Susceptible Rice Genotypes Research Articles

Assessment of Genetic Diversity of Drought Tolerant and Susceptible Rice Genotypes Using Microsatellite Markers

The introgression of wild chromosomal segments into popular rice varieties is one of the potential approaches for developing varieties for drought stress condition. Sixteen genotypes, including nine indica, two tropical japonica and five chromosome segments substitution lines (CSSLs) with different levels of tolerance/susceptibility to drought stress, were selected for diversity study. Sixty-three microsatellite markers were utilized for assessing genetic diversity. A total of 95 alleles were amplified, and out of them, 60 were polymorphic. Six unique alleles, amplified by the microsatellite loci RM276, RM472, RM488, RM537, RM541 and RM28089, were identified in six genotypes, namely FR13A, Brahamanakhi, RUF44, Swarna-sub1, Brahamanakhi and Satyabhama. The highest genetic similarity was found among CSSLs. Polymorphism information content (PIC) value varied from 0 to 1.00 with an average of 0.66 per locus. Twenty-eight microsatellites were found to be polymorphic, which could be used in marker-assisted selection programme. All the sixteen genotypes were grouped into two major clusters at genetic similarity of 0.64. In the cluster I, five CSSLs identified as diverse genotypes had wild ancestor segments responsible for drought tolerance, and hence they could be utilized as potential donors. The popular Indian varieties, Swarna-sub1 and IR64-sub1, could be used as recurrent parents in the future breeding program for developing varieties for abiotic stresses such as submergence and drought.

RNA-Seq analysis of gene expression changes triggered by Xanthomonas oryzae pv. oryzae in a susceptible rice genotype

BackgroundXanthomonas oryzae pv. oryzae (Xoo) is a destructive disease in most of the rice growing regions worldwide. Xoo injects the transcriptional activator-like (TAL) effector protein into the host cell to induce the susceptibility (S) gene(s) for spreading the disease. In the current study, a susceptible rice genotype, JG30, was inoculated with wild Xoo strain PXO99A and its mutant PH without any TAL effector, to retrieve the differentially expressed genes (DEGs) having a role in susceptibility.ResultsRNA-Seq data analysis showed that 1143 genes were significantly differentially expressed (p-value ≤0.05) at 12, 24, 36 and 48 h post inoculation (hpi). Expression patterns, evaluated by quantitative real-time PCR (qRT-PCR), of randomly selected eight genes were similar to the RNA-Seq data. KEGG pathway classified the DEGs into photosynthesis and biosynthesis of phenylpropanoid pathway. Gene ontology (GO) analysis categorized the DEGs into the biological pathway, cellular component, and molecular function. We identified 43 differentially expressed transcription factors (TFs) belonging to different families. Also, clusters of the DEGs representing kinase and peroxidase responsive genes were retrieved. MapMan pathway analysis representing the expression pattern of genes expressed highly in biotic stress and metabolic pathways after PXO99A infection relative to PH.ConclusionsDEGs were identified in susceptible rice genotype inoculated with PXO99A relative to mutant strain PH. The identified 1143 DEGs were predicted to be included in the different biological processes, signaling mechanism and metabolic pathways. The Jasmonic acid (JA) responsive genes were identified to be downregulated in PXO99A infected leaves. This study would be useful for the researchers to reveal the potential functions of genes involved in the rice susceptibility to PXO99A infection.

The metabolic response of suspension-cultured cells from blast-resistant and -susceptible rice (Oryza sativa L.) genotypes to a Pyricularia oryzae elicitor

