Rice Root Tissues Research Articles

Sewage sludge-derived nutrients and biostimulants stimulate rice leaf photosynthesis and root metabolism to enhance carbohydrate, nitrogen and antioxidants accumulation

The production of high quality liquid nitrogen fertilizer with both nutrient comprehensive and biostimulant properties by alkaline thermal hydrolysis of sewage sludge has shown great potential in agricultural production. However, little is known about the effects of sewage sludge-derived nutrients, and biostimulants (SS-NB) on leaf photosynthesis and root growth in rice. Phenotypic, metabolic and microbial analyses were used to reveal the mechanism of SS-NB on rice. Compared to NF treatment, phenotypic parameters (fresh/dry weight, soluble sugar, amino acid, protein) were increased by SS-NB in rice. SS-NB can enhance the photosynthesis of rice leaves by improving the photoconversion efficiency, chlorophyll content, ATP synthase activity, Rubisco and NADPH production. Meanwhile, SS-NB also increased antioxidant capacity (SOD, POD, CAT and proline) in rice leaf and root tissues. Metabolomics revealed that SS-NB application increased the expression levels of metabolites in root and leaf tissues, including carbohydrate, nitrogen and sulfur metabolism, amino acid metabolism, antioxidants, and phytohormone. Most importantly, the regulation of metabolites in rice root tissues is more sensitive than in leaf tissues, especially to the higher levels of antioxidants and phytohormones (IAA and GA) in rice root tissues. Furthermore, SS-NB increased the abundance of photosynthetic autotrophic, organic acids-degrading and denitrifying functional bacteria in rice roots and recruited plant growth-promoting bacteria (Azospirillum and norank_f_JG30-KF-CM45), while the NF treatment group resulted in an imbalance of the microbial community, leading to the dominance of pathogenic bacteria. The results showed that SS-NB had great application potential in crop growth and stress resistance improvement.

Transcriptome and Co-Expression Network Analysis Reveals the Molecular Mechanism of Rice Root Systems in Response to Low-Nitrogen Conditions.

Nitrogen is an important nutrient for plant growth and essential metabolic processes. Roots integrally obtain nutrients from soil and are closely related to the growth and development of plants. In this study, the morphological analysis of rice root tissues collected at different time points under low-nitrogen and normal nitrogen conditions demonstrated that, compared with normal nitrogen treatment, the root growth and nitrogen use efficiency (NUE) of rice under low-nitrogen treatment were significantly improved. To better understand the molecular mechanisms of the rice root system's response to low-nitrogen conditions, a comprehensive transcriptome analysis of rice seedling roots under low-nitrogen and control conditions was conducted in this study. As a result, 3171 differentially expressed genes (DEGs) were identified. Rice seedling roots enhance NUE and promote root development by regulating the genes related to nitrogen absorption and utilization, carbon metabolism, root growth and development, and phytohormones, thereby adapting to low-nitrogen conditions. A total of 25,377 genes were divided into 14 modules using weighted gene co-expression network analysis (WGCNA). Two modules were significantly associated with nitrogen absorption and utilization. A total of 8 core genes and 43 co-expression candidates related to nitrogen absorption and utilization were obtained in these two modules. Further studies on these genes will contribute to the understanding of low-nitrogen adaptation and nitrogen utilization mechanisms in rice.

Isolation and Characterization of Bacillus Consortia for Plant Growth Promotion in Rice (Oryza sativa L.)

