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

Denise L Lindsay; Xin Guan; Nathan E Harms; James T Cronin; Laura A Meyerson; Richard F Lance

doi:10.1002/aps3.11512

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

Appl Plant Sci. 2023 Mar 8;11(2):e11512. doi: 10.1002/aps3.11512. eCollection 2023 Mar-Apr.

Authors

Denise L Lindsay¹, Xin Guan^{2

3}, Nathan E Harms¹, James T Cronin⁴, Laura A Meyerson⁵, Richard F Lance¹

Affiliations

¹ United States Army Engineer Research and Development Center Environmental Laboratory Vicksburg Mississippi 39180 USA.
² Bennett Aerospace Vicksburg Mississippi 39180 USA.
³ Present address: ModernaTX, Moderna Technology Center Norwood Maryland USA.
⁴ Louisiana State University Baton Rouge Louisiana 70803 USA.
⁵ University of Rhode Island Kingston Rhode Island 02881 USA.

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.

© 2023 The Authors. Applications in Plant Sciences published by Wiley Periodicals LLC on behalf of Botanical Society of America. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.