The Rice Oligonucleotide Array Database: an atlas of rice gene expression

Comparative quantitative trait loci analysis framework reveals relationships between salt stress responsive phenotypes and pathways

Soil salinity is a complex abiotic stress that involves several biological pathways. Hence, focusing on a specific or a few salt-tolerant phenotypes is unlikely to provide comprehensive insights into the intricate and interwinding mechanisms that regulate salt responsiveness. In this study, we develop a heuristic framework for systematically integrating and comprehensively evaluating quantitative trait loci (QTL) analyses from multiple stress-related traits obtained by different studies. Making use of a combined set of 46 salinity-related traits from three independent studies that were based on the same chromosome segment substitution line (CSSL) population of rice (Oryza sativa), we demonstrate how our approach can address technical biases and limitations from different QTL studies and calling methods. This allows us to compile a comprehensive list of trait-specific and multi-trait QTLs, as well as salinity-related candidate genes. In doing so, we discover several novel relationships between traits that demonstrate similar trends of phenotype scores across the CSSLs, as well as the similarities between genomic locations that the traits were mapped to. Finally, we experimentally validate our findings by expression analyses and functional validations of several selected candidate genes from multiple pathways in rice and Arabidopsis orthologous genes, including OsKS7 (ENT-KAURENE SYNTHASE 7), OsNUC1 (NUCLEOLIN 1) and OsFRO1 (FERRIC REDUCTASE OXIDASE 1) to name a few. This work not only introduces a novel approach for conducting comparative analyses of multiple QTLs, but also provides a list of candidate genes and testable hypotheses for salinity-related mechanisms across several biological pathways.

Genome-Wide Identification and Analysis of Collar Region-Preferential Genes in Rice

The collar region plays a crucial role in leaf angle formation and plant architecture, which is important for improving crop yield given the challenges of diminishing arable land and changing environmental conditions. To determine collar region-preferential genes (CRPGs) affecting plant architecture and crop yield, we conducted genome-wide transcriptomic analysis. By integrating our RNA sequencing data with public rice anatomical expression data, we identified 657 CRPGs. Verification involved testing six randomly selected CRPGs, all of which exhibited collar-preferential expression. The functional significance of CRPGs was assessed via Gene Ontology enrichment analysis, utilizing MapMan and KEGG, and literature analysis provided additional information for characterized CRPGs. Our findings revealed links between manipulating leaf angle and phytohormone-related pathways and stress responses. Moreover, based on the CRPGs, five transcription factors downstream of the liguleless 1 (LG1) gene were identified. Overall, the identified CRPGs provide potential targets for further research and breeding applications aimed at improving crop productivity by manipulating leaf architecture.

Rice WRKY13 TF protein binds to motifs in the promoter region to regulate downstream disease resistance-related genes

In plants, pathogen resistance is brought about by the binding of certain transcription factor (TF) proteins to the cis-elements of certain target genes. These cis-elements are present upstream in the motif of the promoters of each gene. This ensures the binding of a specific TF to a specific promoter, therefore regulating the expression of that gene. Therefore, the study of each promoter sequence of all the rice genes would help identify the target genes of a specific TF. Rice 1 kb upstream promoter sequences of 55,986 annotated genes were analyzed using the Perl program algorithm to detect WRKY13 binding motifs (bm). The resulting genes were grouped using Gene Ontology and gene set enrichment analysis. A gene with more than 4 TF bm in their promoter was selected. Ten genes reported to have a role in rice disease resistance were selected for further analysis. Cis-acting regulatory element analysis was carried out to find the cis-elements and confirm the presence of the corresponding motifs in the promoter sequences of these genes. The 3D structure of WRKY13 TF and the corresponding ten genes were built, and the interacting residues were determined. The binding capacity of WRKY13 to the promoter of these selected genes was analyzed using docking studies. WRKY13 was considered for docking analysis based on the prior reports of autoregulation. Molecular dynamic simulations provided more details regarding the interactions. Expression data revealed the expression of the genes that helped provide the mechanism of interaction. Further co-expression network helped to characterize the interaction of these selected disease resistance-related genes with the WRKY13 TF protein. This study suggests downstream target genes that are regulated by the WRKY13 TF. The molecular mechanism involving the gene network regulated by WRKY13 TF in disease resistance against rice fungal pathogens is explored.

Genomics and transcriptomics to protect rice (Oryza sativa. L.) from abiotic stressors: -pathways to achieving zero hunger

More over half of the world's population depends on rice as a major food crop. Rice (Oryza sativa L.) is vulnerable to abiotic challenges including drought, cold, and salinity since it grown in semi-aquatic, tropical, or subtropical settings. Abiotic stress resistance has bred into rice plants since the earliest rice cultivation techniques. Prior to the discovery of the genome, abiotic stress-related genes were identified using forward genetic methods, and abiotic stress-tolerant lines have developed using traditional breeding methods. Dynamic transcriptome expression represents the degree of gene expression in a specific cell, tissue, or organ of an individual organism at a specific point in its growth and development. Transcriptomics can reveal the expression at the entire genome level during stressful conditions from the entire transcriptional level, which can be helpful in understanding the intricate regulatory network relating to the stress tolerance and adaptability of plants. Rice (Oryza sativa L.) gene families found comparatively using the reference genome sequences of other plant species, allowing for genome-wide identification. Transcriptomics via gene expression profiling which have recently dominated by RNA-seq complements genomic techniques. The identification of numerous important qtl,s genes, promoter elements, transcription factors and miRNAs involved in rice response to abiotic stress was made possible by all of these genomic and transcriptomic techniques. The use of several genomes and transcriptome methodologies to comprehend rice (Oryza sativa, L.) ability to withstand abiotic stress have been discussed in this review.

OsSNDP3 Functions for the Polar Tip Growth in Rice Pollen Together with OsSNDP2, a Paralog of OsSNDP3

Understanding pollen tube growth is critical for crop yield maintenance. The pollen tube provides a path for sperm cells for fertilization with egg cells. Cells must be subdivided into functionally and structurally distinct compartments for polar tip growth, and phosphoinositides are thought to be one of the facilitators for polarization during pollen tube growth. OsSNDP3 encodes Sec14-nodulin domain-containing protein and localizes in the nucleus and the microdomains of the plasma membrane in tobacco leaf epidermis cells. OsSNDP3 is thought to bind with phosphatidylinositol 4,5-bisphosphate based on the data including the information of basic amino acids in the C-terminal and colocalization with 2X Pleckstrin homology domain of Phospholipase C delta-1. OsSNDP3 interacts with a protein that contains a class I nodulin domain. We discovered that OsSNDP3 plays a significant role in pollen tube germination using CRISPR/Cas9 systems, whereas another pollen-preferential Sec14-nodulin domain-containing protein, OsSNDP2, additively functions with OsSNDP3 during pollen tube germination. Gene Ontology analysis using downregulated genes in ossndp3 indicated that the expression of genes involved in the phosphatidylinositol metabolic process and tip growth was significantly altered in ossndp3. OsSNDP3 aids pollen polar tip growth by binding with phosphatidylinositol 4,5-bisphosphate. We can better understand the roles of phosphoinositides during pollen tube growth by studying the functions of OsSNDP3 and OsSNDP2. And downregulated genes in ossndp3 might be useful targets for future research on polar tip growth.

Global Integrated Genomic and Transcriptomic Analyses of MYB Transcription Factor Superfamily in C3 Model Plant Oryza sativa (L.) Unravel Potential Candidates Involved in Abiotic Stress Signaling

Plant transcription factors (TFs) are significant players in transcriptional regulations, signal transduction, and constitute an integral part of signaling networks. MYB TFs are major TF superfamilies that play pivotal roles in regulation of transcriptional reprogramming, physiological processes, and abiotic stress (AbS) responses. To explore the understanding of MYB TFs, genome and transcriptome-wide identification was performed in the C3 model plant, Oryza sativa (OsMYB). This study retrieved 114 OsMYB TFs that were computationally analyzed for their expression profiling, gene organization, cis-acting elements, and physicochemical properties. Based on the microarray datasets, six OsMYB genes which were sorted out and identified by a differential expression pattern were noted in various tissues. Systematic expression profiling of OsMYB TFs showed their meta-differential expression of different AbS treatments, spatio-temporal gene expression of various tissues and their growth in the field, and gene expression profiling in responses to phytohormones. In addition, the circular ideogram of OsMYB genes in related C4 grass plants conferred the gene synteny. Protein–protein interactions of these genes revealed the molecular crosstalk of OsMYB TFs. Transcriptional analysis (qPCR) of six OsMYB players in response to drought and salinity stress suggested the involvement in individual and combined AbS responses. To decipher how these OsMYB play functional roles in AbS dynamics, further research is a prerequisite.

