DNA Barcoding for Wild Rice [Oryza rufipogon Griff.] of NBU Campus Based on matK gene and Assessment of Genetic Variation Using DREB and BAD2 Gene Sequences
Subhas Chandra Roy
Subhas Chandra Roy, Plant Genetics & Molecular Breeding Laboratory, DRS Department of Botany, University of North Bengal, PO- NBU,Siliguri-734013, WB, India.
Plant Gene and Trait, 2015, Vol. 6, No. 5 doi: 10.5376/pgt.2015.06.0005
Received: 16 May, 2015 Accepted: 07 Jul., 2015 Published: 17 Jul., 2015
© 2015 BioPublisher Publishing Platform
This is an open access article published under the terms of the Creative Commons Attribution License
, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Preferred citation for this article:
Subhas Chandra Roy, DNA barcoding for wild rice [oryza rufipogon Griff.] of NBU campus based on matK gene and assessment of genetic variation using DREB and BAD2 gene sequence. Plant Gene and Trait, 6(4) 1-10 (doi: 10.5376/pgt.2015.06.0005)
DNA barcoding is a technique for characterizing species based on short DNA sequence of a particular genomic region. The chloroplast maturase gene K (matK) sequence of 1420 bp was used to construct unique DNA barcode for wild rice [Oryza rufipogon Grirr.] of NBU campus using BOLD system. The partial matK gene sequence (1420 bp) was annotated and submitted into the GenBank of NCBI (Accession no. KM516199). Gene sequences of DREB transcription factor and BAD2 were analyzed to assess the genetic variation between O. rufipogon (NBU) and other species of rice. The DREB gene is responsible for abiotic stress tolerance whereas BAD2 is a gene for fragrant formation in rice. A thick and discrete band of 916 bp was detected on 1% agarose gel in the DREB lane which proved that wild taxon may provide abiotic stress tolerance. The DNA sequence of 916 bp of DREB gene of O. rufipogon of NBU campus was run in BLAST program of www.gramene.org database, it was matched with DREB gene sequence of wild rice O. rufipogon in the database and aligned in chromosome 1, 4 and 9. Both the DREB and BAD2 gene sequences were run in MEGA6 software for study of genetic relationship among the rice species. Phylogram constructed from this analysis showed close clustering association with other wild rice species. The species O. rufipogon of NBU campus was non-fragrant homozygous because it was given PCR product of 357 bp while used four primers in allele specific gene amplification method.
Wild Rice; Oryza rufipogon; DNA barcode; DREB and BAD2 gene; and Genetic variation