Akshaya Kumar Biswal

Publications (3) View all

• Source

  Available from: Hari Yadla

  Article: Development and validation of class I SSR markers targeting (GATA)n repeat motifs in rice

  Passoupathy Rajendrakumar, Akshaya Kumar Biswal, Kannabiran Sakthivel, Maganti Sheshu Madhav, Chirravuri Neeraja, Sena M. Balachandran, Kommoju Srinivasarao, Podishetty Natarajkumar, Yadla Hari, Kalidindi Sujatha, Raman M. Sundaram
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  ABSTRACT: SSR markers targeting (GATA) n motifs are known to be highly polymorphic and useful in many organisms. (GATA) n motif specific SSR markers covering the whole rice genome are not available. The present study was carried out with an objective to identify class I rice microsatellites in the rice genome with (GATA)n motifs, in-silico, and validate their potential as molecular markers. A total of 243 such motifs were identified; 65 of these were present in the genic region, 59 were in the upstream region and the remaining motifs were found in the intergenic regions. Many of the (GATA) n motifs were found within and/or upstream of genes associated with biotic or abiotic stress tolerance. A total of 230 PCR-based markers targeting all the class I (GATA) n microsatellites were developed and 35 of these markers spread across the rice genome were validated in a set of 24 representative rice varieties belonging to five distinct cultivar groups. All the markers were polymorphic, with average polymorphism information content (PIC) value of 0.61, and the rice cultivars could be uniquely distinguished into different cultivar groups based on marker analysis. These informative markers targeting (GATA) n motifs representing a new set of markers in rice will be highly useful for genetic studies and marker-assisted selection.
  Euphytica 04/2012; 169(2):263-271. · 1.55 Impact Factor
• Article: In silico analysis of microsatellites in organellar genomes of major cereals for understanding their phylogenetic relationships.

  Passoupathy Rajendrakumar, Akshaya Kumar Biswal, Sena M Balachandran, Raman M Sundaram
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  ABSTRACT: Microsatellites are abundant across prokaryotic and eukaryotic genomes. However, comparative analysis of microsatellites in the organellar genomes of plants and their utility in understanding phylogeny has not been reported. The purpose of this study was to understand the organization of microsatellites in the coding and non-coding regions of organellar genomes of major cereals viz., rice, wheat, maize and sorghum. About 5.8-14.3% of mitochondrial and 30.5-43.2% of chloroplast microsatellites were observed in the coding regions. About 83.8-86.8% of known mitochondrial genes had at least one microsatellite while this value ranged from 78.6-82.9% among the chloroplast genomes. Dinucleotide repeats were the most abundant in the coding and non-coding regions of the mitochondrial genome while mononucleotides were predominant in chloroplast genomes. Maize harbored more repeats in the mitochondrial genome, which could be due to the larger size of genome. A phylogenetic analysis based on mitochondrial and chloroplast genomic microsatellites revealed that rice and sorghum were closer to each other, while wheat was the farthest and this corroborated with the earlier reported phylogenies based on nuclear genome co-linearity and chloroplast gene-based analysis.
  In silico biology 02/2008; 8(2):87-104.
• Article: Simple sequence repeats in organellar genomes of rice: frequency and distribution in genic and intergenic regions.

  Passoupathy Rajendrakumar, Akshaya Kumar Biswal, Sena M Balachandran, Kommoju Srinivasarao, Raman M Sundaram
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  ABSTRACT: MOTIVATION: Simple sequence repeats (SSRs) are abundant across genomes. However, the significance of SSRs in organellar genomes of rice has not been completely understood. The availability of organellar genome sequences allows us to understand the organization of SSRs in their genic and intergenic regions. RESULTS: We have analyzed SSRs in mitochondrial and chloroplast genomes of rice. We identified 2528 SSRs in the mitochondrial genome and average 870 SSRs in the chloroplast genomes. About 8.7% of the mitochondrial and 27.5% of the chloroplast SSRs were observed in the genic region. Dinucleotides were the most abundant repeats in genic and intergenic regions of the mitochondrial genome while mononucleotides were predominant in the chloroplast genomes. The rps and nad gene clusters of mitochondria had the maximum repeats, while the rpo and ndh gene clusters of chloroplast had the maximum repeats. We identified SSRs in both organellar genomes and validated in different cultivars and species.
  Bioinformatics 02/2007; 23(1):1-4. · 5.47 Impact Factor