Integrated whole genome and transcriptome analysis reveals the molecular mechanisms for enhanced salt tolerance in an introgression line of rice

Soil salinization reduces crop productivity due to elevated osmotic stress, ionic stress, nutritional disorders, and poor physical conditions. This study explored the molecular genetic basis of salt tolerance by jointly analyzing the genetic variants and transcriptome profiles of a seedling stage salt-tolerant rice ( Oryza sativa L.) introgression line JN100 (JN) in relation to its recurrent parent Jupiter (JU) and donor Nona Bokra (NB). Four major donor segments were detected in JN on chromosomes 1, 2, and 9. While 4258, 3719, and 4241 differentially expressed genes (DEGs) were identified across all three genotypes under saline conditions, there were only 175 and 300 DEGs between JU and JN under control (C) and salt stress (T), respectively. Integration of transcriptomic and genomic sequence data detected 97, 112, and 121 DEGs in the introgressed regions of JU, JN, and NB, respectively. However, 28, 33, and 38 were unique in all three pairs, and there were only 25 DEGs in JN compared to JU under salinity stress. Among CJU-CJN and TJU-TJN, there were six common DEGs, whereas 19 and 8 DEGs were unique across the TJU-TJN and CJU-CJN pairs, respectively. The DEGs located on the introgressed regions comprise mostly transporters (CHXs, NHXs family) and ion channels, transcription factors (bZIP, NAC, and MYB family), abscisic acid (ABA) response, and calcium-mediated signaling cascade, most likely enhancing salt tolerance in JN. Our results underscore the collective contribution of a diverse array of multiple mechanisms and genes such as OsCHX15, OsNTL3/OsNAC74, OsbZIP71 , OsSIT1, OsCCA1, OsABI5, and OsZIFL2 , suggesting the pyramiding approach to accomplish a higher level of salt tolerance in rice. • Whole genome and RNA-Seq data of a salt-tolerant rice introgression line (IL) were integrated. • Four major introgressions in three chromosomes and 25 differentially expressed genes (DEGs) identified under salt stress. • Collective contribution of transporters, TFs, ABA response, and calcium-signaling genes needed for salt tolerance. • Candidate genes identified were OsCHX15, OsNAC74, OsbZIP71 , OsSIT1, OsCCA1, OsABI5, and OsZIFL2. • A pyramiding approach will be appropriate to accomplish a higher level of salt tolerance in rice.