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DNA Fingerprinting of BRRI Hybrid and Their Corresponding Parent

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

Md.Monirul Islam
SSO
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

Abstract/ Executive Summary:

Diversity analysis of BRRI hybrid and their parental materials by molecular markers is required to carry out as morphological data are less reliable. Simple sequence repeat (SSR) markers have become the markers of choice for a wide spectrum of genetic population and evolutionary studies because they are able to detect 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:

End Date:

Program Area: Variety and Species

Commodity: Rice

Objectives:

The aim of the study was for DNA fingerprint and diversity analysis by SSR markers

Methodology:

Sixteen hybrid genotypes (four BRRI released hybrid variety and 12 their parental materials) were used in the present study.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) gel documentation unit.

Source of Information: Proceedings of the BRRI Annual Internal Review for 2009-10

Article Link (Online Journal):

Funding Source:

1. Government

Budget:

Total Budget (Tk.) :

Achievement/Findings:

A total of 73 microsatellite markers were tested for screening the genotypes. Among 73 amplified products, 37% have polymorphic bands giving 81 alleles. Pair-wise genetic dissimilarity co-efficient showed the component lines of BRRI hybrid one, two and four as the most genetically distant to each other whereas BRRI hybrid one, three, four and their respected parents were very close . Cluster analysis based on Dice’ssimilarity coefficient UPGMA system grouped BRRI hybrid and their parental lines into four major clusters at 0.41 cut off similarity co-efficient. Four BRRI hybrid varieties create four distinct clusters along with their components lines.

Knowledge Management: Report/Proceedings