Rice blast, incited by Pyricularia oryzae Cavara, is an important fungal disease of rice (Oryza sativa L.) worldwide. To understand the resistance mechanisms of rice to P. oryzae, we studied metabolic responses of rice suspension-cultured cells to treatment with an elicitor prepared from the mycelial walls of P. oryzae. Suspension-cultured cells of blast- resistant (Usen) and -susceptible (CO39) rice genotypes were profiled for differential metabolic responses at 1, 3, 5 and 7 days after elicitor treatment using gas chromatography coupled to electron impact ionization-time of flight-mass spectroscopy (GC/EI–TOF–MS). A total of 99 metabolites were identified by mass spectral and retention index match to the reference data of the Golm Metabolome Database (GMD). Of the 99 metabolites, 66 metabolites were classified into different chemical classes representing mostly primary metabolites. The remaining 33 metabolites are yet non-identified but are frequently observed metabolites that are part of the GMD reference data and are designated with a unique GMD identifier. Multivariate analysis revealed that the suspension-cultured cells of susceptible and resistant genotypes differ in regard to primary metabolism. Differential responses to the P. oryzae elicitor included significant changes among aromatic amino acids, phenylpropanoids, polyamines and sugars of major carbohydrate metabolism.

Responses of aerobically grown iron chlorosis tolerant and susceptible rice (Oryza sativa L.) genotypes to soil iron management in an Inceptisol

ABSTRACT Iron deficiency is a serious nutritional disorder in aerobic rice, causing chlorosis, poor yields and reduced grain nutritional quality. The problem can be managed by complementing the use of Fe-efficient plant type with a suitable Fe management strategy. In the present paper, we report the effect of eight iron management practices to resolve the problem of iron (Fe) chlorosis through the use of an iron deficiency tolerant (IDTR) and iron deficiency susceptible (IDSR) rice genotype, i.e. Pusa 33 and ADT 39, respectively. Fe deficiency tolerance of these genotypes was related to the root release of PS which enabled a higher uptake of Fe in the IDTR than the IDSR under Fe deficiency. In general, IDTR performed better than the IDSR as evident from a significant increase in total iron, active iron, chlorophyll content and grain and straw yield. IDSR produced the highest grain and straw yield under slow iron release nano clay complex source. Grain Fe content of the IDTR and IDSR increased by 18.9 and 13.4%, respectively, under recommended dose of Fe. The results identified the most effective soil management strategies for the alleviating Fe deficiency chlorosis and improving Fe nutrition of both IDTR and IDSR genotypes.

Biochemical defence responses of resistant and susceptible rice genotypes against blast pathogen Magnaporthe oryzae

Rice blast is the leading fungal disease which is caused by Magnaporthe oryzae that contributes for the significant decline in the rice yield throughout the globe. There is a need for the understanding of biochemical changes in rice plant during blast infection for the development of novel disease control strategies. In the present study, we isolated M. oryzae from the local paddy fields and the fungal isolates (VCF and PON) were identified by ITS-PCR using genomic DNA samples. Further, we inoculated resistant (BR2655 and TUNGA) and susceptible (INTAN and HR12) rice cultivars with PON and VCF isolates. PON isolate showed relatively high virulence compared to VCF and standard MTCC fungal strains. Therefore, we evaluated the effect of PON on the total protein content and plant defence-related key enzymes (peroxidase, polyphenol oxidase, phenylalanine ammonia lyase, β-glucosidase, chitinase and lipoxygenase) activities between 24- and 120-hour post-inoculation (hpi). The results demonstrated the decrease in total protein content in all the inoculated cultivars. In addition, we observed the variation in the activity of peroxidase, polyphenol oxidase, β-glucosidase, chitinase and lipoxygenase at different time points in all the tested rice plants compared to respective controls. However, no significant difference was observed in the phenylalanine ammonia lyase activity relative to its control. Taken together, this study emphasizes on the variation in the activities of plant defence enzymes in different plant cultivars against the tested fungal pathogen and also implementation of defence enzymes as biochemical markers for resistant breeding.

