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Background  The root of  Boehmeria  spp (ramie) is a hepatoprotective Chinese herbal medicine. Medicinal properties vary between  Boehmeria nivea  var.  nivea  and  Boehmeria nivea  var.  tenacissima , which are local species found in Taiwan. As commercial preparations may use either species, there is a need for a rapid and simple assay to identify variants for quality control.    Methods  Four methods were developed and tested for their applicability in differentiating the two species. These methods were random amplified polymorphic DNA (RAPD); sequence characterized amplified regions (SCAR); single nucleotide polymorphisms (SNP) and cleaved amplified polymorphic sequences (CAPS).    Results  Three RAPD markers were developed that produced unique bands in  B. nivea  var.  tenacissima  and  B. nivea  var.  nivea . Based on sequenced RAPD bands, one SCAR marker was developed that produced a single DNA band in  B. nivea  var.  nivea . Two SNP markers differentiated between  B. nivea  var.  nivea  and  B. nivea  var.  tenacissima  based on single nucleotide substitutions. A pair of CAPS oligonucleotides was developed by amplifying a 0.55-kb DNA fragment that exhibited species-specific digestion patterns with restriction enzymes  Alf  III and  Nde  I. Consistent results were obtained with all the four markers on all tested  Boehmeria  lines.    Conclusion  The present study demonstrates the use of the RAPD, SCAR, SNP and CAPS markers for rapid identification of two closely related  Boehmeria  species.

Development and validation of molecular markers for characterization of Boehmeria nivea var. nivea and Boehmeria nivea var. tenacissima