In this study, soil samples from the rhizosphere of various uncultivated weeds were collected from fifteen different locations of Gujarat. Heat treatment was given at 65°C for 20 minutes prior to initial screening for spore-forming Bacillus spp. Among them, 20 nitrogen-fixing (NFB), 27 phosphate solubilising (PSB) and 15 potassium mobilizing (KMB) isolates were screened primarily. After molecular identification only Bacillus isolates were further selected and characterized. Three superior Bacillus isolates were selected from each category by secondary screening. All isolates belonging to different category were compatible in nature and showed significant ammonia production, ARA, phosphate solubilisation, potassium mobilization, siderophore production, IAA production and organic acid producers. The relative expression analysis of three genes NRT2.1 (Nitrate transporter), PT6 (Phosphorus transporter), and AKT1 (Potassium transporter) at transcriptional level were performed in the juvenile root tissues of Rice using qRT-PCR technique at 15th, 30th and 45th days after transplanting with Actin as a internal control. Rice transplants were inoculated with different NPK fixing Bacillus consortia, which significantly improved growth parameters as compared to control in field study. Various growth and yield attributing characters of rice viz., plant height (at 60 DAT, 90 DAT, and at harvesting), number of productive tillers, days to 50 % flowering, 100 seed weight, grain yield, straw yield, as well as dry biomass per hectare were significantly influenced by different treatments. An application of 100 % RDF with NPK consortia (T7) treatment of rice crop resulted in significantly higher plant height (49.25 cm at 60 DAT, 107.00 cm at 90 DAT, 129.50 cm at harvesting), days to 50% flowering (75.63), 100 seed weight (3.53 g), number of productive tillers per plant (12.13), grain yield (6889.00 kg ha-1), straw yield (8754.25 kg ha-1) and dry biomass (7889.25 kg ha-1) followed by the treatments T4 (T2 + N consortia), T5 (T2 + P consortia), T6 (T2 + K consortia), and T2 (RDF (NP) 100%). Nutrient content in grain and straw was differing significantly due to different treatments. However, significantly higher N, P, K, content in straw (1.28 %, 0.15 %, and 1.52 %) and grain (2.06 %, 0.23 %, and 0.25 %) respectively, were recorded under the treatment T7. The spore forming Bacillus consortia was able to survive at a wide range of temperature and pH fluctuations and found to be effective as N-fixers, P-solubilizers, K-mobilizers, siderophore producers, IAA producers with having antagonistic activity against rice pathogen Magnaportha oryzae.

Identification of endophytic and rhizosphere bacteria in rice (Oryza sativa L.) in the experimental field at Payakumbuh State Agriculture Polytechnic, West Sumatra, Indonesia

The decrease of soil fertility and fewer soil microorganisms will lower crop production, particularly rice, thus threatening the national food security program. This study is (a) to isolate and identify the bacteria in the endophytic and rhizosphere of rice plants (b) to study the bacteria from the endophytic and rhizosphere of rice plants which potentially stimulate plant growth. The experiment was carried out at the Laboratory of Food Crop Cultivation at Payakumbuh State Agriculture Polytechnic, Limapuluh Kota Regency, West Sumatra for four months. The sampling method was carried out by random sampling at rice planting in the Payakumbuh State Agriculture Polytechnic Experimental Field. Endophytic bacteria were taken from the root tissue of rice plants, and rhizosphere bacteria were taken from a layer of soil around rice roots. Isolation of bacteria was carried out by using the pour plate and scratchplate methods. Four bacteria were identified using the 16S rRNA sequencing method. The identification results showed that in the rice root tissue found the bacteria Chromobacterium rhizoryzae and Brevibacillus brevis. In the rice rhizosphere, Bacillus pseudomycoides and Bacillus thuringiensis are found. Bacteria are dominated by the Bacillus genera which can stimulate plant growth.

Manganese facilitates cadmium stabilization through physicochemical dynamics and amino acid accumulation in rice rhizosphere under flood-associated low pe+pH

