Conservation of the E-function for floral organ identity in rice revealed by the analysis of tissue culture-induced loss-of-function mutants of the OsMADS1 gene

Transcription factor OsNF-YC1 regulates grain size by coordinating the transcriptional activation of OsMADS1 in Oryza sativa L

Grain weight, grain number per panicle, and the number of panicles are the three factors that determine rice (Oryza sativa L.) yield. Of these, grain weight, which not only directly determines rice yield but also influences appearance and quality, is often considered the most important for rice production. Here, we describe OsNF-YC1, a member of the NF-Y transcription factor family that regulates rice grain size. OsNF-YC1 knockout plants (osnf-yc1), obtained using CRISPR-Cas9 technology, showed reduced grain weight due to reduced width and thickness, with no change in grain length, leading to a slenderer grain shape. Downregulation of OsNF-YC1 using RNA interference resulted in similar grain phenotypes as osnf-yc1. OsNF-YC1 affects grain formation by regulating both cell proliferation and cell expansion. OsNF-YC1 localizes in both the nucleus and cytoplasm, has transcriptional activation activity at both the N-terminus and C-terminus, and is highly expressed in young panicles. OsNF-YC1 interacts with OsMADS1 both in vivo and in vitro. Further analysis showed that the histone-like structural CBFD-NFYB-HMF domain of OsNF-YC1 conserved in the OsNF-YC transcription factor family can directly interact with the MADS-box domain of OsMADS1 to enhance its transcriptional activation activity. This interaction positively regulates the expression of OsMADS55, the direct downstream target of OsMADS1. Therefore, this paper reveals a potential grain size regulation pathway controlled by an OsNF-YC1-OsMADS1-OsMADS55 module in rice.

Genome-wide analysis of the MADS-box gene family of sea buckthorn (Hippophae rhamnoides ssp. sinensis) and their potential role in floral organ development

Sea buckthorn (Hippophae rhamnoides ssp. sinensis) is a deciduous shrub or small tree in the Elaeagnaceae family. It is dioecious, featuring distinct structures in female and male flowers. The MADS-box gene family plays a crucial role in flower development and differentiation of floral organs in plants. However, systematic information on the MADS-box family in sea buckthorn is currently lacking. This study presents a genome-wide survey and expression profile of the MADS-box family of sea buckthorn. We identified 92 MADS-box genes in the H. rhamnoides ssp. Sinensis genome. These genes are distributed across 12 chromosomes and classified into Type I (42 genes) and Type II (50 genes). Based on the FPKM values in the transcriptome data, the expression profiles of HrMADS genes in male and female flowers of sea buckthorn showed that most Type II genes had higher expression levels than Type I genes. This suggesting that Type II HrMADS may play a more significant role in sea buckthorn flower development. Using the phylogenetic relationship between sea buckthorn and Arabidopsis thaliana, the ABCDE model genes of sea buckthorn were identified and some ABCDE model-related genes were selected for qRT-PCR analysis in sea buckthorn flowers and floral organs. Four B-type genes may be involved in the identity determination of floral organs in male flowers, and D-type genes may be involved in pistil development. It is hypothesized that ABCDE model genes may play an important role in the identity of sea buckthorn floral organs. This study analyzed the role of MADS-box gene family in the development of flower organs in sea buckthorn, which provides an important theoretical basis for understanding the regulatory mechanism of sex differentiation in sea buckthorn.

Genome-wide characterization and expression analysis of MADS-box transcription factor gene family in Perilla frutescens

MADS-box transcription factors are widely involved in the regulation of plant growth, developmental processes, and response to abiotic stresses. Perilla frutescens, a versatile plant, is not only used for food and medicine but also serves as an economical oil crop. However, the MADS-box transcription factor family in P. frutescens is still largely unexplored. In this study, a total of 93 PfMADS genes were identified in P. frutescens genome. These genes, including 37 Type I and 56 Type II members, were randomly distributed across 20 chromosomes and 2 scaffold regions. Type II PfMADS proteins were found to contain a greater number of motifs, indicating more complex structures and diverse functions. Expression analysis revealed that most PfMADS genes (more than 76 members) exhibited widely expression model in almost all tissues. The further analysis indicated that there was strong correlation between some MIKCC-type PfMADS genes and key genes involved in lipid synthesis and flavonoid metabolism, which implied that these PfMADS genes might play important regulatory role in the above two pathways. It was further verified that PfMADS47 can effectively mediate the regulation of lipid synthesis in Chlamydomonas reinhardtii transformants. Using cis-acting element analysis and qRT-PCR technology, the potential functions of six MIKCC-type PfMADS genes in response to abiotic stresses, especially cold and drought, were studied. Altogether, this study is the first genome-wide analysis of PfMADS. This result further supports functional and evolutionary studies of PfMADS gene family and serves as a benchmark for related P. frutescens breeding studies.

Transcriptome-wide association analyses reveal the impact of regulatory variants on rice panicle architecture and causal gene regulatory networks

Panicle architecture is a key determinant of rice grain yield and is mainly determined at the 1-2 mm young panicle stage. Here, we investigated the transcriptome of the 1-2 mm young panicles from 275 rice varieties and identified thousands of genes whose expression levels were associated with panicle traits. Multimodel association studies suggested that many small-effect genetic loci determine spikelet per panicle (SPP) by regulating the expression of genes associated with panicle traits. We found that alleles at cis-expression quantitative trait loci of SPP-associated genes underwent positive selection, with a strong preference for alleles increasing SPP. We further developed a method that integrates the associations of cis- and trans-expression components of genes with traits to identify causal genes at even small-effect loci and construct regulatory networks. We identified 36 putative causal genes of SPP, including SDT (MIR156j) and OsMADS17, and inferred that OsMADS17 regulates SDT expression, which was experimentally validated. Our study reveals the impact of regulatory variants on rice panicle architecture and provides new insights into the gene regulatory networks of panicle traits.

Characterization and Gene Mapping of an Open-Glume Oryza sativa L. Mutant

Floral organ development determines agricultural productivity by affecting seed development, seed quality, and final yield. In this study, we described the novel ogl mutant in rice (Oryza sativa L.), which is characterized by an open-glume phenotype, increased pistil number, reduced stamen number, decreased seed setting rate, and smaller rice grains. Genetic analysis showed that the open-glume phenotype might be controlled by a recessive qualitative trait locus. Employing bulked segregant analysis (BSA), one candidate region was identified on rice chromosome 1. The glume opening phenotype cosegregated with SNP (Chr1:1522703), which was located at the start codon of one transcript of OsJAG, resulting in partial loss of OsJAG function. cDNA analysis revealed that OsJAG encodes two transcript variants. Compared to normal plants, the expression of OsJAG.1 was upregulated in open-glume plants. When investigating the glume phenotype, we found that the expression of genes related to floral development changed greatly in open-glume plants. Taken together, this work increases our understanding of the developmental role of OsJAG in rice floral development.

Identification and validation of new MADS-box homologous genes in 3010 rice pan-genome

KEY MESSAGE

Identification and validation of ten new MADS-box homologous genes in 3010 rice pan-genome for rice breeding. The functional genome is significant for rice breeding. MADS-box genes encode transcription factors that are indispensable for rice growth and development. The reported 15,362 novel genes in the rice pan-genome (RPAN) of Asian cultivated rice accessions provided a useful gene reservoir for the identification of more MADS-box candidates to overcome the limitation for the usage of only 75 MADS-box genes identified in Nipponbare for rice breeding. Here, we report the identification and validation of ten MADS-box homologous genes in RPAN. Origin and identity analysis indicated that they are originated from different wild rice accessions and structure of motif analysis revealed high variations in their amino acid sequences. Phylogenetic results with 277 MADS-box genes in 41 species showed that all these ten MADS-box homologous genes belong to type I (SRF-like, M-type). Gene expression analysis confirmed the existence of these ten MADS-box genes in IRIS_313-10,394, all of them were expressed in flower tissues, and six of them were highly expressed during seed development. Altogether, we identified and validated experimentally, for the first time, ten novel MADS-box genes in RPAN, which provides new genetic sources for rice improvement.