Identification of Potential Cytokinin Responsive Key Genes in Rice Treated With Trans-Zeatin Through Systems Biology Approach

Rice is an important staple food grain consumed by most of the population around the world. With climate and environmental changes, rice has undergone a tremendous stress state which has impacted crop production and productivity. Plant growth hormones are essential component that controls the overall outcome of the growth and development of the plant. Cytokinin is a hormone that plays an important role in plant immunity and defense systems. Trans-zeatin is an active form of cytokinin that can affect plant growth which is mediated by a multi-step two-component phosphorelay system that has different roles in various developmental stages. Systems biology is an approach for pathway analysis to trans-zeatin treated rice that could provide a deep understanding of different molecules associated with them. In this study, we have used a weighted gene co-expression network analysis method to identify the functional modules and hub genes involved in the cytokinin pathway. We have identified nine functional modules comprising of different hub genes which contribute to the cytokinin signaling route. The biological significance of these identified hub genes has been tested by applying well-proven statistical techniques to establish the association with the experimentally validated QTLs and annotated by the DAVID server. The establishment of key genes in different pathways has been confirmed. These results will be useful to design new stress-resistant cultivars which can provide sustainable yield in stress-specific conditions.

Toward Integrated Multi-Omics Intervention: Rice Trait Improvement and Stress Management

Rice (Oryza sativa) is an imperative staple crop for nearly half of the world's population. Challenging environmental conditions encompassing abiotic and biotic stresses negatively impact the quality and yield of rice. To assure food supply for the unprecedented ever-growing world population, the improvement of rice as a crop is of utmost importance. In this era, "omics" techniques have been comprehensively utilized to decipher the regulatory mechanisms and cellular intricacies in rice. Advancements in omics technologies have provided a strong platform for the reliable exploration of genetic resources involved in rice trait development. Omics disciplines like genomics, transcriptomics, proteomics, and metabolomics have significantly contributed toward the achievement of desired improvements in rice under optimal and stressful environments. The present review recapitulates the basic and applied multi-omics technologies in providing new orchestration toward the improvement of rice desirable traits. The article also provides a catalog of current scenario of omics applications in comprehending this imperative crop in relation to yield enhancement and various environmental stresses. Further, the appropriate databases in the field of data science to analyze big data, and retrieve relevant information vis-à-vis rice trait improvement and stress management are described.

OsDOF11 Affects Nitrogen Metabolism by Sucrose Transport Signaling in Rice (Oryza sativa L.)

Carbon and nitrogen antagonistically regulate multiple developmental processes. However, the molecular mechanism affecting nitrogen metabolism by sucrose transport remains poorly defined. Previously, we noted that Oryza sativa DNA BINDING WITH ONE FINGER 11 (OsDOF11) mediated sucrose transport by binding to the promoter regions of Sucrose Transporter 1 (SUT1), Oryza sativa Sugars Will Eventually be Exported Transporters 11 (OsSWEET11), and OsSWEET14. Here, we note that OsDOF11 promotes nitrogen uptake and then maintains the ratio of fresh weight to dry weight in seedling plants and the effective leaf blade at flowering stages. Mutants of the sucrose transporter gene OsSWEET14 displayed a phenotype similar to that of OsDOF11. By microarray analysis and qRT-PCR in OsDOF11 mutant plants, OsDOF11 affected the transcription level of amino acid metabolism-related genes. We further found that mainly amino acid contents were reduced in flag leaves but increased in seeds. Both sugar and organic nitrogen changes caused the ratio of fresh weight to dry weight to decrease in OsDOF11 mutant seedling plants and mature leaves, which might result in vigorous reduced metabolic activity and become less susceptible to stress. These results demonstrated that OsDOF11 affected nitrogen metabolism by sugar distribution in rice, which provided new insight that OsDOF11 coordinated with C and N balance to maintain plant growth activity.

A Systemic View of Carbohydrate Metabolism in Rice to Facilitate Productivity

Carbohydrate metabolism is an important biochemical process related to developmental growth and yield-related traits. Due to global climate change and rapid population growth, increasing rice yield has become vital. To understand whole carbohydrate metabolism pathways and find related clues for enhancing yield, genes in whole carbohydrate metabolism pathways were systemically dissected using meta-transcriptome data. This study identified 866 carbohydrate genes from the MapMan toolkit and the Kyoto Encyclopedia of Genes and Genomes database split into 11 clusters of different anatomical expression profiles. Analysis of functionally characterized carbohydrate genes revealed that source activity and eating quality are the most well-known functions, and they each have a strong correlation with tissue-preferred clusters. To verify the transcriptomic dissection, three pollen-preferred cluster genes were used and found downregulated in the gori mutant. Finally, we summarized carbohydrate metabolism as a conceptual model in gene clusters associated with morphological traits. This systemic analysis not only provided new insights to improve rice yield but also proposed novel tissue-preferred carbohydrate genes for future research.

Designing Future Crops: Genomics-Assisted Breeding Comes of Age

Over the past decade, genomics-assisted breeding (GAB) has been instrumental in harnessing the potential of modern genome resources and characterizing and exploiting allelic variation for germplasm enhancement and cultivar development. Sustaining GAB in the future (GAB 2.0) will rely upon a suite of new approaches that fast-track targeted manipulation of allelic variation for creating novel diversity and facilitate their rapid and efficient incorporation in crop improvement programs. Genomic breeding strategies that optimize crop genomes with accumulation of beneficial alleles and purging of deleterious alleles will be indispensable for designing future crops. In coming decades, GAB 2.0 is expected to play a crucial role in breeding more climate-smart crop cultivars with higher nutritional value in a cost-effective and timely manner.

Global Identification of ANTH Genes Involved in Rice Pollen Germination and Functional Characterization of a Key Member, OsANTH3

Pollen in angiosperms plays a critical role in double fertilization by germinating and elongating pollen tubes rapidly in one direction to deliver sperm. In this process, the secretory vesicles deliver cell wall and plasma membrane materials, and excessive materials are sequestered via endocytosis. However, endocytosis in plants is poorly understood. AP180 N-terminal homology (ANTH) domain-containing proteins function as adaptive regulators for clathrin-mediated endocytosis in eukaryotic systems. Here, we identified 17 ANTH domain-containing proteins from rice based on a genome-wide investigation. Motif and phylogenomic analyses revealed seven asparagine-proline-phenylalanine (NPF)-rich and 10 NPF-less subgroups of these proteins, as well as various clathrin-mediated endocytosis-related motifs in their C-terminals. To investigate their roles in pollen germination, we performed meta-expression analysis of all genes encoding ANTH domain-containing proteins in Oryza sativa (OsANTH genes) in anatomical samples, including pollen, and identified five mature pollen-preferred OsANTH genes. The subcellular localization of four OsANTH proteins that were preferentially expressed in mature pollen can be consistent with their role in endocytosis in the plasma membrane. Of them, OsANTH3 represented the highest expression in mature pollen. Functional characterization of OsANTH3 using T-DNA insertional knockout and gene-edited mutants revealed that a mutation in OsANTH3 decreased seed fertility by reducing the pollen germination percentage in rice. Thus, our study suggests OsANTH3-mediated endocytosis is important for rice pollen germination.

Rice PIN Auxin Efflux Carriers Modulate the Nitrogen Response in a Changing Nitrogen Growth Environment

Auxins play an essential role in regulating plant growth and adaptation to abiotic stresses, such as nutrient stress. Our current understanding of auxins is based almost entirely on the results of research on the eudicot Arabidopsis thaliana, however, the role of the rice PIN-FORMED (PIN) auxin efflux carriers in the regulation of the ammonium-dependent response remains elusive. Here, we analyzed the expression patterns in various organs/tissues and the ammonium-dependent response of rice PIN-family genes (OsPIN genes) via qRT-PCR, and attempted to elucidate the relationship between nitrogen (N) utilization and auxin transporters. To investigate auxin distribution under ammonium-dependent response after N deficiency in rice roots, we used DR5::VENUS reporter lines that retained a highly active synthetic auxin response. Subsequently, we confirmed that ammonium supplementation reduced the DR5::VENUS signal compared with that observed in the N-deficient condition. These results are consistent with the decreased expression patterns of almost all OsPIN genes in the presence of the ammonium-dependent response to N deficiency. Furthermore, the ospin1b mutant showed an insensitive phenotype in the ammonium-dependent response to N deficiency and disturbances in the regulation of several N-assimilation genes. These molecular and physiological findings suggest that auxin is involved in the ammonium assimilation process of rice, which is a model crop plant.

Transcriptome-based approaches for clarification of nutritional responses and improvement of crop production

Genome-wide transcriptome profiling is a powerful tool for identifying key genes and pathways involved in plant development and physiological processes. This review summarizes studies that have used transcriptome profiling mainly in rice to focus on responses to macronutrients such as nitrogen, phosphorus and potassium, and spatio-temporal root profiling in relation to the regulation of root system architecture as well as nutrient uptake and transport. We also discuss strategies based on meta- and co-expression analyses with different attributed transcriptome data, which can be used for investigating the regulatory mechanisms and dynamics of nutritional responses and adaptation, and speculate on further advances in transcriptome profiling that could have potential application to crop breeding and cultivation.

