PHYLOGENETIC RELATIONSHIP AMONG THE WILD RICE (Oryza nivara) AND INTRASPECIES OF RICE GENOTYPES BELONGING TO CHHATTISGARH REVEALED BY CHLOROPLAST DNA REGIONS psbA- trnH

JYOTI SINGH¹*, SHUBHA BANERJEE^2
1Department of Plant Molecular Biology and Biotechnology, College of Agriculture, Indira Gandhi Krishi Vishwavidyalaya, Raipur, 492012, Chhattisgarh, India
²Department of Plant Molecular Biology and Biotechnology, College of Agriculture, Indira Gandhi Krishi Vishwavidyalaya, Raipur, 492012, Chhattisgarh, India
* Corresponding Author : jyotisurya777@gmail.com

Received : 31-03-2018     Accepted : 07-04-2018     Published : 15-04-2018
Volume : 10     Issue : 3       Pages : 376 - 379
Genetics 10.3 (2018):376-379
DOI : http://dx.doi.org/10.9735/0975-2862.10.3.376-379

Keywords : Rice, Oryza Species, psbA-trnH, Phylogeny, Variation. BOLD, diversity
Conflict of Interest : None declared
Acknowledgements/Funding : Author thankful to Indira Gandhi Krishi Vishwavidyalaya, Raipur, 492012, Chhattisgarh, India for providing fund under RPF Project.
Author Contribution : All author equally contributed

Background: DNA barcoding technology uses short DNA sequences, for identification of species, understanding evolutionary relationship and also for identification of loci capable of discriminating at intra and inter species level. Method: Nucleotide variation at chloroplast (Cp) region, loci psbA-trnH and phylogenetic diversity among 24 rice genotypes belonging to Chhattisgarh was analyzed. Results: The average nucleotide composition in forward, reverse and both the strand of psbA-trnH loci was 27.8% (A), 35.2% (T/U), 18% (C), and 18.4% (G) with transition/transversion rate ratios are k1 = 6.758 (purines) and k2 = 2.597 (pyrimidines). The overall transition/transversion bias was R = 2.054. The estimated maximum evolutionary divergence sequence was 0.092 minimum 0 and average 0.015 (MEGA 7). The maximum parsimony informative sites were 31 and number of variable sites was reported 103. While nucleotide diversity (per site pi) 0.01459 analyzed in (DNAsp v.5 program). The reported maximum number of haplotypes was 17 and Haplotype diversity (Hd) 0.919. Conclusion: On the basis of nucleotide diversity analysis the discrimination ability of psbA-trnH strand loci was found better as compared to psbA-trnH-r (reverse) or both the strand. The sequencing informative data obtained, from intra-species variation in rice using psbA-trnH-f loci is achievable and proved to be useful for rice genotypes discrimination at intraspecies level. Further validations of rice genotypes can be used for cataloging and characterization of diverse rice genotypes (cultivated and wild) belonging to Chhattisgarh and will advance up in strengthen barcoding of rice genotype present, in various regions of India.

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