Using Transcriptomics to Identify Differential Gene Expression in Response to Salinity among Australian Phragmites australis Clones

Abstract

Common Reed (Phragmites australis) is a frequent component of inland and coastal wetlands in temperate zones worldwide. Ongoing environmental changes have resulted in the decline of this species in many areas and invasive expansion in others. In the Gippsland Lakes coastal waterway system in south-eastern Australia, increasing salinity is thought to have contributed to the loss of fringing P. australis reed beds leading to increased shoreline erosion. A major goal of restoration in this waterway is to address the effect of salinity by planting a genetically diverse range of salt-tolerant P. australis plants. This has prompted an interest in examining the variation in salinity tolerance among clones and the underlying basis of this variation. Transcriptomics is an approach for identifying variation in genes and their expression levels associated with the exposure of plants to environmental stressors. In this paper we present initial results of the first comparative culm transcriptome analysis of P. australis clones. After sampling plants from sites of varied surface water salinity across the Gippsland Lakes, replicates from three clones from highly saline sites (>18 g L-1 TDS) and three from low salinity sites (<6 g L-1) were grown in containers irrigated with either fresh (<0.1 g L-1) or saline water (16 g L-1). An RNA-Seq protocol was used to generate sequence data from culm tissues from the 12 samples allowing an analysis of differential gene expression. Among the key findings, we identified several genes uniquely up- or down-regulated in clones from highly saline sites when irrigated with saline water relative to clones from low salinity sites. These included the higher relative expression levels of genes associated with photosynthesis and lignan biosynthesis indicative of a greater ability of these clones to maintain growth under saline conditions. Combined with growth data from a parallel study, our data suggests local adaptation of certain clones to salinity and provides a basis for more detailed studies.

Spatial Expansion Strategy of the Clonal Modules for <i>Phragmites australis</i> and Response to Environmental Factors in an Inland River Wetland

“…A large number of studies have confirmed that salt stress mainly limits plant growth and development by osmotic stress, disturbance of cell ion balance, and ion toxicity effects [83][84][85][86][87][88]. The salt content of soil in our study was a limiting effect on the growth indexespecially the significant negative correlation between the surface salt and plant height and stem diameter for Phragmites australis (P<0.05).…”

Differentially expressed genes related to oxidoreductase activity and glutathione metabolism underlying the adaptation of Phragmites australis from the salt marsh in the Yellow River Delta, China

“…This is followed by NaCl accumulation (4–24 h), and by a restoration of osmotic homeostasis at a new ionic level by 24 h. Finally, from 24 to 72 h beyond, there is an adjustment to a steady ion balance or ion-induced damage ( Peng et al, 2014 ). Holmes et al (2016) sampled their plant materials after an 8-week salt treatment, while we sampled the materials within 12 h of salt stress, during the NaCl and ROS accumulation period.…”

Comparison of the Photosynthetic Capacity of Phragmites australis in Five Habitats in Saline‒Alkaline Wetlands

“…Some studies have shown that P. australis can regulate its genes, to some extent, to adapt to high-salinity environments. These genetic regulations include higher relative expression levels of genes associated with photosynthesis and lignan biosynthesis, indicative of a greater ability to maintain growth under saline conditions [ 24 ]. At the same time, the distribution of photosynthetically fixed C in roots and soils also changes, for example, with lower contents of photosynthetically fixed C in roots and higher contents in soil [ 25 ].…”