Evaluation of Wheat Gene Expression Under Waterlogging Conditions Using RNA-Seq Analysis.

Waterlogging is a major constraint to global wheat production resulting from oxygen depletion due to soil saturation. Hypoxia leads to pH soil modification and subsequent accumulation of microelements such as iron, aluminum and manganese. Moreover, physiological processes such as photosynthesis, respiration and carbohydrate metabolism are disrupted resulting in an energy crisis and ultimately losses in total yield production. The identification of genes and genome regions associated with tolerance to soil waterlogging is necessary in order to better understand and improve this quantitative trait. Similarly, a better understanding of the biological cross-talk of different stress pathways implicated during waterlogging, such as micro-elemental toxicity and salt stress, are required for a holistic approach to crop improvement. The goal of this study was to evaluate the wheat transcriptome response under waterlogged and non-waterlogged conditions. Two adapted soft red winter wheat cultivars, PIO26R61 and AGS2000 were subjected to waterlogging stress 24 days after sowing in a growth chamber and plant leaf tissues were collected after 24 hours of stress imposition. After total RNA isolation, integrity and quantification was performed using the Bio-rad Experion System. RNA-seq analysis was carried out using 2x100 bp paired-ends sequencing on the HiSeq2500 platform. Around 300 million pair-end reads were developed, covering approximately 16 Gb of the wheat transcriptome. This data is currently being used for analysis of differential changes in the wheat transcriptome under waterlogging stress, SNP identification, splicing events and gene structure and plant response pathway dissection.