Rice Panicle Development Research Articles

Comparative transcriptome analysis of panicle development under heat stress in two rice (Oryza sativa L.) cultivars differing in heat tolerance.

Heat stress inhibits rice panicle development and reduces the spikelet number per panicle. This study investigated the mechanism involved in heat-induced damage to panicle development and spikelet formation in rice cultivars that differ in heat tolerance. Transcriptome data from developing panicles grown at 40 °C or 32 °C were compared for two rice cultivars: heat-tolerant Huanghuazhan and heat-susceptible IR36. Of the differentially expressed genes (DEGs), 4,070 heat stress-responsive genes were identified, including 1,688 heat-resistant-cultivar-related genes (RHR), 707 heat-susceptible-cultivar-related genes (SHR), and 1,675 common heat stress-responsive genes (CHR). A Gene Ontology (GO) analysis showed that the DEGs in the RHR category were significantly enriched in 54 gene ontology terms, some of which improved heat tolerance, including those in the WRKY, HD-ZIP, ERF, and MADS transcription factor families. A Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the DEGs in the RHR and SHR categories were enriched in 15 and 11 significant metabolic pathways, respectively. Improved signal transduction capabilities of endogenous hormones under high temperature seemed to promote heat tolerance, while impaired starch and sucrose metabolism under high temperature might have inhibited young panicle development. Our transcriptome analysis provides insights into the different molecular mechanisms of heat stress tolerance in developing rice.

MiR156f integrates panicle architecture through genetic modulation of branch number and pedicel length pathways

BackgroundRice (Oryza sativa) panicle architecture is the major determinant of the ideal plant architecture that directly influence yield potential. Many genes influencing development of primary branches, secondary branches, spikelet and pedicel would also influence panicle architecture, which is thus a complex trait regulated by genes from various aspects. miR156, an extensively studied miRNA, has recently emerged as promising target for crop improvement because of its role in plant architecture regulation, such as the number of tillers, plant height and the panicle architecture. Increasing evidence suggests that miR156 might play an important role in panicle architecture regulation.Main bodyTo study the detailed function of miR156 in rice panicle architecture regulation, we examined the genetic interaction or transcriptional regulation of miR156/OsSPL to other panicle regulating genes. Our results revealed that expression of many panicle related genes were influenced by miR156. Through biochemical analysis, we further proved that miR156 directly regulated the axillary meristem regulating gene, LAX1, at the transcription level. And the intimate relations between miR156 and LAX1, and miR156 and LAX2 were also uncovered by genetic analysis. On the other hand, a tight genetic linkage between miR156 and RCN2, the panicle branch promoting gene, was also detected, which suggested a buffering mechanism for the miR156 mediated panicle architecture regulation. Furthermore, genetic analysis also demonstrated that miR156 functioned in the same pathway with OsRA2 to regulate pedicel length.Short conclusionAltogether, miR156 integrates several genetic pathways mediated by genes such as LAX1, LAX2, RCN2 and OsRA2, and comprehensively regulates panicle development in rice. Based on these analysis, we concluded that miR156 acts as an important regulator for panicle architecture through influencing various aspects of panicle development.

OsSPL18 controls grain weight and grain number in rice

Grain weight and grain number are two important traits directly determining grain yield in rice. To date, a lot of genes related to grain weight and grain number have been identified; however, the regulatory mechanism underlying these genes remains largely unknown. In this study, we studied the biological function of OsSPL18 during grain and panicle development in rice. Knockout (KO) mutants of OsSPL18 exhibited reduced grain width and thickness, panicle length and grain number, but increased tiller number. Cytological analysis showed that OsSPL18 regulates the development of spikelet hulls by affecting cell proliferation. qRT-PCR and GUS staining analyses showed that OsSPL18 was highly expressed in developing young panicles and young spikelet hulls, in agreement with its function in regulating grain and panicle development. Transcriptional activation experiments indicated that OsSPL18 is a functional transcription factor with activation domains in both the N-terminus and C-terminus, and both activation domains are indispensable for its biological functions. Quantitative expression analysis showed that DEP1, a major grain number regulator, was significantly down-regulated in OsSPL18 KO lines. Both yeast one-hybrid and dual-luciferase (LUC) assays showed that OsSPL18 could bind to the DEP1 promoter, suggesting that OsSPL18 regulates panicle development by positively regulating the expression of DEP1. Sequence analysis showed that OsSPL18 contains the OsmiR156k complementary sequence in the third exon; 5ʹ RLM-RACE experiments indicated that OsSPL18 could be cleaved by OsmiR156k. Taken together, our results uncovered a new OsmiR156k-OsSPL18-DEP1 pathway regulating grain number in rice.