Phosphate-Starvation-Inducible S-Like RNase Genes in Rice Are Involved in Phosphate Source Recycling by RNA Decay

The fine-tuning of inorganic phosphate (Pi) for enhanced use efficiency has long been a challenging subject in agriculture, particularly in regard to rice as a major crop plant. Among ribonucleases (RNases), the RNase T2 family is broadly distributed across kingdoms, but little has been known on its substrate specificity compared to RNase A and RNase T1 families. Class I and class II of the RNase T2 family are defined as the S-like RNase (RNS) family and have showed the connection to Pi recycling in Arabidopsis. In this study, we first carried out a phylogenetic analysis of eight rice and five Arabidopsis RNS genes and identified mono-specific class I and dicot-specific class I RNS genes, suggesting the possibility of functional diversity between class I RNS family members in monocot and dicot species through evolution. We then compared the in silico expression patterns of all RNS genes in rice and Arabidopsis under normal and Pi-deficient conditions and further confirmed the expression patterns of rice RNS genes via qRT-PCR analysis. Subsequently, we found that most of the OsRNS genes were differentially regulated under Pi-deficient treatment. Association of Pi recycling by RNase activity in rice was confirmed by measuring total RNA concentration and ribonuclease activity of shoot and root samples under Pi-sufficient or Pi-deficient treatment during 21 days. The total RNA concentrations were decreased by < 60% in shoots and < 80% in roots under Pi starvation, respectively, while ribonuclease activity increased correspondingly. We further elucidate the signaling pathway of Pi starvation through upregulation of the OsRNS genes. The 2-kb promoter region of all OsRNS genes with inducible expression patterns under Pi deficiency contains a high frequency of P1BS cis-acting regulatory element (CRE) known as the OsPHR2 binding site, suggesting that the OsRNS family is likely to be controlled by OsPHR2. Finally, the dynamic transcriptional regulation of OsRNS genes by overexpression of OsPHR2, ospho2 mutant, and overexpression of OsPT1 lines involved in Pi signaling pathway suggests the molecular basis of OsRNS family in Pi recycling via RNA decay under Pi starvation.

Auxin apical dominance governed by the OsAsp1-OsTIF1 complex determines distinctive rice caryopses development on different branches

In rice (Oryza sativa), caryopses located on proximal secondary branches (CSBs) have smaller grain size and poorer grain filling than those located on apical primary branches (CPBs), greatly limiting grain yield. However, the molecular mechanism responsible for developmental differences between CPBs and CSBs remains elusive. In this transcriptome-wide expression study, we identified the gene Aspartic Protease 1 (OsAsp1), which reaches an earlier and higher transcriptional peak in CPBs than in CSBs after pollination. Disruption of OsAsp1 expression in the heterozygous T-DNA line asp1-1^+/–eliminated developmental differences between CPBs and CSBs. OsAsp1 negatively regulated the transcriptional inhibitor of auxin biosynthesis, OsTAA1 transcriptional inhibition factor 1 (OsTIF1), to preserve indole-3-acetic acid (IAA) apical dominance in CPBs and CSBs. IAA also facilitated OsTIF1 translocation from the endoplasmic reticulum (ER) to the nucleus by releasing the interaction of OsTIF1 with OsAsp1 to regulate caryopses IAA levels via a feedback loop. IAA promoted transcription of OsAsp1 through MADS29 to maintain an OsAsp1 differential between CPBs and CSBs during pollination. Together, these findings provide a mechanistic explanation for the distributed auxin differential between CPBs and CSBs to regulate distinct caryopses development in different rice branches and potential targets for engineering yield improvement in crops.

Rice is a major food crop and an important model plant. Compared with caryopses on apical primary branches (CPBs) of rice, those located on proximal secondary branches (CSBs) display smaller grains and poor grain filling, which greatly limit rice yield potential fulfilment, especially among ‘super’ rice cultivars. In this study, we demonstrated that high indole-3-acetic (IAA) levels upregulated Aspartic Protease 1 (OsAsp1) transcription via MADS29 post-pollination to produce higher OsAsp1 levels in CPBs than in CSBs. OsAsp1 then interacted with OsTAA1 transcriptional inhibition factor 1 (OsTIF1) in the endoplasmic reticulum (ER) to dispel OsTIF1 transcriptional inhibition of OsTAA1, causing IAA content to peak in CPBs at 5 days after fertilisation (DAF). IAA facilitated OsTIF1 translocation from the ER to the nucleus by reducing its interaction with OsAsp1 as feedback regulation of IAA levels in caryopses. Thus, differential auxin levels between CPBs and CSBs are determined by the OsAsp1-OsTIF1 complex, and are essential for the distinct development of CPBs and CSBs, providing potential targets for engineering yield improvement in crops.

Drought-Tolerance Gene Identification Using Genome Comparison and Co-Expression Network Analysis of Chromosome Substitution Lines in Rice

Drought stress limits plant growth and productivity. It triggers many responses by inducing changes in plant morphology and physiology. KDML105 rice is a key rice variety in Thailand and is normally grown in the northeastern part of the country. The chromosome segment substitution lines (CSSLs) were developed by transferring putative drought tolerance loci (QTLs) on chromosome 1, 3, 4, 8, or 9 into the KDML105 rice genome. CSSL104 is a drought-tolerant line with higher net photosynthesis and leaf water potential than KDML105 rice. The analysis of CSSL104 gene regulation identified the loci associated with these traits via gene co-expression network analysis. Most of the predicted genes are involved in the photosynthesis process. These genes are also conserved in Arabidopsis thaliana. Seven genes encoding chloroplast proteins were selected for further analysis through characterization of Arabidopsis tagged mutants. The response of these mutants to drought stress was analyzed daily for seven days after treatment by scoring green tissue areas via the PlantScreen™ XYZ system. Mutation of these genes affected green areas of the plant and stability index under drought stress, suggesting their involvement in drought tolerance.

Systematic Analysis of Cold Stress Response and Diurnal Rhythm Using Transcriptome Data in Rice Reveals the Molecular Networks Related to Various Biological Processes

Rice (Oryza sativa L.), a staple crop plant that is a major source of calories for approximately 50% of the human population, exhibits various physiological responses against temperature stress. These responses are known mechanisms of flexible adaptation through crosstalk with the intrinsic circadian clock. However, the molecular regulatory network underlining this crosstalk remains poorly understood. Therefore, we performed systematic transcriptome data analyses to identify the genes involved in both cold stress responses and diurnal rhythmic patterns. Here, we first identified cold-regulated genes and then identified diurnal rhythmic genes from those (119 cold-upregulated and 346 cold-downregulated genes). We defined cold-responsive diurnal rhythmic genes as CD genes. We further analyzed the functional features of these CD genes through Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses and performed a literature search to identify functionally characterized CD genes. Subsequently, we found that light-harvesting complex proteins involved in photosynthesis strongly associate with the crosstalk. Furthermore, we constructed a protein-protein interaction network encompassing four hub genes and analyzed the roles of the Stay-Green (SGR) gene in regulating crosstalk with sgr mutants. We predict that these findings will provide new insights in understanding the environmental stress response of crop plants against climate change.

Genes of the RAV Family Control Heading Date and Carpel Development in Rice

In plants, correct formation of reproductive organs is critical for successful seedset and perpetuation of the species. Plants have evolved different molecular mechanisms to coordinate flower and seed development at the proper time of the year. Among the plant-specific RELATED TO ABI3 AND VP1 (RAV) family of transcription factors, only TEMPRANILLO1 (TEM1) and TEM2 have been shown to affect reproductive development in Arabidopsis (Arabidopsis thaliana). They negatively regulate the floral transition through direct repression of FLOWERING LOCUS T and GIBBERELLIN 3-OXIDASE1/2, encoding major components of the florigen. Here we identify RAV genes from rice (Oryza sativa), and unravel their regulatory roles in key steps of reproductive development. Our data strongly suggest that, like TEMs, OsRAV9/OsTEM1 has a conserved function as a repressor of photoperiodic flowering upstream of the floral activators OsMADS14 and Hd3a, through a mechanism reminiscent of that one underlying floral transition in temperate cereals. Furthermore, OsRAV11 and OsRAV12 may have acquired a new function in the differentiation of the carpel and the control of seed size, acting downstream of floral homeotic factors. Alternatively, this function may have been lost in Arabidopsis. Our data reveal conservation of RAV gene function in the regulation of flowering time in monocotyledonous and dicotyledonous plants, but also unveil roles in the development of rice gynoecium.

