Interactions between FLORAL ORGAN NUMBER4 and floral homeotic genes in regulating rice flower development

An AP2/ERF transcription factor controls generation of the twin-seedling rice

INTRODUCTION

The floret of rice is a main component of the spikelet, and the ovule of pistil is a critical organ for successful reproduction and determines the number of seeds. However, the molecular mechanisms underlying the ovule development remain elusive.

OBJECTIVE

Twin-seedling rice has great potential for application in rice production. The study was to isolate the gene that controls twin-seedling in rice and explore the molecular function of the gene in floret development.

METHODS

We discovered a twin-seedling rice (tsr) mutant and constructed different segregating populations to clone TSR gene using map-based cloning method. To explore the molecular functions of TSR in determination of the ovary number and development, we applied molecular technologies such as yeast two-hybrid assay, electrophoretic mobility shift assay (EMSA), and dual-LUC transient expression assay to search for the TSR-interacting proteins and the target genes regulated by TSR.

RESULTS

We report here the map-based cloning of TSR which encodes an AP2/ERF transcription factor. Mutations in TSR lead to occurrence of the twin-seedling rice. The tsr mutant showed open hulls of the spikelets and displayed changes in the number of stamens and ovules of the florets. The ovary of tsr mutant contained two conjugated ovules which developed into a mature seed with two viable embryos. Mechanistic studies revealed that TSR regulates the expression levels of genes related to spikelet determination and ovule identity by binding to their promoters. Furthermore, TSR interacted with OsMADS1 and this interaction allowed OsMADS1 to modulate the transcriptional activityy of TSR on gene expression. The molecular study of TSR provides new insights into the formation and development of rice floret and helps breeders generate twin-seedling rice in production.

OsmiRNA5488 Regulates the Development of Embryo Sacs and Targets OsARF25 in Rice (Oryza sativa L.)

Small RNAs are a class of non-coding RNAs that typically range from 20 to 24 nucleotides in length. Among them, microRNAs (miRNAs) are particularly important regulators for plant development. The biological function of the conserved miRNAs has been studied extensively in plants, while that of the species-specific miRNAs has been studied in-depth. In this study, the regulatory role of a rice-specific OsmiRNA5488 (OsmiR5488) was characterized with the miR5488-overexpressed line (miR5488-OE) and miR5488-silenced line (STTM-5488). The seed-setting rate was notably reduced in miR5488-OE lines, but not in STTM-5488 lines. Cytological observation demonstrated the different types of abnormal mature embryo sacs, including the degeneration of embryo sacs and other variant types, in miR5488-OE lines. The percentage of the abnormal mature embryo sacs accounted for the reduced value of the seed-setting rate. Furthermore, OsARF25 was identified as a target of OsmiR5488 via RNA ligase-mediated 3'-amplifification of cDNA ends, dual luciferase assays, and transient expression assays. The primary root length was decreased with the increases in auxin concentrations in miR5488-OE lines compared to wild-type rice. Summarily, our results suggested that OsmiR5488 regulates the seed-setting rate and down-regulates the targeted gene OsARF25.

LAX1, functioning with MADS-box genes, determines normal palea development in rice

Normal floral organ development in rice is necessary for grain formation. Many MADS-box family genes that belong to ABCDE model have been widely implicated in rice flower development. The LAX1 allele encodes a plant-specific basic helix-loop-helix (bHLH) transcription factor, which is the main regulator of axillary meristem formation in rice. However, the molecular mechanisms of LAX1 allele together with MADS-box family genes underlying palea development have not been reported. We found a short palea mutant plant in a population of indica rice variety 9311 treated with cobalt 60. We report the map-based cloning and characterization of lax1-7, identified as a new mutant allele of the LAX1 locus, and the role of its wild-type allele LAX1 in rice palea development. Through complementary experiments, combined with genetic and molecular biological analyses, the function of the LAX1 allele was determined. We showed that LAX1 allele is expressed specifically in young spikelets and encodes a nucleus-localized protein. In vitro and in vivo experiments revealed that the LAX1 protein physically interacts with OsMADS1, OsMADS6 and OsMADS7. The LAX1 allele is pleiotropic for the maintenance of rice palea identity via cooperation with MADS-box genes and other traits, including axillary meristem initiation, days to heading, plant height, panicle length and spikelet fertility.