Differential expression of proteins in resistant and susceptible rice genotypes against blast infection

Blast is one of the most important diseases affecting rice cultivation worldwide. The current study employed Two-Dimensional Difference Gel Electrophoresis (2D-DIGE) plus Matrix-assisted laser desorption/ionization time-of-flight-mass spectroscopy (MALDI-TOF MS) and TOF/TOF tandem MS/MS to investigate the differentially regulated proteins in the highly resistant (HR) genotype, FL 127 and highly susceptible (HS) genotype, Rustic against blast pathogen in rice. The differential expression of seventy eight protein spots were observed in 2D-gel analysis of HR and HS genotypes. The comparision of protein expression ratio between HR and HS genotypes showed that twenty protein spots were predominant in differential expression against blast pathogen. Of which, seventeen were upregulated and three were down regulated. Characterization of these proteins using MALDI-TOF (MS) and TOF/TOF tandem MS/MS analysis with protein databases revealed that most of their functions either directly or indirectly related to plant defense and stress response, transcription and photosynthesis. The knowledge on various proteins characterized in this study suggested their possible role in expressing resistance by gentotype FL 127 against P. oryzae. Further, the knowledge generated in this study would be useful in the development of molecular markers for screening blast resistance using molecular biology approaches.

Effects of initial nematode population density and water regime on resistance and tolerance to the rice root-knot nematode Meloidogyne graminicola in African and Asian rice genotypes

ABSTRACTThe rice root-knot nematode (RKN), Meloidogyne graminicola, is an important pathogen affecting rice production in South and Southeast Asia. Efficacy of resistance and tolerance in selected M. graminicola-resistant African rice genotypes TOG5674, TOG5675 and CG14 and -susceptible Asian rice genotypes IR64 and UPLRi-5 were examined under a range of initial population densities (Pi) and water regimes. Resistance to M. graminicola in resistant rice genotypes was not broken with increasing pathogen pressure (Pi = 15,000 to 60,000 J2/plant). Resistant rice genotypes were even tolerant to the damage and yield loss caused by high pathogen pressure. On the other hand, increasing Pi levels caused more damage on susceptible rice genotypes. Final nematode population densities in the root systems of resistant and susceptible rice genotypes were significantly lower under flooded conditions than under upland and drought conditions. TOG5674, TOG5675 and CG14 were more tolerant to M. graminicola infection even when grown under upland and drought conditions while IR64 and UPLRi-5 were highly sensitive.

Aldo-ketoreductase 1 (AKR1) improves seed longevity in tobacco and rice by detoxifying reactive cytotoxic compounds generated during ageing

BackgroundMaintenance of seed viability is an important factor for seedling vigour and plant establishment. Lipid peroxidation mediated reactive carbonyl compounds (RCC’s) and non-enzymatic modifications of proteins through Maillard and Amadori products reduce seed viability and seedling vigour.ResultsIn this study, the relevance of RCCs on genotypic variation in rice seed viability and overexpression of an aldo-ketoreductase (AKR1) enzyme that detoxify cytotoxic compounds to improve seed viability and vigour was studied. Physiological and biochemical approaches were integrated to quantify the variation in seed viability and seedling vigour in rice genotypes after exposing to ageing treatment. AKR1 was overexpressed in a susceptible rice genotype and tobacco to study the relevance of reduced RCC’s on seed viability and seedling vigour. The glycation and lipid peroxidation compounds accumulated after accelerated ageing treatments in rice genotypes. The accumulation of malondialdehyde, methyl glyoxal, Maillard and Amadori products affected the seed viability and germination as they showed a significant negative relationship. The transgenic rice and tobacco seeds expressing AKR1 showed lower levels of cytotoxic compounds and glycation products that resulted in improved seed viability and seedling vigour in rice and tobacco.ConclusionsThe study demonstrates that, reactive cytotoxic compounds affect the seed viability during storage. Detoxification of reactive cytotoxic compounds by Aldo-keto reductases is one of the mechanisms to improve the seed longevity during storage.

Genome-wide changes in microRNA expression during short and prolonged heat stress and recovery in contrasting rice cultivars.

