Deciphering salt-responsive NB-ARC genes in rice transcriptomic data: A bioinformatics approach with gene expression validation

The salt-tolerant rice can be developed by finding exotic germplasm that possesses tolerant traits through a series of selections. Determination of functional marker genes is essential to perform a concise and fast method for selection. This research focuses on pinpointing candidate genes suitable for functional markers. We conducted an in silico analysis of the NB-ARC gene family across three transcriptomic datasets of rice under salt stress. This included examining cis-regulatory elements in the promoter regions, protein domains/motifs, and predicting subcellular localizations to narrow down our gene selection. From 19 different rice varieties evaluated under salt stress, we identified the most tolerant and susceptible ones for further investigation. Two varieties with contrasting tolerance levels were selected for validation. Real-time polymerase chain reaction was employed to determine the gene expression for validation. Among the 139 NB-ARC genes studied, 28 exhibited differential expression in all 3 transcriptome datasets. The candidate genes LOC_Os04g43440, LOC_Os11g15700, and LOC_Os11g39310 were selected, primarily based on their predicted subcellular localization within the nucleus. Out of 19 varieties, Inpari 35, FL478, and Siak Raya are considered salt-tolerant varieties. Notably, among the three salt-tolerant varieties – Inpari 35, FL478, and Siak Raya – Inpari 35 emerged as the most resilient, displaying robust growth parameters during the seedling stage. Conversely, IR29 was found to be the most susceptible. Expression analysis revealed that LOC_Os04g43440 in Inpari 35 showed increased expression at 24 h of salt stress exposure, while LOC_Os11g15700 exhibited upregulation after 48 h. Remarkably, LOC_Os11g39310 displayed a remarkable 21.78-fold increase at 24 h, followed by a decline at 48 h. LOC_Os11g39310 stands out as a promising marker essential for guiding selection in breeding programs aimed at cultivating salt-tolerant rice varieties.