~ 686 ~ International Journal of Chemical Studies 2018; 6(1): 686-690 P-ISSN: 2349–8528 E-ISSN: 2321–4902 IJCS 2018; 6(1): 686-690 © 2018 IJCS Received: 17-11-2017 Accepted: 18-12-2017 Jyoti Singh Department of Plant Molecular Biology and Biotechnology, College of Agriculture, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, India Datta P Kakade Department of Plant Molecular Biology and Biotechnology, College of Agriculture, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, India Shubha Banerjee Department of Plant Molecular Biology and Biotechnology, College of Agriculture, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, India Correspondence Jyoti Singh Department of Plant Molecular Biology and Biotechnology, College of Agriculture, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, India Fingerprint: Visual description of variation in multiple sequence alignments of intra-species of rice genotypes belonging to Chhattisgarh Jyoti Singh, Datta P Kakade and Shubha Banerjee Abstract The usefulness of genetic material for use as DNA barcodes is under stable evolution and advancement as new barcodes offering better resolution and efficiency of amplification for specific species groups are identified. The panel of 24 rice genotypes including diverse germplasm lines, elite lines, landraces and wild rice belonging to Chhattisgarh were amplified using atpH-atpI, petA-psbJ, trnK, rbcL, matK, trnlc- trnld, psbA-trnH aligned sets of seven chloroplast specific loci, sequences were analyzed using fingerprint available at http://evol.mcmaster.ca/fingerprint. Fingerprint helps to identify similarities, differences, and patterns within a multiple sequence alignment which is biologically valuable because it permits visualization of the distribution of a particular feature and inferences about the structure, function, and evolution of the sequences in analysis also represent identity, variability, charge, hydrophobicity, solvent accessibility, and structure along with new visualizations based on composition, heterogeneity, heterozygosity, dN/dS and nucleotide diversity. The visualization based on composition, heterogeneity, dN/dS and nucleotide diversity on 24 were performed. The results shows even though matK and rbcl loci shows lesser number of haplotypes but are variable throughout the region. On the other part psbA-trnH shows variability in the specific region through showed good discrimination power in molecular phylogenetic analysis. Keywords: Cytochromec oxidase I, DNA barcoding, fingerprint, multiple sequence alignment, polymorphism, sequence diversity Introduction Rice is the most important and widely cultivated crop in the world. Rice has more than forty thousand varieties species all across the globe. Asia is the home of rice as more than two billion people are getting 60-70 per cent of their energy requirement from rice and its derived products (Rekha et al., 2015) [15] . Chhattisgarh is traditionally rich in rice diversity containing the wild progenitors of cultivated rice. The recent development of DNA barcoding provides a novel opportunity in delimitating closely related species. DNA barcoding helps to identify species on the basis of single- DNA region or a combination of a few DNA regions in the absence of taxonomic knowledge (Hebert et al., 2003) [10] , for these reason the DNA barcode regions should be of short lengths with high recovery rates (success rate for amplifying and sequencing) and have high species differentiation rate (CBOL plant working Group, 2009, Hollingsworth et al., 2008, and Li et al., 2011) [3, 11, 13] . At present chloroplast regions were regarded as ideal candidates compared to the mitochondrial regions for plant barcoding by virtue of their faster mutation rate, and recombination, uniparental inheritance and higher recovery rate (Kress et al., 2005) [12] The Barcode of Life Initiative has employed COI as the standard gene because it is able to discriminate between many closely related animal species (Hebert et al 2003) [10] and there is evidence to suggest that it also works well in algae (Saunders 2005) [16] , arthropods (Smith et al 2005) [17] , fish (Ward et al 2005) [19] and some plants (Kress et al 2005) [12] . Identifying sequence changes in homologous sites provides insights about the structure functional genomics, and evolution of a protein. Unfortunately, numerous programs which require download and installation of software, support complicated documentation, impose a fee or limit the number of sequences allowed in the input file, graphical multiple alignment editors, such as clustal_x (Thompson et al. 1997) [18] , Seaview (Galtier et al. 1996) [9] , and JALVIEW (Clamp et al. 2004) [4] , that display an alignment in its entirety. The problem is that it becomes difficult to summarize the characteristics or diversity of as ite relative to other sites within a multiple sequence alignment.