OsMADS1 Regulates Grain Quality, Gene Expressions, and Regulatory Networks of Starch and Storage Protein Metabolisms in Rice

OsMADS1 plays a vital role in regulating floret development and grain shape, but whether it regulates rice grain quality still remains largely unknown. Therefore, we used comprehensive molecular genetics, plant biotechnology, and functional omics approaches, including phenotyping, mapping-by-sequencing, target gene seed-specific RNAi, transgenic experiments, and transcriptomic profiling to answer this biological and molecular question. Here, we report the characterization of the 'Oat-like rice' mutant, with poor grain quality, including chalky endosperms, abnormal morphology and loose arrangement of starch granules, and lower starch content but higher protein content in grains. The poor grain quality of Oat-like rice was found to be caused by the mutated OsMADS1^Olr allele through mapping-by-sequencing analysis and transgenic experiments. OsMADS1 protein is highly expressed in florets and developing seeds. Both OsMADS1-eGFP and OsMADS1^Olr-eGFP fusion proteins are localized in the nucleus. Moreover, seed-specific RNAi of OsMADS1 also caused decreased grain quality in transgenic lines, such as the Oat-like rice. Further transcriptomic profiling between Oat-like rice and Nipponbare grains revealed that OsMADS1 regulates gene expressions and regulatory networks of starch and storage protein metabolisms in rice grains, hereafter regulating rice quality. In conclusion, our results not only reveal the crucial role and preliminary mechanism of OsMADS1 in regulating rice grain quality but also highlight the application potentials of OsMADS1 and the target gene seed-specific RNAi system in improving rice grain quality by molecular breeding.

DEGENERATED LEMMA (DEL) regulates lemma development and affects rice grain yield

In grass, the lemma is a unique floral organ structure that directly determines grain size and yield. Despite a great deal of research on grain enlargement caused by changes in glume cells, the importance of normal development of the glume for normal grain development has been poorly studied. In this study, we investigated a rice spikelet mutant, degenerated lemma (del), which developed florets with a slightly degenerated or rod-like lemma. More importantly, del also showed a significant reduction in grain length and width, seed setting rate, and 1000-grain weight, which led to a reduction in yield. The results indicate that the mutation of the DEL gene further affects rice grain yield. Map-based cloning shows a single-nucleotide substitution from T to A within Os01g0527600/DEL/OsRDR6, causing an amino acid mutation of Leu-34 to His-34 in the del mutant. Compared with the wild type, the expression of DEL in del was significantly reduced, which might be caused by single base substitution. In addition, the expression level of tasiR-ARF in del was lower than that of the wild type. RT-qPCR results show that the expression of some floral organ identity genes was changed, which indicates that the DEL gene regulates lemma development by modulating the expression of these genes. The present results suggest that the normal expression of DEL is necessary for the formation of lemma and the normal development of grain morphology and therefore has an important effect on the yield.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01297-6.

The ABC of Flower Development in Monocots: The Model of Rice Spikelet

The initial seminal studies of flower developmental genetics were made from observations in several eudicot model species, particularly Arabidopsis and Antirrhinum. However, an increasing amount of research in monocot model and crop species is finally giving the credit that monocots deserve for their position in the evolutionary history of Angiosperms, their astonishing diversification and adaptation, their diversified floral structures, their pivotal function in most ecosystems on Earth and, finally, their importance in agriculture and farming, economy, landscaping and feeding mankind. Rice is a staple crop and the major monocot model to study the reproductive phase and flower evolution. Inspired by this, this chapter reviews a story of highly conserved functions related to the ABC model of flower development. Nevertheless, this model is complicated in rice by cases of gene neofunctionalization, like the recruitment of MADS-box genes for the development of the unique organs known as lemma and palea, subfunctionalization, and rewiring of conserved molecular pathways.

Tracing the Evolution of the SEPALLATA Subfamily across Angiosperms Associated with Neo- and Sub-Functionalization for Reproductive and Agronomically Relevant Traits

SEPALLATA transcription factors (SEP TFs) have been extensively studied in angiosperms as pivotal components of virtually all the MADS-box tetrameric complex master regulators of floral organ identities. However, there are published reports that suggest that some SEP members also regulate earlier reproductive events, such as inflorescence meristem determinacy and inflorescence architecture, with potential for application in breeding programs in crops. The SEP subfamily underwent a quite complex pattern of duplications during the radiation of the angiosperms. Taking advantage of the many whole genomic sequences now available, we present a revised and expanded SEP phylogeny and link it to the known functions of previously characterized genes. This snapshot supports the evidence that the major SEP3 clade is highly specialized for the specification of the three innermost floral whorls, while its sister LOFSEP clade is functionally more versatile and has been recruited for diverse roles, such as the regulation of extra-floral bract formation and inflorescence determinacy and shape. This larger pool of angiosperm SEP genes confirms previous evidence that their evolution was driven by whole-genome duplications rather than small-scale duplication events. Our work may help to identify those SEP lineages that are the best candidates for the improvement of inflorescence traits, even in far distantly related crops.

Fine Mapping of Rice Specific MR1, a Gene Determines Palea Identity

The hull (palea and lemma) is the specific organ of grass florets. Although many genes related to the hull development have been cloned, the genetic mechanisms behind the development are still unclear, and the evolutionary relationship has different explanations and heated arguments between the palea and lemma. In this study, we found a specific mr1 mutant with a reduced palea, showing an enlarged mrp and degraded bop. Phenotype observations and molecular evidences showed that the bop was converted to the mrp-like organ. Our findings first reveal that the bop and mrp are homologous structures, and the palea and lemma are the same whorl floral organs. MR1 may prevent the transformation of the bop into mrp by regulating the expressions of hull identity genes. Meantime, the mr1 mutant showed altered grain size and grain quality, with defective physical and chemical contents. MR1 was controlled by a single recessive gene and was finally located on chromosome 1, with a physical distance of 70 kb. More work will be needed for confirming the target gene of MR1, which would contribute to our understanding of grain formation and the origin between the lemma, bop, and mrp.

SEPALLATA--like genes of Isatis indigotica can affect the architecture of the inflorescences and the development of the floral organs

BACKGROUND

The architecture of inflorescence and the development of floral organs can influence the yield of seeds and have a significant impact on plant propagation. E-class floral homeotic MADS-box genes exhibit important roles in regulation of floral transition and differentiation of floral organs. Woad (Isatis indigotica) possesses unique inflorescence, floral organs and fruit. However, very little research has been carried out to determine the function of MADS-box genes in this medicinal cruciferous plant species.

RESULTS

SEPALLATA orthologs in I. indigotica were cloned by degenerate PCR. The sequence possessing the highest identity with SEP2 and SEP4 of Arabidopsis were named as IiSEP2 and IiSEP4, respectively. Constitutive expression of IiSEP2 in Columbia (Col-0) ecotype of Arabidopsis led to early flowering, and the number of the flowers and the lateral branches was reduced, indicating an alteration in architecture of the inflorescences. Moreover, the number of the floral organs was declined, the sepals were turned into carpelloid tissues bearing stigmatic papillae and ovules, and secondary flower could be produced in apetalous terminal flowers. In 35S::IiSEP4-GFP transgenic Arabidopsis plants in Landsberg erecta (Ler) genetic background, the number of the floral organs was decreased, sepals were converted into curly carpelloid structures, accompanied by generation of ovules. Simultaneously, the size of petals, stamens and siliques was diminished. In 35S::IiSEP4-GFP transgenic plants of apetalous ap1 cal double mutant in Ler genetic background, the cauliflower phenotype was attenuated significantly, and the petal formation could be rescued. Occasionally, chimeric organs composed of petaloid and sepaloid tissues, or petaloid and stamineous tissues, were produced in IiSEP4 transgenic plants of apl cal double mutant. It suggested that overexpression of IiSEP4 could restore the capacity in petal differentiation. Silencing of IiSEP4 by Virus-Induced Gene Silencing (VIGS) can delay the flowering time, and reduce the number and size of the floral organs in woad flowers.

