication of wheat spike as well as the association of the BSL trait with FHB susceptibility.

Rice transcription factor MADS32 regulates floral patterning through interactions with multiple floral homeotic genes

Floral patterning is regulated by intricate networks of floral identity genes. The peculiar MADS32 subfamily genes, absent in eudicots but prevalent in monocots, control floral organ identity. However, how the MADS32 family genes interact with other floral homeotic genes during flower development is mostly unknown. We show here that the rice homeotic transcription factor OsMADS32 regulates floral patterning by interacting synergistically with E class protein OsMADS6 in a dosage-dependent manner. Furthermore, our results indicate important roles for OsMADS32 in defining stamen, pistil, and ovule development through physical and genetic interactions with OsMADS1, OsMADS58, and OsMADS13, and in specifying floral meristem identity with OsMADS6, OsMADS3, and OsMADS58, respectively. Our findings suggest that OsMADS32 is an important factor for floral meristem identity maintenance and that it integrates the action of other MADS-box homeotic proteins to sustain floral organ specification and development in rice. Given that OsMADS32 is an orphan gene and absent in eudicots, our data substantially expand our understanding of flower development in plants.

Developmental mechanisms involved in the diversification of flowers

We all appreciate the fantastic diversity of flowers. How flowers diversified, however, remains largely enigmatic. The mechanisms underlying the diversification of flowers are complex because the overall appearance of a flower is determined by many factors, such as the shape and size of its receptacle, and the arrangement, number, type, shape and colour of floral organs. Modifications of the developmental trajectories of a flower and its components, therefore, can lead to the generation of new floral types. In this Review, by summarizing the recent progress in studying the initiation, identity determination, morphogenesis and maturation of floral organs, we present our current understanding of the mechanisms underlying the diversification of flowers.

Rice Flower Development Revisited: Regulation of Carpel Specification and Flower Meristem Determinacy

The ABC model in flower development represents a milestone of plant developmental studies and is essentially conserved across a wide range of angiosperm species. Despite this overall conservation, individual genes in the ABC model are not necessarily conserved and sometimes play a species-specific role, depending on the plant. We previously reported that carpels are specified by the YABBY gene DROOPING LEAF (DL) in rice (Oryza sativa), which bears flowers that are distinct from those of eudicots. In contrast, another group reported that carpels are specified by two class C genes, OsMADS3 and OsMADS58. Here, we have addressed this controversial issue by phenotypic characterization of floral homeotic gene mutants. Analysis of a complete loss-of-function mutant of OsMADS3 and OsMADS58 revealed that carpel-like organs expressing DL were formed in the absence of the two class C genes. Furthermore, no known flower organs including carpels were specified in a double mutant of DL and SUPERWOMAN1 (a class B gene), which expresses only class C genes in whorls 3 and 4. These results suggest that, in contrast to Arabidopsis, class C genes are not a key regulator for carpel specification in rice. Instead, they seem to be involved in the elaboration of carpel morphology rather than its specification. Our phenotypic analysis also revealed that, similar to its Arabidopsis ortholog CRABS CLAW, DL plays an important function in regulating flower meristem determinacy in addition to carpel specification.

Genome-Wide Identification and Characterization of wALOG Family Genes Involved in Branch Meristem Development of Branching Head Wheat

The branched spike phenotype is an important supernumerary spikelet trait of Triticum turgidum L. associated with the production of significantly more grains per spike, thereby offering a higher potential yield. However, the genetic basis of branch meristem (BM) development remains to be fully elucidated in wheat. TAW1, an ALOG (Arabidopsis LSH1 and Oryza G1) family gene, has been shown to function as a unique regulator in promoting BM development in rice. In this study, we found that the development pattern of the BMs of the branched spike in wheat was similar to the indeterminate BMs of rice. Moreover, phylogenetic analysis classified the ALOG genes into 12 groups. This family of genes was found to have evolved independently in eudicots and monocots and was evolutionarily conserved between wheat and rice as well as during wheat polyploidization. Furthermore, experiments revealed that TtALOG2-1A, a TAW1-homologous gene, plays a significant role in regulating the transition of indeterminate BM fate. Finally, large-scale RNA-sequencing studies and quantitative real-time polymerase chain reaction (qRT-PCR) experiments revealed that members of the TtALOGs may act upstream of the TtMADS22, TtMADS47, and TtMADS55 genes to promote indeterminate BM activities. Our findings further knowledge on BM development in wheat.

