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DNA Fingerprinting of Four Rice Varieties

Dr. Md .Shamsher Ali
CSO
Biotechnology Division, BRRI-Gazipur

Dr.Md.Enamul Hoque
CSO and Head (In Charge)
Biotechnology Division, BRRI-Gazipur

Dr.Hosneara Hossain
SSO
Biotechnology Division, BRRI-Gazipur

Md Monirul Islam
SSO
Biotechnology Division ,BRRI-Gazipur

S M Hisam Al Rabbi
SO
Biotechnology Division, BRRI-Gazipur

Ripon Kumar Roy
SO
Biotechnology Division, BRRI-Gazipur

M A Taher
SO
Biotechnology Division, BRRI-Gazipur

Abstract/ Executive Summary:

Diversity analysis of rice varieties by molecular markers is required to carry out breeding programmes between diversed parents as morphological data are not reliable. Single Sequence Repeat (SSR) markers have become the markers of choice for a wide spectrum of genetic population and evolutionary studies because they can detect a significantly higher degree of polymorphism in technically efficient and cost-effective way.

Keywords: DNA fingerprinting, Markers, Diversity analysis

Location: Biotechnology Division, BRRI-Gazipur

Start Date: 01-01-2008

End Date:

Program Area: Variety and Species

Commodity: Rice

Objectives:

The experiment was carried out for DNA fingerprint and diversity analysis by SSR markers.

Methodology:

Four elite rice varieties (BRRI dhan50, Basmati386, BMDA Basmati and BHR1) were used in the present study among them BRRI dhan50, Basmati386 and BMDA Basmati are premium quality aromatic rice.DNA was extracted from young leaves of 21 days old plants by mini DNA preparation method (modified CTAB). The concentration of extracted DNA was estimated by Nano Drop Spectrophotometer. Each PCR was carried out in a 10 μL reaction volume containing 1 μL of MgCl2 free 10X PCR buffer, 1.2 μL of 25 mM MgCl2, 0.2 μL of 10 mM dNTPs, 0.2 μL of 5 U/μL Taq DNA polymerase, 0.5 μL of 10 μM forward and reverse primers and 2 μL (10ng) of DNA using a 96 well thermal cycler. The temperature profile use for PCR amplification comprised 94° C for 5 min (initial denaturation) followed by 35 cycles of 94° C for 1 min (denaturation), 55° C for 1 min (annealing), 72° C for 2 min (extension) with a final extension for 7 min at 72° C at the end of 35 cycles. The annealing temperatures were adjusted based on the specific requirements of each primer combination. The PCR products were mixed with gel loading dye and electrophoresed in 8% polyacrylamide gel using vertical polyacrylamide gels for high throughput manual genotyping. Four μL of amplification products were resolved by running gel in 1X TBE buffer for 1.5 - 2.5 hrs depending upon the allele size at around 75 volts and 180 mA electricity. The gels were stained in 1 μg/ml ethidium bromide solution and were documented using UVPRO (Uvipro Platinum, EU) geldocumentation unit.

Source of Information: Proceedings of the BRRI Annual Internal Review for 2008-09

Article Link (Online Journal):

Funding Source:

1. Government

Budget:

Total Budget (Tk.) :

Achievement/Findings:

All of the 4 rice varieties are much diverged. The genetic similarity analysis using UPGMA clustering system generated 3 major genetic clusters at a cut-off similarity co-efficient level of 0.25. Both BR50 and BHR1 remain alone in their clusters. Only Basmati 386 and BMDA Basmati are grouped in same cluster and from pair-wise genetic dissimilarity co-efficient , we got that they have dissimilarity co-efficient 0.750 meaning 25% similarity. Rest varieties are very much diverged.

Knowledge Management: Report/Proceedings