Uncovering the Water Stress Response of Reed Canary Grass (Phalaris arundinacea) from Differential Expression of the Reference Transcriptome

The collaborative FP7 EU project GrassMargins explores the potential of perennial grasses as bioenergy crops on marginal lands. These lands are likely to give poor or unreliable yields for food crops to the farmer. Perennial energy crops would avoid direct competition with food production on these lands, and provide added benefits such as protection from erosion, better nutrient efficiency, and a low input cropping system. The C3 grass Phalaris arundinacea has great potential applications as a crop on poor soils for bioenergy, forage, and phytoremediation. As under such conditions the plants are likely to encounter various abiotic stresses, we explored the plant response to water stress using RNA-Seq experiments.

During the water stress trial, physiological measurements were taken to monitor the extent of stress the plants were experiencing. Leaf samples were taken for later RNA analysis in RNA-Seq experiments based on the Illumina HiSeq 2000 system. A Phalaris reference transcriptome of approximately 18000 transcripts has been constructed from a normalized RNA-Seq library sequenced on the Roche 454 platform. Reads were mapped onto this reference and transcript read counts were analysed for differential expression.

We identified differentially expressed Phalaris sequences between various stress treatments, control conditions, and genotypes by applying the novel algorithm RoDEO, see http://researcher.watson.ibm.com/project/5513. RoDEO employs a non-parametric method assessing stable as well as differentially expressed genes, and is particularly resilient when dealing with a limited number of replicates. RoDEO is discussed in more detail at the PAG XXIII Gene Expression Analysis Workshop.