CONCLUSION

All the results showed that SEPALLATA-like genes could influence the architecture of the inflorescence and the determinacy of the floral meristems, and was also related to development of the floral organs.

Rice SEPALLATA genes OsMADS5 and OsMADS34 cooperate to limit inflorescence branching by repressing the TERMINAL FLOWER1-like gene RCN4

The spatiotemporal control of meristem identity is critical for determining inflorescence architecture, and thus yield, of cereal plants. However, the precise mechanisms underlying inflorescence and spikelet meristem determinacy in cereals are still largely unclear. We have generated loss-of-function and overexpression mutants of the paralogous OsMADS5 and OsMADS34 genes in rice (Oryza sativa), and analysed their panicle phenotypes. Using chromatin immunoprecipitation, electrophoretic mobility-shift and dual-luciferase assays, we have also identified RICE CENTRORADIALIS 4 (RCN4), a TFL1-like gene, as a direct downstream target of both OsMADS proteins, and have analysed RCN4 mutants. The osmads5 osmads34 mutant lines had significantly enhanced panicle branching with increased secondary, and even tertiary and quaternary, branches, compared to wild-type (WT) and osmads34 plants. The osmads34 mutant phenotype could largely be rescued by also knocking out RCN4. Moreover, transgenic panicles overexpressing RCN4 had significantly increased branching, and initiated development of c. 7× more spikelets than WT. Our results reveal a role for OsMADS5 in panicle development, and show that OsMADS5 and OsMADS34 play similar functions in limiting branching and promoting the transition to spikelet meristem identity, in part by repressing RCN4 expression. These findings provide new insights to better understand the molecular regulation of rice inflorescence architecture.

Nitrate-responsive transcriptome analysis reveals additional genes/processes and associated traits viz. height, tillering, heading date, stomatal density and yield in japonica rice

Our transcriptomic analysis expanded the repertoire of nitrate-responsive genes/processes in rice and revealed their phenotypic association with root/shoot, stomata, tiller, panicle/flowering and yield, with agronomic implications for nitrogen use efficiency. Nitrogen use efficiency (NUE) is a multigenic quantitative trait, involving many N-responsive genes/processes that are yet to be fully characterized. Microarray analysis of early nitrate response in excised leaves of japonica rice revealed 6688 differentially expressed genes (DEGs), including 2640 hitherto unreported across multiple functional categories. They include transporters, enzymes involved in primary/secondary metabolism, transcription factors (TFs), EF-hand containing calcium binding proteins, hormone metabolism/signaling and methytransferases. Some DEGs belonged to hitherto unreported processes viz. alcohol, lipid and trehalose metabolism, mitochondrial membrane organization, protein targeting and stomatal opening. 1158 DEGs were associated with growth physiology and grain yield or phenotypic traits for NUE. We identified seven DEGs for shoot apical meristem, 66 for leaf/culm/root, 31 for tiller, 70 for heading date/inflorescence/spikelet/panicle, 144 for seed and 78 for yield. RT-qPCR validated nitrate regulation of 31 DEGs belonging to various important functional categories/traits. Physiological validation of N-dose responsive changes in plant development revealed that relative to 1.5 mM, 15 mM nitrate significantly increased stomatal density, stomatal conductance and transpiration rate. Further, root/shoot growth, number of tillers and grain yield declined and panicle emergence/heading date delayed, despite increased photosynthetic rate. We report the binding sites of diverse classes of TFs such as WRKY, MYB, HMG etc., in the 1 kb up-stream regions of 6676 nitrate-responsive DEGs indicating their role in regulating nitrate response/NUE. Together, these findings expand the repertoire of genes and processes involved in genomewide nitrate response in rice and reveal their physiological, phenotypic and agronomic implications for NUE.

A Novel Embryo Phenotype Associated With Interspecific Hybrid Weakness in Rice Is Controlled by the MADS-Domain Transcription Factor OsMADS8

A novel hybrid weakness gene, DTE9, associated with a dark tip embryo (DTE) trait, was observed in CR6078, an introgression line derived from a cross between the Oryza sativa spp. japonica "Hwayeong" (HY) and the wild relative Oryza rufipogon. CR6078 seeds exhibit protruding embryos and flowers have altered inner floral organs. DTE9 was also associated with several hybrid weakness symptoms including decreased grain weight. Map-based cloning and transgenic approaches revealed that DTE9 is an allele of OsMADS8, a MADS-domain transcription factor. Genetic analysis indicated that two recessive complementary genes were responsible for the expression of the DTE trait. No sequence differences were observed between the two parental lines in the OsMADS8 coding region; however, numerous single nucleotide polymorphisms were detected in the promoter and intronic regions. We generated overexpression (OX) and RNA interference (RNAi) transgenic lines of OsMADS8 in HY and CR6078, respectively. The OsMADS8-OX lines showed the dark tip embryo phenotype, whereas OsMADS8-RNAi recovered the normal embryo phenotype. Changes in gene expression, including of ABCDE floral homeotic genes, were observed in the OsMADS8-OX and OsMADS8-RNAi lines. Overexpression of OsMADS8 led to decreased expression of OsEMF2b and ABA signaling-related genes including OsVP1/ABI3. HY seeds showed higher ABA content than CR6078 seeds, consistent with OsMADS8/DTE9 regulating the expression of genes related ABA catabolism in CR6078. Our results suggest that OsMADS8 is critical for floral organ determination and seed germination and that these effects are the result of regulation of the expression of OsEMF2b and its role in ABA signaling and catabolism.

A homologous gene of OsREL2/ASP1, ASP-LSL regulates pleiotropic phenotype including long sterile lemma in rice

BACKGROUND

Panicle is a harvesting organ of rice, and its morphology and development are closely associated with grain yield. The current study was carried on a mutant screened through an EMS (ethyl-methane sulphonate) mutagenized population of a Japonica cultivar Kitaake (WT).

RESULTS

A mutant, named as asp-lsl (aberrant spikelet-long sterile lemma), showed a significant decrease in plant height, number of tillers, thousand-grains weight, seed setting rate, spikelet length, kernel length and effective number of grains per panicle as compared to WT. Asp-lsl showed a pleiotropic phenotype coupled with the obvious presence of a long sterile lemma. Cross-sections of lemma showed an increase in the cell volume rather than the number of cells. Genetic segregation analysis revealed its phenotypic trait is controlled by a single recessive nuclear gene. Primary and fine mapping indicated that candidate gene controlling the phenotype of asp-lsl was located in an interval of 212 kb on the short arm of chromosome 8 between RM22445 and RM22453. Further sequencing and indels markers analysis revealed LOC_Os08g06480 harbors a single base substitution (G→A), resulting in a change of 521st amino acid(Gly→Glu. The homology comparison and phylogenetic tree analysis revealed mutation was occurred in a highly conserved domain and had a high degree of similarity in Arabidopsis, corn, and sorghum. The CRISPR/Cas9 mutant line of ASP-LSL produced a similar phenotype as that of asp-lsl. Subcellular localization of ASP-LSL revealed that its protein is localized in the nucleus. Relative expression analysis revealed ASP-LSL was preferentially expressed in panicle, stem, and leaves. The endogenous contents of GA, CTK, and IAA were found significantly decreased in asp-lsl as compared to WT.

CONCLUSIONS

Current study presents the novel phenotype of asp-lsl and also validate the previously reported function of OsREL2 (ROMOSA ENHANCER LOCI2), / ASP1(ABERRANT SPIKELET AND PANICLE 1).

