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Authors Holmes, GD; Hall, NE; Gendall, AR; Boon, PI; James, EA
Author Full Name Holmes, Gareth D.; Hall, Nathan E.; Gendall, Anthony R.; Boon, Paul I.; James, Elizabeth A.
Title Using Transcriptomics to Identify Differential Gene Expression in Response to Salinity among Australian Phragmites australis Clones
Source FRONTIERS IN PLANT SCIENCE
Language English
Document Type Article
Author Keywords clonality; common reed; differential gene expression; Phragmites australis; salinity; salt tolerance; transcriptomics
Keywords Plus K+ TRANSPORTER; SALT TOLERANCE; COMMON REED; CRYPTIC INVASION; DIVERSITY; WETLAND; STRESS; POPULATION; RESISTANCE; HAPLOTYPE
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.
Author Address [Holmes, Gareth D.; James, Elizabeth A.] Royal Bot Gardens Victoria, Melbourne, Vic, Australia; [Hall, Nathan E.] La Trobe Univ, La Trobe Inst Mol Sci, Bundoora, Vic, Australia; [Hall, Nathan E.; Gendall, Anthony R.] La Trobe Univ, AgriBio, Dept Anim Plant & Soil Sci, Bundoora, Vic, Australia; [Boon, Paul I.] Victoria Univ, Inst Sustainabil & Innovat, Footscray Pk, Vic, Australia
Reprint Address James, EA (corresponding author), Royal Bot Gardens Victoria, Melbourne, Vic, Australia.
E-mail Address elizabeth.james@rbg.vic.gov.au
ORCID Number Hall, Nathan/0000-0001-8942-0498; Gendall, Anthony/0000-0002-2255-3939
Funding Agency and Grant Number Gippsland Lakes Environmental Fund (GLEF)
Funding Text We thank Doug Frood (Pathways Bushland and Environment) for advice and help in the establishment of the plant material, Lana Civelle, and Gina Marino (Victoria University) for the maintenance of the growth trial and allowing access for sampling. Parks Victoria allowed access to source populations. Tracie Webster (DEJTR) and Stephen Doyle (La Trobe University) provided advice during cDNA library preparation. This work was funded by the Gippsland Lakes Environmental Fund (GLEF).
Times Cited 8
Total Times Cited Count (WoS, BCI, and CSCD) 8
Publisher FRONTIERS MEDIA SA
Publisher City LAUSANNE
Publisher Address AVENUE DU TRIBUNAL FEDERAL 34, LAUSANNE, CH-1015, SWITZERLAND
ISSN 1664-462X
29-Character Source Abbreviation FRONT PLANT SCI
ISO Source Abbreviation Front. Plant Sci.
Publication Date APR 13
Year Published 2016
Volume 7
Article Number 432
Digital Object Identifier (DOI) 10.3389/fpls.2016.00432
Page Count 12
Web of Science Category Plant Sciences
Subject Category Plant Sciences
Document Delivery Number DJ0DM
Unique Article Identifier WOS:000373872000001
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