MicroRNAs (miRNAs) are known to regulate expression of genes under stress. We report here the deep sequencing of small RNAs expressed during control, short and prolonged heat stress and recovery. Genome-wide identification of miRNAs in tolerant (Nagina 22) and susceptible (Vandana) rice cultivars was performed in 16 samples representing root and shoot of 13-day-old seedlings. The expression profile of miRNAs was analysed in 36 pairwise combinations to identify the genotype-, treatment- and tissue-dependent expression of miRNAs. Small-RNA sequencing of 16 libraries yielded ~271 million high-quality raw sequences; 162 miRNA families were identified. The highly expressed miRNAs in rice tissues were miR166, miR168, miR1425, miR529, mR162, miR1876, and miR1862. Expression of osa-miR1436, osa-miR5076, osa-miR5161, and osa-miR6253 was observed only in stressed tissue of both genotypes indicating their general role in heat stress response. Expression of osa-miR1439, osa-miR1848, osa-miR2096, osa-miR2106, osa-miR2875, osa-miR3981, osa-miR5079, osa-miR5151, osa-miR5484, osa-miR5792, and osa-miR5812 was observed only in Nagina 22 during high temperature, suggesting a specific role of these miRNAs in heat stress tolerance. This study provides details of the repertoire of miRNAs expressed in root and shoot of heat susceptible and tolerant rice genotypes under heat stress and recovery.

Oviposition Preference and Larval Performance of Cnaphalocrocis medinalis (Lepidoptera: Pyralidae) on Rice Genotypes.

Cnaphalocrocis medinalis Guenée is a noxious rice pest during cultivated periods. Cnaphalocrocis medinalis moths lay eggs on leaf surfaces, and larvae longitudinally roll the leaves to hide inside the leaf buds and feed on the upper epidermis and mesophyll tissues. In this study, we evaluated the female oviposition preference and larval performance of C. medinalis on six insect-resistant and six insect-susceptible rice genotypes. Female moth choice and no-choice oviposition preferences were studied. The number of eggs laid on the leaf varies among selected rice genotypes; however, female adults prefer to lay more eggs on both some resistant and susceptible rice genotypes. Furthermore, newly hatched larvae showed no observed differences in preference for both specific resistant and susceptible rice genotypes. The time taken by larvae for leaf selection varied significantly after inoculation on different genotypes at the maximum tillering and heading stages of rice plants. Compared with susceptible genotypes, leaf selection time was prolonged in resistant genotypes. In addition, the time taken for folding primary vegetative and flag leaves by larvae varied among the selected rice genotypes; larvae required more time to fold leaves of resistant than susceptible genotypes. In host antibiosis tests, larval and pupal survival and pupal weight were higher in susceptible than resistant genotypes. The results showed that the time required by larvae for leaf rolling and host antibiosis should be considered as the most crucial factors for rice genotypes resistant to C. medinalis.

Transcriptome Analysis Reveals the Response of Iron Homeostasis to Early Feeding by Small Brown Planthopper in Rice.

It has been documented that planthopper attacks change iron (Fe) content of rice plants. To investigate whether planthopper attacks change rice Fe homeostasis at the molecular level, the response of rice Fe homeostasis to early feeding by small brown planthopper (SBPH) was examined by transcriptome profiling. Results showed that the concentration of Fe and nicotianamine decreased in resistant rice genotype and increased in susceptible rice genotype after attack by SBPH. Transcriptome profiling showed that 13 and 21 Fe homeostasis-related genes encoded enzymes that were involved in phytosiderophore biosynthesis and that Fe transporters and regulators displayed altered expression in resistant and susceptible rice genotypes, respectively, after attack by SBPH. This revealing response of Fe homeostasis to planthopper attack in rice at the molecular level provided new insight into rice plants' response to planthopper attack and uncovered a novel physiological response of rice to planthopper attack, which extended our knowledge of the early interaction between rice and SBPH.

