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A gDNA Microarray for Genotyping Salvia Species

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Abstract

Salvia is an important genus from the Lamiaceae with approximately 1,000 species. This genus is distributed globally and cultivated for ornamental, culinary, and medicinal uses. We report the construction of the first fingerprinting array for Salvia species enriched with polymorphic and divergent DNA sequences and demonstrate the potential of this array for fingerprinting several economically important members of this genus. In order to generate the Salvia subtracted diversity array (SDA) a suppression subtractive hybridization (SSH) was performed between a pool of Salvia species and a pool of angiosperms and non-angiosperms to selectively isolate Salvia-specific sequences. A total of 285-subtracted genomic DNA (gDNA) fragments were amplified and arrayed. DNA fingerprints were obtained for fifteen Salvia genotypes including three that were not part of the original subtraction pool. Hierarchical cluster analysis indicated that the Salvia-specific SDA was capable of differentiating S. officinalis and S. miltiorrhiza from their closely related species and was also able to reveal genetic relationships consistent with geographical origins. In addition, this approach was capable of isolating highly polymorphic sequences from chloroplast and nuclear DNA without preliminary sequence information. Therefore, SDA is a powerful technique for fingerprinting non-model plants and for identifying new polymorphic loci that may be developed as potential molecular markers.

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Acknowledgments

The authors gratefully acknowledge the support from the Rural Industries Research and Development Corporation, RMIT University and the Australian Postgraduate Scholarship awarded to Alexandra Olarte. We acknowledge the technical support from A/Prof. Reg Lehmann from MediHerb Australia and Claudia Salazar for their assistance with the graphics in this study.

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Authors and Affiliations

  1. Health Innovations Research Institute, School of Applied Sciences, RMIT University, Melbourne, VIC, 3000, Australia

    Alexandra Olarte, Nitin Mantri, Gregory Nugent & Edwin Pang

  2. Health Innovations Research Institute, School of Health Sciences, RMIT University, Melbourne, VIC, 3000, Australia

    Chun Guang Li & Charlie Xue

  3. Southern Cross Plant Science and Medicinal Plant Herbarium, Southern Cross University, Lismore, NSW, 2480, Australia

    Hans Wohlmuth

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  1. Alexandra Olarte
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  2. Nitin Mantri
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Correspondence to Nitin Mantri.

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Olarte, A., Mantri, N., Nugent, G. et al. A gDNA Microarray for Genotyping Salvia Species. Mol Biotechnol 54, 770–783 (2013). https://doi.org/10.1007/s12033-012-9625-5

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