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Use of SSR, RAPD markers and protein profiles based analysis to differentiate Eleusine coracana genotypes differing in their protein content

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Abstract

Fifty-two genotypes of Eleusine coracana collected from Uttarakhand hills were subjected to simple sequence repeat (SSR), random amplified polymorphic DNA (RAPD)-PCR and protein profiling analysis to investigate the variation in protein content. The main objective of the present study was to detect variability among E. coracana and also assess the discriminating ability of these three molecular methods. A total of 21 RAPD and 24 SSR primers were assayed for their specificity in detecting genetic variability in E. coracana, of which 20 RAPD and 21 SSR primers were highly reproducible and were found suitable for use in PCR analysis. Assessing genetic diversity among E. coracana genotypes by RAPD-PCR using 20 polymorphic primers yielded 56 different RAPD markers which clustered the genotypes into different groups on the basis of protein content. Similarly, SSR-PCR with 21 polymorphic primers clustered the genotypes into different groups. On the other hand, biochemical typing of E. coracana using whole seed proteins generated profiles that showed no major difference indicating the technique to be not useful in typing genotypes of this crop. However, a few of the genotypes showed the presence of a unique band of 32 kDa that needs to be further investigated to understand the role of the protein from nutritional point of view, if any. In the present study, significant negative correlation (r = −0.69*) was found between the protein and calcium content of finger millet genotypes. Sodium Dodecyl Sulphate Polyacrylamide Gel Electrophoresis based seed storage proteins generated profiles showed no major differences in banding pattern among 52 finger millet genotypes while quantitative estimation of seed storage protein fractions using Lowry method revealed that glutelin was highest followed by prolamin, globulin and albumin.

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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 authors thank the, Ranichauri Hill Campus G.B. Pant University of Agriculture and Technology for providing the seed samples of the germplasm analyzed in present study.

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  1. Department of Molecular Biology and Genetic Engineering, College of Basic Sciences & Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar, 263 145, India

    Anil Kumar, Netrapal Sharma & Preety Panwar

  2. Vivekanad Parvatiya Krishi Anusandhan Kendra, Almora, India

    Arun K. Gupta

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Correspondence to Anil Kumar.

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Kumar, A., Sharma, N., Panwar, P. et al. Use of SSR, RAPD markers and protein profiles based analysis to differentiate Eleusine coracana genotypes differing in their protein content. Mol Biol Rep 39, 4949–4960 (2012). https://doi.org/10.1007/s11033-011-1291-3

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