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

Holmes GD, Hall NE, Gendall AR, Boon PI, James EA - Front Plant Sci (2016)

Bottom Line: Ongoing environmental changes have resulted in the decline of this species in many areas and invasive expansion in others.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.

View Article: PubMed Central - PubMed

Affiliation: Royal Botanic Gardens Victoria, Melbourne VIC, Australia.

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.

No MeSH data available.


Related in: MedlinePlus

Source sites of Phragmites australis clones from the Gippsland Lakes, south-eastern Australia used in this study. Population codes are as listed in Table 1. The artificial opening of the lake system to Bass Strait is immediately south-west of the Lakes Entrance township while blue lines indicate inflowing rivers.
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Figure 1: Source sites of Phragmites australis clones from the Gippsland Lakes, south-eastern Australia used in this study. Population codes are as listed in Table 1. The artificial opening of the lake system to Bass Strait is immediately south-west of the Lakes Entrance township while blue lines indicate inflowing rivers.

Mentions: Sections of rhizome from six P. australis clones were harvested in September 2014 from several sites across the Gippsland Lakes area of south-eastern Australia (Figure 1; Table 1). These sites are described in Boon et al. (2015c). Rhizome sections were stored at 4°C in damp hessian bags until potted out. The surface-water salinities of the sites (Table 1) were determined using the total dissolved solids (TDS) function of a TPS WP-81 water-quality meter with a k = 10 temperature-compensating conductivity sensor (TPS Instruments, Brisbane, QLD, Australia). Although once-off ‘spot’ measurements, the surface-water salinities measured at each site agreed closely with long-term spatial patterns of water salinity across the Gippsland Lakes reported by Webster et al. (2001). To check whether P. australis plants could persist in apparently saline environments by accessing shallow lenses of fresh ground water, we also measured interstitial water salinity at various depths in the sediment at each site. These data will be reported in a separate paper. In summary, there was a good correlation (r2 = 0.41, n = 37) between salinity in surface water and interstitial water across the sites, strongly suggesting that the plants from saline sites were not subsidized by ground water lower in salinity than the overlaying water column (Boon et al., 2015c). Rhizomes of each clone were divided into short sections (typically 5-10 cm) and planted into 150 mm diameter plastic pots containing commercial potting medium with no added nutrients (Richgro All-purpose Potting mix, Richgro Garden Products, Jandakot, WA, Australia). Each pot was placed in a 9 L plastic bucket and positioned randomly in an outdoor trial plot at Victoria University, Werribee (Melbourne) in mid-October 2014. Six replicates of each of the six clones were prepared for each salinity treatment. During a preliminary four-week plant establishment phase, pots were kept wet by maintaining 1–2 cm of mains-sourced fresh water (<0.1 g L-1 TDS) in each bucket. This initial low water level was required to facilitate the development of the young plants (Doug Frood, pers. comm.). After the establishment period, water levels were increased to the height of the potting medium (i.e., the plants were inundated but not fully flooded). Nine weeks after planting, the water in each pot was replaced with mains water containing a dissolved salt mix of Oceanpure synthetic sea salt OP-50 (Commodity Axis, Camarillo, CA, USA) in a progression of 0, 2, 4, 8, or 16 g L-1. The highest salt concentration applied was approximately half of that found in typical sea water. At the same time, 5 g of slow-release fertilizer (Osmocote all-purpose, Scotts Australia, Bella Vista, NSW, Australia; 13.4% N, 1.0% P, 5.2% K, 7.5% S, 2.2% Ca, 0.3% Mg, 1.7% Fe, plus trace elements) was added to each pot. Water levels within each bucket were maintained by topping up with fresh water every two to three days and the water completely replaced with fresh solutions of the appropriate salinity every two weeks.


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

Holmes GD, Hall NE, Gendall AR, Boon PI, James EA - Front Plant Sci (2016)

Source sites of Phragmites australis clones from the Gippsland Lakes, south-eastern Australia used in this study. Population codes are as listed in Table 1. The artificial opening of the lake system to Bass Strait is immediately south-west of the Lakes Entrance township while blue lines indicate inflowing rivers.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4829608&req=5

Figure 1: Source sites of Phragmites australis clones from the Gippsland Lakes, south-eastern Australia used in this study. Population codes are as listed in Table 1. The artificial opening of the lake system to Bass Strait is immediately south-west of the Lakes Entrance township while blue lines indicate inflowing rivers.
Mentions: Sections of rhizome from six P. australis clones were harvested in September 2014 from several sites across the Gippsland Lakes area of south-eastern Australia (Figure 1; Table 1). These sites are described in Boon et al. (2015c). Rhizome sections were stored at 4°C in damp hessian bags until potted out. The surface-water salinities of the sites (Table 1) were determined using the total dissolved solids (TDS) function of a TPS WP-81 water-quality meter with a k = 10 temperature-compensating conductivity sensor (TPS Instruments, Brisbane, QLD, Australia). Although once-off ‘spot’ measurements, the surface-water salinities measured at each site agreed closely with long-term spatial patterns of water salinity across the Gippsland Lakes reported by Webster et al. (2001). To check whether P. australis plants could persist in apparently saline environments by accessing shallow lenses of fresh ground water, we also measured interstitial water salinity at various depths in the sediment at each site. These data will be reported in a separate paper. In summary, there was a good correlation (r2 = 0.41, n = 37) between salinity in surface water and interstitial water across the sites, strongly suggesting that the plants from saline sites were not subsidized by ground water lower in salinity than the overlaying water column (Boon et al., 2015c). Rhizomes of each clone were divided into short sections (typically 5-10 cm) and planted into 150 mm diameter plastic pots containing commercial potting medium with no added nutrients (Richgro All-purpose Potting mix, Richgro Garden Products, Jandakot, WA, Australia). Each pot was placed in a 9 L plastic bucket and positioned randomly in an outdoor trial plot at Victoria University, Werribee (Melbourne) in mid-October 2014. Six replicates of each of the six clones were prepared for each salinity treatment. During a preliminary four-week plant establishment phase, pots were kept wet by maintaining 1–2 cm of mains-sourced fresh water (<0.1 g L-1 TDS) in each bucket. This initial low water level was required to facilitate the development of the young plants (Doug Frood, pers. comm.). After the establishment period, water levels were increased to the height of the potting medium (i.e., the plants were inundated but not fully flooded). Nine weeks after planting, the water in each pot was replaced with mains water containing a dissolved salt mix of Oceanpure synthetic sea salt OP-50 (Commodity Axis, Camarillo, CA, USA) in a progression of 0, 2, 4, 8, or 16 g L-1. The highest salt concentration applied was approximately half of that found in typical sea water. At the same time, 5 g of slow-release fertilizer (Osmocote all-purpose, Scotts Australia, Bella Vista, NSW, Australia; 13.4% N, 1.0% P, 5.2% K, 7.5% S, 2.2% Ca, 0.3% Mg, 1.7% Fe, plus trace elements) was added to each pot. Water levels within each bucket were maintained by topping up with fresh water every two to three days and the water completely replaced with fresh solutions of the appropriate salinity every two weeks.

Bottom Line: Ongoing environmental changes have resulted in the decline of this species in many areas and invasive expansion in others.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.

View Article: PubMed Central - PubMed

Affiliation: Royal Botanic Gardens Victoria, Melbourne VIC, Australia.

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.

No MeSH data available.


Related in: MedlinePlus