Establishment of Novel Simple Sequence Repeat Markers in Phragmites australis and Application in Wetlands of Nanhui Dongtan, Shanghai
by
,
Shaozu Ma
1,†, 
Yifei Shen
1,†,
Min Li
2,
Ruitong Jiang
1,
Luyi Cai
1,
Tingting Wu
1,
Linxi Gao
1,
Meiqin Wu
1,* and
Peimin He
1,* 1
College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai 201306, China
2
Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
*
Authors to whom correspondence should be addressed.
†
These authors equally contributed to this work.
Biology 2025, 14(4), 356; https://doi.org/10.3390/biology14040356
Submission received: 24 February 2025
/
Revised: 21 March 2025
/
Accepted: 25 March 2025
/
Published: 28 March 2025
(This article belongs to the Special Issue Global Fisheries Resources, Fisheries, and Carbon-Sink Fisheries)
Simple Summary
Common reeds (Phragmites australis), vital wetland plants, face challenges from environmental changes. To understand how coastal reeds adapt, we created 15 genetic markers to study four reed groups in Shanghai’s wetlands. Results revealed high genetic diversity overall, but one group (DD) showed lower diversity, likely due to salt stress and competition from invasive Spartina alterniflora. The reeds split into two clusters, shaped by both geography and environmental conditions, yet maintained some genetic mixing. This work helps identify resilient reed populations, supports conservation efforts to sustain reeds in changing environments and informs strategies to protect wetlands, which are crucial for biodiversity and coastal health.
Abstract
Common reed (Phragmites australis) is a widely distributed perennial herb of high ecological significance in wetlands worldwide. This research developed 15 SSR markers through whole-genome sequencing and assessed the genetic diversity across four representative reed populations (DB, JPDP, YJRHK, DD) in the coastal wetlands of Nanhui Dongtan, Shanghai. A total of 113.5 alleles (Na) were detected, averaging 7.567 alleles per locus, with an expected heterozygosity (He) of 0.690 and a Shannon diversity index (I) of 1.485. Polymorphism information content (PIC) values (ranging from 0.577 to 0.872, average 0.770) indicated strong resolution power for discriminating subtle genetic differences across populations. Among the four populations, JPDP displayed the highest genetic diversity parameters (Na = 12.667; I = 2.020), whereas DD exhibited the lowest, consistent with intensive demographic screening under saline stress and competition from Spartina alterniflora. Bayesian clustering analysis (STRUCTURE) and UPGMA dendrograms further revealed that the four populations split into two major subgroups, which underlines both the influence of geographic and ecological factors on genetic structuring and the persistence of gene flow. In sum, the newly developed SSR markers demonstrated robustness and sensitivity in elucidating the overall high genetic diversity but moderate genetic differentiation of reed populations in Nanhui Dongtan. These findings not only offer insights into local adaptation mechanisms in coastal wetlands but also provide a technical basis for the conservation and utilization of P. australis.