Periodic flooding in paddy soils impacts redox behavior and induces variations in pe+pH levels. Manganese (Mn) is capable of reducing cadmium (Cd) uptake by rice. However, the processes involved in how Mn alters Cd mobilization under different pe+pH environments remain poorly understood. To investigate the mechanisms of Mn-mediated soil Cd-stabilization and subsequent inhibition of Cd uptake from flooded soils, we examined Cd immobilization in soil pot incubations, transcriptional changes in Cd-transport genes, and metabolomic analyses of roots and rhizosphere soils with or without Mn application. We found a decrease in extractable Cd concentration largely depended on irrigation-associated low pe+pH, exogenous Mn enhancement of Fe−Mn (oxyhydro)oxide-mediated Cd transformation, and Cd deposition in rice Fe/Mn plaques. Mn application led to striking effects on the expression of Cd-related genes eg. IRT, HMA, and NRAMP in rice root tissue. Exposure to Mn under variable pe+pH levels resulted in metabolic reprogramming of soil and rice roots. Mn induced amino acid synthesis in rice roots, leading to rhizosphere accumulation of free L-lysine, glycine, and glutamine, which can reportedly bind metal ions, forming complexes with Cd. Thus, secreted amino acids, low pe+pH, and free Mn can together comprise a multi-faceted approach to managing Cd toxicity in rice.

Plant growth promoting Bacillus consortia regulates the expression of NRT2.1, PT6, and AKT1 genes in rice

The inoculation of rice transplants with consortium of nitrogen fixing Bacillus, phosphate solubilizing Bacillus, and potassium mobilizing Bacillus in field condition was carried out. The relative expression analysis of three transport related genes NRT2.1 (Nitrate transporter), PT6 (Phosphurus transporter), and AKT1 (Potassium transporter) at transcriptional level were performed in the juvenile root tissues of Rice using qRT-PCR technique at 15th, 30th and 45th days after transplanting with Actin as a indigenous control. The expression of NRT2.1 (Nitrate transporter) increases in treatment T7 to 2.60 fold at 15 DAT and then expression decreases at 30 and 45 DAT, as the availability of N fertilizer reduces compared to absolute control. The expression of PT6 (Phosphurus transporter) decreases in treatment T7 to 0.48 fold at 15 DAT and then expression increases at 30 and 45 DAT, as the availability of P fertilizer reduces compared to absolute control. The expression of AKT1 (Nitrate transporter) increases in treatment T7 to 1.95 fold at 15 DAT and then expression decreases at 30 and 45 DAT, as the availability of K fertilizer reduces compared to absolute control.

Preventive Effects of Fluoro-Substituted Benzothiadiazole Derivatives and Chitosan Oligosaccharide against the Rice Seedling Blight Induced by Fusarium oxysporum.

Rice seedling blight, caused by Fusarium oxysporum, significantly affects global rice production levels. Fluoro-substituted benzothiadiazole derivatives (FBT) and chitosan oligosaccharide (COS) are elicitors that can enhance plant resistance to pathogen infection. However, there is a lack of information regarding FBT and COS used as elicitors in rice seedlings blight. Therefore, the aim of this study was to evaluate the effect of FBT and COS treatments on rice seedling blight and elucidate the molecular mechanisms of the two elicitors for inducing resistance using proteomic technique. Results indicated that FBT and COS significantly reduced the disease incidence and index, and relived the root growth inhibition caused by F. oxysporum (p < 0.05). Biochemical analyses demonstrated that these two elicitors effectively enhanced activities of defense enzymes. Moreover, the proteomic results of rice root tissues disclosed more differentially expressed proteins in diterpenoid biosynthesis pathway that were particularly stimulated by two elicitors compared to the other pathways studied, resulting in the accumulation of antimicrobial substance, momilactone. Findings of this study could provide sound theoretical basis for further applications of FBT and COS used as rice elicitors against seedling blight.

Whole genome shotgun sequence of Bacillus paralicheniformis strain KMS 80, a rhizobacterial endophyte isolated from rice (Oryza sativa L.).

