Manikandan Ramesh

Agrobacterium-mediated transformation of leaf base derived callus tissues of popular indica rice (Oryza sativa L. sub sp. indica cv. ADT 43)

A simple and efficient protocol for the Agrobacterium-mediated transformation of an agronomically useful abiotic sensitive popular indica rice cv. ADT 43 has been developed. Initiation of calli were best achieved from the leaf bases of 4 days old rice seedlings on LS medium supplemented with 2.5mg/L 2,4-D and 1.0mg/L thiamine-HCl. Rice calli immersed in Agrobacterium suspension (strain EHA 105, OD(600)=0.8) were co-cultured on LS30-AsPC medium for 2 days at 25±2°C in the dark. Based on GUS expression analysis, 10min co-cultivation time with 100μM acetosyringone was found optimum for the delivery of gus gene. Calli were proved to be very sensitive to Agrobacterium infection and we found that the level of necrotic response can be minimized after co-cultivation with 30% LS, 10g/L PVP, 10% coconut water and 250mg/L timentin which improved the final transformation efficiency to 9.33%. Molecular and genetic analysis of transgenic plants reveals the integration, expression and inheritance of transgene in the progeny (T(1)) of these plants. The copy number of transgenes has been found to vary from 1 to 2 in transgenic plants (T(0) and T(1)).

High frequency plant regeneration from embryogenic callus of a popular indica rice ( Oryza sativa L.)

The aim of the study is to establish a routine procedure for high frequency plant regeneration from in vitro raised embryogenic callus of abiotic salt sensitive indica rice (Oryza sativa L.) cultivar ADT 43. The effect of synthetic auxin 2,4-D on callus induction was optimized to achieve high frequency plant regeneration from fresh embryogenic callus without further subculture. Friable, nodular and creamish-white embryogenic callus cultures were raised from mature rice seeds on LS medium supplemented with 2.5 mg L−1 2,4-D and 1.0 mg L−1 thiamine-HCL. Plant regeneration was achieved by the 24 days old embryogenic callus on MS medium supplemented with 1.0 mg L−1 BAP and 1.5 mg L−1NAA. In vitro regenerated plants with multiple tillers and roots were transferred to sterile soil and maintained in the growth chamber. The regenerated plants exhibited normal growth and were phenotypically similar to plants maintained in the garden. Using the present protocol, 25–30 plantlets were regenerated from 50 individual mature seed derived callus within two to three months. This protocol has the potential for large-scale production of elite plants after genetic transformation.

Improved Agrobacterium-mediated transformation and direct plant regeneration in four cultivars of finger millet (Eleusine coracana (L.) Gaertn.)

We have developed an improved Agrobacterium-mediated transformation and rapid regeneration system for four cultivars (‘CO(Ra)-14’, ‘PR-202’, ‘Try-1’ and ‘Paiyur-2’) of finger millet using optimized transformation and direct plant regeneration conditions. The shoot apical meristems (SAMs) were used as explants in this study. Agrobacterium strain EHA105 carrying binary vector pCAMBIA1301 was used to optimize the transformation conditions. Concentration of hygromycin, the optical density of the culture, infection time, age of the explants, co-cultivation period, the concentrations of acetosyringone and antibiotics were optimized to improve the transformation frequency. The highest frequency of mean transient gus expression (85.1%) was achieved in cultivar ‘CO(Ra)-14’. The entire transformation procedure, from initiating SAMs to planting putative transgenic plantlets in the greenhouse, was completed within 45 days with the highest stable transformation frequency of 11.8% for ‘CO(Ra)-14’. PCR, gus staining and Southern blot analyses were performed in T0 and T1 generations to confirm the gene integration. Six events from T0 had a single copy of the transgene and showed a normal Mendelian pattern of segregation. To our knowledge, this is the first report on the high frequency transformation of finger millet by Agrobacterium and subsequent recovery of transgenic plants via direct plant regeneration without a callus phase, in short duration (45 days). The proposed protocol could be supportive in breaking through the bottleneck in transformation and regeneration of finger millet cultivars.