Analysis of Altered Flowering Related Genes in a Multi-Silique Rapeseed (Brassica napus L.) Line zws-ms Based on Combination of Genome, Transcriptome and Proteome Data

Based on previous researches, we further investigated the multi-silique trait in rapeseed (Brassica napus L.) line zws-ms. In this study, we used a relatively comprehensive list of flowering related genes in rapeseed and compared them between zws-ms and its near-isogenic line (NIL) zws-217. Genes were studied on genome, transcriptome and proteome levels and then we focused on genes with non-synonymous single nucleotide polymorphism (SNP) or frame-shift insertion-deletion (InDel), finding some genes on the list which changes their sequences. Then, combined with their annotation and the information of their orthologs, certain genes such as BnaA09g05900D, ortholog of AGAMOUS-LIKE 42 (AGL42), which encodes an MADS-box protein, were assumed as probably responsible for the multi-silique trait. Also, we analyzed the Differentially Accumulated Proteins (DAPs) between zws-ms and zws-217, revealing some genes involved in homologous recombination and mismatch repair pathways. Since the development of flowers/siliques is crucial to crops and it influences the yield of rapeseed, this study paved a way to deeply understand the mechanism of the multi-pistil flower formation, which may facilitate researches on rapeseed production in future.

Identification and characterization of a novel gene controlling floral organ number in rice (Oryza sativa L.)

Floral organ number is crucial for successful seed setting and mature grain development. Although some genes and signaling pathways controlling floral organ number have been studied, the underlying mechanism is complicated and requires further investigation. In this study, a floral organ number mutant was generated by the ethyl methanesulfonate treatment of the Korean japonica rice cultivar Ilpum. In the floral organ number mutant, 37% of the spikelets showed an increase in the number of floral organs, especially stamens and pistils. Histological analysis revealed that the number of ovaries was determined by the number of stigmas; spikelets with two or three stigmas contained only one ovary, whereas spikelets with four stigmas possessed two ovaries. The floral organ number mutant showed pleiotropic phenotypes including multiple grains, early flowering, short plant height, and reduced tiller number compared with the wild-type. Genetic and MutMap analyses revealed that floral organ number is controlled by a single recessive gene located between the 8.0 and 20.0 Mb region on chromosome 8. Calculation of SNP-index confirmed Os08g0299000 as the candidate gene regulating floral organ number, which was designated as FLORAL ORGAN NUMBER7 (FON7). A single nucleotide polymorphism (G to A) was discovered at the intron splicing donor site of FON7, which caused the skipping of the entire sixth exon in the mutant, resulting in the deletion of 144 bp. Furthermore, the T-DNA-tagged line displayed the same floral organ number phenotype as the fon7 mutant. These results provide valuable insight into the mechanism of floral organ differentiation and formation in rice.

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.

OsbZIP47 Is an Integrator for Meristem Regulators During Rice Plant Growth and Development

