Publications (5)13.33 Total impact
-
Dataset: 2010 gupta fig sugarcane
-
Article: Rice genomics moves ahead
[show abstract] [hide abstract]
ABSTRACT: Rice is one of the pillars of world-wide food security. Improvement in its yield is necessary to mitigate hunger of millions of people who depend on rice as a staple. Decoding rice genome sequence is expected to complement efforts being made to improve rice and its yield. The information about more than 32,000 genes, regulatory elements, repeat DNA, and DNA markers opens-up new horizons for molecular analysis and genetic enhancement not only for rice but also for other cereal crops. In the post-genomic era, significant progress has been made on defining transcriptome and epigenome as well as gene discovery by way of forward and reverse genetic approaches. Efforts are onto fill the gap between the genome and the phenotype. This may lead to regular practice of genomics-assisted breeding of rice. KeywordsGene function-Genome analysis-Epigenomics-Transcriptomics-Genomics-assisted breeding-RiceMolecular Breeding 04/2012; 26(2):257-273. · 2.85 Impact Factor -
Article: Carotenoid biosynthesis genes in rice: structural analysis, genome-wide expression profiling and phylogenetic analysis.
[show abstract] [hide abstract]
ABSTRACT: Carotenoids, important lipid-soluble antioxidants in photosynthetic tissues, are known to be completely absent in rice endosperm. Many studies, involving transgenic manipulations of carotenoid biosynthesis genes, have been performed to get carotenoid-enriched rice grain. Study of genes involved in their biosynthesis can provide further information regarding the abundance/absence of carotenoids in different tissues. We have identified 16 and 34 carotenoid biosynthesis genes in rice and Populus genomes, respectively. A detailed analysis of the domain structure of carotenoid biosynthesis enzymes in rice, Populus and Arabidopsis has shown that highly conserved catalytic domains, along with other domains, are present in these proteins. Phylogenetic analysis of rice genes with Arabidopsis and other characterized carotenoid biosynthesis genes has revealed that homologous genes exist in these plants, and the duplicated gene copies probably adopt new functions. Expression of rice and Populus genes has been analyzed by full-length cDNA- and EST-based expression profiling. In rice, this analysis was complemented by real-time PCR, microarray and signature-based expression profiling, which reveal that carotenoid biosynthesis genes are highly expressed in light-grown tissues, have differential expression pattern during vegetative/reproductive development and are responsive to stress.MGG Molecular & General Genetics 11/2009; 283(1):13-33. · 2.58 Impact Factor -
Article: The water-deficit stress- and red-rot-related genes in sugarcane.
[show abstract] [hide abstract]
ABSTRACT: Sugarcane is an important international commodity as a valuable agricultural crop especially in developing countries. Sequencing was carried out to generate >35,000 expressed sequence tags (ESTs) from healthy as well as red-rot-infected tissue of Indian subtropical variety of sugarcane. Subsequent clustering with existing sugarcane ESTs in public databases identified 4,087 clusters, including 85 clusters that preferentially express upon Colletotrichum falcatum (red-rot) infection, which were previously unreported. Real-time reverse transcription-PCR profiling of selected EST clusters identified several sugarcane clusters that show differential expression in response to biotic and abiotic stress conditions. Twenty-five stress-related clusters showed >2-fold relative expression during water-deficit stress in sugarcane. Similarly, EST clusters could be identified, which exhibit association with red-rot disease when assessed in red-rot-susceptible and red-rot-resistant varieties of sugarcane. Such EST clusters are good candidates for in-depth analysis to elucidate stress-responsive pathways in sugarcane and facilitate genetic manipulation to tailor this crop for tolerance to various stresses.Functional & Integrative Genomics 10/2009; 10(2):207-14. · 3.83 Impact Factor -
Article: Genome-wide identification, organization and phylogenetic analysis of Dicer-like, Argonaute and RNA-dependent RNA Polymerase gene families and their expression analysis during reproductive development and stress in rice.
[show abstract] [hide abstract]
ABSTRACT: Important developmental processes in both plants and animals are partly regulated by genes whose expression is modulated at the post-transcriptional level by processes such as RNA interference (RNAi). Dicers, Argonautes and RNA-dependent RNA polymerases (RDR) form the core components that facilitate gene silencing and have been implicated in the initiation and maintenance of the trigger RNA molecules, central to process of RNAi. Investigations in eukaryotes have revealed that these proteins are encoded by variable number of genes with plants showing relatively higher number in each gene family. To date, no systematic expression profiling of these genes in any of the organisms has been reported. In this study, we provide a complete analysis of rice Dicer-like, Argonaute and RDR gene families including gene structure, genomic localization and phylogenetic relatedness among gene family members. We also present microarray-based expression profiling of these genes during 14 stages of reproductive and 5 stages of vegetative development and in response to cold, salt and dehydration stress. We have identified 8 Dicer-like (OsDCLs), 19 Argonaute (OsAGOs) and 5 RNA-dependent RNA polymerase (OsRDRs) genes in rice. Based on phylogeny, each of these genes families have been categorized into four subgroups. Although most of the genes express both in vegetative and reproductive organs, 2 OsDCLs, 14 OsAGOs and 3 OsRDRs were found to express specifically/preferentially during stages of reproductive development. Of these, 2 OsAGOs exhibited preferential up-regulation in seeds. One of the Argonautes (OsAGO2) also showed specific up-regulation in response to cold, salt and dehydration stress. This investigation has identified 23 rice genes belonging to DCL, Argonaute and RDR gene families that could potentially be involved in reproductive development-specific gene regulatory mechanisms. These data provide an insight into probable domains of activity of these genes and a basis for further, more detailed investigations aimed at understanding the contribution of individual components of RNA silencing machinery during reproductive phase of plant development.BMC Genomics 11/2008; 9:451. · 4.07 Impact Factor
Top co-authors
Top Journals
Institutions
-
2012
-
University of Delhi
Delhi, NCT, India
-