Loss of function of Oryza sativa Argonaute 18 induces male sterility and reduction in phased small RNAs

In this manuscript, we show that Oryza sativa indica Argonaute protein AGO18 is required for male gametophyte development likely to through a small RNA-mediated mechanism. Monocots have evolved unique gene silencing pathways due to the presence of unique members of Dicer-like and Argonaute (AGO) family members. Among the monocot AGO homologs, AGO18 occupies a unique position. Previous reports have implicated this protein in viral resistance as well as in gametogenesis, likely through its competition with AGO1 clade members for micro(mi)RNAs and other small (s)RNAs. Although expression of rice AGO18 in specific stages of male gametogenesis has been documented, its major functions in plant development remain poorly understood. Here, we show that Oryza sativa indica AGO18 is involved in male gametophyte development. Knockdown (KD) of AGO18 in transgenic rice lines resulted in stunted plants that are male sterile, whereas their carpels were functional. Transcriptome analysis revealed downregulation of several pollen development-associated genes in KD lines. sRNA sequencing in vegetative and reproductive tissues of KD lines indicated reduction of miRNAs and phased secondary sRNAs implicated in male gametophyte development. Our results indicate a distinct role for rice AGO18 in male fertility.

Fast Track to Discover Novel Promoters in Rice

Promoters are key components for the application of biotechnological techniques in crop plants. Reporter genes such as GUS or GFP have been used to test the activity of promoters for diverse applications. A huge number of T-DNAs carrying promoterless GUS near their right borders have been inserted into the rice genome, and 105,739 flanking sequence tags from rice lines with this T-DNA insertion have been identified, establishing potential promoter trap lines for 20,899 out of 55,986 genes in the rice genome. Anatomical meta-expression data and information on abiotic stress related to these promoter trap lines enable us to quickly identify new promoters associated with various expression patterns. In the present report, we introduce a strategy to identify new promoters in a very short period of time using a combination of meta-expression analysis and promoter trap lines.

Rice Senescence-Induced Receptor-Like Kinase (OsSRLK) Is Involved in Phytohormone-Mediated Chlorophyll Degradation

Chlorophyll breakdown is a vital catabolic process of leaf senescence as it allows the recycling of nitrogen and other nutrients. In the present study, we isolated rice senescence-induced receptor-like kinase (OsSRLK), whose transcription was upregulated in senescing rice leaves. The detached leaves of ossrlk mutant (ossrlk) contained more green pigment than those of the wild type (WT) during dark-induced senescence (DIS). HPLC and immunoblot assay revealed that degradation of chlorophyll and photosystem II proteins was repressed in ossrlk during DIS. Furthermore, ultrastructural analysis revealed that ossrlk leaves maintained the chloroplast structure with intact grana stacks during dark incubation; however, the retained green color and preserved chloroplast structures of ossrlk did not enhance the photosynthetic competence during age-dependent senescence in autumn. In ossrlk, the panicles per plant was increased and the spikelets per panicle were reduced, resulting in similar grain productivity between WT and ossrlk. By transcriptome analysis using RNA sequencing, genes related to phytohormone, senescence, and chlorophyll biogenesis were significantly altered in ossrlk compared to those in WT during DIS. Collectively, our findings indicate that OsSRLK may degrade chlorophyll by participating in a phytohormone-mediated pathway.

Genome-Wide Transcriptome Analysis of Rice Seedlings after Seed Dressing with Paenibacillus yonginensis DCY84T and Silicon

Plant-growth-promoting bacteria (PGPB) are beneficial microorganisms that can also protect against disease and environmental stress. Silicon (Si) is the second most abundant element in soil, and is known to increase plant growth, grain yield, resistance to biotic stress, and tolerance to abiotic stress. Combined treatment of PGPB and Si has been shown to further enhance plant growth and crop yield. To determine the global effects of the PGPB and Si on rice growth, we compared rice plants treated with Paenibacillus yonginensis DCY84^T (DCY84^T) and Si with untreated rice. To identify the genes that respond to DCY84^T+Si treatment in rice, we performed an RNA-Seq transcriptome analysis by sampling treated and untreated roots on a weekly basis for three weeks. Overall, 576 genes were upregulated, and 394 genes were downregulated in treated roots, using threshold fold-changes of at least 2 (log₂) and p-values < 0.05. Gene ontology analysis showed that phenylpropanoids and the L-phenylalanine metabolic process were prominent in the upregulated genes. In a metabolic overview analysis using the MapMan toolkit, pathways involving phenylpropanoids and ethylene were strongly associated with upregulated genes. The functions of seven upregulated genes were identified as being associated with drought stress through a literature search, and a stress experiment confirmed that plants treated with DCY84^T+Si exhibited greater drought tolerance than the untreated control plants. Furthermore, the predicted protein–protein interaction network analysis associated with DCY84^T+ Si suggests mechanisms underlying growth promotion and stress tolerance.

Phenylalanine ammonia-lyase family is closely associated with response to phosphate deficiency in rice

BACKGROUND

Phenylalanine ammonia-lyase (PAL) catalyzes the first step in the biosynthetic phenylpropanoid pathway (PPP) via deamination of phenylalanine to trans-cinnamic acid, a precursor for the lignin and flavonoid biosynthetic pathways. Although its role is well-established in various plants, the functional significance of PAL genes in rice remains poorly understood.

OBJECTIVE

This study aims to find out the global feature of rice PAL genes associated with phosphate use efficiency.

METHODS

To identify the biological functions of individual rice PAL genes, we performed meta-expression profiling analysis based on phylogenomics of rice PAL genes and confirmed the expression patterns using Quantitative real-time PCR (qPCR).

RESULTS

We identified nine genes that were remarkably up-regulated during long-term phosphate (Pi) starvation and recovery processes through RNA-Seq data analysis. Expression patterns of the nine rice PAL genes under Pi starvation were further confirmed by qPCR, indicating that the function of PAL genes is strongly associated with Pi starvation response in rice.

CONCLUSION

Our study reports the functional significance of rice PAL genes involved in adaptation to low Pi growth conditions and provides useful information to improve Pi use efficiency in crop plant.

Genome-Wide Computational Identification of Biologically Significant Cis-Regulatory Elements and Associated Transcription Factors from Rice

The interactions between transcription factors (TFs) and cis-acting regulatory elements (CREs) provide crucial information on the regulation of gene expression. The determination of TF-binding sites and CREs experimentally is costly and time intensive. An in silico identification and annotation of TFs, and the prediction of CREs from rice are made possible by the availability of whole genome sequence and transcriptome data. In this study, we tested the applicability of two algorithms developed for other model systems for the identification of biologically significant CREs of co-expressed genes from rice. CREs were identified from the DNA sequences located upstream from the transcription start sites, untranslated regions (UTRs), and introns, and downstream from the translational stop codons of co-expressed genes. The biologically significance of each CRE was determined by correlating their absence and presence in each gene with that gene's expression profile using a meta-database constructed from 50 rice microarray data sets. The reliability of these methods in the predictions of CREs and their corresponding TFs was supported by previous wet lab experimental data and a literature review. New CREs corresponding to abiotic stresses, biotic stresses, specific tissues, and developmental stages were identified from rice, revealing new pieces of information for future experimental testing. The effectiveness of some-but not all-CREs was found to be affected by copy number, position, and orientation. The corresponding TFs that were most likely correlated with each CRE were also identified. These findings not only contribute to the prioritization of candidates for further analysis, the information also contributes to the understanding of the gene regulatory network.

A Systematic View Exploring the Role of Chloroplasts in Plant Abiotic Stress Responses

Chloroplasts are intracellular semiautonomous organelles central to photosynthesis and are essential for plant growth and yield. The significance of the function of chloroplast-related genes in response to climate change has not been well studied in crops. In the present study, the initial focus was on genes that were predicted to be located in the chloroplast genome in rice, a model crop plant, with genes either preferentially expressed in the leaf or ubiquitously expressed in all organs. The characteristics were analyzed by Gene Ontology (GO) enrichment and MapMan functional classification tools. It was then identified that 110 GO terms (45 for leaf expression and 65 for ubiquitous expression) and 1,695 genes mapped to MapMan overviews were strongly associated with chloroplasts. In particular, the MapMan cellular response overview revealed a close association between heat stress response and chloroplast-related genes in rice. Moreover, features of these genes in response to abiotic stress were analyzed using a large-scale publicly available transcript dataset. Consequently, the expression of 215 genes was found to be upregulated in response to high temperature stress. Conversely, genes that responded to other stresses were extremely limited. In other words, chloroplast-related genes were found to affect abiotic stress response mainly through high temperature response, with little effect on response to drought and salinity stress. These results suggest that genes involved in diurnal rhythm in the leaves participate in the reaction to recognize temperature changes in the environment. Furthermore, the predicted protein–protein interaction network analysis associated with high temperature stress is expected to provide a very important basis for the study of molecular mechanisms by which chloroplasts will respond to future climate changes.