Stem cell homeostasis by the WUSCHEL-CLAVATA (WUS-CLV) feedback loop is generally conserved across species; however, its links with other meristem regulators can be species-specific, rice being an example. We characterized the role of rice OsbZIP47 in vegetative and reproductive development. The knockdown (KD) transgenics showed meristem size abnormality and defects in developmental progression. The size of the shoot apical meristem (SAM) in 25-day OsbZIP47KD plants was increased as compared to the wild-type (WT). Inflorescence of KD plants showed reduced rachis length, number of primary branches, and spikelets. Florets had defects in the second and third whorl organs and increased organ number. OsbZIP47KD SAM and panicles had abnormal expression for CLAVATA peptide-like signaling genes, such as FON2-LIKE CLE PROTEIN1 (FCP1), FLORAL ORGAN NUMBER 2 (FON2), and hormone pathway genes, such as cytokinin (CK) ISOPENTEYLTRANSFERASE1 (OsIPT1), ISOPENTEYLTRANSFERASE 8 (OsIPT8), auxin biosynthesis OsYUCCA6, OsYUCCA7 and gibberellic acid (GA) biosynthesis genes, such as GRAIN NUMBER PER PANICLE1 (GNP1/OsGA20OX1) and SHORTENED BASAL INTERNODE (SBI/OsGA2ox4). The effects on ABBERANT PANICLE ORGANIZATION1 (APO1), OsMADS16, and DROOPING LEAF (DL) relate to the second and third whorl floret phenotypes in OsbZIP47KD. Protein interaction assays showed OsbZIP47 partnerships with RICE HOMEOBOX1 (OSH1), RICE FLORICULA/LEAFY (RFL), and OsMADS1 transcription factors. The meta-analysis of KD panicle transcriptomes in OsbZIP47KD, OsMADS1KD, and RFLKD transgenics, combined with global OSH1 binding sites divulge potential targets coregulated by OsbZIP47, OsMADS1, OSH1, and RFL. Further, we demonstrate that OsbZIP47 redox status affects its DNA binding affinity to a cis element in FCP1, a target locus. Taken together, we provide insights on OsbZIP47 roles in SAM development, inflorescence branching, and floret development.

SMALL REPRODUCTIVE ORGANS, a SUPERMAN-like transcription factor, regulates stamen and pistil growth in rice

Organ size is determined mainly by cell division and cell expansion. Several genetic factors regulating development of plant lateral organs have been characterized, but those involved in determining reproductive organ size and separation in rice (Oryza sativa) remain unknown. We have isolated the rice gene SMALL REPRODUCTIVE ORGANS (SRO) encoding a nucleus-localized Cys2His2 (C₂ H₂ ) zinc finger protein orthologous to Arabidopsis transcription factor (TF) SUPERMAN (SUP). Combined developmental, genetic, histological and transcriptomic analyses were used to determine the function of SRO in regulating reproductive organ size. SRO affects genes involved in cell division, cell expansion and phytohormone signalling in the rice flower. SRO is specifically expressed in the first stages of stamen filament development to regulate their correct formation and separation. In addition, SRO noncell-autonomously regulates the size and functionality of male and female reproductive organs. The B-class MADS-box gene OsMADS16/SPW1 is epistatic to SRO, whereas SRO regulates reproductive organ specification and floral meristem determinacy synergistically with C-class genes OsMADS3 and OsMADS58. These findings provide insights into how an evolutionarily conserved TF has a pivotal role in reproductive organ development in core eudicots and monocots, through partially conserved expression, function and regulatory network.

Molecular Control of Carpel Development in the Grass Family

Carpel is the ovule-bearing female reproductive organ of flowering plants and is required to ensure its protection, an efficient fertilization, and the development of diversified types of fruits, thereby it is a vital element of most food crops. The origin and morphological changes of the carpel are key to the evolution and adaption of angiosperms. Progresses have been made in elucidating the developmental mechanisms of carpel establishment in the model eudicot plant Arabidopsis thaliana, while little and fragmentary information is known in grasses, a family that includes many important crops such as rice (Oryza sativa), maize (Zea mays), barley (Hordeum vulgare), and wheat (Triticum aestivum). Here, we highlight recent advances in understanding the mechanisms underlying potential pathways of carpel development in grasses, including carpel identity determination, morphogenesis, and floral meristem determinacy. The known role of transcription factors, hormones, and miRNAs during grass carpel formation is summarized and compared with the extensively studied eudicot model plant Arabidopsis. The genetic and molecular aspects of carpel development that are conserved or diverged between grasses and eudicots are therefore discussed.