Genome-wide identification of the pectate lyase-like (PLL) gene family and functional analysis of two PLL genes in rice

Pectate lyase catalyses the eliminative cleavage of de-esterified pectin, which is a major component of primary cell walls in many higher plants. Pectate lyase-like (PLL) genes have been identified in various plant species and are involved in a broad range of physiological processes associated with pectin degradation. Previous studies have functionally identified two PLL genes in rice (Oryza sativa. L). However, the knowledge concerning genome-wide analysis of this family remains limited, and functions of the other PLL genes have not been thoroughly elucidated to date. In this study, we identified 12 PLL genes based on a genome-wide investigation in rice. A complete overview of this gene family is presented, including chromosomal locations, exon-intron structure, cis-acting elements and conserved motifs. PLL protein sequences from multiple plant species were compared and divided into five groups based on phylogenetic analysis. Quantitative RT-PCR analysis revealed that only a portion of OsPLL genes (4 of 12) exhibits detectable expression levels. Notably, OsPLL1, OsPLL3, OsPLL4 and OsPLL12 exhibit strong and preferential expression in panicles suggesting that the potential roles of these genes are crucial during rice panicle development. Moreover, knockdown of OsPLL3 and OsPLL4 by artificial microRNA (amiRNA) disrupted normal pollen development and resulted in partial male sterility. These results could provide valuable information for characterising the functions and dissecting the molecular mechanisms of the OsPLL genes.

Normalized difference vegetation index for rice management in El Espinal, Colombia

Se evaluaron las imágenes aéreas y el NDVI como herramientas para la supervisión del arroz a gran escala. El índice de vegetación de diferencia normalizada (NDVI) se utilizó para identificar problemas en el desarrollo de la variedad de arroz FEDEARROZ-2000, la cual es resistente al virus de la hoja blanca y al daño directo de la "sogata". Se estimó la dinámica temporal del NDVI para FEDEARROZ-2000. En la Etapa de Desarrollo de la Panícula del Arroz (EDPA), el NDVI inferior a 0,8 se relacionó con áreas con problemas de nivelación, estrés hídrico y diferencias en el estado de las plantas. El NDVI de la EDPA tuvo una correlación positiva significativa con las panículas/m2, el peso de los 1000 granos, y con el rendimiento (Coeficiente de correlación de Pearson R≥0.86; Probabilidad≤0.04). El NDVI en la etapa lechosa ayudó a identificar ambientes de producción y a programar áreas para la cosecha.

Transcriptomic analysis of field-grown rice (Oryza sativa L.) reveals responses to shade stress in reproductive stage

The number of spikelets per panicle is a key factor affecting rice (Oryza sativa L.) yield, and is regulated by many different environmental cues, such as light intensity. In this study, we found that shade led to a reduction in the number of secondary branches and fewer spikelets per panicle. Rice grown in the shade had an increased spikelet degradation rate. We studied the genes that respond to shade in rice using transcriptome sequencing, which revealed that rice floral genes OsFKF1 and OsDof12 expression levels were suppressed by shading. However, Heading date 1 (Hd1), Heading date 3a (Hd3a), and Early heading date 1 (Ehd1) were induced and RICE FLOWERING LOCUS T 1 (RFT1) was suppressed without any obvious change in heading time. Furthermore, the expression level of spikelet differentiation-related genes OsFOR1, FON1, OsPBP1 and OsSPL16 were influenced by shade stress, may led to changes in spike structural. Shade affected the expression of growth-related genes that are involved in metabolism, DNA synthesis/chromatin structure, and the environmental adaptation pathway. Genes involved in chloroplast development were downregulated in leaves under shade. In addition, genes that regulate energy expenditure were suppressed by shade in both young panicles and leaves, indicating that damage to the leaf photosynthetic apparatus reduces the energetic costs of the plant. Organic synthesis-related genes were suppressed in young panicles of plants under shade, suggesting that shade slows panicle development. The identification of novel differentially expressed genes provides new insights into the effects of light deficiency on young panicle development in rice.