SiMADS34, an E-class MADS-box transcription factor, regulates inflorescence architecture and grain yield in Setaria italica

A novel MADS-box member SiMADS34 is essential for regulating inflorescence architecture and grain yield in Setaria italica. MADS-box transcription factors participate in regulating various developmental processes in plants. Inflorescence architecture is one of the most important agronomic traits and is closely associated with grain yield in most staple crops. Here, we isolated a panicle development mutant simads34 from a foxtail millet (Setaria italica (L.) P. Beauv.) EMS mutant library. The mutant showed significantly altered inflorescence architecture and decreased grain yield. Investigation of agronomic traits revealed increased panicle width by 16.8%, primary branch length by 10%, and number of primary branches by 30.9%, but reduced panicle length by 25.2%, and grain weight by 25.5% in simads34 compared with wild-type plants. Genetic analysis of a simads34 × SSR41 F₂ population indicated that the simads34 phenotype was controlled by a recessive gene. Map-based cloning and bulked-segregant analysis sequencing demonstrated that a single G-to-A transition in the fifth intron of SiMADS34 in the mutant led to an alternative splicing event and caused an early termination codon in this causal gene. SiMADS34 mRNA was expressed in all of the tissues tested, with high expression levels at the heading and panicle development stages. Subcellular localization analysis showed that simads34 predominantly accumulated in the nucleus. Transcriptome sequencing identified 241 differentially expressed genes related to inflorescence development, cell expansion, cell division, meristem growth and peroxide stress in simads34. Notably, an SPL14-MADS34-RCN pathway was validated through both RNA-seq and qPCR tests, indicating the putative molecular mechanisms regulating inflorescence development by SiMADS34. Our study identified a novel MADS-box member in foxtail millet and provided a useful genetic resource for inflorescence architecture and grain yield research.

Transcriptome analysis reveals rice MADS13 as an important repressor of the carpel development pathway in ovules

In angiosperms, floral homeotic genes encoding MADS-domain transcription factors regulate the development of floral organs. Specifically, members of the SEPALLATA (SEP) and AGAMOUS (AG) subfamilies form higher-order protein complexes to control floral meristem determinacy and to specify the identity of female reproductive organs. In rice, the AG subfamily gene OsMADS13 is intimately involved in the determination of ovule identity, since knock-out mutant plants develop carpel-like structures in place of ovules, resulting in female sterility. Little is known about the regulatory pathways at the base of rice gynoecium development. To investigate molecular mechanisms acting downstream of OsMADS13, we obtained transcriptomes of immature inflorescences from wild-type and Osmads13 mutant plants. Among a total of 476 differentially expressed genes (DEGs), a substantial overlap with DEGs from the SEP-family Osmads1 mutant was found, suggesting that OsMADS1 and OsMADS13 may act on a common set of target genes. Expression studies and preliminary analyses of two up-regulated genes encoding Zinc-finger transcription factors indicated that our dataset represents a valuable resource for the identification of both OsMADS13 target genes and novel players in rice ovule development. Taken together, our study suggests that OsMADS13 is an important repressor of the carpel pathway during ovule development.

Characterization of a new rice OsMADS1 null mutant generated by homologous recombination-mediated gene targeting

A new, stable, null mutant of OsMADS1 generated by homologous recombination-based gene targeting in an indica rice confirms its regulatory role for floral meristem identity, its determinate development and floral organ differentiation. OsMADS1, an E-class MADS-box gene, is an important regulator of rice flower development. Studies of several partial loss-of-function and knockdown mutants show varied floret organ defects and degrees of meristem indeterminacy. The developmental consequences of a true null mutant on floret meristem identity, its determinate development and differentiation of grass-specific organs such as the lemma and palea remain unclear. In this study, we generated an OsMADS1 null mutant by homologous recombination-mediated gene targeting by inserting a selectable marker gene (hpt) in OsMADS1 and replacing parts of its cis-regulatory and coding sequences. A binary vector was constructed with diphtheria toxin A chain gene (DT-A) as a negative marker to eliminate random integrations and the hpt marker for positive selection of homologous recombination. Precise disruption of the endogenous OsMADS1 locus in the rice genome was confirmed by Southern hybridization. The homozygous osmads1ko null mutant displayed severe defects in all floral organs including the lemma and palea. We also noticed striking instances of floral reversion to inflorescence and vegetative states which has not been reported for other mutant alleles of OsMADS1 and further reinforces the role of OsMADS1 in controlling floral meristem determinacy. Our data suggest, OsMADS1 commits and maintains determinate floret development by regulating floral meristem termination, carpel and ovule differentiation genes (OsMADS58, OsMADS13) while its modulation of genes such as OsMADS15, OsIG1 and OsMADS32 could be relevant in the differentiation and development of palea. Further, our study provides an important perspective on developmental stage-dependent modulation of some OsMADS1 target genes.

Characterization of the 'Oat-Like Rice' Caused by a Novel Allele OsMADS1Olr Reveals Vital Importance of OsMADS1 in Regulating Grain Shape in Oryza sativa L

BACKGROUND

Grain shape is a critical agronomic trait affecting grain yield and quality. Exploration and functional characterization of grain shape-related genes will facilitate rice breeding for higher quality and yield.

RESULTS

Here, we characterized a recessive mutant named Oat-like rice for its unique grain shape which highly resembles oat grains. The Oat-like rice displayed abnormal floral organs, an open hull formed by remarkably elongated leafy lemmas and paleae, occasionally formed conjugated twin brown rice, an aberrant grain shape and a low seed setting rate. By map-based cloning, we discovered that Oat-like rice harbors a novel allele of OsMADS1 gene (OsMADS1^Olr), which has a spontaneous point mutation that causes the substitution of an amino acid that is highly conserved in the MADS-box domain of the MADS-box family. Further linkage analysis indicated that the point mutation in the OsMADS1^Olr is associated with Oat-like rice phenotype, and expression analysis of the OsMADS1 by qRT-PCR and GUS staining also indicated that it is highly expressed in flower organs as well as in the early stages of grain development. Furthermore, OsMADS1^Olr-overexpressing plants showed similar phenotypes of Oat-like rice in grain shape, possibly due to the dominant negative effect. And OsMADS1-RNAi plants also displayed grain phenotypes like Oat-like rice. These results suggested that OsMADS1^Olr is responsible for the Oat-like rice phenotype including aberrant grain shape. Moreover, the expression levels of representative genes related to grain shape regulation were apparently altered in Oat-like rice, OsMADS1^Olr-overexpressing and OsMADS1-RNAi transgenic plants. Finally, compared with Oat-like rice, OsMADS1^Olr-overexpressing and OsMADS1-RNAi plants, mild phenotype of seed-specific OsMADS1-RNAi transgenic plants indicated that OsMADS1 may has has a direct regulation role in grain development and the grain phenotypes of Oat-like rice, OsMADS1^Olr-overexpressing and OsMADS1-RNAi plants are majorly caused by the abnormal lemma and palea development.

CONCLUSIONS

Altogether, our results showed that grain shape and a low seed setting rate of the notable 'Oat-like rice' are caused by a spontaneous point mutation in the novel allele OsMADS1^Olr. Furthermore, our findings suggested that OsMADS1 mediates grain shape possibly by affecting the expression of representative genes related to grain shape regulation. Thus, this study not only revealed that OsMADS1 plays a vital role in regulating grain shape of rice but also highlighted the importance and value of OsMADS1 to improve the quality and yield of rice by molecular breeding.

A set of AP2-like genes is associated with inflorescence branching and architecture in domesticated rice

Rice yield is influenced by inflorescence size and architecture, and inflorescences from domesticated rice accessions produce more branches and grains. Neither the molecular control of branching nor the developmental differences between wild and domesticated rice accessions are fully understood. We surveyed phenotypes related to branching, size, and grain yield across 91 wild and domesticated African and Asian accessions. Characteristics related to axillary meristem identity were the main phenotypic differences between inflorescences from wild and domesticated accessions. We used whole transcriptome sequencing in developing inflorescences to measure gene expression before and after the transition from branching axillary meristems to determinate spikelet meristems. We identified a core set of genes associated with axillary meristem identity in Asian and African rice, and another set associated with phenotypic variability between wild and domesticated accessions. AP2/EREBP-like genes were enriched in both sets, suggesting that they are key factors in inflorescence branching and rice domestication. Our work has identified new candidates in the molecular control of inflorescence development and grain yield, and provides a detailed description of the effects of domestication on phenotype and gene expression.

Characterization and fine mapping of nonstop glumes 2 (nsg2) mutant in rice (Oryza sativa L.)

