Transcriptomic Analysis of Short-Term Salt-Stress Response in Mega Hybrid Rice Seedlings

Salinity is a major abiotic stressor that leads to productivity losses in rice (Oryza sativa L.). In this study, transcriptome profiling and heterosis-related genes were analyzed by ribonucleic acid sequencing (RNA-Seq) in seedlings of a mega rice hybrid, Liang-You-Pei-Jiu (LYP9), and its two parents 93–11 and Pei-ai64s (PA64s), under control and two different salinity levels, where we found 8292, 8037, and 631 salt-induced differentially expressed genes (DEGs), respectively. Heterosis-related DEGs were obtained higher after 14 days of salt treatment than after 7 days. There were 631 and 4237 salt-induced DEGs related to heterosis under 7-day and 14-day salt stresses, respectively. Gene functional classification showed the expression of genes involved in photosynthesis activity after 7-day stress treatment, and in metabolic and catabolic activity after 14 days. In addition, we correlated the concurrence of an expression of DEGs for the bHLH transcription factor and a shoot length/salinity-related quantitative trait locus qSL7 that we fine-mapped previously, providing a confirmed case of heterosis-related genes. This experiment reveals the transcriptomic divergence of the rice F1 hybrid and its parental lines under control and salt stress state, and enlightens about the significant molecular mechanisms developed over time in response to salt stress.