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International Journal of Current Microbiology and Applied Sciences (IJCMAS)
IJCMAS is now DOI (CrossRef) registered Research Journal. The DOIs are assigned to all published IJCMAS Articles.
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National Academy of Agricultural Sciences (NAAS)
NAAS Score: *5.38 (2019)
[Effective from January 1, 2019]
For more details click here

ICV 2017: 100.00
Index Copernicus ICI Journals Master List 2017 - IJCMAS--ICV 2017: 100.00
For more details click here

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Original Research Articles

PRINT ISSN : 2319-7692
Online ISSN : 2319-7706
Issues : 12 per year
Publisher : Excellent Publishers
Email : editorijcmas@gmail.com / submit@ijcmas.com
Editor-in-chief: Dr.M.Prakash
Index Copernicus ICV 2017: 100.00
NAAS RATING 2018: 5.38

Int.J.Curr.Microbiol.App.Sci.2017.6(5): 2746-2756
DOI: 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 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 information is available on universal barcode for plants. Candidate loci belonging to chloroplast genome (CpG) and nuclear genome have been analyzed in various plants to identify universal barcoding loci capable of inter and intraspecies discrimination. 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. Results indicated that only one of the chloroplast CGS primer pair “psbA-trnH” showed (100%) amplification efficiency followed by “rbcL” (89.61%), “atpH-atpl” (68.39%), “matK” (66.2%) and “petA-psbJ” (62.33%). While 9 primers showed lower amplification efficiency between 5.19% and 52.81%. Based on amplification efficiency, reproducibility and amplicon size (as per Consortium for the Barcode of Life standard) five primers were selected for amplicon sequencing and further study of phylogenetic and phylogeographical relationships among above genotypes.


Keywords: Rice, DNA Barcoding, Chloroplast ‘DNA, rbcl, ‘matK, Species
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How to cite this article:

Jyoti Singh, Datta P. Kakade, Mayur R. Wallalwar, Rishiraj Raghuvanshi, Miranda Kongbrailatpam, Satish B. Verulkar and Shubha Banerjee. 2017. Evaluation of Potential DNA Barcoding Loci from Plastid Genome: Intraspecies Discrimination in Rice (Oryza species).Int.J.Curr.Microbiol.App.Sci. 6(5): 2746-2756. doi: https://doi.org/10.20546/ijcmas.2017.605.308