In cereal crops, the grain number per panicle and the grain yield are greatly affected by the number of florets in a spikelet. In wild-type rice, a spikelet only produces one fertile floret and beneath the floret are a pair of sterile lemmas and a pair of rudimentary glumes. This study characterized a rice spikelet mutant nonstop glumes 2 (nsg2). In the nsg2 mutant, both the sterile lemmas and rudimentary glumes were elongated, and part of sterile lemma looked like a lemma in appearance, shape and size. Detailed histological analysis and qPCR analysis revealed that the sterile lemmas in the nsg2 mutant had homeotically transformed into lemma-like organs. This phenotype indicates that NSG2 is involved in the regulation of spikelet development and supports the long-held view that sterile lemmas were derived from the lemmas of the two lateral florets. This implies that the rice spikelet has the potential to be restored to the "three florets spikelet", which may have existed in its ancestors. Genetic analysis reveals that the nsg2 trait is controlled by a single recessive gene. The NSG2 gene was finally mapped between markers R-20 and R-39 on chromosome 7 with a physical region of 180 kb. The two MYB family factors LOC_Os07g44030 and LOC_Os07g44090 might be involved in the development of the spikelet and floral organ, and they were considered as candidate genes of NSG2. These results provide a foundation for map-based cloning and function analysis of NSG2, as well as evidence to support "three-florets spikelet" breeding in rice.

Screening and analysis of proteins interacting with OsMADS16 in rice (Oryza sativa L.)

OsMADS16, a class B floral organ identity gene, plays a pivotal role in stamen formation in rice. To date, little is known about the interacting partners of OsMADS16 except for several MADS-box proteins. In this study, we constructed a high-quality cDNA library of young panicles (< 5 cm in length) and performed yeast two-hybrid (Y2H) screening using OsMADS16 as bait. Eleven candidate proteins interacting with OsMADS16 were identified by Y2H and validated by BiFC and Co-IP assays. Subcellular localization results further confirmed the possibility of the interactions of OsMADS16 with 10 of the candidate proteins in natural rice cells. Bioinformatics analysis indicated that these partners exerted various molecular, cellular and physiological functions. Some of them were known or likely to be related to reproductive events, such as stamen primordium initiation, differentiation and development (OsMADS2, OsMADS4 and OsCOP9) and pollen development (OsbHLH40 and Os6PGDH). Our results provide an important reference for further research on OsMADS16-mediated regulation mechanism on floral organ development and pollen formation.

Expression pattern of ABCDE model genes in floral organs of bolting garlic clone

A correct understanding of the ABCDE model genes expression, especially genes involved in the development of the reproductive floral organs, in bolting and fertile garlic clones improves the process of its fertilization and breeding programs. Therefore, Real-Time PCR was employed to evaluate the temporal and spatial expression patterns of some floral organ identity genes in the inflorescence and different floret organs in the two stages of green and purple florets of bolting garlic clone. Relative expression of the studied genes, except AsSTK, in the mature inflorescence increased significantly during the early stages of initiation and differentiation of floral organs. Relative expression of the AsAP1 in the tepal and carpel, and AsAP2 in the tepal, stamen and carpel increased significantly. The highest relative expression levels of the AsAP1 and AsAP2 were found in the tepal of green florets and in the carpel of purple florets, respectively. AsAP3 and AsPI expression increased significantly in the stamen and carpel, and the highest relative expression of these two genes were observed in the green floret tepal. Relative expression of the AsAG increased significantly only in the reproductive floral organs and decreased significantly both in the carpel and stamen at floret maturity. The AsSEP1, 3 were expressed in all floral organs, but the AsSTK was only expressed in the carpel and its relative expression increased significantly at floret maturity. Finally, since considerable expression levels of the above genes were observed in the floral organs, these genes seem to be influential in the formation of floral organs in bolting garlic.

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.

Alternative splicing of OsLG3b controls grain length and yield in japonica rice

Grain size, one of the important components determining grain yield in rice, is controlled by the multiple quantitative trait loci (QTLs). Intensive artificial selection for grain size during domestication is evidenced in modern cultivars compared to their wild relatives. Here, we report the molecular cloning and characterization of OsLG3b, a QTL for grain length in tropical japonica rice that encodes MADS-box transcription factor 1 (OsMADS1). Six SNPs in the OsLG3b region led to alternative splicing, which were associated with grain length in an association analysis of candidate region. Quantitative PCR analysis indicated that OsLG3b expression was higher during the panicle and seed development stages. Analysis of haplotypes and introgression regions revealed that the long-grain allele of OsLG3b might have arisen after domestication of tropical japonica and spread to subspecies indica or temperate japonica by natural crossing and artificial selection. OsLG3b is therefore a target of human selection for adaptation to tropical regions during domestication and/or improvement of rice. Phylogenetic analysis and pedigree records showed that OsLG3b had been employed by breeders, but the gene still has much breeding potential for increasing grain length in indica. These findings will not only aid efforts to elucidate the molecular basis of grain development and domestication, but also facilitate the genetic improvement of rice yield.

Genetic Evidence for the Role of a Rice Vacuolar Invertase as a Molecular Sink Strength Determinant

BACKGROUND

Rice is a major crop feeding the majority of the global population, and increasing its sink strength is one of the modes to alleviate the declining availability of food for the rapidly growing world population. We demonstrate a role for an important rice vacuolar invertase isoform, OsINV3, in sink strength determination.

RESULTS

OsINV3 mutants showed shorter panicles with lighter and smaller grains, owing to a smaller cell size on the outer and inner surfaces of the palea and lemma as observed by scanning electron microscopy. Further, strong promoter::GUS expression was observed in the palea, lemma and the rachis branches in the young elongating panicles, which supported the role of OsINV3 in cell expansion and thus, in spikelet size and panicle length determination. Size of the spikelet was found to directly influence the grain weight, which was confirmed by the lack of differences in weights of hulled grain for differently segregated alleles in the heterozygous lines. Assessment of field grown mutants not only revealed a drastic reduction in the percentage of ripened grain, 1000-grain weight and final yield, but also significantly reduced partitioning of assimilates to the panicles, whereby the total dry weight remained unaffected. Determination of the non-structural carbohydrate contents revealed a lower hexose-to-sucrose ratio in the panicles of the mutants from panicle initiation to 10 days after heading, a stage that identifies as the critical pre-storage phase of grain filling, whereas the starch contents were not affected. In addition, strong promoter::GUS expression was observed in the dorsal end of ovary during the pre-storage phase until 6 days after flowering, highlighting a function for OsINV3 in monitoring the initial grain filling stage.

CONCLUSIONS

OsINV3 was found to regulate spikelet size by playing a key role in cell expansion, driving the movement of assimilates for grain filling by modulating the hexose-to-sucrose ratio, contributing in grain weight determination and thus, the grain yield.

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.

Differences in meristem size and expression of branching genes are associated with variation in panicle phenotype in wild and domesticated African rice

Background

The African rice Oryza glaberrima was domesticated from its wild relative Oryza barthii about 3000 years ago. During the domestication process, panicle complexity changed from a panicle with low complexity in O. barthii, to a highly branched panicle carrying more seeds in O. glaberrima. To understand the basis of this differential panicle development between the two species, we conducted morphological and molecular analyses of early panicle development.

Results

Using X-ray tomography, we analyzed the morphological basis of early developmental stages of panicle development. We uncovered evidence for a wider rachis meristem in O. glaberrima than in O. barthii. At the molecular level, spatial and temporal expression profiles of orthologs of O. sativa genes related to meristem activity and meristem fate control were obtained using in situ hybridization and qRT-PCR. Despite highly conserved spatial expression patterns between O. glaberrima and O. barthii, differences in the expression levels of these early acting genes were detected.

Conclusion

The higher complexity of the O. glaberrima panicle compared to that of its wild relative O. barthii is associated with a wider rachis meristem and a modification of expression of branching-related genes. Our study indicates that the expression of genes in the miR156/miR529/SPL and TAW1 pathways, along with that of their target genes, is altered from the unbranched stage of development. This suggests that differences in panicle complexity between the two African rice species result from early alterations to gene expression during reproductive development.