Variations in the Structure and Evolution of Rice WRKY Genes in Indica and Japonica Genotypes and their Co-expression Network in Mediating Disease Resistance

WRKY transcription factor (TF) family regulates many functions in plant growth and development and also during biotic and abiotic stress. In this study, 101 WRKY TF gene models in indica and japonica rice were used to conduct evolutionary analysis, gene structure analysis, and motif composition. Co-expression analysis was carried out first by selecting the differentially expressing genes that showed a significant change in response to the pathogens from Rice Oligonucleotide Array Database (ROAD). About 82 genes showed responses to infection by Magnaporthe oryzae or Xanthomonas oryzae pv. oryzae. Co-expression gene network was constructed using direct neighborhood and context associated inbuilt mode in RiceNetv2 tool. Only 41 genes showed interaction with 2299 non-WRKY genes. Variations exist in the structure and evolution of WRKY genes among indica and japonica genotypes which have important implications in their differential roles including disease resistance. WRKY genes mediate a complex networking and co-express along with other WRKY and non-WRKY genes to mediate resistance against fungal and bacterial pathogens in rice.

Infrastructures of systems biology that facilitate functional genomic study in rice

Rice (Oryza sativa L.) is both a major staple food for the worldwide population and a model crop plant for studying the mode of action of agronomically valuable traits, providing information that can be applied to other crop plants. Due to the development of high-throughput technologies such as next generation sequencing and mass spectrometry, a huge mass of multi-omics data in rice has been accumulated. Through the integration of those data, systems biology in rice is becoming more advanced.To facilitate such systemic approaches, we have summarized current resources, such as databases and tools, for systems biology in rice. In this review, we categorize the resources using six omics levels: genomics, transcriptomics, proteomics, metabolomics, integrated omics, and functional genomics. We provide the names, websites, references, working states, and number of citations for each individual database or tool and discuss future prospects for the integrated understanding of rice gene functions.

Gene network mediated by WRKY13 to regulate resistance against sheath infecting fungi in rice (Oryza sativa L.)

OsWRKY13 TF gene is known to play a regulatory role of signaling in physiological pathways related to either development or disease resistance in rice plants. Rice cultivars IR 50 and TRY 3, resistant and susceptible respectively to sheath blight, TRY 3 and CO 43 resistant and susceptible respectively to sheath rot were challenged with fungal pathogens and disease scoring was carried out. Percent Disease Index (PDI) was significantly higher in susceptible varieties than resistant varieties. RT-PCR and qPCR analyses of WRKY13 using RNA extracted from the plant tissues revealed higher WRKY13 expression in resistant varieties (both diseases) upon pathogen challenge compared to uninfected control and also the susceptible varieties. To compute and evaluate the possible molecular mechanism for observed resistance correlated to WRKY13 gene expression, rice gene expression profiles against bacterial leaf blight and leaf blast disease from ROAD database were used to prioritize the locus IDs that were used as input in RiceNet v2 tool. The expression of WRKY13-regulated TIFY9 gene was predicted and validated using RT-PCR and qRT-PCR along with WRKY12 and PR2. All three genes showed induced expression in R. solani challenged sheath blight resistant variety. WRKY12 and PR2 expression in S. oryzae challenged sheath rot resistant variety was higher. Agrobacterium mediated transformation was carried out in rice plants using overexpression construct of WRKY13 (agroinfection in seeds of varieties susceptible to sheath blight and sheath rot, followed by selection in antibiotic media, germinating and hardening of putative transgenic lines). Based on qPCR analysis, the expression level of WRKY13 and the co-expression levels of WRKY12, TIFY9 and PR2 were found higher in PCR-positive T₁ plants compared to wild-type. Infection bioassays in the transgenic plants of both varieties revealed enhanced resistance to the pathogens. A mechanism by which WRKY13 would influence the MAPK cascade with TIFY9 acting as a mediator, is proposed.

RSL Class II Transcription Factors Guide the Nuclear Localization of RHL1 to Regulate Root Hair Development

Root hairs are important for absorption of nutrients and water from the rhizosphere. The Root Hair Defective-Six Like (RSL) Class II family of transcription factors is expressed preferentially in root hairs and has a conserved role in root hair development in land plants. We functionally characterized the seven members of the RSL Class II subfamily in the rice (Oryza sativa) genome. In root hairs, six of these genes were preferentially expressed and four were strongly expressed. Phenotypic analysis of each mutant revealed that Os07g39940 plays a major role in root hair formation, based on observations of a short root hair phenotype in those mutants. Overexpression (OX) for each of four family members in rice resulted in an increase in the density and length of root hairs. These four members contain a transcription activation domain and are targeted to the nucleus. They interact with rice Root Hairless1 (OsRHL1), a key regulator of root hair development. When heterologously expressed in epidermal cells of Nicotiana benthamiana leaves, OsRHL1 was predominantly localized to the cytoplasm. When coexpressed with each of the four RSL Class II members, however, OsRLH1 was translocated to the nucleus. Transcriptome analysis using Os07g39940-OX plants revealed that 86 genes, including Class III peroxidases, were highly up-regulated. Furthermore, reactive oxygen species levels in the root hairs were increased in Os07g39940-OX plants but were drastically reduced in the os07g39940 and rhl1 mutants. Our results demonstrate that RSL Class II members function as essential regulators of root hair development in rice.

Rice Genome-Scale Network Integration Reveals Transcriptional Regulators of Grass Cell Wall Synthesis

Grasses have evolved distinct cell wall composition and patterning relative to dicotyledonous plants. However, despite the importance of this plant family, transcriptional regulation of its cell wall biosynthesis is poorly understood. To identify grass cell wall-associated transcription factors, we constructed the Rice Combined mutual Ranked Network (RCRN). The RCRN covers >90% of annotated rice (Oryza sativa) genes, is high quality, and includes most grass-specific cell wall genes, such as mixed-linkage glucan synthases and hydroxycinnamoyl acyltransferases. Comparing the RCRN and an equivalent Arabidopsis network suggests that grass orthologs of most genetically verified eudicot cell wall regulators also control this process in grasses, but some transcription factors vary significantly in network connectivity between these divergent species. Reverse genetics, yeast-one-hybrid, and protoplast-based assays reveal that OsMYB61a activates a grass-specific acyltransferase promoter, which confirms network predictions and supports grass-specific cell wall synthesis genes being incorporated into conserved regulatory circuits. In addition, 10 of 15 tested transcription factors, including six novel Wall-Associated regulators (WAP1, WACH1, WAHL1, WADH1, OsMYB13a, and OsMYB13b), alter abundance of cell wall-related transcripts when transiently expressed. The results highlight the quality of the RCRN for examining rice biology, provide insight into the evolution of cell wall regulation, and identify network nodes and edges that are possible leads for improving cell wall composition.

A web-based tool for the prediction of rice transcription factor function

Transcription factors (TFs) are an important class of regulatory molecules. Despite their importance, only a small number of genes encoding TFs have been characterized in Oryza sativa (rice), often because gene duplication and functional redundancy complicate their analysis. To address this challenge, we developed a web-based tool called the Rice Transcription Factor Phylogenomics Database (RTFDB) and demonstrate its application for predicting TF function. The RTFDB hosts transcriptome and co-expression analyses. Sources include high-throughput data from oligonucleotide microarray (Affymetrix and Agilent) as well as RNA-Seq-based expression profiles. We used the RTFDB to identify tissue-specific and stress-related gene expression. Subsequently, 273 genes preferentially expressed in specific tissues or organs, 455 genes showing a differential expression pattern in response to 4 abiotic stresses, 179 genes responsive to infection of various pathogens and 512 genes showing differential accumulation in response to various hormone treatments were identified through the meta-expression analysis. Pairwise Pearson correlation coefficient analysis between paralogous genes in a phylogenetic tree was used to assess their expression collinearity and thereby provides a hint on their genetic redundancy. Integrating transcriptome with the gene evolutionary information reveals the possible functional redundancy or dominance played by paralog genes in a highly duplicated genome such as rice. With this method, we estimated a predominant role for 83.3% (65/78) of the TF or transcriptional regulator genes that had been characterized via loss-of-function studies. In this regard, the proposed method is applicable for functional studies of other plant species with annotated genome.

Chromatin interacting factor OsVIL2 increases biomass and rice grain yield

Grain number is an important agronomic trait. We investigated the roles of chromatin interacting factor Oryza sativa VIN3-LIKE 2 (OsVIL2), which controls plant biomass and yield in rice. Mutations in OsVIL2 led to shorter plants and fewer grains whereas its overexpression (OX) enhanced biomass production and grain numbers when compared with the wild type. RNA-sequencing analyses revealed that 1958 genes were up-regulated and 2096 genes were down-regulated in the region of active division within the first internodes of OX plants. Chromatin immunoprecipitation analysis showed that, among the downregulated genes, OsVIL2 was directly associated with chromatins in the promoter region of CYTOKININ OXIDASE/DEHYDROGENASE2 (OsCKX2), a gene responsible for cytokinin degradation. Likewise, active cytokinin levels were increased in the OX plants. We conclude that OsVIL2 improves the production of biomass and grain by suppressing OsCKX2 chromatin.