Differential biochemical response of rice (Oryza sativa L.) genotypes against rice blast (Magnaporthe oryzae)

The disease-free (control) and blast infected leaf samples of 11 rice genotypes were evaluated for activity profile of defense-related and antioxidative enzymes. The amplification genomic DNA with two SSR markers RM124 and RM224 were also performed for identification of blast resistance and susceptible genotypes. The activity of chitinase, PAL and β-glucosidase of post pathogen-infected leaf samples increased significantly in all rice genotypes, thought the increase was comparable less in to blast susceptible genotypes Chimansal and EK-70. The activity of antioxidative enzymes was comparatively higher in the infected leaf of blast resistant genotypes recording highest increase in NLR-20104 and KJT-5. The activity of defense-related and antioxidative enzymes in the disease-free leaf samples differed among the genotypes and was even higher in the two blast susceptible genotypes. RM144 and RM224 SSR primers clearly amplified in blast resistant KJT-5, NLR-20104, KJT-2, Tetep genotypes whereas RM144 missing in susceptible Chimansal but prominently present in susceptible genotype EK-70. This study revealed that higher level of induction of defense-related and antioxidative enzymes and presence of specific amplified fragments with RM144 and RM224 could be useful for screening the resistant and susceptible rice genotypes against Magnaporthe oryzae.

Seedling stage low temperature response in tolerant and susceptible rice genotypes suggests role of relative water content and members of OsSNAC gene family

ABSTRACTLow temperature (LT) severely affects rice growth and grain yield. Recently, we reported contrasting genotypes including ARR 09 and Takyer for seedling stage long duration low temperature response. Here we show that susceptible rice genotypes show an increase in lipid peroxide levels and decrease in relative water content (RWC) to a higher extent in comparison to tolerant genotypes in response to 3 h LT. Stress induced NAC family members (OsNAC1, OsNAC2, OsNAC3, and OsNAC5) showed a higher transcript accumulation in tolerant genotypes than in sensitive genotypes after LT treatment suggesting stress tolerance might be due to higher expression of stress-responsive transcription factors. Furthermore, ARR 09 can be used as an important genetic resource to better understand LT tolerance mechanism.

Activity profile of defence-related enzymes in rice genotypes (Oryza sativa L.) against rice blast (Magnaporthe oryzae)

The control and infected leaf samples of blast resistant and susceptible rice genotypes were evaluated for activities of defence-related enzymes viz., total phenol content, chitinase, phenylalanine ammonia lyase (PAL), β-glycosidase, antioxidative enzymes, superoxide dismutase, peroxidase and ascorbate peroxidase. The level of total phenol content and the activity profile of chitinase, PAL and β-glycosidase significantly increased in both blast-resistant and susceptible rice genotypes with comparatively higher level induction Tetep, NLR-20104 and Swarnadhan the blast-resistant genotypes. The antioxidative enzymes were comparatively higher in the leaf samples of blast-resistant genotypes recording highest increase in NLR-20104 and KJT-5. The constitutive levels of total phenols and activity of defence-related and antioxidative enzymes in the control leaf samples differed among the genotypes and were even higher in the two blast susceptible genotypes (EK-70 and Chimansal). However, the level of induction as evident from the activity profile differences between control and infected leaf samples suggests higher level of induction was more which is indicative of the induced defence response. The genotype recording maximum induction of defence-related and antioxidative enzymes activity could be useful criteria in screening for blast resistant genotype in rice.

Induction of Submergence Specific Protein in Rice Varieties

Submergence stress is considered as the third most important limitation of rice production contributing to its low productivity in lowland and rainfed ecosystem. Grain yield reduced after submergence. The reduction was minimum in FR-13A (51.4%) followed by NDR-9830148 (51.6%) and was maximum in NDR-9830102 (96.6%) followed by Mahsuri (90.2%). The maximum elongation per cent was recorded in TCA-48 (50.1%) followed by NDR-9930077 (42.2%) and was minimum in NDR 9830148 (16.2%) followed by NDR 9930056 (17.7%). Mean effect showed that in stress condition number of grains per panicle decreased by 20.6% as compared to control. Yield contributing components, sterility, grain yield and number of grains per panicle and test weight of variety FR-13A, Swarna Sub-1, NDR-9830148 and TCA-48 were less affected by submergence in comparison to Mahsuri and other varieties. Five rice varieties, TCA-48, FR-13A and NDR 9730018 tolerant genotypes and Swarna and NDR 9830102 susceptible rice genotypes were used to find if new protein bands are synthesized under submergence. A specific band of 25 kDa was present in tolerant varieties but absent in susceptible varieties on 15% SDS PAGE. The presence of some specific proteins in tolerant varieties indicated that additional proteins were induced after submergence.