A Genome-wide View of Transcriptome Dynamics During Early Spike Development in Bread Wheat

Wheat spike development is a coordinated process of cell proliferation and differentiation with distinctive phases and architecture changes. However, the dynamic alteration of gene expression in this process remains enigmatic. Here, we characterized and dissected bread wheat spike into six developmental stages, and used genome-wide gene expression profiling, to investigate the underlying regulatory mechanisms. High gene expression correlations between any two given stages indicated that wheat early spike development is controlled by a small subset of genes. Throughout, auxin signaling increased, while cytokinin signaling decreased. Besides, many genes associated with stress responses highly expressed during the double ridge stage. Among the differentially expressed genes (DEGs), were identified 375 transcription factor (TF) genes, of which some homologs in rice or Arabidopsis are proposed to function in meristem maintenance, flowering time, meristem initiation or transition, floral organ development or response to stress. Gene expression profiling demonstrated that these genes had either similar or distinct expression pattern in wheat. Several genes regulating spike development were expressed in the early spike, of which Earliness per se 3 (Eps-3) was found might function in the initiation of spikelet meristem. Our study helps uncover important genes associated with apical meristem morphology and development in wheat.

A Dynamic Co-expression Map of Early Inflorescence Development in Setaria viridis Provides a Resource for Gene Discovery and Comparative Genomics

The morphological and functional diversity of plant form is governed by dynamic gene regulatory networks. In cereal crops, grain and/or pollen-bearing inflorescences exhibit vast architectural diversity and developmental complexity, yet the underlying genetic framework is only partly known. Setaria viridis is a small, rapidly growing grass species in the subfamily Panicoideae, a group that includes economically important cereal crops such as maize and sorghum. The S. viridis inflorescence displays complex branching patterns, but its early development is similar to that of other panicoid grasses, and thus is an ideal model for studying inflorescence architecture. Here we report a detailed transcriptional resource that captures dynamic transitions across six sequential stages of S. viridis inflorescence development, from reproductive onset to floral organ differentiation. Co-expression analyses identified stage-specific signatures of development, which include homologs of previously known developmental genes from maize and rice, suites of transcription factors and gene family members, and genes of unknown function. This spatiotemporal co-expression map and associated analyses provide a foundation for gene discovery in S. viridis inflorescence development, and a comparative model for exploring related architectural features in agronomically important cereals.

Quantitative Trait Transcripts Mapping Coupled with Expression Quantitative Trait Loci Mapping Reveal the Molecular Network Regulating the Apetalous Characteristic in Brassica napus L

The apetalous trait of rapeseed (Brassica napus, AACC, 2n = 38) is important for breeding an ideal high-yield rapeseed with superior klendusity to Sclerotinia sclerotiorum. Currently, the molecular mechanism underlying the apetalous trait of rapeseed is unclear. In this study, 14 petal regulators genes were chosen as target genes (TGs), and the expression patterns of the 14 TGs in the AH population, containing 189 recombinant inbred lines derived from a cross between apetalous "APL01" and normal "Holly," were analyzed in two environments using qRT-PCR. Phenotypic data of petalous degree (PDgr) in the AH population were obtained from the two environments. Both quantitative trait transcript (QTT)-association mapping and expression QTL (eQTL) analyses of TGs expression levels were performed to reveal regulatory relationships among TGs and PDgr. QTT mapping for PDgr determined that PLURIPETALA (PLP) was the major negative QTT associated with PDgr in both environments, suggesting that PLP negatively regulates the petal development of line "APL01." The QTT mapping of PLP expression levels showed that CHROMATIN-REMODELING PROTEIN 11 (CHR11) was positively associated with PLP expression, indicating that CHR11 acts as a positive regulator of PLP expression. Similarly, QTT mapping for the remaining TGs identified 38 QTTs, associated with 13 TGs, and 31 QTTs, associated with 10 TGs, respectively, in the first and second environments. Additionally, eQTL analyses of TG expression levels showed that 12 and 11 unconditional eQTLs were detected in the first and second environment, respectively. Based on the QTTs and unconditional eQTLs detected, we presented a hypothetical molecular regulatory network in which 14 petal regulators potentially regulated the apetalous trait in "APL01" through the CHR11-PLP pathway. PLP acts directly as the terminal signal integrator negatively regulating petal development in the CHR11-PLP pathway. These findings will aid in the understanding the molecular mechanism underlying the apetalous trait of rapeseed.