Genome-wide analysis of root hair-preferential genes in rice

BACKGROUND

Root hairs are valuable in taking up nutrients and water from the rhizosphere and serving as sites of interactions with soil microorganisms. By increasing the external surface area of the roots or interacting with rhizobacteria, root hairs directly and indirectly promote plant growth and yield. Transcriptome data can be used to understand root-hair development in rice.

RESULT

We performed Agilent 44 K microarray experiments with enriched root-hair samples and identified 409 root hair-preferential genes in rice. The expression patterns of six genes were confirmed using a GUS reporter system and quantitative RT-PCR analysis. Gene Ontology (GO) analysis demonstrated that 13 GO terms, including oxygen transport and cell wall generation, were highly over-represented in those genes. Although comparative analysis between rice and Arabidopsis revealed a large proportion of orthologous pairs, their spatial expression patterns were not conserved. To investigate the molecular network associated with root hair-preferential genes in rice, we analyzed the PPI network as well as coexpression data. Subsequently, we developed a refined network consisting of 24 interactions between 10 genes and 18 of their interactors.

CONCLUSION

Identification of root hair-preferential genes and in depth analysis of those genes will be a useful reference to accelerate the understanding of root-hair development in rice.

Dynamics of the Methylome and Transcriptome during the Regeneration of Rice

Oryza sativa indica (cv. IR64) and Oryza sativa japonica (cv. TNG67) vary in their regeneration efficiency. Such variation may occur in response to cultural environments that induce somaclonal variation. Somaclonal variations may arise from epigenetic factors, such as DNA methylation. We hypothesized that somaclonal variation may be associated with the differential regeneration efficiency between IR64 and TNG67 through changes in DNA methylation. We generated the stage-associated methylome and transcriptome profiles of the embryo, induced calli, sub-cultured calli, and regenerated calli (including both successful and failed regeneration) of IR64 and TNG67. We found that stage-associated changes are evident by the increase in the cytosine methylation of all contexts upon induction and decline upon regeneration. These changes in the methylome are largely random, but a few regions are consistently targeted at the later stages of culture. The expression profiles showed a dominant tissue-specific difference between the embryo and the calli. A prominent cultivar-associated divide in the global methylation pattern was observed, and a subset of cultivar-associated differentially methylated regions also showed stage-associated changes, implying a close association between differential methylation and the regeneration programs of these two rice cultivars. Based on these findings, we speculate that the differential epigenetic regulation of stress response and developmental pathways may be coupled with genetic differences, ultimately leading to differential regeneration efficiency. The present study elucidates the impact of tissue culture on callus formation and delineates the impact of stage and cultivar to determine the dynamics of the methylome and transcriptome in culture.

Rice tolerance to suboptimal low temperatures relies on the maintenance of the photosynthetic capacity

The purpose of this research was to identify differences between two contrasting rice cultivars in their response to suboptimal low temperatures stress. A transcriptomic analysis of the seedlings was performed and results were complemented with biochemical and physiological analyses. The microarray analysis showed downregulation of many genes related with PSII and particularly with the oxygen evolving complex in the sensitive cultivar IR50. Complementary studies indicated that the PSII performance, the degree of oxygen evolving complex coupling with the PSII core and net photosynthetic rate diminished in this cultivar in response to the stress. However, the tolerant cultivar Koshihikari was able to maintain its energy equilibrium by sustaining the photosynthetic capacity. The increase of oleic acid in Koshihikari could be related with membrane remodelling of the chloroplasts and hence contribute to tolerance. Overall, these results work as a ground for future analyses that look forward to characterize possible mechanisms to tolerate this stress.

ARMOUR - A Rice miRNA: mRNA Interaction Resource

ARMOUR was developed as A Rice miRNA:mRNA interaction resource. This informative and interactive database includes the experimentally validated expression profiles of miRNAs under different developmental and abiotic stress conditions across seven Indian rice cultivars. This comprehensive database covers 689 known and 1664 predicted novel miRNAs and their expression profiles in more than 38 different tissues or conditions along with their predicted/known target transcripts. The understanding of miRNA:mRNA interactome in regulation of functional cellular machinery is supported by the sequence information of the mature and hairpin structures. ARMOUR provides flexibility to users in querying the database using multiple ways like known gene identifiers, gene ontology identifiers, KEGG identifiers and also allows on the fly fold change analysis and sequence search query with inbuilt BLAST algorithm. ARMOUR database provides a cohesive platform for novel and mature miRNAs and their expression in different experimental conditions and allows searching for their interacting mRNA targets, GO annotation and their involvement in various biological pathways. The ARMOUR database includes a provision for adding more experimental data from users, with an aim to develop it as a platform for sharing and comparing experimental data contributed by research groups working on rice.

Genome-wide analyses of late pollen-preferred genes conserved in various rice cultivars and functional identification of a gene involved in the key processes of late pollen development

BACKGROUND

Understanding late pollen development, including the maturation and pollination process, is a key component in maintaining crop yields. Transcriptome data obtained through microarray or RNA-seq technologies can provide useful insight into those developmental processes. Six series of microarray data from a public transcriptome database, the Gene Expression Omnibus of the National Center for Biotechnology Information, are related to anther and pollen development.

RESULTS

We performed a systematic and functional study across the rice genome of genes that are preferentially expressed in the late stages of pollen development, including maturation and germination. By comparing the transcriptomes of sporophytes and male gametes over time, we identified 627 late pollen-preferred genes that are conserved among japonica and indica rice cultivars. Functional classification analysis with a MapMan tool kit revealed a significant association between cell wall organization/metabolism and mature pollen grains. Comparative analysis of rice and Arabidopsis demonstrated that genes involved in cell wall modifications and the metabolism of major carbohydrates are unique to rice. We used the GUS reporter system to monitor the expression of eight of those genes. In addition, we evaluated the significance of our candidate genes, using T-DNA insertional mutant population and the CRISPR/Cas9 system. Mutants from T-DNA insertion and CRISPR/Cas9 systems of a rice gene encoding glycerophosphoryl diester phosphodiesterase are defective in their male gamete transfer.

CONCLUSION

Through the global analyses of the late pollen-preferred genes from rice, we found several biological features of these genes. First, biological process related to cell wall organization and modification is over-represented in these genes to support rapid tube growth. Second, comparative analysis of late pollen preferred genes between rice and Arabidopsis provide a significant insight on the evolutional disparateness in cell wall biogenesis and storage reserves of pollen. In addition, these candidates might be useful targets for future examinations of late pollen development, and will be a valuable resource for accelerating the understanding of molecular mechanisms for pollen maturation and germination processes in rice.

Peroxiredoxins and Redox Signaling in Plants

SIGNIFICANCE

Peroxiredoxins (Prxs) are thiol peroxidases with multiple functions in the antioxidant defense and redox signaling network of the cell. Our progressing understanding assigns both local and global significance to plant Prxs, which are grouped in four Prx types. In plants they are localized to the cytosol, mitochondrion, plastid, and nucleus. Antioxidant defense is fundamentally connected to redox signaling, cellular communication, and acclimation. The thiol-disulfide network is central part of the stress sensing and processing response and integrates information input with redox regulation. Recent Advances: Prxs function both as redox sensory system within the network and redox-dependent interactors. The processes directly or indirectly targeted by Prxs include gene expression, post-transcriptional reactions, including translation, post-translational regulation, and switching or tuning of metabolic pathways, and other cell activities. The most advanced knowledge is available for the chloroplast 2-CysPrx wherein recently a solid interactome has been defined. An in silico analysis of protein structure and coexpression reinforces new insights into the 2-CysPrx functionality.

CRITICAL ISSUES

Up to now, Prxs often have been investigated for local properties of enzyme activity. In vitro and ex vivo work with mutants will reveal the ability of Prxs to interfere with multiple cellular components, including crosstalk with Ca²⁺-linked signaling pathways, hormone signaling, and protein homeostasis.

FUTURE DIRECTIONS

Complementation of the Prxs knockout lines with variants that mimic specific states, namely devoid of peroxidase activity, lacking the oligomerization ability, resembling the hyperoxidized decamer, or with truncated C-terminus, should allow dissecting the roles as thiol peroxidase, oxidant, interaction partner, and chaperone. Antioxid. Redox Signal. 28, 609-624.