Development of Rice Stink Bug,Oebalus pugnaxF., Nymphs on Rice Kernels and Effects of Nymphal Feeding on Rice Yields

The rice stink bug, Oebalus pugnax F., is of major economic importance to producers and millers of rice, Oryza sativa L. (Poaceae), because of the damaging effects of feeding during kernel development. Adult rice stink bugs cause yield loss and discoloration of rice kernels when feeding on panicles from anthesis to hard-dough stages of grain development, but damage by nymphs developing from the first to fifth instars has not been adequately studied. An experiment assessed the effect of rice stink bug nymphs on rice yield by caging egg masses on individual panicles and removing insects when adults emerged. A positive relationship between insect abundance and two measures of yield loss, unfilled kernels and milling loss, was very significant. Approximately 35% of eggs developed into fifth-instar nymphs in less than 21 days -- before kernels matured. Findings suggested that eggs and nymphs during early stages of rice panicle development should be considered in insecticidal treatment thresholds for rice stink bugs.

MiR529a modulates panicle architecture through regulating SQUAMOSA PROMOTER BINDING-LIKE genes in rice (Oryza sativa).

MiR529a affects rice panicle architecture by targeting OsSPL2,OsSPL14 and OsSPL17 genes that could regulate their downstream panicle related genes. The panicle architecture determines the grain yield and quality of rice, which could be regulated by many transcriptional factors. The SQUAMOSA PROMOTER BINDING-LIKE (SPL) transcription factors are involved in the regulation of panicle development, which are targeted by miR156 and miR529. The expression profile demonstrated that miR529a is preferentially expressed in the early panicle of rice and it might regulate panicle development in rice. However, the regulation mechanism of miR529-SPL is still not clear. In this study, we predicted five miR529a putative target genes, OsSPL2, OsSPL14, OsSPL16, OsSPL17 and OsSPL18, while only the expression of OsSPL2, OsSPL14, and OsSPL17 was regulated by miR529a in the rice panicle. Overexpression of miR529a dramatically affected panicle architecture, which was regulated by OsSPL2, OsSPL14, and OsSPL17. Furthermore, the 117, 35, and 25 pathway genes associated with OsSPL2, OsSPL14 and OsSPL17, respectively, were predicted, and they shared 20 putative pathway genes. Our results revealed that miR529a could play a vital role in the regulation of panicle architecture through regulating OsSPL2, OsSPL14, OsSPL17 and the complex networks formed by their pathway and downstream genes. These findings will provide new genetic resources for reshaping ideal plant architecture and breeding high yield rice varieties.

Dynamic patterns of expression for genes regulating cytokinin metabolism and signaling during rice inflorescence development.

Inflorescence development in cereals, including such important crops as rice, maize, and wheat, directly affects grain number and size and is a key determinant of yield. Cytokinin regulates meristem size and activity and, as a result, has profound effects on inflorescence development and architecture. To clarify the role of cytokinin action in inflorescence development, we used the NanoString nCounter system to analyze gene expression in the early stages of rice panicle development, focusing on 67 genes involved in cytokinin biosynthesis, degradation, and signaling. Results point toward key members of these gene families involved in panicle development and indicate that the expression of many genes involved in cytokinin action differs between the panicle and vegetative tissues. Dynamic patterns of gene expression suggest that subnetworks mediate cytokinin action during different stages of panicle development. The variation of expression during panicle development is greater among genes encoding proteins involved in cytokinin metabolism and negative regulators of the pathway than for the genes in the primary response pathway. These results provide insight into the expression patterns of genes involved in cytokinin action during inflorescence development in a crop of agricultural importance, with relevance to similar processes in other monocots. The identification of subnetworks of genes expressed at different stages of early panicle development suggests that manipulation of their expression could have substantial effects on inflorescence architecture.