Identification and analysis of novel salt responsive candidate gene based SSRs (cgSSRs) from rice (Oryza sativa L.).

BackgroundMajority of the Asian people depend on rice for nutritional energy. Rice cultivation and yield are severely affected by soil salinity stress worldwide. Marker assisted breeding is a rapid and efficient way to develop improved variety for salinity stress tolerance. Genomic microsatellite markers are an elite group of markers, but there is possible uncertainty of linkage with the important genes. In contrast, there are better possibilities of linkage detection with important genes if SSRs are developed from candidate genes. To the best of our knowledge, there is no such report on SSR markers development from candidate gene sequences in rice. So the present study was aimed to identify and analyse SSRs from salt responsive candidate genes of rice.ResultsIn the present study, based on the comprehensive literature survey, we selected 220 different salt responsive genes of rice. Out of them, 106 genes were found to contain 180 microsatellite loci with, tri-nucleotide motifs (56%) being most abundant, followed by di-(41%) and tetra nucleotide (2.8%) motifs. Maximum loci were found in the coding sequences (37.2%), followed by in 5′UTR (26%), intron (21.6%) and 3′UTR (15%). For validation, 19 primer sets were evaluated to detect polymorphism in diversity analysis among the two panels consisting of 17 salt tolerant and 17 susceptible rice genotypes. Except one, all primer sets exhibited polymorphic nature with an average of 21.8 alleles/primer and with a mean PIC value of 0.28. Calculated genetic similarity among genotypes was ranged from 19%-89%. The generated dendrogram showed 3 clusters of which one contained entire 17 susceptible genotypes and another two clusters contained all tolerant genotypes.ConclusionThe present study represents the potential of salt responsive candidate gene based SSR (cgSSR) markers to be utilized as novel and remarkable candidate for diversity analysis among rice genotypes differing in salinity response.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0498-1) contains supplementary material, which is available to authorized users.

Differential induction of peroxidase and polyphenol oxidase isozymes in suspension-cultured cells of blast resistant and susceptible genotypes of rice in response to treatment with Magnaporthe grisea elicitor and toxin

The effect of elicitor from mycelial walls of Magnaporthe grisea, the rice blast fungus and α-picolinic acid, one of the toxins produced by M. grisea on induction of peroxidase (PO), polyphenol oxidase (PPO) in suspension-cultured rice (Oryza sativa L.) cells was studied. Cultured cells of blast resistant (Usen) and susceptible (CO39) rice genotypes were treated with elicitor (50 μg of glucose equivalents per ml) or α-picolinic acid (400 ppm). The cells were harvested at different time intervals and analysed for the induction of PO and PPO. PO isozyme analysis indicated that the elicitor strongly induced the activities of PO-2 and PO-3 in cultured cells of Usen 3 days after treatment. In Usen, toxin also induced the activities of PO-3 and PO-4. However, similar levels of activities corresponding to these isozymes were recorded 7 days after treatment. In CO39, the activities of PO-1 and PO-2 were induced 3 days after elicitor treatment. In contrast, the toxin suppressed the activity of PO-2. The elicitor induced the activities of PPO-1, PPO-2 and PPO-3 in both Usen and CO39. In Usen, steady increase of PPO-3 was observed and higher level of activity was recorded 5 days after treatment. In CO39, higher level of PPO-3 was observed 1 day after treatment and declined thereafter. However, the activities of PPO-1 and PPO-2 increased 3 days after treatment in CO39. In the toxin-treated cells of Usen, higher level of activity of PPO-3 was observed 3 days after treatment.

