to Sodium Chloride Salinity Using High Throughput RNA Sequencing

Salinity and drought stress are the primary cause of crop losses worldwide. In saline sodic soils sodium chloride (NaCl) disrupts normal plant growth and development. The complex interactions of plant systems with abiotic stress have made RNA sequencing a more holistic and appealing approach to study transcriptome level responses in a single cell and/or tissue. Our objective was to determine the leaf and root transcriptome response of Petunia ‘Mitchell diploid’ to acute NaCl stress. Petunia plants were established in hydroponic containers in controlled environment chambers. At experiment initiation the nutrient solution was amended with 150 mM NaCl (salt treatment) or not amended with NaCl (control). Leaf and root tissue samples were taken 0, 6, 24, and 48 h after experiment initiation. Initially we determined the Petunia transcriptome response to NaCl stress by Illumina sequencing of 0, 6, and 24 h leaf samples followed by a de novo assembly of our 196 million reads with Trinity software. Using our reference transcriptome we identified more than 7,000 genes that were differentially expressed within 24 h of acute NaCl stress in leaf. The proposed transcriptome can also be used as an excellent tool for biological and bioinformatics in the absence of an available Petunia genome and it is available at the SOL Genomics Network (SGN) http://solgenomics.net. Genes related to regulation of reactive oxygen species, transport, and signal transduction as well as novel and undescribed transcripts were among those most differentially expressed in response to salt stress. Gene Ontology analyses indicated that much of the NaCl damage happened at 24 h inducing genotoxicity, affecting transport and organelles due to the high concentration of Na⁺ ions. Work is ongoing to examine the root transcriptome response. The candidate genes identified in this study can be applied as markers for breeding or to genetically engineer plants to enhance salt tolerance. The data from this work will enable researchers to perform accurate downstream analysis to further understand the effect of salt stress in both roots and leaves.