Transcriptome sequencing of the roots of RPY geng (japonica) and Chao 2R (indica) at 2-week seedlings under salt stress

Rice (Oryza sativa L.) seedlings are particularly sensitive to salt stress and their growth and yield are seriously threatened by high-intensity salt stress. However, the molecular mechanism of the difference in salt tolerance between different rice varieties, especially between subspecies, is still unclear. We herein investigated differentially expressed genes (DEGs) under salt stress in contrasting rice genotypes, namely RPY geng (japonica, tolerant variety) and Chao 2R (indica, susceptible variety).Rice seedlings were grown in 96-well PCR plate as supporting materials in Yoshida solution (Coolaber, Beijing, China), 26 Celsius, with a 16/8 h light/dark photoperiod, 60% relative humidity in plant growth incubators (ZSX1500GS, Jingshen Instrument, Shanghai, China) for 14 days, and Yoshida solution was replaced every two days 12. Fourteen-day-old seedlings of RPY geng and Chao 2R were changed into 100 mM NaCl Yoshida solution for salt stress treatment (Figure S1). Then, we sampled root tissues at 0-day (0d), 3-day (3d), and 7-day (7d), respectively. Three independent biological replicates were prepared for each treatment/control group, and at least 30 seedlings with uniform growth were sampled for each biological replicate. After all samples were collected and immediately stored in liquid nitrogen for the next step of RNA extraction.