Performance of Compressive Sensing Based Energy Detection

Detailed workflow for Physical position search (DOCX 36 kb

RiceMetaSys for salt and drought stress responsive genes in rice: a web interface for crop improvement

Abstract Background Genome-wide microarray has enabled development of robust databases for functional genomics studies in rice. However, such databases do not directly cater to the needs of breeders. Here, we have attempted to develop a web interface which combines the information from functional genomic studies across different genetic backgrounds with DNA markers so that they can be readily deployed in crop improvement. In the current version of the database, we have included drought and salinity stress studies since these two are the major abiotic stresses in rice. Results RiceMetaSys, a user-friendly and freely available web interface provides comprehensive information on salt responsive genes (SRGs) and drought responsive genes (DRGs) across genotypes, crop development stages and tissues, identified from multiple microarray datasets. ‘Physical position search’ is an attractive tool for those using QTL based approach for dissecting tolerance to salt and drought stress since it can provide the list of SRGs and DRGs in any physical interval. To identify robust candidate genes for use in crop improvement, the ‘common genes across varieties’ search tool is useful. Graphical visualization of expression profiles across genes and rice genotypes has been enabled to facilitate the user and to make the comparisons more impactful. Simple Sequence Repeat (SSR) search in the SRGs and DRGs is a valuable tool for fine mapping and marker assisted selection since it provides primers for survey of polymorphism. An external link to intron specific markers is also provided for this purpose. Bulk retrieval of data without any limit has been enabled in case of locus and SSR search. Conclusions The aim of this database is to facilitate users with a simple and straight-forward search options for identification of robust candidate genes from among thousands of SRGs and DRGs so as to facilitate linking variation in expression profiles to variation in phenotype. Database URL: http://14.139.229.20

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Identification and characterization of PEBP family genes reveal CcFT8 a probable candidate for photoperiod insensitivity in C. cajan

Understanding the molecular mechanism underlying photoperiod sensitivity will play a crucial role in extending the cropping area of Cajanus cajan, a photoperiod sensitive major grain legume of India and Africa. In flowering plants, Flowering locus T (FT) gene is involved in the production of florigen molecule which is essential for induction of flowering, influenced largely by the duration of photoperiod. To understand the structural and regulatory nature of this gene, a genome-wide survey was carried out, revealing the presence of 13 PEBP (FT) family genes in C. cajan. Based on the gene expression profiling of 13 PEBP genes across the 30 tissues of C. cajan, CcFT6 and CcFT8 were found to be probable Flowering locus T genes responsible for the production of florigen as both of them showed expression in reproductive leaf. Expression analysis in photoperiod sensitive, MAL3 genotype revealed that CcFT6 is upregulated under SD. However, in photoperiod insensitive genotype (ICP20338) CcFT6 and CcFT8 were upregulated in SD and LD, respectively. Hence, in ICP20338 under SD, flowering induction occurs with the involvement of CcFT6 while under LD, flowering induction seems to be associated with the expression of CcFT8. CcFT6 was found to be expressed only under favourable photoperiodic condition (SD) in both MAL3 and ICP20338 and may be regulated through a photoperiod dependent pathway. The presence of additional florigen producing gene, CcFT8 in ICP20338 which has the ability to flower in a photoperiod independent manner under LD conditions might provide some clues on its photoperiod insensitive nature. This study will provide a detailed characterization of the genes involved in photoperiodic regulation of flowering in C. cajan

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Additional file 1: Table S1. of RiceMetaSys for salt and drought stress responsive genes in rice: a web interface for crop improvement

Detailed information about the microarray datasets retrieved from NCBI GEO database. (DOCX 17 kb

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Not AvailableIn 2007, with the help of DBT, a research project to create mutant resources for functional genomics in rice was launched through a national initiative involving ICAR-National Research Centre on Plant Biotechnology, New Delhi; ICAR-Indian Agricultural Research Institute, New Delhi; Tamil Nadu Agricultural University, Coimbatore; ICAR-Indian Institute of Rice Research, Hyderabad; University of Agricultural Sciences, Bangalore and Punjab Agricultural University, Ludhiana. Genetically well-defined material is a prerequisite for functional genomics. Thus, the project aimed to generate EMS mutants in the background of an upland and short duration aus genotype, Nagina22, characterize the mutants and use them in crop improvement. As of now, nearly 85,000 rice M2 mutant populations have been created under the project. Based on field phenotyping, gain and or loss of function mutants for tolerance to herbicide spray, drought, salinity and resistance to rice leaf and panicle blast, sheath blight and high phosphorus (P) use efficiency under low P field have been identified. Notably, the herbicide-tolerant mutant identified is under the process of registration for distribution to public and private rice breeders under appropriate material transfer agreement. Besides this, the project also aims to serve as a ‘National Repository of rice EMS mutant resource’ for the researchers involved in rice biology and improvement in the country.Not Availabl

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Not AvailableNBS-encoding genes play a critical role in the plant defense system. Wild relatives of crop plants are rich reservoirs of plant defense genes. Here, we performed a stringent genome-wide identification of NBS-encoding genes in three cultivated and eight wild Oryza species, representing three different genomes (AA, BB, and FF) from four continents. A total of 2688 NBS-encoding genes were identified from 11 Oryza genomes. All the three progenitor species of cultivated rice, namely O. barthii, O. rufipogon, and O. nivara, were the richest reservoir of NBS-encoding genes (214, 313, and 307 respectively). Interestingly, the two Asian cultivated species showed a contrasting pattern in the number of NBS-encoding genes. While indica subspecies maintained nearly equal number of NBS genes as its progenitor (309 and 313), the japonica subspecies had retained only two third in the course of evolution (213 and 307). Other major sources for NBS-encoding genes could be (i) O. longistaminata since it had the highest proportion of NBS-encoding genes and (ii) O. glumaepatula as it clustered distinctly away from the rest of the AA genome species. The present study thus revealed that NBS-encoding genes can be exploited from the primary gene pool for disease resistance breeding in rice.Not Availabl

Chloroplast Genome Sequence of Clusterbean (Cyamopsis tetragonoloba L.): Genome Structure and Comparative Analysis

Clusterbean (Cyamopsis tetragonoloba L.), also known as guar, belongs to the family Leguminosae, and is an annual herbaceous legume. Guar is the main source of galactomannan for gas mining industries. In the present study, the draft chloroplast genome of clusterbean was generated and compared to some of the previously reported legume chloroplast genomes. The chloroplast genome of clusterbean is 152,530 bp in length, with a quadripartite structure consisting of large single copy (LSC) and small single copy (SSC) of 83,025 bp and 17,879 bp in size, respectively, and a pair of inverted repeats (IRs) of 25,790 bp in size. The chloroplast genome contains 114 unique genes, which includes 78 protein coding genes, 30 tRNAs, 4 rRNAs genes, and 2 pseudogenes. It also harbors a 50 kb inversion, typical of the Leguminosae family. The IR region of the clusterbean chloroplast genome has undergone an expansion, and hence, the whole rps19 gene is included in the IR, as compared to other legume plastid genomes. A total of 220 simple sequence repeats (SSRs) were detected in the clusterbean plastid genome. The analysis of the clusterbean plastid genome will provide useful insights for evolutionary, molecular and genetic engineering studies