Three TOB1-related YABBY genes are required to maintain proper function of the spikelet and branch meristems in rice

YABBY genes play important roles in the development of lateral organs such as leaves and floral organs in Angiosperms. However, the function of YABBY genes is poorly understood in monocots. We focused on three rice (Oryza sativa) YABBY genes, TONGARI-BOUSHI (TOB1, TOB2, TOB3), which are closely related to Arabidopsis (Arabidopsis thaliana) FILAMENTOUS FLOWER (FIL). To elucidate the function of these YABBY genes, we employed a reverse genetic approach. TOB genes were expressed in bract and lateral organ primordia, but not in meristems. RNAi knockdown of TOB2 or TOB3 in the tob1 mutant caused abnormal spikelet development. Furthermore, simultaneous knockdown of both TOB2 and TOB3 in tob1 affected not only spikelet, but also inflorescence development. In severe cases, the inflorescences comprised naked branches without spikelets. Analysis of inflorescence development at an early stage showed that the observed phenotypic defects were closely associated with a failure to initiate and maintain reproductive meristems. These results indicate that the TOB genes regulate the maintenance and fate of all reproductive meristems. It is likely that the function of FIL/TOB clade YABBY genes has been conserved between Arabidopsis and rice to maintain the proper function of meristems, even though these genes are expressed in lateral organ primordia.

Genetic Enhancer Analysis Reveals that FLORAL ORGAN NUMBER2 and OsMADS3 Co-operatively Regulate Maintenance and Determinacy of the Flower Meristem in Rice

Meristems such as the shoot apical meristem and flower meristem (FM) act as a reservoir of stem cells, which reproduce themselves and supply daughter cells for the differentiation of lateral organs. In Oryza sativa (rice), the FLORAL ORGAN NUMBER2 (FON2) gene, which is similar to Arabidopsis CLAVATA3, is involved in meristem maintenance. In fon2 mutants, the numbers of floral organs are increased due to an enlargement of the FM. To identify new factors regulating meristem maintenance in rice, we performed a genetic screening of mutants that enhanced the fon2 mutation, and found a mutant line (2B-424) in which pistil number was dramatically increased. By using a map-based approach and next-generation sequencing, we found that the line 2B-424 had a complete loss-of-function mutation (a large deletion) in OsMADS3, a class C MADS-box gene that is known to be involved in stamen specification. Disruption of OsMADS3 in the fon2 mutant by CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats-CRISPR-associated protein 9) technology caused a flower phenotype similar to that of 2B-424, confirming that the gene responsible for enhancement of fon2 was OsMADS3. Morphological analysis showed that the fon2 and osmads3 mutations synergistically affected pistil development and FM determinacy. We also found that whorl 3 was duplicated in mature flowers and the FM was enlarged at an early developmental stage in severe osmads3 single mutants. These findings suggest that OsMADS3 is involved not only in FM determinacy in late flower development but also in FM activity in early flower development.

Polar patterning of the spikelet is disrupted in the two opposite lemma mutant in rice

Angiosperms produce diverse flowers and the pattern of floral symmetry is a major factor for flower diversification. Bilaterally symmetric flowers have evolved multiple times in different angiosperm lineages from radially symmetric ancestors. Whereas most monocots produce radially symmetric flowers, grasses such as rice (Oryza sativa) and maize (Zea mays) generate bilaterally symmetric flowers and spikelets. In this paper, we focused on the two opposite lemma (tol) mutant, which displays a pleiotropic phenotype in the spikelet. Close morphological examination revealed that a typical spikelet phenotype of the tol mutant was principally based on the mirror image duplication of the lemma-side half of the spikelet. Other spikelet phenotypes can be explained as the derivation from the spikelet with this duplication. A polar pattern of organ formation along the lemma-palea axis was disrupted by this duplication. Accordingly, tol mutation seems to change the spikelet from bilateral symmetry (monosymmetry) to disymmetry. Thus, the tol mutant provides good genetic material to investigate the regulation of spikelet symmetry in rice.

Analysis of a rice fickle spikelet1 mutant that displays an increase in flower and spikelet organ number with inconstant expressivity

In rice (Oryza sativa), floral organs develop in the spikelet, an inflorescence unit unique to grass species. The floral organs, such as carpels, stamens and lodicules, are enclosed by two spikelet organs, the palea and lemma. The number of floral organs is genetically regulated. Mutations in the FLORAL ORGAN NUMBER (FON) genes cause an increase in the number of carpels and stamens due to an enlargement of the floral meristem. The spikelet organs, such as lemma and palea, are less affected in the fon mutants. We found a mutant, fickle spikelet1 (fsp1), that displayed an increased number not only of floral organs but also of spikelet organs. Because the fsp1 spikelets showed a pleiotropic phenotype, we classified them into four types. The expressivity of the fsp1 phenotype varied from plant to plant, and also from panicle to panicle within a single plant. In addition, the frequency of each fsp1 spikelet type also varied considerably among plants and among panicles within a plant. When the fsp1 mutants were grown in a growth chamber, an extra abnormality, namely a defect in pollen development, was observed. Furthermore, the expressivity of the mutant phenotype increased dramatically in mutant plants grown in a growth chamber. Thus, the expressivity of the fsp1 phenotype seems to be strongly influenced by environmental conditions.