In vitro mass propagation and conservation of Nilgirianthus ciliatus through nodal explants: A globally endangered, high trade medicinal plant of Western Ghats

Abstract Nilgirianthus ciliatus is a globally endangered aromatic slender shrub of Western Ghats with extensive applications in Ayurveda. It is endangered due to its indiscriminate collection and overexploitation to meet the requirements of the pharmaceuticals. This study deals with the preservation of this endangered plant through in vitro nodal culture. Nodal explants were initially cultured on Murashige and Skoog (MS) medium supplemented with 6-benzylaminopurine (BA) or 6-furfurylaminopurine individually for primary shoot induction. For multiple shoot induction, primary shoots were transferred onto MS medium containing BA individually or in combination with auxins. Clusters of multiple shoots (up to 24.3) occurred with highest frequency (93.2%) on MS medium fortified with BA (3 mg l−1) and indole-3-acetic acid (0.1 mg l−1). In vitro regenerated plantlets were rooted on half-strength MS medium with maximum rooting frequency (82.2%) obtained in the presence of indole-3-butyric acid (1.0 mg l−1). The rooted plantlets were acclimatized to soil with 100% survival rate. Results of this study allowed us to develop an efficient regeneration system that will permit to carry out restoration programmes of N. ciliatus in Western Ghats. In future, this protocol will be an invaluable tool to produce synthetic seeds for cryopreservation and long-term conservation.

Global Transcriptome Analysis of Combined Abiotic Stress Signaling Genes Unravels Key Players in Oryza sativa L.: An In silico Approach

Combined abiotic stress (CAbS) affects the field grown plants simultaneously. The multigenic and quantitative nature of uncontrollable abiotic stresses complicates the process of understanding the stress response by plants. Considering this, we analyzed the CAbS response of C3 model plant, Oryza sativa by meta-analysis. The datasets of commonly expressed genes by drought, salinity, submergence, metal, natural expression, biotic, and abiotic stresses were data mined through publically accessible transcriptomic abiotic stress (AbS) responsive datasets. Of which 1,175, 12,821, and 42,877 genes were commonly expressed in meta differential, individual differential, and unchanged expressions respectively. Highly regulated 100 differentially expressed AbS genes were derived through integrative meta-analysis of expression data (INMEX). Of this 30 genes were identified from AbS gene families through expression atlas that were computationally analyzed for their physicochemical properties. All AbS genes were physically mapped against O. sativa genome. Comparative mapping of these genes demonstrated the orthologous relationship with related C4 panicoid genome. In silico expression analysis of these genes showed differential expression patterns in different developmental tissues. Protein–protein interaction of these genes, represented the complexity of AbS. Computational expression profiling of candidate genes in response to multiple stresses suggested the putative involvement of OS05G0350900, OS02G0612700, OS05G0104200, OS03G0596200, OS12G0225900, OS07G0152000, OS08G0119500, OS06G0594700, and Os01g0393100 in CAbS. These potential candidate genes need to be studied further to decipher their functional roles in AbS dynamics.

Analysis of genetic variation in sorghum (Sorghum bicolor (L.) Moench) genotypes with various agronomical traits using SPAR methods

Genetic variation among 45 genotypes of sorghum (Sorghum bicolor L.) representing seven subpopulations was assessed using three single primer amplification reaction (SPAR) methods viz., inter-simple sequence repeat (ISSR), random amplified polymorphic DNA (RAPD) and directed amplification of minisatellite-region DNA (DAMD). Totally 15 ISSR, 8 RAPD and 7 DAMD primers generated 263 amplification products, accounting for 84.6% polymorphism across all the genotypes. The Mantels test of correlation revealed the best correlation between ISSR and cumulative data with a correlation coefficient (r) of 0.84. Assessment of population diversity indicated that the maximum intra population genetic diversity was recorded among high FeZn lines (HFL) having maximum values of Neis genetic diversity (h) (0.244), Shannon information index (I) (0.368) and the percentage of polymorphic loci (Pp) (72.65%) while the corresponding lowest values of 0.074, 0.109 and 17.95% respectively were observed among the members of MDT subpopulation. The mean coefficient of gene differentiation (GST) and the gene flow (Nm) between populations were observed to be 0.396 and 0.7680 respectively. The analysis of molecular variance (AMOVA) suggested that maximum genetic variation exists within populations (95%) than among populations (5%). Thus the information obtained from this study could be utilized in sorghum breeding programmes for the development of varieties with improved nutrition and agronomic values in future.

Antibiofilm Activity of Dendrophthoe falcata against Different Bacterial Pathogens

Dendrophthoe falcata is a hemiparasitic plant commonly used for ailments such as ulcers, asthma, impotence, paralysis, skin diseases, menstrual troubles, pulmonary tuberculosis, and wounds. In this context, the validations of the traditional claim that the leaf extract of D. falcata possesses antibiofilm and anti-quorum sensing activity against different bacterial pathogens were assessed. The bacterial biofilms were quantified by crystal violet staining. Among the 17 bacterial pathogens screened, the methanolic fraction of the leaf extract clearly demonstrated antibiofilm activity for Proteus mirabilis, Vibrio vulnificus, Aeromonas hydrophila, Shigella sonnei, Chromobacterium violaceum ATCC 12472, Vibrio parahaemolyticus, Vibrio harveyi, Vibrio alginolyticus, Vibrio cholerae, and Proteus vulgaris. At biofilm inhibitory concentrations, biofilm formation was reduced by up to 70-90 %. Furthermore, the potential quorum-sensing activity of the leaf extract was tested by agar well diffusion using Chromobacterium violaceum (ATCC 12472 & CV O26) reporter strains. The inhibition of violacein production may be due to direct or indirect interference on QS by active constituents or the interactive effect of different phytocompounds present in the extracts. This is the first report on antibiofilm and QS activity of D. falcata leaf extracts, signifying the scope for development of complementary medicine for biofilm-associated infections.