NetMiner-an ensemble pipeline for building genome-wide and high-quality gene co-expression network using massive-scale RNA-seq samples

Accurately reconstructing gene co-expression network is of great importance for uncovering the genetic architecture underlying complex and various phenotypes. The recent availability of high-throughput RNA-seq sequencing has made genome-wide detecting and quantifying of the novel, rare and low-abundance transcripts practical. However, its potential merits in reconstructing gene co-expression network have still not been well explored. Using massive-scale RNA-seq samples, we have designed an ensemble pipeline, called NetMiner, for building genome-scale and high-quality Gene Co-expression Network (GCN) by integrating three frequently used inference algorithms. We constructed a RNA-seq-based GCN in one species of monocot rice. The quality of network obtained by our method was verified and evaluated by the curated gene functional association data sets, which obviously outperformed each single method. In addition, the powerful capability of network for associating genes with functions and agronomic traits was shown by enrichment analysis and case studies. In particular, we demonstrated the potential value of our proposed method to predict the biological roles of unknown protein-coding genes, long non-coding RNA (lncRNA) genes and circular RNA (circRNA) genes. Our results provided a valuable and highly reliable data source to select key candidate genes for subsequent experimental validation. To facilitate identification of novel genes regulating important biological processes and phenotypes in other plants or animals, we have published the source code of NetMiner, making it freely available at https://github.com/czllab/NetMiner.

OsbZIP48, a HY5 Transcription Factor Ortholog, Exerts Pleiotropic Effects in Light-Regulated Development

Plants have evolved an intricate network of sensory photoreceptors and signaling components to regulate their development. Among the light signaling components identified to date, HY5, a basic leucine zipper (bZIP) transcription factor, has been investigated extensively. However, most of the work on HY5 has been carried out in Arabidopsis (Arabidopsis thaliana), a dicot. In this study, based on homology search and phylogenetic analysis, we identified three homologs of AtHY5 in monocots; however, AtHYH (HY5 homolog) homologs are absent in the monocots analyzed. Out of the three homologs identified in rice (Oryza sativa), we have functionally characterized OsbZIP48OsbZIP48 was able to complement the Athy5 mutant. OsbZIP48 protein levels are developmentally regulated in rice. Moreover, the OsbZIP48 protein does not degrade in dark-grown rice and Athy5 seedlings complemented with OsbZIP48, which is in striking contrast to AtHY5. In comparison with AtHY5, which does not cause any change in hypocotyl length when overexpressed in Arabidopsis, the overexpression of full-length OsbZIP48 in rice transgenics reduced the plant height considerably. Microarray analysis revealed that OsKO2, which encodes ent-kaurene oxidase 2 of the gibberellin biosynthesis pathway, is down-regulated in OsbZIP48^OE and up-regulated in OsbZIP48^KD transgenics as compared with the wild type. Electrophoretic mobility shift assay showed that OsbZIP48 binds directly to the OsKO2 promoter. The RNA interference lines and the T-DNA insertional mutant of OsbZIP48 showed seedling-lethal phenotypes despite the fact that roots were more proliferative during early stages of development in the T-DNA insertional mutant. These data provide credible evidence that OsbZIP48 performs more diverse functions in a monocot system like rice in comparison with its Arabidopsis ortholog, HY5.

Transcriptional changes measured in rice roots after exposure to arsenite-contaminated sediments

Transcriptional analyses are discussed to provide a deeper understanding of the molecular mechanisms underlying toxic effects. Thus, they can complement classic ecotoxicological test methods and potentially allow the identification of biomarkers associated to the exposure of chemical stressors and or adverse biological effects. This feasibility study intended to identify a set of potential gene expression biomarkers for arsenite-exposure in rice roots that could complement the informative value of an existing sediment-contact test with rice. A sediment-contact test with Oryza sativa with the parameters inhibition of root and shoot elongation as phenotypic endpoints was used as basis. Rice plants were exposed to arsenite-spiked sediments. Transcriptomic changes in response to arsenite were observed by means of cDNA-microarray analysis regarding the whole-transcriptome at two sublethal arsenite concentrations. In order to identify candidate biomarker genes, differentially expressed genes were identified. Arsenite-induced differentially expressed genes were significantly associated with gene ontology (GO)-terms that indicated a general stress response. Of the differentially expressed genes, five genes were selected and their expression was measured at seven arsenite concentrations by means of qPCR in order to obtain their expression profiles. Three candidate biomarker genes showed a dose-dependent upregulation, while two showed no clear dose-dependent expression. The expression of all candidate biomarkers was also assessed in rice plants grown on two arsenic-contaminated natural sediments, but only one biomarker gene showed the expected upregulation.

Meta-expression analysis of unannotated genes in rice and approaches for network construction to suggest the probable roles

This work suggests 2020 potential candidates in rice for the functional annotation of unannotated genes using meta-analysis of anatomical samples derived from microarray and RNA-seq technologies and this information will be useful to identify novel morphological agronomic traits. Although the genome of rice (Oryza sativa) has been sequenced, 14,365 genes are considered unannotated because they lack putative annotation information. According to the Rice Genome Annotation Project Database ( http://rice.plantbiology.msu.edu/ ), the proportion of functionally characterized unannotated genes (0.35%) is quite limited when compared with the approximately 3.9% of annotated genes with assigned putative functions. Researchers require additional information to help them investigate the molecular mechanisms associated with those unannotated genes. To determine which of them might regulate morphological or physiological traits in the rice genome, we conducted a meta-analysis of expression data that covered a wide range of tissue/organ samples. Overall, 2020 genes showed cultivar-, tissue-, or organ-preferential patterns of expression. Representative candidates from featured groups were validated by RT-PCR, and the GUS reporter system was used to validate the expression of genes that were clustered according to their leaf or root preference. Taking a molecular and genetics approach, we examined meta-expression data and found that 127 genes were differentially expressed between japonica and indica rice cultivars. This is potentially significant for future agronomic applications. We also used a T-DNA insertional mutant and performed a co-expression network analysis of Sword shape dwarf1 (SSD1), a gene that regulates cell division. This network was refined via RT-PCR analysis. Our results suggested that SSD1 represses the expression of four genes related to the processes of DNA replication or cell division and provides insight into possible molecular mechanisms. Together, these strategies present a valuable tool for in-depth characterization of currently unannotated genes.

Mapping the microRNA Expression Profiles in Glyoxalase Over-expressing Salinity Tolerant Rice

In the recent years, glyoxalase pathway has been an active area of research in both human and plants. This pathway is reported to confer stress tolerance in plants, by modulating the glutathione homeostasis to achieve detoxification of a potent cytotoxic and mutagenic compound, methylglyoxal. The microRNAs (miRNAs) are also reported to play significant role in stress tolerance for plants. However, the cross-talk of miRNAs with the metabolism regulated by glyoxalase in the salinity-tolerance is unexplored. We therefore investigated whether expression profiles of miRNAs are altered in response to glyoxalase overexpression, and if any of these are also responsible for modulating the stress responses of plants. In this study, the Next Generation Sequencing (NGS) was employed to profile miRNA expression levels from glyoxalase overexpressing transgenic lines. The associated targets of differentially expressed miRNAs were predicted and their functional annotation was carried out using Gene Ontology (GO) and KEGG Orthology (KO), which showed their involvement in several crucial biological pathways. The analysis of NGS datasets also identified other isoforms or isomiRs of selected miRNAs, which may have an active role in developing tolerance against salt stress. Different aspects of miRNA modifications were also studied in glyoxalase overexpressing lines.

High Performance of Photosynthesis and Osmotic Adjustment Are Associated With Salt Tolerance Ability in Rice Carrying Drought Tolerance QTL: Physiological and Co-expression Network Analysis

Understanding specific biological processes involving in salt tolerance mechanisms is important for improving traits conferring tolerance to salinity, one of the most important abiotic stresses in plants. Under drought and salinity stresses, plants share overlapping responsive mechanisms such as physiological changes and activation of signaling molecules, which induce and transmit signals through regulator genes in a regulatory network. In this study, two near isogenic lines of rice carrying chromosome segments of drought tolerance QTL on chromosome 8 from IR68586-F2-CA-31 (DH103) in the genetic background of sensitive cultivar "Khao Dawk Mali 105; KDML105" (designated as CSSL8-94 and CSSL8-95) were used to investigate physiological responses to salt stress [namely growth, Na⁺/K⁺ ratio, water status, osmotic adjustment, photosynthetic parameters, electrolyte leakage (EL), malondialdehyde (MDA), proline and sugar accumulations], compared with the standard salt tolerant (Pokkali; PK) and their recurrent parent (KDML105) rice cultivars. Physiological examination indicated that both CSSLs showed superior salt-tolerant level to KDML105. Our results suggested that salt tolerance ability of these CSSL lines may be resulted from high performance photosynthesis, better osmotic adjustment, and less oxidative stress damage under salt conditions. Moreover, to explore new candidate genes that might take part in salt tolerance mechanisms, we performed co-expression network analysis for genes identified in the CSSL rice, and found that Os08g419090, the gene involved with tetrapyrrole and porphyrin biosynthetic process (chlorophyll biosynthetic process), Os08g43230 and Os08g43440 (encoded TraB family protein and cytochrome P450, respectively) might have unprecedented roles in salt stress tolerance.

