Transcriptome Study of Rice Roots Status under High Alkaline Stress at Seedling Stage

Alkaline stress is harmful to plant growth and development, it would induce endogenic ionic concentration and osmotic pressure, trigger relevant genes expression with transcription factor binding, signal transduction and hormone synthesis. In this study, we selected "Dongdao-4", a salt-alkali stress tolerance rice cultivar, which was subjected to extreme high pH (pH = 11.5) alkaline stress at the trefoil stage for 7 days. Using the RNA-seq technology, we analyzed variations in genes expressed between the fourth and the seventh day of treatment. The number of differentially expressed genes (DEGs) was 3804, 2534, 207 and 3276 for fourth day-stress vs. fourth day-control, seventh day-stress vs. seventh day-control, seventh day-control vs. fourth day-control and seventh day-stress vs. fourth day-stress, respectively. Gene ontology (GO) results revealed that DEGs were mainly enriched in apoptotic process, electron carrier activity, receptor activity, molecular transducer activity. The Kyoto Encyclopedia of Genes and Genomes (KEGG) results implied that DEGs were mainly enriched in metabolic pathways, biosynthesis of secondary metabolites. In particular, DEGs were distributed in genes related to the transcription factor, leucine rich repeats (LRRs) and hormones. We also report here for the first-time identification of 125 genes specifically expressed during the alkaline stress. Our results provided important information assisting with the exploration of the molecular mechanisms of rice plants subjected to high pH condition and can facilitate rice abiotic tolerance breeding.