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Evaluation of potential DNA barcoding loci from plastid genome: Intraspecies discrimination in rice (Oryza species)

In this study, relative potential of 24 candidate loci (Dong et al, 2012) from plastid genome were validated on set of 231 diverse rice genotypes, for selection of suitable barcoding loci for DNA barcoding in rice. | Int.J.Curr.Microbiol.App.Sci 2017 6 5 2746-2756 International Journal of Current Microbiology and Applied Sciences ISSN 2319-7706 Volume 6 Number 5 2017 pp. 2746-2756 Journal homepage http www.ijcmas.com Original Research Article https doi.org 10.20546 ijcmas.2017.605.308 Evaluation of Potential DNA Barcoding Loci from Plastid Genome Intraspecies Discrimination in Rice Oryza species Jyoti Singh Datta P. Kakade Mayur R. Wallalwar Rishiraj Raghuvanshi Miranda Kongbrailatpam Satish B. Verulkar and Shubha Banerjee Department of Plant Molecular Biology and Biotechnology College of Agriculture Indira Gandhi Krishi Vishwavidyalaya Raipur Chhattisgarh-492012 India Corresponding author ABSTRACT DNA barcoding is a technique that makes use of short sequences from a standardized region of a genome to provide quick and reliable identification of species among all forms Keywords of life. The presence of uniqueness and variability required for DNA barcoding is well reported in animal system based on mitochondrial gene CO1.On the other hand limited Rice DNA information is available on universal barcode for plants. Candidate loci belonging to Barcoding chloroplast genome CpG and nuclear genome have been analyzed in various plants to Chloroplast identify universal barcoding loci capable of inter and intraspecies discrimination. In this DNA rbcl study relative potential of 24 candidate loci Dong et al 2012 from plastid genome were matK Species. validated on set of 231 diverse rice genotypes for selection of suitable barcoding loci for Article Info DNA barcoding in rice. Results indicated that only one of the chloroplast CGS primer pair psbA-trnH showed 100 amplification efficiency followed by rbcL 89.61 Accepted 26 April 2017 atpH-atpl 68.39 matK 66.2 and petA-psbJ 62.33 . While 9 primers Available Online showed lower amplification efficiency between 5.19 and 52.81 . Based on 10 May 2017 amplification efficiency reproducibility and amplicon size as per Consortium for the Barcode of