Comparative Proteomic Analysis Reveals Nitrogen Fertilizer Increases Spikelet Number per Panicle in Rice by Repressing Protein Degradation and 14-3-3 Proteins

The spikelet number per panicle is established in the early stages of panicle development. Nitrogen fertilizer application before panicle initiation is known to increase spikelet number, which is one of the most important traits in rice productivity determination. However, the basic proteomic mechanism remains poorly understood. The present study shows that nitrogen fertilizer significantly increased spikelet number and grain yield in rice. Proteomic variations were further analyzed in young panicles at the secondary panicle branch initiation and spikelet meristem initiation under nitrogen fertilizer treatment. Proteomic analysis identified 63 proteins with significant differential accumulation in young panicles under nitrogen fertilizer treatment. Proteolysis represents the largest functional category, which suggests that protein degradation is an important pathway in the response to nitrogen fertilizer. Importantly, nitrogen fertilizer significantly reduced 14-3-3 proteins, which interact with key enzymes associated with carbon and nitrogen metabolism, and the rice FT homologue Hd3a. Real-time PCR revealed that Hd3a signaling is also repressed by nitrogen fertilizer in leaves. This study contributes to a better understanding of the regulation of nitrogen fertilizers in the flowering pathway leading to panicle development. The identification of novel genes provides new insight into the profound impacts of nitrogen fertilizer on panicle development in rice.

Clustered spikelets 4, encoding a putative cytochrome P450 protein CYP724B1, is essential for rice panicle development

Rice (Oryza sativa L.) inflorescence (panicle) architecture is an important agronomic trait, serving as one of the determinants of rice yield. A number of genes related to panicle development have been cloned and functionally characterized so far. However, more information is needed for fully understanding of the mechanism underlying the panicle development. In the present study, we identified a clustered spikelets 4 (cl4) mutant in the 93-11 genetic background. Compared to its wild-type 93-11, cl4 mutant has a typical clustered spikelets phenotype with all primary branches clustered on the base of the main rachis and 2–3 abnormal spikelets clustered on the primary branches. Moreover, cl4 mutant also shows shorter plant height than that of the wild type. Map-based cloning strategy is performed to clone the CL4 gene. As a result, CL4 is demonstrated to encode a putative cytochrome P450 protein CYP724B1, which is involved in brassinosteroid biosynthesis. To confirm our mapping result, the CL4 RNAi transgenic plants are generated. And the transgenic plants also show similar phenotype as the cl4 mutant. These results provide strong evidence that CL4 plays an important role in rice panicle development as well as plant height regulation.

OsSLI1, a homeodomain containing transcription activator, involves abscisic acid related stress response in rice (Oryza sativa L.).

Homeodomain-leucine zipper type I (HD-Zip I) proteins are involved in the regulation of plant development and response to environmental stresses. In this study, OsSLI1 (Oryza sativa stress largely induced 1), encoding a member of the HD-Zip I subfamily, was isolated from rice. The expression of OsSLI1 was dramatically induced by multiple abiotic stresses and exogenous abscisic acid (ABA). In silico sequence analysis discovered several cis-acting elements including multiple ABREs (ABA-responsive element binding factors) in the upstream promoter region of OsSLI1. The OsSLI1-GFP fusion protein was localized in the nucleus of rice protoplast cells and the transcriptional activity of OsSLI1 was confirmed by the yeast hybrid system. Further, it was found that OsSLI1 expression was enhanced in an ABI5-Like1 (ABL1) deficiency rice mutant abl1 under stress conditions, suggesting that ABL1 probably negatively regulates OsSLI1 gene expression. Moreover, it was found that OsSLI1 was regulated in panicle development. Taken together, OsSLI1 may be a transcriptional activator regulating stress-responsive gene expression and panicle development in rice.

A point mutation in the zinc finger motif of RID1/EHD2/OsID1 protein leads to outstanding yield-related traits in japonica rice variety Wuyunjing 7

