DNA assays for genetic discrimination of three Phragmites australis subspecies in the United States

Abstract

Abstract Premise To genetically discriminate subspecies of the common reed (Phragmites australis), we developed real‐time quantitative (qPCR) assays for identifying P. australis subsp. americanus, P. australis subsp. australis, and P. australis subsp. berlandieri. Methods and Results Utilizing study‐generated chloroplast DNA sequences, we developed three novel qPCR assays. Assays were verified on individuals of each subspecies and against two non‐target species, Arundo donax and Phalaris arundinacea. One assay amplifies only P. australis subsp. americanus, one amplifies P. australis subsp. australis and/or P. australis subsp. berlandieri, and one amplifies P. australis subsp. americanus and/or P. australis subsp. australis. This protocol enhances currently available rapid identification methods by providing genetic discrimination of all three subspecies. Conclusions The newly developed assays were validated using P. australis samples from across the United States. Application of these assays outside of this geographic range should be preceded by additional testing.

Keywords

• aquatic invasive species
• chloroplast genome sequencing
• environmental genetics
• hydrolysis probe real‐time quantitative PCR
• plant identification