Bacillus paralicheniformis strain KMS 80 (MTCC No. 12704) is an isolate from the root tissues of rice (Oryza sativa L.) that displays biological nitrogen fixation and plant growth promoting abilities. Here, we report the complete genome sequence of this strain, which contains 4,566,040 bp, 4424 protein-coding genes, 8692 promoter sequences, 67 tRNAs, 20 rRNA genes with six copies of 5S rRNAs along with a single copy of 16S-23S rRNA and genome average GC-content of 45.50%. Twenty one genes involved in nitrogen metabolism pathway and two main transcriptional factor genes, glnR and tnrA responsible for regulation of nitrogen fixation in Bacillus sp. were predicted from the whole genome of strain KMS 80. Analysis of the ~ 4.57 Mb genome sequence will give support to understand the genetic determinants of host range, endophytic colonization behaviour as well as to enhance endophytic nitrogen fixation and other plant beneficial role of B. paralicheniformis in rice.

Molecular characterization of rice arsenic-induced RING finger E3 ligase 2 (OsAIR2) and its heterogeneous overexpression in Arabidopsis thaliana.

Arsenic (As) accumulation adversely affects the growth and productivity of plants and poses a serious threat to human health and food security. In this study, we identified one As-responsive Really Interesting New Gene (RING) E3 ubiquitin ligase gene from rice root tissues during As stress. We named it Oryza sativa As-Induced RING E3 ligase 2 (OsAIR2). Expression of OsAIR2 was induced under various abiotic stress conditions, including heat, salt, drought and As exposure. Results of an in vitro ubiquitination assay showed that OsAIR2 possesses an E3 ligase activity. Within the cell, OsAIR2 was found to be localized to the Golgi apparatus. Using yeast two-hybrid (Y2H) assay, the 3-ketoacyl-CoA thiolase (KAT) protein was identified as an interaction partner. We found that the O. sativa KAT1 (OsKAT1) is localized to the cytosol and peroxisomes. Moreover, in vitro pull-down assay verified the physical interaction between OsAIR2 and OsKAT1. Interestingly, in vitro ubiquitination assay and in vivo proteasomal degradation assay revealed that OsAIR2 ubiquitinates OsKAT1 and promotes the degradation of OsKAT1 via the 26S proteasome degradation pathway. Heterogeneous overexpression of OsAIR2 in Arabidopsis improved the seed germination and increased the root length under arsenate stress conditions. Therefore, these results suggest that OsAIR2 may be associated with the plant response to As stress and acts as a positive regulator of As stress tolerance.

Draft Genome Sequence of Pseudomonas stutzeri Strain KMS 55, an Endophytic Diazotroph Isolated from Rice Roots.

ABSTRACTPseudomonas stutzeri strain KMS 55 (MTCC 12703) is an isolate from the root tissues of rice (Oryza sativa L.) that displays a high biological nitrogen fixation ability. Here, we report the complete genome sequence of this strain, which contains 4,637,820 bp, 4,289 protein-coding genes, 5,006 promoter sequences, 62 tRNAs, a single copy of 5S-16S-23S rRNA, and a genome average GC content of 51.18%. Analysis of the ~4.64-Mb genome sequence will give support to increased understanding of the genetic determinants of host range, endophytic colonization behavior, endophytic nitrogen fixation, and other plant-beneficial roles of Pseudomonas stutzeri.

Colonization of the vegetative stage of rice plants by the false smut fungus Villosiclava virens, as revealed by a combination of species‐specific detection methods

Rice false smut disease caused by the ascomycete fungus Villosiclava virens (Clavicipitaceae) reduces rice yield worldwide. It invades rice panicles and forms dark‐green false smut balls composed of thick‐walled conidia. Although the infection process during the booting stage is well studied, its infection route before this is unclear. It was hypothesized that the thick‐walled conidia in soil penetrate rice roots, and the fungus latently colonizes roots and tiller buds at the vegetative stage. This hypothesis was tested using species‐specific detection methods. First, real‐time PCR with species‐specific primers and probe was used to estimate thick‐walled conidial number in the paddy field soil. Secondly, nested PCR with species‐specific primers showed that fungal DNA was detected in roots and shoot apices of rice plants in the vegetative stage. Thirdly, colourimetric in situ hybridization with a species‐specific oligonucleotide probe targeting 18S rRNA suggested that sparse mycelia or tightly condensed mycelia were present on the external surface of tiller buds enveloped by juvenile leaf sheaths at the vegetative stage. Thin hyphae were found around leaf axils at the surface of elongated stems at the heading stage, and the fungal hyphae grew in the rice root tissues. In addition, it was demonstrated that eGFP‐tagged transformants of the fungus invaded rice roots and colonized the surface of roots and leaf sheaths under artificial conditions.

