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Genetic Variability in Bangladeshi Aromatic Rice Through Rapd Analysis

Mehfuz Hasan
Department of Genetics and Plant Breeding, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Salna, Gazipur 1706, Bangladesh.

Mohammad Sharif Raihan
Department of Genetics and Plant Breeding, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Salna, Gazipur 1706, Bangladesh.

Abstract/ Executive Summary:

Genetic polymorphism and relationships among 30 commercial varieties of Bangladeshi aromatic rice (Oryza sativa L.) were established using random amplified polymorphic DNA (RAPD) primers. Out of fifty 10-mer RAPD primers screened initially, four were chosen and used in a comparative analysis of different varieties of indigenous Bangladeshi aromatic rice. Of the 33 total RAPD fragments amplified, 7 (21.21%) were found to be shared by individuals of all eight varieties. The remaining 26 fragments were found to be polymorphic (78.79%). Pair-wise estimates of similarity ranged from 0.101 to 0.911. Highest genetic diversity was determined between Radhunipagol and Dubsail varieties (0.911). The amount of genetic diversity within aromatic rice germplasm was quite high as determined by the genetic similarity coefficients between varieties. Genetic similarities obtained from RAPD data were also used to create a cluster diagram. Cluster analysis using an un-weighted pair-group method with arithmetic averages (UPGMA) was used to group the varieties and the 30 aromatic rice varieties were grouped into 6 clusters where cluster I includes the maximum number of varieties (9). Cluster VI includes minimum number of varieties (2). This study offered a rapid and reliable method for the estimation of variability between different varieties which could be utilized by the breeders for further improvement of the local aromatic rice varieties.

Keywords: Aromatic rice, Genetic variation, Polymorphism, Random amplified polymorphic DNA, Un-weighted pair-group

Location: Department of Genetics and Plant Breeding, BSMRAU, Salna, Gazipur, Bangladesh.

Start Date:

End Date:

Program Area: Variety and Species

Commodity: Rice

Objectives:

To measure variability among Bangladeshi aromatic rice varieties grown under different names throughout the country based on RAPD markers.

Methodology:

Thirty indigenous rice varieties collected from different regions of Bangladesh were studied. The seeds of collected varieties were grown in pots. Leaf samples were collected from two-week old plants and for use in DNA assays. Genomic DNA was extracted according to modified CTAB (cetyltrimethylammonium bromide) method. Approximately 200 g of rice leaf tissue was chilled and ground to a very fine powder by mortar and pestle. The powdered tissue was transferred to a 1.5ml micro centrifuge tube containing 700 μl of pre-warmed (65°C) DNA extraction buffer. The contents were incubated for 40 minutes at 65°C in shaking water bath. 700 μl of chloroform: isoamylalcohol (24 : 1) was added for extraction. The mixture was centrifuged for 15 min at 14000 rpm. The aqueous phase was transferred to another fresh tube and isopropanol (2/3 of the aqueous phase) was added and mixed gently to precipitate DNA. The mixture was centrifuged for 20 min at 14000 rpm. The supernatant was discarded and the pellet was washed with 70% ethanol. The pellet was dried completely and dissolved in TE buffer. The purity and concentration of DNA were determined by using the spectrophotometer at wavelengths of 260 nm and 280 nm. The working concentration was prepared by diluting DNA to obtain 25 ng/μl strength. RAPD amplification was performed in a reaction volume of 25 μl containing 10 X reaction buffer (100 mMTris, 500 mM KCl, 0.1% gelatin, pH 9.0) with 1.5 mM MgCl2, 5 pM of primer, 0.2 mM dNTPs (dATP, dCTP, dGTP and dTTP), 2 U Taq DNA polymerase and 25 ng of template DNA. PCR amplification used the following profile: 45 cycles of 94°C for 1 min, 35°C for 1 min, and 72°C for 1 min with an extension of 72°C for 10 min. The resulting products were electrophoretically analyzed through 1.5% agarose gel stained with ethidium bromide (5 μg /ml) in TBE buffer (90 mM Tris–borate and 2 mM EDTA, pH 8.0). After staining in 0.5 μg/ml ethidium bromide solution, gels were photographed on a UV transilluminator. The genomes were scored for presence or absence of polymorphic bands and intensity of these polymorphic bands. Index of genetic variation was calculated and dendrograms were constructed through UPGMA method by using computer software. Fifty decamer random primers were initially screened for the presence of bands. Out of them, four primers (OPA 14, OPC 07, OPC 15 and OPF 17) were selected as they produced polymorphic and reproducible banding profiles.

Source of Information: Turkish Journal of Agriculture - Food Science and Technology, 3(3): 107-111, 2015, ISSN: 2148-127X

Article Link (Online Journal):

Funding Source:

Budget:

Total Budget (Tk.) :

Achievement/Findings:

Genetic variation is important in maintaining the developmental stability and biological potential of an organism. In essence, the present work revealed ample genetic variation among the studied aromatic rice germ plasm. Significant levels of genetic variation were observed between each pair of rice cultivars which indicated rich genetic resources in aromatic rice of Bangladesh. Information on this genetic variation from the present study might be useful for breeders in making decision for improvement of rice cultivars through selective breeding and cross breeding programs. Besides this, breeders could make a strategy for conservation of cultivars having diverse gene pools. As literature on genetic analysis of Bangladeshi aromatic rice using molecular markers is very scarce, present study could help the researchers in this regard in future.

Knowledge Management: Journal