Electronic supplementary material

The online version of this article (doi:10.1186/s13227-017-0065-y) contains supplementary material, which is available to authorized users.

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

The floral meristem (FM) is self-maintaining at the early stages of flower development, but it is terminated when a fixed number of floral organs are produced. The FLORAL ORGAN NUMBER4 (FON4; also known as FON2) gene, an ortholog of Arabidopsis CLAVATA3 (CLV3), is required for regulating FM size and determinacy in rice. However, its interactions with floral homeotic genes remain unknown. Here, we report the genetic interactions between FON4 and floral homeotic genes OsMADS15 (an A-class gene), OsMADS16 (also called SUPERWOMAN1, SPW1, a B-class gene), OsMADS3 and OsMADS58 (C-class genes), OsMADS13 (a D-class gene), and OsMADS1 (an E-class gene) during flower development. We observed an additive phenotype in the fon4 double mutant with the OsMADS15 mutant allele dep (degenerative palea). The effect on the organ number of whorl 2 was enhanced in fon4 spw1. Double mutant combinations of fon4 with osmads3, osmads58, osmads13, and osmads1 displayed enhanced defects in FM determinacy and identity, respectively, indicating that FON4 and these genes synergistically control FM activity. In addition, the expression patterns of all the genes besides OsMADS13 had no obvious change in the fon4 mutant. This work reveals how the meristem maintenance gene FON4 genetically interacts with C, D, and E floral homeotic genes in specifying FM activity in monocot rice.

Gene expression profiling of reproductive meristem types in early rice inflorescences by laser microdissection

In rice, inflorescence architecture is established at early stages of reproductive development and contributes directly to grain yield potential. After induction of flowering, the complexity of branching, and therefore the number of seeds on the panicle, is determined by the activity of different meristem types and the timing of transitions between them. Although some of the genes involved in these transitions have been identified, an understanding of the network of transcriptional regulators controlling this process is lacking. To address this we used a precise laser microdissection and RNA-sequencing approach in Oryza sativa ssp. japonica cv. Nipponbare to produce quantitative data that describe the landscape of gene expression in four different meristem types: the rachis meristem, the primary branch meristem, the elongating primary branch meristem (including axillary meristems), and the spikelet meristem. A switch in expression profile between apical and axillary meristem types followed by more gradual changes during transitions in axillary meristem identity was observed, and several genes potentially involved in branching were identified. This resource will be vital for a mechanistic understanding of the link between inflorescence development and grain yield.

Flower development: the evolutionary history and functions of the AGL6 subfamily MADS-box genes

AGL6 is an ancient subfamily of MADS-box genes found in both gymnosperms and angiosperms. Its functions remained elusive despite the fact that the MADS-box genes and the ABC model have been studied for >20 years. Nevertheless, recent discoveries in petunia, rice, and maize support its involvement in the 'E' function of floral development, very similar to the closely related AGL2 (SEPALLATA) subfamily which has been well characterized. The known functions of AGL6 span from ancient conserved roles to new functions acquired in specific plant families. The AGL6 genes are involved in floral meristem regulation, in floral organs, and ovule (integument) and seed development, and have possible roles in both male and female germline and gametophyte development. In grasses, they are also important for the development of the first whorl of the flower, whereas in Arabidopsis they may play additional roles before floral meristem formation. This review covers these recent insights and some other aspects that are not yet fully elucidated, which deserve more studies in the future.

G1/ELE Functions in the Development of Rice Lemmas in Addition to Determining Identities of Empty Glumes

Rice empty glumes, also named sterile lemmas or rudimentary lemmas according to different interpretations, are distinct from lemmas in morphology and cellular pattern. Consistently, the molecular mechanism to control the development of lemmas is different from that of empty glumes. Rice LEAFY HULL STERILE1(OsLHS1) and DROOPING LEAF(DL) regulate the cellular pattern and the number of vascular bundles of lemmas respectively, while LONG STERILE LEMMA1 (G1)/ELONGATED EMPTY GLUME (ELE) and PANICLE PHYTOMER2 (PAP2)/OsMADS34 determine identities of empty glumes. Though some progress has been made, identities of empty glumes remain unclear, and genetic interactions between lemma genes and glume genes have been rarely elucidated. In this research, a new G1/ELE mutant g1-6 was identified and the phenotype was analyzed. Similar to previously reported mutant lines of G1/ELE, empty glumes of g1-6 plants transform into lemma-like organs. Furthermore, Phenotypes of single and double mutant plants suggest that, in addition to their previously described gene-specific functions, G1/ELE and OsLHS1 play redundant roles in controlling vascular bundle number, cell volume, and cell layer number of empty glumes and lemmas. Meanwhile, expression patterns of G1/ELE in osmads1-z flowers and OsLHS1 in g1-6 flowers indicate they do not regulate each other at the level of transcription. Finally, down-regulation of the empty glume gene OsMADS34/PAP2 and ectopic expression of the lemma gene DL, in the g1-6 plants provide further evidence that empty glumes are sterile lemmas. Generally, our findings provided valuable information for better understanding functions of G1 and OsLHS1 in flower development and identities of empty glumes.

OsMADS1 Represses microRNA172 in Elongation of Palea/Lemma Development in Rice

Specification of floral organ identity is critical for the establishment of floral morphology and inflorescence architecture. Although multiple genes are involved in the regulation of floral organogenesis, our understanding of the underlying regulating network is still fragmentary. MADs-box genes are principle members in the ABCDE model that characterized floral organs. OsMADS1 specifies the determinacy of spikelet meristem and lemma/palea identity in rice. However, the pathway through which OsMADS1 regulates floral organs remains elusive; here, we identified the microRNA172 (miR172) family as possible regulators downstream of OsMADS1. Genetic study revealed that overexpression of each miR172 gene resulted in elongated lemma/palea and indeterminacy of the floret, which resemble the phenotype of osmads1 mutant. On the contrary, overexpression of each target APETALA2 (AP2) genes resulted in shortened palea/lemma. Expression level and specificity of miR172 was greatly influenced by OsMADS1, as revealed by Northern blot analysis and In situ hybridization. Genetically, AP2-3 and AP2-2 over expression rescued the elongation and inconsistent development of the lemma/palea in OsMADS1RNAi transgenic plants. Our results suggested that in rice, OsMADS1 and miR172s/AP2s formed a regulatory network involved in floral organ development, particularly the elongation of the lemma and the palea.

Interactions of OsMADS1 with Floral Homeotic Genes in Rice Flower Development

During reproductive development, rice plants develop unique flower organs which determine the final grain yield. OsMADS1, one of SEPALLATA-like MADS-box genes, has been unraveled to play critical roles in rice floral organ identity specification and floral meristem determinacy. However, the molecular mechanisms underlying interactions of OsMADS1 with other floral homeotic genes in regulating flower development remains largely elusive. In this work, we studied the genetic interactions of OsMADS1 with B-, C-, and D-class genes along with physical interactions among their proteins. We show that the physical and genetic interactions between OsMADS1 and OsMADS3 are essential for floral meristem activity maintenance and organ identity specification; while OsMADS1 physically and genetically interacts with OsMADS58 in regulating floral meristem determinacy and suppressing spikelet meristem reversion. We provided important genetic evidence to support the neofunctionalization of two rice C-class genes (OsMADS3 and OsMADS58) during flower development. Gene expression profiling and quantitative RT-PCR analyses further revealed that OsMADS1 affects the expression of many genes involved in floral identity and hormone signaling, and chromatin immunoprecipitation (ChIP)-PCR assay further demonstrated that OsMADS17 is a direct target gene of OsMADS1. Taken together, these results reveal that OsMADS1 has diversified regulatory functions in specifying rice floral organ and meristem identity, probably through its genetic and physical interactions with different floral homeotic regulators.