Dual mode ratiometric recognition of zinc acetate: nanomolar detection with in vitro tracking of endophytic bacteria in rice root tissue.

Several naphthalene-based aldazine derivatives were developed as efficient colorimetric and fluorescence probes for selective ratiometric recognition of traces of zinc acetate. The derivative structures were characterized by single-crystal X-ray diffraction. The probes were used for in vitro tracking of zinc acetate in endophytic bacteria within rice root tissue and to image zinc acetate in human breast cancer cells (MCF7) by normal and fluorescence microscopy. Density functional theoretical studies were in close agreement with the experimental findings.

Tuning of azine derivatives for selective recognition of Ag+ with the in vitro tracking of endophytic bacteria in rice root tissue.

Several azine derivatives have been prepared and structurally characterized by spectroscopic and single-crystal X-ray diffraction analysis. Two of them, viz. naphthalene based (A10) and anthracene based (A11) show fluorescence enhancement in the presence of Ag+ in aqueous-methanol. Moreover, A11 efficiently tracks Ag+in vitro endophytic bacteria infected rice root tissue. Experimental results have been substantiated by theoretical DFT calculations.

Fluorescence resonance energy transfer (FRET)-based technique for tracking of endophytic bacteria in rice roots

Visualization of endophytes inside the host tissue has remained a prime interest to the plant microbiologist throughout the last decade. Assessment of a root colonization pattern of a nitrogen-fixing polyvalent plant-growth-promoting endophyte, Azotobacter chroococcum Avi2 (16S rRNA gene NCBI acc. no. KP099933), of Oryza sativa var. Swarna, by a plasmid containing green fluorescent protein (GFP) gene failed because the bacteria formed a cyst on exposure to CaCl2 during the transformation process of the green fluorescent protein gene. A new technique based on fluorescence resonance energy transfer (FRET) was developed to visualize the intracellular location of the bacterium of rice root as an alternative to track the bacterium where the use of GFP is restricted. An Al3+-specific rhodamine-based novel fluorescent ligand (λex = 400 nm, λem = 455 nm), (E)-3′,6′-bis(diethylamino)-2-(2-(pyren-4-ylmethyleneamino)ethyl)spiro[isoindoline-1,9′xanthen]-3-one, was synthesized and used to visualize 100 μM aluminium nitrate treated A. chroococcum inside rice root tissues. Within 6 h of incubation, a clear, stable and distinguishable green fluorescence was observed under the fluorescence microscope form Al3+-treated A. chroococcum colonized in the rice roots when incubated with a ligand. The results confirmed colonization of the bacteria inside the roots.

Identifikasi Nematoda Puru Akar, Meloidogyne graminicola, pada Tanaman Padi di Jawa Barat

Root knot nematodes (RKN), Meloidogyne spp. is one of the most important rice pathogen in some regions in the world. Information of RKN on rice plants in West Java is very important because West Java is one of the largest national rice production center. The purpose of this study was to determine and identify the presence of Meloidogyne spp. on rice plants in West Java. Rice plant samples were taken from 7 rice-growing districts in West Java. Typical symptoms of infected rice plants by Meloidogyne spp. are stunting and the formation of root galls. RKN was found to infect rice plants in several areas in Bogor, Cirebon, and Sukabumi. All stadia of the RKN development which include eggs, second, third, and fourth stage jeveniles, adult females and males were found inside the rice root tissues based on nematode staining observation. Morphometric measurements of the body and stylet length, maximum body width, length of the second stage juveniles, and female perineal pattern, indicated that Meloidogyne species found was M. graminicola .