Integrated omics analysis of root-preferred genes across diverse rice varieties including Japonica and indica cultivars

Plant root systems play essential roles in developmental processes, such as the absorption of water and inorganic nutrients, and structural support. Gene expression is affected by growth conditions and the genetic background of plants. To identify highly conserved root-preferred genes in rice across diverse growth conditions and varieties, we used two independent meta-anatomical expression profiles based on a large collection of Affymetrix and Agilent 44K microarray data sets available for public use. We then identified 684 loci with root-preferred expression, which were validated with in silico analysis using both meta-expression profiles. The expression patterns of four candidate genes were confirmed in vivo by monitoring expression of β-glucuronidase under control of the candidate-gene promoters, providing new tools to manipulate agronomic traits associated with roots. We also utilized real-time PCR to examine the root-preferential expression of 14 genes across four rice varieties, including japonica and indica cultivars. Using a database of rice genes with known functions, we identified the reported functions of 39 out of the 684 candidate genes. Sixteen genes are directly involved in root development, while the remaining are involved in processes indirectly related to root development (i.e., soil-stress tolerance or growth retardation). This indicates the importance of our candidate genes for studies on root development and function. Gene ontology enrichment analysis in the 'biological processes' category revealed that root-preferred genes in rice are closely associated with nutrient transport-related genes, indicating that the primary role of roots is the uptake of nutrients from soil. In addition, predicted protein-protein interaction analysis suggested a molecular network for root development composed of 215 interactions associated with 44 root-preferred or root development-related genes. Taken together, our data provide an important foundation for future research on root development in rice.

Melonet-DB, a Grand RNA-Seq Gene Expression Atlas in Melon (Cucumis melo L.)

Melon (Cucumis melo L.) is an important Cucurbitaceae crop produced worldwide, exhibiting wide genetic variations and comprising both climacteric and non-climacteric fruit types. The muskmelon cultivar "'Earl's favorite Harukei-3 (Harukei-3)"' known for its sweetness and rich aroma is used for breeding of high-grade muskmelon in Japan. We conducted RNA sequencing (RNA-seq) transcriptome studies in 30 different tissues of the 'Harukei-3' melon. These included root, stems, leaves, flowers, regenerating callus and ovaries, in addition to the flesh and peel sampled at seven stages of fruit development. The expression patterns of 20,752 genes were determined with fragments per kilobase of transcript per million fragments sequenced (FPKM) >1 in at least one tissue. Principal component analysis distinguished 30 melon tissues based on the global gene expression profile and, further, the weighted gene correlation network analysis classified melon genes into 45 distinct coexpression groups. Some coexpression groups exhibited tissue-specific gene expression. Furthermore, we developed and published web application tools designated "'Gene expression map viewer"' and "'Coexpression viewer"' on our website Melonet-DB (http://melonet-db.agbi.tsukuba.ac.jp/) to promote functional genomics research in melon. By using both tools, we analyzed melon homologs of tomato fruit ripening regulators such as E8, RIPENING-INHIBITOR (RIN) and NON-RIPENING (NOR). The "'Coexpression viewer"' clearly distinguished fruit ripening-associated melon RIN/NOR/CNR homologs from those expressed in other tissues. In addition, several other MADS-box, NAM/ATAF/CUC (NAC) and homeobox transcription factor genes were identified as fruit ripening-associated genes. Our tools provide useful information for research not only on melon but also on other fleshy fruit plants.

Comparative Expression Analysis of Rice and Arabidopsis Peroxiredoxin Genes Suggests Conserved or Diversified Roles Between the Two Species and Leads to the Identification of Tandemly Duplicated Rice Peroxiredoxin Genes Differentially Expressed in Seeds

BACKGROUND

Peroxiredoxins (PRXs) have recently been identified as plant antioxidants. Completion of various genome sequencing projects has provided genome-wide information about PRX genes in major plant species. Two of these -- Oryza sativa (rice) and Arabidopsis -- each have 10 PRX members. Although significant progress has been made in understanding their biological roles in Arabidopsis, those functions in rice, a model crop plant, have not been well studied.

RESULTS

We performed a comparative expression analysis of rice and Arabidopsis PRXs. Our phylogenetic analysis revealed that one subgroup contains three rice and three Arabidopsis Type-II PRXs that are expressed ubiquitously. This suggests that they are involved in housekeeping functions to process reactive oxygen species (ROS). Within the second subgroup, expression of Os1-CysPrxA (LOC_Os7g44430) and AtOs1-CysPrx is conserved in seeds while Os1-CysPrxB (LOC_Os7g44440) shows a root-preferential pattern of expression. We used transgenic plants expressing the GUS reporter gene under the control of the promoters of these two tandem duplicates to confirm their meta-expression patterns. Our GUS expression data from developing seeds and those that were germinating indicated that Os1-CysPrxB is involved in root development, as initiated from the embryo, while Os1-CysPrxA has roles in regulating endosperm development near the aleurone layer. For the third and fourth subgroups, the rice PRXs are more likely to show leaf/shoot-preferential expression, while those from Arabidopsis are significantly expressed in the flowers and seeds in addition to the leaf/shoot. To determine the biological meaning of those expression patterns that were dominantly identified in rice PRXs, we analyzed three rice genes showing leaf/shoot-preferential expression in a mutant of the light-responsive 1-deoxy-D-xylulose 5-phosphate reductoisomerase (dxr) gene and found that two of them were significantly down-regulated in the mutant.

CONCLUSION

A global expression analysis of the PRX family in rice identified tandem duplicates, Os1-CysPrxA and Os1-CysPrxB, in the 1-CysPrx subgroup that are differentially expressed in developing seeds and germinating seeds. Analysis of the cis-acting regulatory elements (CREs) revealed unique CREs responsible for embryo and root or endosperm-preferential expression. In addition, the presence of leaf/shoot-preferential PRXs in rice suggests that they are required in that crop because those plants must tolerate a higher light intensity in their normal growth environment when compared with that of Arabidopsis. Downregulation of two PRXs in the dxr mutant causing an albino phenotype, implying that those genes have roles in processing ROS produced during photosynthesis. Network analysis of four PRXs allowed us to model regulatory pathways that explain the underlying protein interaction network. This will be a useful hypothetical model for further study.

RiceAntherNet: a gene co-expression network for identifying anther and pollen development genes

In plants, normal anther and pollen development involves many important biological events and complex molecular regulatory coordination. Understanding gene regulatory relationships during male reproductive development is essential for fundamental biology and crop breeding. In this work, we developed a rice gene co-expression network for anther development (RiceAntherNet) that allows prediction of gene regulatory relationships during pollen development. RiceAntherNet was generated from 57 rice anther tissue microarrays across all developmental stages. The microarray datasets from nine rice male sterile mutants, including msp1-4, ostdl1a, gamyb-2, tip2, udt1-1, tdr, eat1-1, ptc1 and mads3-4, were used to explore and test the network. Among the changed genes, three clades showing differential expression patterns were constructed to identify genes associated with pollen formation. Many of these have known roles in pollen development, for example, seven genes in Clade 1 (OsABCG15, OsLAP5, OsLAP6, DPW, CYP703A3, OsNP1 and OsCP1) are involved in rice pollen wall formation. Furthermore, Clade 1 contained 12 genes whose predicted orthologs in Arabidopsis have been reported as key during pollen development and may play similar roles in rice. Genes in Clade 2 are expressed earlier than Clade 1 (anther stages 2-9), while genes in Clade 3 are expressed later (stages 10-12). RiceAntherNet serves as a valuable tool for identifying novel genes during plant anther and pollen development. A website is provided (https://www.cpib.ac.uk/anther/riceindex.html) to present the expression profiles for gene characterization. This will assist in determining the key relationships between genes, thus enabling characterization of critical genes associated with anther and pollen regulatory networks.

OsMTP11 is localised at the Golgi and contributes to Mn tolerance

Membrane transporters play a key role in obtaining sufficient quantities of manganese (Mn) but also in protecting against Mn toxicity. We have characterized OsMTP11, a member of the Cation Diffusion Facilitator/Metal Tolerance Protein (CDF/MTP) family of metal cation transporters in Oryza sativa. We demonstrate that OsMTP11 functions in alleviating Mn toxicity as its expression can rescue the Mn-sensitive phenotype of the Arabidopsis mtp11-3 knockout mutant. When expressed stably in Arabidopsis and transiently in rice and tobacco, it localises to the Golgi. OsMTP11 partially rescues the Mn-hypersensitivity of the pmr1 yeast mutant but only slightly alleviates the Zn sensitivity of the zrc1 cot1 yeast mutant. Overall, these results suggest that OsMTP11 predominantly functions as a Mn-transporting CDF with lower affinity for Zn. Site-directed mutagenesis studies revealed four substitutions in OsMTP11 that appear to alter its transport activity. OsMTP11 harbouring a substitution of leucine 150 to a serine fully rescued pmr1 Mn-sensitivity at all concentrations tested. The other substitutions, including those at conserved DxxxD domains, reduced complementation of pmr1 to different levels. This indicates their importance for OsMTP11 function and is a starting point for refining transporter activity/specificity.