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Efficiency of RAPD, SSR and Cytochrome P450 gene based markers in accessing genetic variability amongst finger millet (Eleusine coracana) accessions

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Abstract

Finger millet (Eleusine coracana L.) is an important crop used for food, forage, and industrial products. Three DNA marker techniques, random amplified polymorphic DNA (RAPD), simple sequence repeat (SSR) and cytochrome P450 gene based markers were used for the detection of genetic polymorphism in 83 accessions of finger millet collected from various geographical regions of India and Africa. A total of 18 RAPD, 10 SSR and 10 pairs of cytochrome P450 gene based markers were generated 56.17, 70.19 and 54.29% polymorphism, respectively. Mean polymorphism information content (PIC) for each of these marker systems (0.280 for RAPD, 0.89 for SSR and 0.327 for cytochrome P450 gene based markers) suggested that SSR marker were highly effective in determining polymorphism. The phenograms based on the three markers data indicate that genotypes from different geographical regions are clearly distinguishable as separate clusters. Mantel test employed for detection of goodness of fit established cophenetic correlation values above 0.90 for all the three marker systems. The dendrograms and PCA plots derived from the binary data matrices of the three marker systems are highly concordant. High bootstrap values were obtained at major nodes of phenograms through WINBOOT software. Based on the results of present study, SSR and cytochrome P450 gene based markers appear to be particularly useful for the estimation of genetic diversity. This study reveals the potential of RAPD, SSR and gene based markers for characterizing germplasm of Eleusine coracana and narrow down the vast germplasm into distinct core groups.

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Abbreviations

PCA:

Principal component analysis

PCR:

Polymerase chain reaction

PIC:

Polymorphism information content

RAPD:

Random amplified polymorphic DNA

UPGMA:

Unweighted pair group method with arithmetic averages

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Acknowledgments

The authors wish to acknowledge the Department of Biotechnology, Govt. of India for providing financial support in the form of Programme Support for research and development in Agricultural Biotechnology at G.B. Pant University of Agriculture and Technology, Pantnagar (Grant No. BT/PR7849/AGR/02/374/2006). The first author was supported by fellowship from DBT, India during the project programme. The authors thank the All India Co-ordinated Small Millets Improvement Project, ICAR, UAS, GKVK, Bangalore for providing the seed samples of germplasm analysed in present study. We are highly thankful to Dr. T. Mohapatra for his kind academic inputs in data analysis and interpretation of data.

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  1. Department of Molecular Biology and Genetic Engineering, G.B. Pant University of Agriculture and Technology, Pantnagar, 263145, India

    Preety Panwar, R. K. Saini, Netrapal Sharma, Dinesh Yadav & Anil Kumar

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  1. Preety Panwar
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  2. R. K. Saini
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Correspondence to Anil Kumar.

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Panwar, P., Saini, R.K., Sharma, N. et al. Efficiency of RAPD, SSR and Cytochrome P450 gene based markers in accessing genetic variability amongst finger millet (Eleusine coracana) accessions. Mol Biol Rep 37, 4075–4082 (2010). https://doi.org/10.1007/s11033-010-0067-5

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