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Genetic Diversity Analysis in Aus Genotypes Using Ssr Markers

Md. Shamsher Ali
Chief Scientific Officer
Biotechnology Division, Bangladesh Rice Research Institute, Gazipur-1701

Md. Enamul Hoque
Principal Scientific Officer
Biotechnology Division, Bangladesh Rice Research Institute, Gazipur-1701

Ripon Kumar Roy
Scientific Officer
Biotechnology Division, Bangladesh Rice Research Institute, Gazipur-1701

Abstract/ Executive Summary:

Ninety four (six BRRI released and 88 local) Aus genotypes were screened against 91 SSR markers for DNA fingerprinting. Among them 51 primers showed polymorphism. One hundred and 95 alleles were detected at loci of 51 microsatellite markers across 94 Aus genotypes. Genetic dissimilarity co-efficient was recognized between every two genotypes based on DNA profile. The highest genetic dissimilarity (1.000) was found among the Aus genotypes of Ausa Bogi (Aus2), Aus gram binni (Aus7), Monshi murali (Aus26), Kachilon (2) (Aus44), Panki rat (Aus45), Agaua (Aus46), Chandra moni (Aus69) and Khusni (Aus72) . Whereas the lowest genetic dissimilarity was between BRRI dhan42 and BRRI dhan43 (0.1176). Genetic dissimilarity co-efficient revealed that most local Aus genotypes have broad genetic base as they indicated more genetic dissimilarity. On the other hand, BRRI released modern Aus variety showed narrow genetic base as indicated less then low genetic dissimilarity co-efficient. The genetic similarity analysis using UPGMA clustering system generated 11 major genetic clusters at a cut-off similarity co-efficient level of 0.37. The highest number of genotypes clustered in group 9 (22) and lowest in group 3 (1) and 6 (1).

Keywords: Genetic diversity, Aus genotype, SSR markers

Location: BRRI Head Quater, Gazipur

Start Date: 01-07-2009

End Date: 30-06-2010

Program Area: Conservation and Biodiversity

Commodity: Rice

Objectives:

To assess extent of genetic variation in traditional and improved varieties
To establish their relationship for breeding purpose

Methodology:

Ninety four (six BRRI released and 88 local) Aus genotypes have been screened against 91 SSR markers for this study. DNA was extracted from young leaves of 21 days old plants by mini preparation DNA 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 MgCl₂free 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 3 µL (10ng) of DNA using a 96 well thermal cycler. The temperature profile use was of 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. 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. Three µL of PCR products were resolved by running gel in 1X TBE buffer for 1.5 - 2.5 hrs depending upon the allele size at around 80-90 volts and 300-500 mA electricity. The gels were stained in 50µl ethidium bromide solution with 500 ml distil water (1 µg/ml ethidium bromide) and documented using UVPRO (Uvipro Platinum, EU) gel documentation unit.

Source of Information: Proceedings of the BRRI Annual Internal Review for 2009-2010

Article Link (Online Journal):

Funding Source:

1. Government

Budget: 300000

Total Budget (Tk.) : 300000

Achievement/Findings:

BRRI released modern Aus variety showed narrow genetic base as indicated less then low genetic dissimilarity co-efficient. The genetic similarity analysis using UPGMA clustering system generated 11 major genetic clusters at a cut-off similarity co-efficient level of 0.37.

Knowledge Management: Report/Proceedings