DNA barcoding for identification of water-onion (Crinum thaianum), an endangered species in Thailand

Crinum thaianum, also known as water-onion, has been widely used as an ornamental plant in fish tanks and aquariums, an indicator of water quality in natural water sources, and a component in some skincare products.Unfortunately, it is now listed as an endangered species because of the ongoing reduction in its natural area due to habitat destruction, a result of flood protection measures and illegal harvesting for exportation and domestic consumption.This study reported for the first time the use of DNA barcoding, a molecular technique for species-specific identification of this endangered species.Four DNA barcoding regions in six water-onion samples were studied, i.e., the chloroplast-encoded maturase K (matK), ribulose-bisphosphate carboxylase large subunit (rbcL) and transfer RNAhistidine (trnH)-photosystem II protein D1 (psbA) intergenic spacer, and the nuclear-encoded the internal transcribed spacer of ribosomal DNA (ITS of rDNA).The six water-onion samples were collected from different locations and 13 other Crinum species.The results showed a high genetic similarity among the six water-onion samples.Four nucleotide substitutions were identified in two different regions (trnH-psbA and ITS) in the 6 water-onion samples.Although all 4 regions could be used to distinguish the species from each other, the ITS of rDNA region gave the best result for Crinum species discrimination, based on the bootstrap value of the phylogenetic tree and the optimum genetic distance length.This technique could be an efficient tool for species-specific identification and for supporting conservation practices in the future.