BackgroundFlowering time, which is often associated with the length of the growth period in rice, determines the adaptability of a plant to various environments. However, little is known about how flowering-time genes affect panicle development and yield formation potential in rice after inducing the transition from vegetative growth to reproductive growth.ResultsTo explore the relationship between floral induction and yield formation and the molecular mechanism of panicle development in rice, a novel mutant, ghd10, was identified from japonica variety Wuyunjing 7 plants subjected to ethyl methane sulfonate (EMS) treatment. The ghd10 mutant exhibited delayed flowering time, tall stalks and increased panicle length and primary branch number. Map-based cloning revealed that Ghd10 encodes a transcription factor with Cys-2/His-2-type zinc finger motifs. Ghd10 is orthologous to INDETERMINATE1 (ID1), which promotes flowering in maize (Zea mays) and is identical to the previously cloned genes Rice Indeterminate1 (RID1), Early heading date2 (Ehd2) and OsId1. Transient expression analysis of the Ghd10-GFP fusion protein in tobacco mesophyll cells showed that this protein is expressed in the nucleus. Ghd10 mRNA accumulated most abundantly in developing leaves and panicle structures, but rarely in roots. Expression analysis revealed that the expression levels of Ehd1, Hd1, RFT1, Hd3a and OsMADS15 decreased dramatically under both short-day and long-day conditions in ghd10.ConclusionThese results indicate that Ghd10, which encodes a promoter of flowering, influences plant height and panicle development by regulating the expression levels of some flowering-related genes, such as Ehd1, Hd1, OsMADS15 and others. The ghd10 allele is a useful resource for improvement of panicle traits in rice grown in tropical and low-latitude areas.Electronic supplementary materialThe online version of this article (doi:10.1186/1939-8433-6-24) contains supplementary material, which is available to authorized users.

A Novel Nuclear Protein Phosphatase 2C Negatively Regulated by ABL1 is Involved in Abiotic Stress and Panicle Development in Rice

Type 2C protein phosphatase plays an important role in the signal transduction of stress response in plants. In this paper, we identified a novel stress-induced type 2C protein phosphatase gene OsSIPP2C1 from rice. OsSIPP2C1 contains a complete open reading frame of 1,074bp, encoding a protein with 357 amino acids. OsSIPP2C1 expression was up-regulated by high salt, PEG6000 and exogenous ABA, and enhanced in the abl1 mutant under normal, salt, or drought condition. Interestingly, OsSIPP2C1 expression was increased during the early panicle development. Subcellular localization assay using rice protoplast cells indicated that OsSIPP2C1 was predominantly located in the nucleus. Together, it is suggested that a nuclear PP2C protein OsSIPP2C1 negatively regulated by ABL1 is involved in abiotic stress and panicle development in rice.

Flowering Time Genes Heading date 1 and Early heading date 1 Together Control Panicle Development in Rice

Although flowering time is often associated with plant size, little is known about how flowering time genes affect plant architecture. We grew four rice lines having different flowering time genotypes (hd1 ehd1, hd1 Ehd1, Hd1 ehd1 and Hd1 Ehd1) under distinct photoperiod conditions. By using genotype–treatment combinations that resulted in similar flowering times, we were able to compare the effects of flowering time genes on traits related to plant architecture. The results revealed that the combination of Heading-date 1 (Hd1) and Early heading date 1 (Ehd1) can reduce the number of primary branches in a panicle, resulting in smaller spikelet numbers per panicle; this occurs independently of the control of flowering time. In addition, expression of the Hd3a and Rice Flowering-locus T 1 (RFT1) florigen genes was up-regulated in leaves of the Hd1 Ehd1 line at the time of the floral transition. We further revealed that Hd1 and/or Ehd1 caused up-regulation of Terminal Flower 1-like genes and precocious expression of panicle formation-related genes at shoot apical meristems during panicle development. Therefore, two key flowering time genes, Hd1 and Ehd1, can control panicle development in rice; this may affect crop yields in the field through florigen expression in leaf.

PANICLE PHYTOMER2 (PAP2), encoding a SEPALLATA subfamily MADS-box protein, positively controls spikelet meristem identity in rice

In rice panicle development, new meristems are generated sequentially in an organized manner and acquire their identity in a time- and position-dependent manner. In the panicle of the panicle phytomer2-1 (pap2-1) mutant, the pattern of meristem initiation is disorganized and newly formed meristems show reduced competency to become spikelet meristems, resulting in the transformation of early arising spikelets into rachis branches. In addition, rudimentary glumes and sterile lemmas, the outermost organs of the spikelet, elongate into a leafy morphology. We propose that PAP2 is a positive regulator of spikelet meristem identity. Map-based cloning revealed that PAP2 encodes OsMADS34, a member of the SEPALLATA (SEP) subfamily of MADS-box proteins. PAP2/OsMADS34 belongs to the LOFSEP subgroup of MADS-box genes that show grass-specific diversification caused by gene duplication events. All five SEP subfamily genes in rice are expressed exclusively during panicle development, while their spatial and temporal expression patterns vary. PAP2 expression starts the earliest among the five SEP genes, and a low but significant level of PAP2 mRNA was detected in the inflorescence meristem, in branch meristems immediately after the transition, and in glume primordia, consistent with its role in the early development of spikelet formation. Our study provides new evidence supporting the hypothesis that the genes of the LOFSEP subgroup control developmental processes that are unique to grass species.