Patterns of gene expression during Arabidopsis flower development from the time of initiation to maturation

Background

The formation of flowers is one of the main model systems to elucidate the molecular mechanisms that control developmental processes in plants. Although several studies have explored gene expression during flower development in the model plant Arabidopsis thaliana on a genome-wide scale, a continuous series of expression data from the earliest floral stages until maturation has been lacking. Here, we used a floral induction system to close this information gap and to generate a reference dataset for stage-specific gene expression during flower formation.

Results

Using a floral induction system, we collected floral buds at 14 different stages from the time of initiation until maturation. Using whole-genome microarray analysis, we identified 7,405 genes that exhibit rapid expression changes during flower development. These genes comprise many known floral regulators and we found that the expression profiles for these regulators match their known expression patterns, thus validating the dataset. We analyzed groups of co-expressed genes for over-represented cellular and developmental functions through Gene Ontology analysis and found that they could be assigned specific patterns of activities, which are in agreement with the progression of flower development. Furthermore, by mapping binding sites of floral organ identity factors onto our dataset, we were able to identify gene groups that are likely predominantly under control of these transcriptional regulators. We further found that the distribution of paralogs among groups of co-expressed genes varies considerably, with genes expressed predominantly at early and intermediate stages of flower development showing the highest proportion of such genes.

Conclusions

Our results highlight and describe the dynamic expression changes undergone by a large number of genes during flower development. They further provide a comprehensive reference dataset for temporal gene expression during flower formation and we demonstrate that it can be used to integrate data from other genomics approaches such as genome-wide localization studies of transcription factor binding sites.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1699-6) contains supplementary material, which is available to authorized users.

A role for TRIANGULAR HULL1 in fine-tuning spikelet morphogenesis in rice

The lemma and palea, which enclose the pistil, stamens, and lodicules, are the most conspicuous organs in the rice spikelet. We isolated a mutant line (ng6569) in which the lemma and palea were narrower than those of the wild type, and found that the mutant had a defect in TRIANGULAR HULL1 (TH1), which encodes a nuclear protein with an ALOG domain. Detailed morphological analysis indicated that the th1 mutation caused a reduction in the size of tubercles, which are convex structures on the surface of the lemma and palea. This reduction was more pronounced in the apical region of the lemma than in the basal region, resulting in the formation of a beak-like spikelet. By contrast, the number of tubercle rows and their spatial distribution on the lemma were not affected in the th1 mutant. Thus, the TH1 gene seems to be involved in fine-tuning the morphogenesis of the lemma and palea. In situ hybridization analysis revealed that TH1 was highly expressed in the primordia of the lemma and palea, but only weakly expressed in the primordia of the sterile lemma and rudimentary glume. We then examined the effect of th1 mutation on the lemma-like structure formed in the long sterile lemma/glume1 (g1) and extra glume1 (eg1) mutants. The result showed that the th1 mutation strongly affected the morphology of the extra lemma of eg1, but had no significant effect on the transformed lemma of g1.

Co-ordination of Flower Development Through Epigenetic Regulation in Two Model Species: Rice and Arabidopsis

Angiosperms produce flowers for reproduction. Flower development is a multistep developmental process, beginning with the initiation of the floral meristems, followed by floral meristem identity specification and maintenance, organ primordia initiation, floral organ identity specification, floral stem cell termination and finally floral organ maturation. During flower development, each of a large number of genes is expressed in a spatiotemporally regulated manner. Underlying these molecular and phenotypic events are various genetic and epigenetic pathways, consisting of diverse transcription factors, chromatin-remodeling factors and signaling molecules. Over the past 30 years, genetic, biochemical and genomic assays have revealed the underlying genetic frameworks that control flower development. Here, we will review the transcriptional regulation of flower development in two model species: Arabidopsis thaliana and rice (Oryza sativa). We focus on epigenetic regulation that functions to co-ordinate transcription pathways in flower development.

Overexpression of the JAZ factors with mutated jas domains causes pleiotropic defects in rice spikelet development

In a determinate meristem, such as a floral meristem, a genetically determined number of organs are produced before the meristem is terminated. In rice, iterative formation of organs during flower development with defects in meristem determinacy, classically called 'proliferation', is caused by several mutations and observed in dependence on environmental conditions. Here we report that overexpression of several JAZ proteins, key factors in jasmonate signaling, with mutations in the Jas domains causes an increase in the numbers of organs in florets, aberrant patterns of organ formation and repetitious organ production in spikelets. Our results imply that JAZ factors modulate mechanisms that regulate meristem functions during spikelet development.