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Molecular characterization of Dendrobium nobile Lindl., an endangered medicinal orchid, based on randomly amplified polymorphic DNA

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Abstract

Dendrobium nobile Lindl., is an orchid species of immense biopharmaceutical and horticultural importance. The knowledge of its existent genetic variations within wild accessions is crucial for formulation of sustainable utilization strategies. It is distributed in a large landscape area and can grow at altitudes ranging from 800 to 2,000 m. Given that Orchidaceae is one of the largest families of flowering plants, reports on their existing genetic diversity are extremely limited. Molecular study on D. nobile can provide valuable information about the genetic diversity level and genetic relatedness of this important medicinal orchid species. Knowledge of genetic structure of a species also provides resources of a species with its current feature and future evolutionary potential. The genetic structure of D. nobile from Northeast India was investigated using randomly amplified polymorphic DNA (RAPD).The PIC value of RAPD primers was 0.74 and Rp values ranged between 6.80 and 13.23. Overall the Shannon Index, Global coefficient of genetic differentiation (G ST), showed that relative genetic diversity of the populations was fairly high. However, the low value of gene flow (Nm = 0.27) was revealed by the RAPD marker. The results of analysis of molecular variance (AMOVA) revealed that variation amongst the populations was significantly higher than within the populations. A combination of UPGMA and STRUCTURE analysis was employed to estimate the genetic relationships of D. nobile germplasm; interestingly, both the methods presented similar grouping pattern with few differences. Results revealed that 60 individuals belonging to six natural populations in Northeast India were clustered into two major groups. The data represented in this study suggested that the RAPD method was a valuable tool for estimation of genetic diversity and genetic relatedness of the D. nobile germplasm. The present findings are useful outcomes for germplasm conservation and formulation of new breeding strategies for this extremely important medicinal orchid species.

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Abbreviations

PCR:

Polymerase chain reaction

RAPD:

Random amplified polymorphic DNA

PIC :

Polymorphic information content

AMOVA:

Analysis of molecular variance

Rp :

Resolving power

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Acknowledgments

This research work was supported by the Centre for Advanced Studies (CAS) in Botany, University Grants Commission (UGC), India and research grant to PB in the form of Meritorious Student Fellowship which is gratefully acknowledged. PB also acknowledges Dr. Shrawan Kumar, Dr. Santosh Kumar Sharma and Dr. Sourav Kumar Das for their technical assistance provided during the course of this study.

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Authors and Affiliations

  1. Plant Biotechnology Laboratory, Department of Botany, Centre for Advanced Studies, North-Eastern Hill University, Shillong, 793022, Meghalaya, India

    Paromik Bhattacharyya & Suman Kumaria

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  1. Paromik Bhattacharyya
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  2. Suman Kumaria
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Correspondence to Suman Kumaria.

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606_2014_1065_MOESM1_ESM.jpg

Fig. S1 The highest probability of the RAPD data was attained when samples were clustered into two groups (K = 2) as shown by the peak value of ∆K (Evanno et al., 2005). (JPEG 42 kb)

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Supplementary material 3 (DOC 33 kb)

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Bhattacharyya, P., Kumaria, S. Molecular characterization of Dendrobium nobile Lindl., an endangered medicinal orchid, based on randomly amplified polymorphic DNA. Plant Syst Evol 301, 201–210 (2015). https://doi.org/10.1007/s00606-014-1065-1

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