OsSPL9 Regulates Grain Number and Grain Yield in Rice

Rice grain yield consists of several key components, including tiller number, grain number per panicle (GNP), and grain weight. Among them, GNP is mainly determined by panicle branches and spikelet formation. In this study, we identified a gene affecting GNP and grain yield, OsSPL9, which encodes SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) family proteins. The mutation of OsSPL9 significantly reduced secondary branches and GNP. OsSPL9 was highly expressed in the early developing young panicles, consistent with its function of regulating panicle development. By combining expression analysis and dual-luciferase assays, we further confirmed that OsSPL9 directly activates the expression of RCN1 (rice TERMINAL FLOWER 1/CENTRORADIALIS homolog) in the early developing young panicle to regulate the panicle branches and GNP. Haplotype analysis showed that Hap3 and Hap4 of OsSPL9 might be favorable haplotypes contributing to high GNP in rice. These results provide new insights on high grain number breeding in rice.

Cloning of long sterile lemma (lsl2), a single recessive gene that regulates spike germination in rice (Oryza sativa L.)

BACKGROUND

Rice is a typical monocotyledonous plant and an important cereal crop. The structural units of rice flowers are spikelets and florets, and floral organ development and spike germination affect rice reproduction and yield.

RESULTS

In this study, we identified a novel long sterile lemma (lsl2) mutant from an EMS population. First, we mapped the lsl2 gene between the markers Indel7-22 and Indel7-27, which encompasses a 25-kb region. The rice genome annotation indicated the presence of four candidate genes in this region. Through gene prediction and cDNA sequencing, we confirmed that the target gene in the lsl2 mutant is allelic to LONG STERILE LEMMA1 (G1)/ELONGATED EMPTY GLUME (ELE), hereafter referred to as lsl2. Further analysis of the lsl2 and LSL2 proteins showed a one-amino-acid change, namely, the mutation of serine (Ser) 79 to proline (Pro) in lsl2 compared with LSL2, and this mutation might change the function of the protein. Knockout experiments showed that the lsl2 gene is responsible for the long sterile lemma phenotype. The lsl2 gene might reduce the damage induced by spike germination by decreasing the seed germination rate, but other agronomic traits of rice were not changed in the lsl2 mutant. Taken together, our results demonstrate that the lsl2 gene will have specific application prospects in future rice breeding.

CONCLUSIONS

The lsl2 gene is responsible for the long sterile lemma phenotype and might reduce the damage induced by spike germination by decreasing the seed germination rate.

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.

Regulation of meristem maintenance and organ identity during rice reproductive development

Grasses have evolved complex inflorescences, where the primary unit is the specialized short branch called a spikelet. Detailed studies of the cumulative action of the genetic regulators that direct the progressive change in axillary meristem identity and their terminal differentiation are crucial to understanding the complexities of the inflorescence and the development of a determinate floret. Grass florets also pose interesting questions concerning the morphologies and functions of organs as compared to other monocots and eudicots. In this review, we summarize our current knowledge of the regulation of the transitions that occur in grass inflorescence meristems, and of the specification of floret meristems and their determinate development. We primarily use rice as a model, with appropriate comparisons to other crop models and to the extensively studied eudicot Arabidopsis. The role of MADS-domain transcription factors in floral organ patterning is well documented in many eudicots and in grasses. However, there is evidence to suggest that some of these rice floral regulators have evolved distinctive functions and that other grass species-specific factors and regulatory pathways occur - for example the LOFSEP 'E' class genes OsMADS1 and OsMAD34, and ramosa genes. A better understanding of these systems and the epigenetic regulators and hormone signaling pathways that interact with them will provide new insights into the rice inflorescence meristem and the differentiation of its floret organs, and should indicate genetic tools that can be used to control yield-related traits in both rice and other cereal crops.