Molecular identification and interaction assay of the gene (OsUbc13) encoding a ubiquitin-conjugating enzyme in rice

The ubiquitin (Ub)-conjugating enzyme, Ubc13, has been known to be involved in error-free DNA damage tolerance (or post-replication repair) via catalyzing Lys63-linked polyubiquitin chains formation together with a Ubc variant. However, its functions remain largely unknown in plant species, especially in monocotyledons. In this study, we cloned a Ub-conjugating enzyme, OsUbc13, that shares the conserved domain of Ubc with AtUBC13B in Oryza sativa L., which encodes a protein of 153 amino acids; the deduced sequence shares high similarities with other homologs. Real-time quantitative polymerase chain reaction (PCR) indicated that OsUbc13 transcripts could be detected in all tissues examined, and the expression level was higher in palea, pistil, stamen, and leaf, and lower in root, stem, and lemma; the expression of OsUbc13 was induced by low temperature, methylmethane sulfate (MMS), and H(2)O(2), but repressed by mannitol, abscisic acid (ABA), and NaCl. OsUbc13 was probably localized in the plasma and nuclear membranes. About 20 proteins, which are responsible for the positive yeast two-hybrid interaction of OsUbc13, were identified. These include the confirmed OsVDAC (correlated with apoptosis), OsMADS1 (important for development of floral organs), OsB22EL8 (related to reactive oxygen species (ROS) scavenging and DNA protection), and OsCROC-1 (required for formation of Lys63 polyubiquitylation and error-free DNA damage tolerance). The molecular characterization provides a foundation for the functional study of OsUbc13.

Down-regulation of a LBD-like gene, OsIG1, leads to occurrence of unusual double ovules and developmental abnormalities of various floral organs and megagametophyte in rice

The indeterminate gametophyte1 (ig1) mutation was first characterized to modulate female gametophyte development in maize (Zea mays). However, the function of its rice orthologue, OsIG1, remains unknown. For this, we first analysed OsIG1 localization from differential tissues in rice. Real-time quantitative PCR (qRT-PCR) and histochemical staining results demonstrated that the expression signal of OsIG1 was strongly detected in young inflorescence, moderately in mature flower and weakly in leaf. Furthermore, RNA in situ hybridization analyses exhibited that OsIG1 was strongly expressed in inflorescence meristems, floral meristems, empty-glume- and floret- primordia, especially in the primordia of stamens and immature ovules, and the micropylar side of the mature ovary. In OsIG1-RNAi lines, wrinkled blade formation was accompanied by increased leaf inclination angle. Cross-section further showed that the number of bulliform cells located between the vasculatures was significantly increased, indicating that OsIG1 is involved in division and differentiation of bulliform cell and lateral growth during leaf development. OsIG1-RNAi suppression lines showed pleiotropic phenotypes, including degenerated palea, glume-like features and open hull. In addition, a single OsIG1-RNAi floret is characterized by frequently developing double ovules with abnormal embryo sac development. Additionally, down-regulation of OsIG1 differentially affected the expression of genes associated with the floral organ development including EG1, OsMADS6 and OsMADS1. Taken together, these results demonstrate that OsIG1 plays an essential role in the regulation of empty-glume identity, floral organ number control and female gametophyte development in rice.

The polycomb group gene EMF2B is essential for maintenance of floral meristem determinacy in rice

Polycomb Repressive Complex 2 (PRC2) represses the transcriptional activity of target genes through trimethylation of lysine 27 of histone H3. The functions of plant PRC2 have been chiefly described in Arabidopsis, but specific functions in other plant species, especially cereals, are still largely unknown. Here we characterize mutants in the rice EMF2B gene, an ortholog of the Arabidopsis EMBRYONIC FLOWER2 (EMF2) gene. Loss of EMF2B in rice results in complete sterility, and mutant flowers have severe floral organ defects and indeterminacy that resemble loss-of-function mutants in E-function floral organ specification genes. Transcriptome analysis identified the E-function genes OsMADS1, OsMADS6 and OsMADS34 as differentially expressed in the emf2b mutant compared with wild type. OsMADS1 and OsMADS6, known to be required for meristem determinacy in rice, have reduced expression in the emf2b mutant, whereas OsMADS34 which interacts genetically with OsMADS1 was ectopically expressed. Chromatin immunoprecipitation for H3K27me3 followed by quantitative (q)RT-PCR showed that all three genes are presumptive targets of PRC2 in the meristem. Therefore, in rice, and possibly other cereals, PRC2 appears to play a major role in floral meristem determinacy through modulation of the expression of E-function genes.

Post-translational regulation of rice MADS29 function: homodimerization or binary interactions with other seed-expressed MADS proteins modulate its translocation into the nucleus

OsMADS29 is a seed-specific MADS-box transcription factor that affects embryo development and grain filling by maintaining hormone homeostasis and degradation of cells in the nucellus and nucellar projection. Although it has a bipartite nuclear localization signal (NLS) sequence, the transiently expressed OsMADS29 monomer does not localize specifically in the nucleus. Dimerization of the monomers alters the intracellular localization fate of the resulting OsMADS29 homodimer, which then translocates into the nucleus. By generating domain-specific deletions/mutations, we show that two conserved amino acids (lysine(23) and arginine(24)) in the NLS are important for nuclear localization of the OsMADS29 homodimer. Furthermore, the analyses involving interaction of OsMADS29 with 30 seed-expressed rice MADS proteins revealed 19 more MADS-box proteins, including five E-class proteins, which interacted with OsMADS29. Eleven of these complexes were observed to be localized in the nucleus. Deletion analysis revealed that the KC region (K-box and C-terminal domain) plays a pivotal role in homodimerization. These data suggest that the biological function of OsMADS29 may not only be regulated at the level of transcription and translation as reported earlier, but also at the post-translational level by way of the interaction between OsMADS29 monomers, and between OsMADS29 and other MADS-box proteins.

The pleiotropic SEPALLATA-like gene OsMADS34 reveals that the 'empty glumes' of rice (Oryza sativa) spikelets are in fact rudimentary lemmas

The single floret of the rice (Oryza sativa) spikelet is subtended by a pair of enigmatic organs usually termed 'empty glumes' or 'sterile lemmas'. As the identity of these organs remains essentially unknown, we refer to them as 'organs of unknown identity' (OUIs). Here we present a novel mutant of the rice SEPALLATA-like gene OsMADS34 which develops, in addition to disorganized branches and sterile seeds, elongated OUIs. The function and evolution of OsMADS34 were studied. Morphological and molecular markers indicate that the elongated OUIs have adopted lemma identity. Evolutionary analyses show that the ancestral genes of the OsM34 subclade evolved under positive selection, and that three specific motifs occur in the C-terminal region of proteins in the OsM34 subclade. Yeast two-hybrid assays revealed that the C-terminal region of OsMADS34 plays a crucial role in mediating protein interactions. Sequence analyses for the wild rice Oryza grandiglumis which has elongated OUIs revealed the association of OsMADS34 functionality with OUI identity. Our findings support the hypothesis that OUIs originated from the lemmas of degenerate florets under the negative control of OsMADS34. As OUIs neither are homologues to glumes nor have the identity of lemmas any more, but originated from these organs, we suggest calling them 'rudimentary lemmas'.

Grass flower development

Grasses bear unique flowers lacking obvious petals and sepals in special inflorescence units, the florets and the spikelet. Despite this, grass floral organs such as stamens and lodicules (petal homologs) are specified by ABC homeotic genes encoding MADS domain transcription factors, suggesting that the ABC model of eudicot flower development is largely applicable to grass flowers. However, some modifications need to be made for the model to fit grasses well: for example, a YABBY gene plays an important role in carpel specification. In addition, a number of genes are involved in the development of the lateral organs that constitute the spikelet. In this review, we discuss recent progress in elucidating the genes required for flower and spikelet development in grasses, together with those involved in fate determination of the spikelet and flower meristems.