Meloidogyne incognita - rice (Oryza sativa) interaction: a new model system to study plant-root-knot nematode interactions in monocotyledons.

BackgroundPlant-parasitic nematodes developed strategies to invade and colonize their host plants, including expression of immune suppressors to overcome host defenses. Meloidogyne graminicola and M. incognita are root-knot nematode (RKN) species reported to damage rice (Oryza sativa L.) cultivated in upland and irrigated systems. Despite M. incognita wide host range, study of the molecular plant - RKN interaction has been so far limited to a few dicotyledonous model plants. The aim of this study was to investigate if the rice cv. Nipponbare widely used in rice genomic studies could be used as a suitable monocotyledon host plant for studying M. incognita pathogenicity mechanisms. Here we compared the ability of M. graminicola and M. incognita to develop and reproduce in Nipponbare roots. Next, we tested if RKNs modulates rice immunity-related genes expression in galls during infection and express the Mi-crt gene encoding an immune suppressor.ResultsRoot galling, mature females, eggs and newly formed J2s nematodes were obtained for both species in rice cultivated in hydroponic culture system after 4-5 weeks. Meloidogyne graminicola reproduced at higher rates than M. incognita on Nipponbare and the timing of infection was shorter. In contrast, the infection characteristics compared by histological analysis were similar for both nematode species. Giant cells formed from 2 days after infection (DAI) with M. graminicola and from 6 DAI with M. incognita. Real-time PCR (qRT-PCR) data indicated that RKNs are able to suppress transcription of immune regulators genes, such as OsEDS1, OsPAD4 and OsWRKY13 in young galls. Four M. incognita reference genes (Mi-eif-3, Mi-GDP-2, Mi-Y45F10D.4, and Mi-actin) were selected for normalizing nematode gene expression studies in planta and in pre-parasitic J2s. Meloidogyne incognita expressed the immune suppressor calreticulin gene (Mi-crt) in rice roots all along its infection cycle.ConclusionRKNs repress the transcription of key immune regulators in rice, likely in order to lower basal defence in newly-formed galls. The calreticulin Mi-CRT can be one of the immune-modulator effectors secreted by M. incognita in rice root tissues. Together, these data show that rice is a well suited model system to study host- M. incognita molecular interactions in monocotyledons.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-014-0023-4) contains supplementary material, which is available to authorized users.

Improvement of nitrogen accumulation and metabolism in rice (Oryza sativa L.) by the endophyte Phomopsis liquidambari

The fungal endophyte Phomopsis liquidambari can enhance nitrogen (N) uptake and metabolism of rice plants under hydroponic conditions. To investigate the effects of P. liquidambari on N accumulation and metabolism in rice (Oryza sativa L.) under field conditions during the entire growing season (S1, the seedling stage; S2, the tillering stage; S3, the heading stage; S4, the ripening stage), we utilized pot experiments to examine metabolic and physiological levels in both shoot and root tissues of rice, with endophyte (E+) and without endophyte (E−), in response to three different N levels. We found that under low-N treatment, P. liquidambari symbiosis increased the rice yield and N use efficiency by 12% and by 11.59%, respectively; that the total N contents in E+ rice plants at the four growth stages were separately increased by 29.05%, 14.65%, 21.06% and 18.38%, respectively; and that the activities of nitrate reductase and glutamine synthetase in E+ rice roots and shoots were significantly increased by fungal infection during the S1 to S3 stages. Moreover, P. liquidambari significantly increased the free NH4+, NO3-, amino acid and soluble protein contents in infected rice tissues under low-N treatment during the S1 to S3 stages. The obtained results offer novel data concerning the systemic changes induced by P. liquidambari in rice during the entire growth period and confirm the hypothesis that the rice–P. liquidambari interaction improved the N accumulation and metabolism of rice plants, consequently increasing rice N utilization in nutrient-limited soil.