Histopathology of the rice root-knot nematode, Meloidogyne graminicola, on Oryza sativa and O. glaberrima

The root-knot nematode,Meloidogyne graminicola, can cause substantial rice yield losses. Understanding the mechanisms of resistance to this nematode species in known resistant rice genotypes may help to improve rice genotypes, aiming at developing and implementing environment-friendly and cost-effective nematode management strategies. Using susceptible and resistant rice genotypes, a comparative analysis of histological response mechanisms was made during two phases of the nematode colonisation:i) root penetration; andii) subsequent establishment and development byM. graminicolasecond-stage juveniles (J2). Two types of defence response mechanisms could be distinguished in the resistant rice genotypes. The early defence response consisted of a hypersensitive response (HR)-like reaction in the early stage of infection characterised by necrosis of cells directly affected by nematode feeding. This HR-like reaction was observed only in theM. graminicola-resistantOryza glaberrimagenotypes and not in theM. graminicola-susceptibleO. sativagenotypes. The late defence response took place after the induction of giant cells by the J2. Giant cells usually collapsed and degenerated before J2 developed into adults. Structural features of the roots of the susceptibleO. sativashowed greater root and stele diam. and cortex thickness than the resistantO. glaberrimagenotypes. Desired features of plants with resistance toM. graminicolaelucidated in this study can be used for selection of plants for breeding programmes.

Identification and characterization of salt responsive miRNA-SSR markers in rice (Oryza sativa)

Salinity is an important abiotic stress that affects agricultural production and productivity. It is a complex trait that is regulated by different molecular mechanisms. miRNAs are non-coding RNAs which are highly conserved and regulate gene expression. Simple sequence repeats (SSRs) are robust molecular markers for studying genetic diversity. Although several SSR markers are available now, challenge remains to identify the trait-specific SSRs which can be used for marker assisted breeding. In order to understand the genetic diversity of salt responsive-miRNA genes in rice, SSR markers were mined from 130 members of salt-responsive miRNA genes of rice and validated among the contrasting panels of tolerant as well as susceptible rice genotypes, each with 12 genotypes. Although 12 miR-SSRs were found to be polymorphic, only miR172b-SSR was able to differentiate the tolerant and susceptible genotypes in 2 different groups. It had also been found that miRNA genes were more diverse in susceptible genotypes than the tolerant one (as indicated by polymorphic index content) which might interfere to form the stem-loop structure of premature miRNA and their subsequent synthesis in susceptible genotypes. Thus, we concluded that length variations of the repeats in salt responsive miRNA genes may be responsible for a possible sensitivity to salinity adaptation. This is the first report of characterization of trait specific miRNA derived SSRs in plants.

Differential gene expression in gall midge susceptible rice genotypes revealed by suppressive subtraction hybridization (SSH) cDNA libraries and microarray analysis.

BackgroundA major pest of rice, the Asian rice gall midge (Orseolia oryzae Wood-Mason), causes significant yield losses in the rice growing regions throughout Asia. Feeding by the larvae induces susceptible plants to produce nutritive tissue to support growth and development. In order to identify molecular signatures during compatible interactions, genome wide transcriptional profiling was performed using SSH library and microarray technology.ResultsResults revealed up-regulation of genes related to primary metabolism, nutrient relocation, cell organization and DNA synthesis. Concomitantly, defense, secondary metabolism and signaling genes were suppressed. Further, real-time PCR validation of a selected set of 20 genes, in three susceptible rice varieties (TN1, Kavya and Suraksha) during the interaction with the respective virulent gall midge biotypes, also revealed variation in gene expression in Kavya as compared to TN1 and Suraksha.ConclusionsThese studies showed that virulent insects induced the plants to step up metabolism and transport nutrients to their feeding site and suppressed defense responses. But Kavya rice mounted an elevated defense response during early hours of virulent gall midge infestation, which was over-powered later, resulting in host plant susceptibility.Electronic supplementary materialThe online version of this article (doi:10.1186/1939-8433-5-8) contains supplementary material, which is available to authorized users.