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Assessment of Genetic Diversity in Zingiberaceae Through Nucleotide Binding Site-Based Motif-Directed Profiling

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Abstract

Functional motif-directed profiling was performed with 15 nucleotide binding site (NBS) primer–enzyme combinations to identify and elucidate the phylogenetic relationships among 15 genotypes of the family Zingiberaceae. We retrieved 167 polymorphic bands (24.85 %), with an average of 11.13 bands per primer. Mean polymorphism rates were detected using MseI (26 %), RsaI (21 %), and AluI (28 %) as restriction enzymes. The polymorphism information content (PIC) for each NBS primer–enzyme combination ranged from 0.48 to 0.76 with a mean value of 0.65. The 38 NBS profiling markers had PIC values ranging from 0.3 to 0.6 and exhibited good power to discriminate between genotypes. Comparison of NBS profiling with microsatellite data for the same set of genotypes exhibited a correlation value of 0.78, P ≤ 0.001. Our study suggests that genetic variability assessment could be more efficient if it targeted genes that exhibit functionally relevant variation, rather than random markers.

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Acknowledgments

The authors are grateful to Prof. Manoj Ranjan Nayak, President, Siksha O Anusandhan University, for his encouragement and support.

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  1. Centre of Biotechnology, Siksha O Anusandhan University, Bhubaneswar, 751003, India

    Raj Kumar Joshi, Sujata Mohanty, Basudeba Kar & Sanghamitra Nayak

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  1. Raj Kumar Joshi
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  2. Sujata Mohanty
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  3. Basudeba Kar
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  4. Sanghamitra Nayak
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Correspondence to Raj Kumar Joshi.

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Supplementary material 1 (DOC 49 kb)

10528_2012_9507_MOESM2_ESM.tif

Supplementary material 2. Polymorphism revealed by a part of the NBS profiling gel obtained with primer NBS9 and restriction enzyme AluI for 15 zingiberaceous taxa (TIFF 229 kb)

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Joshi, R.K., Mohanty, S., Kar, B. et al. Assessment of Genetic Diversity in Zingiberaceae Through Nucleotide Binding Site-Based Motif-Directed Profiling. Biochem Genet 50, 642–656 (2012). https://doi.org/10.1007/s10528-012-9507-3

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