Isolation and characterization of two novel root-specific promoters in rice (Oryza sativa L.)

Novel root-specific promoters are important for developing methods to drive root-specific gene expression for nutrient and water absorption. RT-PCR (reverse transcription polymerase chain reaction) analysis identified high expression levels of Os03g01700 and Os02g37190 in root tissues across developmental stages in comparison with the constitutive genes OsAct1 (rice Actin1 gene), OsUbi1 (rice polyubiquitin rubi1 gene), and OsCc1 (rice cytochrome c gene). The copy numbers of Os03g01700 and Os02g37190 were evaluated by qRT-PCR. The results showed that Os03g01700 and Os02g37190 transcripts were highly accumulated in the examined root tissues but were not detected in young embryos or leaves at the indicated days after germination or in the panicle, in contrast to the ubiquitous expression of OsAct1, OsUbi1, and OsCc1. Additionally, the promoter regions of these two genes were linked to the GUSplus reporter gene and transformed into rice. GUS staining of the transgenic plants showed that the Os03g01700 and Os02g37190 promoters were active in primary and secondary roots throughout the developmental stages, except in root hairs. The GUSPlus transcript levels were also highly root-specific in the transgenic rice. Overall, the two promoters are highly active in the root tissues of rice and can be useful for the root-specific enhancement of target gene(s).

NDUCTION OF SYSTEMIC RESISTANCE IN RICE BY PSEUDOMONAS FLUORESCENT AGAINST RICE ROOT KNOT NEMATODE MELOIDOGYNE GRAMINICOLA

Induction ofdefense enzymes phenol, peroxidase (PO), polyphenol oxidase (PPO),phenyl ammonia lyase (PAL), super oxide dismutase (SOD) and chitinase by Pseudomonasfluorescens isolate Pf1, against challenge inoculation of Meloidogynegraminicola in rice was studied in vitro. The activity of phenol,PO,PPO, PAL and chitinase was higher in the bacterized rice plants. Theanalysis of isoform profiles revealed unique PO, PPO and SOD isoforms inducedin plants treated with P. fluorescens. The present study implies earlierand higher accumulation of phenols and defense enzymes viz., PO, PPO,PAL and chitinase in rice root tissue resulting in significant reduction innematode infection.

Transcriptome analysis of rice mature root tissue and root tips in early development by massive parallel sequencing

Despite the major physiological dissimilarities between mature root regions and their tips, differences in their gene expression profiles remain largely unexplored. In this research, the transcriptome of rice (Oryza sativa L. subsp. japonica) mature root tissue and root tips was monitored using mRNA-Seq at two time points. Almost 50 million 76 bp reads were mapped onto the rice genome sequence, expression patterns for different tissues and time points were investigated, and at least 1106 novel transcriptionally active regions (nTARs) expressed in rice root tissue were detected. More than 30 000 genes were found to be expressed in rice roots, among which were 1761 root-enriched and 306 tip-enriched transcripts. Mature root tissue appears to respond more strongly to external stimuli than tips, showing a higher expression of, for instance, auxin-responsive and abscisic acid-responsive genes, as well as the phenylpropanoid pathway and photosynthesis upon light. The root tip-enriched transcripts are mainly involved in mitochondrial electron transport, organelle development, secondary metabolism, DNA replication and metabolism, translation, and cellular component organization. During root maturation, genes involved in cell wall biosynthesis and modification, response to oxidative stress, and secondary metabolism were activated. For some nTARs, a potential role in root development can be put forward based on homology to genes involved in CLAVATA signalling, cell cycle regulators, and hormone signalling. A subset of differentially expressed genes and novel transcripts was confirmed using (quantitative) reverse transcription-PCR. These results uncover previously unrecognized tissue-specific expression profiles and provide an interesting starting point to study the different regulation of transcribed regions of these tissues.