Identification of native and invasive subspecies of common reed (Phragmites australis) in Alberta, Canada, by RNase-H-dependent PCR

Abstract

Colonies of the invasive subspecies of common reed (Phragmites australis (Cav.) Trin. ex Steud) were found in Alberta in 2016. To facilitate the rapid subspecies identification necessary to support management of this invasive subspecies, a simple and time-saving protocol was developed to differentiate the invasive from the native subspecies. This protocol was based on the RNase-H-dependent PCR (rhPCR) technique, which utilizes the DNA polymorphism found in two chloroplast DNA regions. Compared with the widely used restriction fragment length polymorphism (RFLP) protocol, the rhPCR had the same level of accuracy for subspecies identification, but is simpler and less time-consuming. Using both the rhPCR and RFLP techniques, 27 samples of P. australis derived from 21 colonies in nine Alberta counties were tested to determine their subspecies identity. Fourteen colonies were identified as invasive subspecies, and seven were native subspecies. Based on these preliminary data, we concluded that the invasive subspecies has established across Alberta, and now may be more common than the native subspecies. In addition, RFLP results confirmed that the rhPCR was accurate and could be used independently to identify P. australis subspecies in future studies.