Transcriptome Characterization and Expression Analyses in Salt-Tolerant and Salt-Sensitive Cultivars of Oryza sativa after Exposure to Salt Stress

Rice is a major cereal crop that is responsible for feeding the world population. Rice varieties must be developed and improved to provide high quality grain and yield in addition to being tolerant and resistant to abiotic and biotic stresses. Salt stress is an abiotic stress that ultimately reduces the grain yield and quality in rice. To better understand the transcriptional regulation a rice undergoes during salt exposure, we constructed genome-wide transcriptomes of two Oryza sativa Indica group varieties under salt stress; the natural salt-tolerant, Pokkali and the salt-sensitive breeding line, IR29.

More than 105,000 transcripts represent the de novo transcriptome assemblies of IR29 and Pokkali. The assemblies successfully mapped to ~99% of the Japonica genome, but only ~90% of the currently available gene models. Over five time points (1, 2, 5, 10, 24 hours post salt exposure) IR29 had 6,595 unique transcripts differentially expressed whereas Pokkali had 7,209 in response to salt stress. Sequence reads were aligned to the reference Japonica genome and led to the identification of ~190,000 single nucleotide polymorphisms and ~40,000 simple sequence repeat (SSR) sites that have potential as genetic markers.

In collaboration with the Gramene database and EBI Gene Expression ATLAS, this project’s gene expression data is available for public access via direct database queries as well as using ATLAS widgets and Webservices. The Expression Atlas provides information on gene expression profiles from RNA-Seq and Microarray experiments using standardized protocols.