Expression Pattern of GS3 During Panicle Development in Rice under Drought Stress: Quantification Normalized Against Selected Housekeeping Genes in Real-Time PCR

Expression Pattern of GS3 During Panicle Development in Rice under Drought Stress: Quantification Normalized Against Selected Housekeeping Genes in Real-Time PCR

Relative Susceptibility of Stages of Rice Panicle Development to Male and Female Oebalus pugnax1

In field experiments conducted in 2005 and 2006, panicles of rice, Oryza sativa L., were infested for 48 h with one male or female rice stink bug, Oebalus pugnax (F.), at heading, milk, soft and hard dough stages of development. Number of grains, number and weight of filled grains, number and weight of empty grains, and percentage whole kernels per panicle were not significantly affected by infestation at any stage of panicle development, nor were any significant differences found in percentage peck caused by male or female O. pugnax. In 2005, percentage peck was significantly lower in uninfested panicles and panicles infested during hard dough than in panicles infested during heading, milk or soft dough. No differences were found in percentage peck caused by O. pugnax during heading, milk or soft dough. In 2006, no significant differences were found in percentage peck produced by O. pugnax in panicles infested during heading, milk, soft dough or hard dough. Higher percentage peck in hard dough may have been the result of late drainage of the field.

Most Susceptible Stage of Rice Panicle Development to <I>Oebalus pugnax</I> (Hemiptera: Pentatomidae)

Oebalus pugnax (F.) (Hemiptera: Pentatomidae) damage to rice, Orya savita L., reduces rough and head rice yields, and grain quality. O. pugnax feeds on developing kernels, introducing pathogenic fungi and causing a discoloration of the grain known as "peck." The objective of this study was to determine the stage of rice panicle development most susceptible to O. pugnax attack. During 2005 and 2006, in greenhouse and field experiments, rice plants were caged at the boot stage and then infested with adult or nymphal O. pugnax. Plants were infested during one of three stages of panicle development: heading, milk, or soft dough. Insects were allowed to feed on the plants for the duration of each stage and then killed. After maturation, panicles were harvested, and grain was hulled and milled. Grain weight, percentage of pecky grain, and percentage of whole grain after milling were recorded. No differences were found in the weight of rough, brown, or milled rice infested with O. pugnax during different stages of panicle development. Number of filled grains per cage was not affected by O. pugnax, and number of empty grains per cage was affected in two of four experiments. Higher percentage of peck was found in grain from panicles infested during dough and milk than in grain from panicles infested during heading. Adult O. pugnax caused higher percentage of peck than nymphs in all stages of panicle development. An inverse relationship was found between percentage of peck and percentage of whole grain weight only in one of the experiments.

Genome‐wide analysis of spatial and temporal gene expression in rice panicle development

The basic structure of a rice inflorescence (the panicle) is determined by the pattern of branch formation, which is established at the early stages of panicle development. In this study we conducted global transcriptome profiling of the early stages of rice panicle development from phase transition to floral organ differentiation. To generate a meristem-specific gene-expression profile, shoot apical meristems (SAMs) and subsequently formed, very young panicles were collected manually and used for cDNA microarray analysis. We identified 357 out of 22,000 genes that are expressed differentially in the early stages of panicle development, and the 357 genes were classified into seven groups based on their temporal expression patterns. The most noticeable feature is that a fairly small number of genes, which are extensively enriched in transcription factors, are upregulated in the SAM immediately after phase transition. In situ hybridization analysis showed that each gene analysed exhibits a unique and interesting localization of mRNA. Remarkably, one of the transcription factors was proven to be a close downstream component of the pathway in which LAX, a major regulator of panicle branching, acts. These results suggest that our strategy--careful collection of meristems, global transcriptome analysis and subsequent in situ hybridization analysis--is useful not only to obtain a genome-wide view of gene expression, but also to reveal genetic networks controlling rice panicle development.