Dissecting the role of MADS-box genes in monocot floral development and diversity

Many monocot plants have high social and economic value. These include grasses such as rice (Oryza sativa), wheat (Triticum aestivum), and barley (Hordeum vulgare), which produce soft commodities for many food and beverage industries, and ornamental flowers such ase lily (Lilium longiflorum) and orchid (Oncidium Gower Ramsey), which represent an important component of international flower markets. There is constant pressure to improve the development and diversity of these species, with a significant emphasis on flower development, and this is particularly relevant considering the impact of changing environments on reproduction and thus yield. MADS-box proteins are a family of transcription factors that contain a conserved 60 amino acid MADS-box motif. In plants, attention has been devoted to characterization of this family due to their roles in inflorescence and flower development, which holds promise for the modification of floral architecture for plant breeding. This has been explored in diverse angiosperms, but particularly the dicot model Arabidopsis thaliana. The focus of this review is on the less well characterized roles of the MADS-box proteins in monocot flower development and how changes in MADS-box proteins throughout evolution may have contributed to creating a diverse range of flowers. Examining these changes within the monocots can identify the importance of certain genes and pinpoint those which might be useful in future crop improvement and breeding strategies.

Loss of LOFSEP Transcription Factor Function Converts Spikelet to Leaf-Like Structures in Rice

SEPALLATA (SEP)-like genes, which encode a subfamily of MADS-box transcription factors, are essential for specifying floral organ and meristem identity in angiosperms. Rice (Oryza sativa) has five SEP-like genes with partial redundancy and overlapping expression domains, yet their functions and evolutionary conservation are only partially known. Here, we describe the biological role of one of the SEP genes of rice, OsMADS5, in redundantly controlling spikelet morphogenesis. OsMADS5 belongs to the conserved LOFSEP subgroup along with OsMADS1 and OsMADS34OsMADS5 was expressed strongly across a broad range of reproductive stages and tissues. No obvious phenotype was observed in the osmads5 single mutants when compared with the wild type, which was largely due to the functional redundancy among the three LOFSEP genes. Genetic and molecular analyses demonstrated that OsMADS1, OsMADS5, and OsMADS34 together regulate floral meristem determinacy and specify the identities of spikelet organs by positively regulating the other MADS-box floral homeotic genes. Experiments conducted in yeast also suggested that OsMADS1, OsMADS5, and OsMADS34 form protein-protein interactions with other MADS-box floral homeotic members, which seems to be a typical, conserved feature of plant SEP proteins.

Regulatory network and genetic interactions established by OsMADS34 in rice inflorescence and spikelet morphogenesis

Grasses display highly diversified inflorescence architectures that differ in the arrangement of spikelets and flowers and determine cereal yields. However, the molecular basis underlying grass inflorescence morphogenesis remains largely unknown. Here we investigate the role of a functionally diversified SEPALLATA MADS-box transcription factor, OsMADS34, in regulating rice (Oryza sativa L.) inflorescence and spikelet development. Microarray analysis showed that, at the very early stages of inflorescence formation, dysfunction of OsMADS34 caused altered expression of 379 genes that are associated with protein modification and degradation, transcriptional regulation, signaling and metabolism activity. Genetic analysis revealed that OsMADS34 controls different aspects of inflorescence structure, branching and meristem activity synergistically with LAX PANICLE1 (LAX1) and FLORAL ORGAN NUMBER4 (FON4), as evidenced by the enhanced phenotypes of osmads34 lax1 and osmads34 fon4 compared with the single mutants. Additionally, double mutant between osmads34 and the sterile lemma defective mutant elongated empty glume (ele) displayed an enhanced phenotype, that is, longer and wider sterile lemmas that were converted into lemma/palea-like organs, suggesting that ELE and OsMADS34 synergistically control the sterile lemma development. OsMADS34 may act together with OsMADS15 in controlling sterile lemma development. Collectively, these findings provide insights into the regulatory function of OsMADS34 in rice inflorescence and spikelet development.