Protein change in plant evolution: tracing one thread connecting molecular and phenotypic diversity

Proteins change over the course of evolutionary time. New protein-coding genes and gene families emerge and diversify, ultimately affecting an organism's phenotype and interactions with its environment. Here we survey the range of structural protein change observed in plants and review the role these changes have had in the evolution of plant form and function. Verified examples tying evolutionary change in protein structure to phenotypic change remain scarce. We will review the existing examples, as well as draw from investigations into domestication, and quantitative trait locus (QTL) cloning studies searching for the molecular underpinnings of natural variation. The evolutionary significance of many cloned QTL has not been assessed, but all the examples identified so far have begun to reveal the extent of protein structural diversity tolerated in natural systems. This molecular (and phenotypic) diversity could come to represent part of natural selection's source material in the adaptive evolution of novel traits. Protein structure and function can change in many distinct ways, but the changes we identified in studies of natural diversity and protein evolution were predicted to fall primarily into one of six categories: altered active and binding sites; altered protein-protein interactions; altered domain content; altered activity as an activator or repressor; altered protein stability; and hypomorphic and hypermorphic alleles. There was also variability in the evolutionary scale at which particular changes were observed. Some changes were detected at both micro- and macroevolutionary timescales, while others were observed primarily at deep or shallow phylogenetic levels. This variation might be used to determine the trajectory of future investigations in structural molecular evolution.

Molecular evolution and patterns of duplication in the SEP/AGL6-like lineage of the Zingiberales: a proposed mechanism for floral diversification

The diversity of floral forms in the plant order Zingiberales has evolved through alterations in floral organ morphology. One striking alteration is the shift from fertile, filamentous stamens to sterile, laminar (petaloid) organs in the stamen whorls, attributed to specific pollination syndromes. Here, we examine the role of the SEPALLATA (SEP) genes, known to be important in regulatory networks underlying floral development and organ identity, in the evolution of development of the diverse floral organs phenotypes in the Zingiberales. Phylogenetic analyses show that the SEP-like genes have undergone several duplication events giving rise to multiple copies. Selection tests on the SEP-like genes indicate that the two copies of SEP3 have mostly evolved under balancing selection, probably due to strong functional restrictions as a result of their critical role in floral organ specification. In contrast, the two LOFSEP copies have undergone differential positive selection, indicating neofunctionalization. Reverse transcriptase-polymerase chain reaction, gene expression from RNA-seq data, and in situ hybridization analyses show that the recovered genes have differential expression patterns across the various whorls and organ types found in the Zingiberales. Our data also suggest that AGL6, sister to the SEP-like genes, may play an important role in stamen morphology in the Zingiberales. Thus, the SEP-like genes are likely to be involved in some of the unique morphogenetic patterns of floral organ development found among this diverse order of tropical monocots. This work contributes to a growing body of knowledge focused on understanding the role of gene duplications and the evolution of entire gene networks in the evolution of flower development.

OsMADS16 genetically interacts with OsMADS3 and OsMADS58 in specifying floral patterning in rice

Rice (Oryza sativa) has unique floral patterns that contribute to grain yield. However, the molecular mechanism underlying the specification of floral organ identities in rice, particularly the interaction among floral homeotic genes, remains poorly understood. Here, we show that the floral homeotic gene OsMADS16 (also called SUPERWOMAN1, SPW1, a B-class gene) acts together with the rice C-class genes OsMADS3 and OsMADS58 in specifying floral organ patterning. OsMADS16 and the two C-class genes have an overlapping expression pattern in the third whorl founder cells. Compared with the single mutants, both spw1-1 osmads3-4 and spw1-1 osmads58 double mutants exhibit additional whorls of glume-like organs within the flower, particularly an extra whorl of six glume-like structures formed at the position of the wild-type stamens. These ectopic glume-like structures were shown to have palea identity through cellular observation and in situ hybridization analysis using marker genes. Our results suggest that B- and C-class genes play a key role in suppressing indeterminate growth within the floral meristem, particularly whorl-3 primordia. We also hypothesize that, in contrast to previous assumptions, the specialized spikelet organ in rice, the palea, is the counterpart of the sepal in eudicots, and the lemma is homologous to the bract.

Rice LHS1/OsMADS1 controls floret meristem specification by coordinated regulation of transcription factors and hormone signaling pathways

SEPALLATA (SEP) MADS box transcription factors mediate floral development in association with other regulators. Mutants in five rice (Oryza sativa) SEP genes suggest both redundant and unique functions in panicle branching and floret development. leafy hull sterile1/OsMADS1, from a grass-specific subgroup of LOFSEP genes, is required for specifying a single floret on the spikelet meristem and for floret organ development, but its downstream mechanisms are unknown. Here, key pathways and directly modulated targets of OsMADS1 were deduced from expression analysis after its knockdown and induction in developing florets and by studying its chromatin occupancy at downstream genes. The negative regulation of OsMADS34, another LOFSEP gene, and activation of OsMADS55, a SHORT VEGETATIVE PHASE-like floret meristem identity gene, show its role in facilitating the spikelet-to-floret meristem transition. Direct regulation of other transcription factor genes like OsHB4 (a class III homeodomain Leu zipper member), OsBLH1 (a BEL1-like homeodomain member), OsKANADI2, OsKANADI4, and OsETTIN2 show its role in meristem maintenance, determinacy, and lateral organ development. We found that the OsMADS1 targets OsETTIN1 and OsETTIN2 redundantly ensure carpel differentiation. The multiple effects of OsMADS1 in promoting auxin transport, signaling, and auxin-dependent expression and its direct repression of three cytokinin A-type response regulators show its role in balancing meristem growth, lateral organ differentiation, and determinacy. Overall, we show that OsMADS1 integrates transcriptional and signaling pathways to promote rice floret specification and development.

Characterization of Osmads6-5, a null allele, reveals that OsMADS6 is a critical regulator for early flower development in rice (Oryza sativa L.)

AGL6-clade genes are a subfamily of MADS-box genes and preferentially expressed in floral organs. OsMADS6 and OsMADS17 are two AGL6-like genes in rice. OsMADS17 has been shown to play a minor role in floral development and appears to result from a duplication of OsMADS6. OsMADS6 was initially named as MFO1 for mosaic floral organs based on its moderate mutant phenotypes. So far, four moderate or weak mutant alleles of OsMADS6 have been described, providing valuable insights into its role in flower development. Here, we report a null allele of OsMADS6 (Osmads6-5), which exhibited a strong mutant phenotype in spikelet without affecting vegetative traits, causing all floral organs except lemma homeotically transformed into lemma-like organs (LLOs) as well as an indeterminate floral meristem, thus resulting in a mutant floret consisting of reiterating whorls of lemma and LLOs. In consistently, over-expression of OsMADS6 led to additional lodicule-, stamen- and carpel-like organs. Expression analysis showed that OsMADS6 controls the formation of the incipient primordia of lodicule, stamen and carpel via regulating the expression of class B, C and SEP-like MADS-box genes. Taken together, our results revealed that OsMADS6 acts as a critical regulator for early flower development in rice and provide novel insights into the molecular mechanism of OsMADS6.

CHIMERIC FLORAL ORGANS1, encoding a monocot-specific MADS box protein, regulates floral organ identity in rice

The control of floral organ identity by homeotic MADS box genes is well established in eudicots. However, grasses have highly specialized outer floral organs, and the identities of the genes that regulate the highly specialized outer floral organs of grasses remain unclear. In this study, we characterized a MIKC-type MADS box gene, CHIMERIC FLORAL ORGANS (CFO1), which plays a key role in the regulation of floral organ identity in rice (Oryza sativa). The cfo1 mutant displayed defective marginal regions of the palea, chimeric floral organs, and ectopic floral organs. Map-based cloning demonstrated that CFO1 encoded the OsMADS32 protein. Phylogenetic analysis revealed that CFO1/OsMADS32 belonged to a monocot-specific clade in the MIKC-type MADS box gene family. The expression domains of CFO1 were mainly restricted to the marginal region of the palea and inner floral organs. The floral organ identity gene DROOPING LEAF (DL) was expressed ectopically in all defective organs of cfo1 flowers. Double mutant analysis revealed that loss of DL function mitigated some of the defects of floral organs in cfo1 flowers. We propose that the CFO1 gene plays a pivotal role in maintaining floral organ identity through negative regulation of DL expression.