Comparative analysis of expressed sequence tags (ESTs) between drought-tolerant and -susceptible genotypes of chickpea under terminal drought stress

<p>Abstract</p> <p>Background</p> <p>Chickpea (<it>Cicer arietinum </it>L.) is an important grain-legume crop that is mainly grown in rainfed areas, where terminal drought is a major constraint to its productivity. We generated expressed sequence tags (ESTs) by suppression subtraction hybridization (SSH) to identify differentially expressed genes in drought-tolerant and -susceptible genotypes in chickpea.</p> <p>Results</p> <p>EST libraries were generated by SSH from root and shoot tissues of IC4958 (drought tolerant) and ICC 1882 (drought resistant) exposed to terminal drought conditions by the dry down method. SSH libraries were also constructed by using 2 sets of bulks prepared from the RNA of root tissues from selected recombinant inbred lines (RILs) (10 each) for the extreme high and low root biomass phenotype. A total of 3062 unigenes (638 contigs and 2424 singletons), 51.4% of which were novel in chickpea, were derived by cluster assembly and sequence alignment of 5949 ESTs. Only 2185 (71%) unigenes showed significant BLASTX similarity (<1E-06) in the NCBI non-redundant (nr) database. Gene ontology functional classification terms (BLASTX results and GO term), were retrieved for 2006 (92.0%) sequences, and 656 sequences were further annotated with 812 Enzyme Commission (EC) codes and were mapped to 108 different KEGG pathways. In addition, expression status of 830 unigenes in response to terminal drought stress was evaluated using macro-array (dot blots). The expression of few selected genes was validated by northern blotting and quantitative real-time PCR assay.</p> <p>Conclusion</p> <p>Our study compares not only genes that are up- and down-regulated in a drought-tolerant genotype under terminal drought stress and a drought susceptible genotype but also between the bulks of the selected RILs exhibiting extreme phenotypes. More than 50% of the genes identified have been shown to be associated with drought stress in chickpea for the first time. This study not only serves as resource for marker discovery, but can provide a better insight into the selection of candidate genes (both up- and downregulated) associated with drought tolerance. These results can be used to identify suitable targets for manipulating the drought-tolerance trait in chickpea.</p

CicArVarDB: SNP and InDel database for advancing genetics research and breeding applications in chickpea

Molecular markers are valuable tools for breeders to help accelerate crop improvement. High throughput sequencing technologies facilitate the discovery of large-scale variations such as single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs). Sequencing of chickpea genome along with re-sequencing of several chickpea lines has enabled the discovery of 4.4 million variations including SNPs and InDels. Here we report a repository of 1.9 million variations (SNPs and InDels) anchored on eight pseudomolecules in a custom database, referred as CicArVarDB that can be accessed at http://cicarvardb.icrisat.org/. It includes an easy interface for users to select variations around specific regions associated with quantitative trait loci, with embedded webBLAST search and JBrowse visualisation. We hope that this database will be immensely useful for the chickpea research community for both advancing genetics research as well as breeding applications for crop improvement

Effect of impurities on performance of biodiesel: A review

575-579This paper reviews effect of impurities formed during transesterification process and how biodiesel can be made free fromimpurities. It also highlights effect on performance of long term storage of biodiesel

Sorption of ammonia on crystalline polyelectrolyte tantalum tungstate

296-298A crystalline polyelectrolyte tantalum tungstate (Ta:W::2.568:1) has been selected for the sorption of ammonia. Its BET surface area, electron micrograph and IR spectra have been reported. The sorption of ammonia at 50° and its desorption at 50° and 150°C have been carried out. Ammonia sorption may be utilized to control the pollution caused by exhaust gases of automobiles

Aptamer based electrochemical sensor for detection of human lung adenocarcinoma A549 cells

We report results of the studies relating to development of an aptamer-based electrochemical biosensor for detection of human lung adenocarcinoma A549 cells. The aminated 85-mer DNA aptamer probe specific for the A549 cells has been covalently immobilized onto silane self assembled monolayer (SAM) onto ITO surface using glutaraldehyde as the crosslinker. The results of cyclic voltammetry and differential pulse voltammetry studies reveal that the aptamer functionalized bioelectrode can specifically detect lung cancer cells in the concentration range of 10(3) to 10(7) cells/ml with detection limit of 10(3) cells/ml within 60 s. The specificity studies of the bioelectrode have been carried out with control KB cells. No significant change in response is observed for control KB cells as compared to that of the A549 target cells

Enhanced electromagnetic shielding behaviour of multilayer graphene anchored luminescent TiO2 in PPY matrix

Present research is focussed on the development of a novel composite material for highly-efficient absorption of electromagnetic interference (EMI) pollution. Herein, we report synthesis and characterization of polypyrrole (PPY) composite containing multi-layered graphene (MLG) anchored with titanium dioxide (TiO2) via in-situ oxidative polymerization of pyrrole. The tuning of the microwave signals has achieved via composites with different weight ratios of MLG and TiO2. The maximum Total shielding effectiveness (SET), 53 dB was observed for PPY/MLG/TiO2 (5% composite) in the frequency range of 12.4-18 GHz. The observed results suggest that the composite material could be a new alternative for building block of electromagnetic shielding applications

New insight into the shape-controlled synthesis and microwave shielding properties of iron oxide covered with reduced graphene oxide

We proposed various approaches for the shape-controlled synthesis of iron oxide-RGO composites to evaluate the effect of different morphologies on their microwave shielding properties. The nature of various ferrite structures (flakes, cubes and rods) covered by reduced graphene oxide multilayers has been investigated using X-ray diffraction, Raman spectroscopy, FT-IR, scanning electron microscopy, high-resolution transmission electron microscopy and X-ray photoelectron spectroscopic techniques. The electromagnetic interference (EMI) shielding effectiveness of iron oxide of different shapes coated with reduced graphene oxide was investigated in the Ku band frequency range (12.4-18 GHz). The rod shaped iron oxide covered with reduced graphene oxide sheets demonstrates the highest shielding effectiveness value of similar to 33.30 dB (>99.9% attenuation) as compared to flake and cube shaped iron oxides due to the combined effect of magnetic losses (hysteresis, eddy current loss and effective anisotropy) and dielectric losses (space charge polarization, interfacial polarization, surface defects, multiple scattering, etc.). These innovative proposed structures and their obtained EMI shielding results deliver a new insight into the morphology dependent nature of iron oxides covered with RGO nanosheets and create new opportunities for next generation EMI materials

A snapshot on SNPs in four chickpea genotypes compared to the reference genome.

<p>The Venn diagram shows distribution of SNPs detected between four genotypes (Pistol, Hat Trick, Slasher and Genesis 90). The genotype CDC Frontier was used as a reference sequence. For instance, a total of 95,329 SNPs were found to be concordant between Pistol and Hat Trick genotypes. Similarly, amongst all the four genotypes 62,291 SNPs were found to be in common.</p

Comparison of key features of the ISMU pipeline with similar pipelines.

<p>ISMU is one of the few tools that provide an easy to use graphical interface (GUI) packed with a wide choice of open source tools (alignment and variant calling) for handling NGS data. The information describing features of other pipelines is derived from Fisher et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0101754#pone.0101754-Fischer1" target="_blank">[60]</a> and compared. The symbols “Y” and “N” represent, presence and absence of the feature in the pipeline. Numbers (1. 5, 2) indicate number of tool included in the pipeline. “n.m” refers to feature not mentioned.</p