The transcriptome landscape of Kumrogarh, a unique rice landrace showing the simultaneous presence of Sub1 and SK loci for submergence tolerance.

Abstract

To decipher the molecular mechanism behind submergence tolerance in a typical rice genotype (var. Kumrogarh), leaf transcriptome analysis was performed on submerged plant tissue with 7 and 14 days of induced submergence, followed by cataloguing the differentially expressed transcripts. Subsequent bioinformatics analysis identified 5,267 differentially expressed genes (DEGs), of which 2,657 were upregulated and 2,610 were downregulated in four comparative combinations: T7-C7, T14-T7, T14-T7, and C14-C7. A group of 41 co-expressed genes was found across all sets, while 1427, 558 and 83 transcripts were uniquely expressed in the T7-C7, T14-T7, and C14-C7 combinations, respectively. Constructed Ven diagram showed that 1428, 65, and 44 transcripts were commonly expressed in the paired combinations "T7-C7" and "T14-T7", "C14-C7" and "T7-C7", and "C14-C7" and "T14-T7". Gene ontology study functionally categorized the DEGs into molecular functions, biological processes, and cellular components. Additionally, nine transcription factor families were identified, including MYB, WRKY, bZIP, bHLH, SET domain, NAC domain, C2H2 zinc finger, E2F, and HSF, along with a set of differentially regulated signalling genes. Twelve genes related to submergence adaptation were selected for final validation through quantitative real-time PCR-based expression analysis, which demonstrated a strong association with a coefficient (R ² = 0.716) after aligning with the RNA-Seq data. Derived results showed upregulation of gibberellin receptor GID1L2 (LOC_Os02g35940.1), ethylene-responsive element-binding protein (LOC_Os06g08360.1), glyceraldehyde-3-phosphate dehydrogenase (LOC_Os04g38600.1), decarboxylase (LOC_Os08g04540.1), sucrose synthase (LOC_Os03g22120.1), aldehyde dehydrogenase (LOC_Os12g07810.1), endonuclease/exonuclease/phosphatase family domain-containing protein (LOC_Os01g08780.1), polygalacturonase inhibitor 1 precursor (LOC_Os07g38130.1), transmembrane amino acid transporter protein (LOC_Os01g41420.1), and SAM-dependent carboxyl methyltransferase (LOC_Os02g48770.1). This study provides a comprehensive profile of leaf transcriptomics in a traditionally tall-type rice landrace containing both submergence-tolerant Sub1 and SK alleles, highlighting an area of research that remains largely unexplored. These remarkable findings have driven this investigation to decipher the interplay among these key genetic factors by hypothesizing a model leading to the development of a genetic network associated with improved survival under prolonged deep submergence of such a unique rice genotype.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-025-04277-7.