Curcumin from Curcuma longa affects the virulence of Pectobacterium wasabiae and P. carotovorum subsp. carotovorum via quorum sensing regulation

In plant soft-rotting bacteria Pectobacterium, quorum sensing (QS) regulates the secretion of an arsenal of plant cell wall degrading extracellular enzymes (PCWDEs) and flagella-mediated motility via two different signaling molecules such as 3-oxohexanoyl-L-homoserine lactone (3-oxo-C6-AHL) and 3-oxooctanoyl-L-homoserine lactone (3-oxo- C8-AHL). In the present investigation, the phytochemical compound curcumin was assessed for its QS inhibitory potential against AHL-dependent PCWDEs production and motility in P. wasabiae SCC3193, P. carotovorum subsp. Carotovorum Pcc21 and P. carotovorum subsp. Carotovorum Pcc. Interestingly, curcumin at sub-MIC effectively inhibited the production of PCWDEs as well as the swimming and swarming motility of all tested pathogens in a non-bactericidal fashion. Subsequently, the in vitro root pathogenicity assay in Arabidopsis thaliana unveiled the rescuing efficacy of curcumin against the pathogenicity of tested plant pathogens by attenuating its QS mediated virulence factors production. Besides, studies with QS mutant strain Pcc21-M10 also evidenced the QSI property of curcumin.

Efficient In vitro plant regeneration through leaf base derived callus cultures of abiotic stress sensitive popular Asian Indica rice cultivar IR 64 (Oryza sativa L.)

A simple and efficient protocol has been developed for high frequency plant regeneration through callus cultures derived from leaf bases of abiotic stress sensitive Asian indica rice variety IR 64. Leaf base segments (4-5 mm diameter) were obtained from 6-day-old dark grown seedlings germinated on halfstrength Murashige and Skoog medium and cultured on MS medium supplemented with different concentrations of 2,4-Dichlorophenoxyacetic acid (2.2-18 μM) and Kinetin (0.2-1.7 μM). Among the various combinations, 13.5 μM 2,4-D and 1.3 μM Kn resulted in high callus induction frequency (87.5%) with a maximum fresh weight of 0.22 g per segment. The regeneration frequency was 75.5% with multiple shoots within 3 weeks of transfer on MS medium supplemented with 13.3 μM 6-benzylamino purine and 8 μM Naphthaleneacetic acid. The shoots readily rooted on half-strength MS medium without any hormonal supplements. In vitro regenerated plantlets with multiple shoots and roots were transferred to sterile soil and vermiculite mix and maintained in shade house for 30 days. Complete plantlets were then transferred to nursery and acclimatized to the external environment until seed set. RAPD profile reveals monomorphism and thus confirming the genetic stability of the regenerated plants. This method has the potential for both direct as well as indirect method of transformation for the production of genetically modified plants.

Global analysis of threonine metabolism genes unravel key players in rice to improve the abiotic stress tolerance

The diversity in plant metabolites with improved phytonutrients is essential to achieve global food security and sustainable crop yield. Our study using computational metabolomics genome wide association study (cmGWAS) reports on a comprehensive profiling of threonine (Thr) metabolite in rice. Sixteen abiotic stress responsive (AbSR) – Thr metabolite producing genes (ThrMPG), modulate metabolite levels and play a significant role determining both physiological and nutritional importance of rice. These AbSR-ThrMPG were computationally analysed for their protein properties using OryzaCyc through plant metabolic network analyser. A total of 1373 and 1028 SNPs were involved in complex traits and genomic variations. Comparative mapping of AbSR-ThrMPG revealed the chromosomal colinearity with C4 grass species. Further, computational expression pattern of these genes predicted a differential expression profiling in diverse developmental tissues. Protein interaction of protein coding gene sequences revealed that the abiotic stresses (AbS) are multigenic in nature. In silico expression of AbSR-ThrMPG determined the putative involvement in response to individual AbS. This is the first comprehensive genome wide study reporting on AbSR –ThrMPG analysis in rice. The results of this study provide a pivotal resource for further functional investigation of these key genes in the vital areas of manipulating AbS signaling in rice improvement.