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<p>Small open reading frames (sORFs) represent an underexplored source of functional peptides in plant genomes. This study aimed to identify drought-responsive sORFs in <i>Oryza sativa</i> subsp. <i>indica</i> and to evaluate their potential roles in drought stress adaptation, addressing the question of whether sORFs contribute to physiological and molecular drought tolerance mechanisms in rice. Stress-responsive sORFs were identified through <i>in silico</i> prediction combined with transcriptomic analysis across multiple abiotic stress conditions. Functional annotation was performed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses, and signal peptide prediction was used to infer potential secretory functions. Three <i>O. sativa</i> subsp. <i>indica</i> rice cultivars (MR 219, MR 220, and MR 297) were subjected to drought stress for physiological assessment. Oxidative stress markers and antioxidant gene expression were analyzed, and candidate sORF expression was validated using RT-PCR. Differentially expressed sORFs (DE sORFs) were significantly enriched in GO terms related to structural molecule activity and binding, while KEGG analysis highlighted MAPK signaling and antioxidant defense pathways. Several sORFs were predicted to encode secretory peptides. Among the tested cultivars, MR 297 showed enhanced drought tolerance with reduced leaf rolling and stable chlorophyll content, whereas MR 219 exhibited higher oxidative damage, indicated by elevated malondialdehyde and proline levels. Antioxidant genes were strongly upregulated under drought stress, particularly in MR 219. Expression of selected sORFs (<i>OsisORF_0050</i>, <i>OsisORF_3394</i>, and <i>OsisORF_3007</i>) was confirmed under drought conditions. This study reveals sORFs as previously overlooked contributors to drought stress responses in <i>O. sativa</i> subsp. <i>indica</i> rice and provides a foundation for their functional characterization and potential application in crop improvement.</p>

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Genome-wide identification of sORFs in Oryza sativa subsp. indica and their comparative transcriptomic analysis under stress

  • 期刊论文

  • 发表日期：

    2026年6月22日

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  • Sheue Ni Ong,
  • Boon Chin Tan,
  • Kousuke Hanada,
  • Hui Zhao,
  • Chee How Teo

摘要

Small open reading frames (sORFs) represent an underexplored source of functional peptides in plant genomes. This study aimed to identify drought-responsive sORFs in Oryza sativa subsp. indica and to evaluate their potential roles in drought stress adaptation, addressing the question of whether sORFs contribute to physiological and molecular drought tolerance mechanisms in rice. Stress-responsive sORFs were identified through in silico prediction combined with transcriptomic analysis across multiple abiotic stress conditions. Functional annotation was performed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses, and signal peptide prediction was used to infer potential secretory functions. Three O. sativa subsp. indica rice cultivars (MR 219, MR 220, and MR 297) were subjected to drought stress for physiological assessment. Oxidative stress markers and antioxidant gene expression were analyzed, and candidate sORF expression was validated using RT-PCR. Differentially expressed sORFs (DE sORFs) were significantly enriched in GO terms related to structural molecule activity and binding, while KEGG analysis highlighted MAPK signaling and antioxidant defense pathways. Several sORFs were predicted to encode secretory peptides. Among the tested cultivars, MR 297 showed enhanced drought tolerance with reduced leaf rolling and stable chlorophyll content, whereas MR 219 exhibited higher oxidative damage, indicated by elevated malondialdehyde and proline levels. Antioxidant genes were strongly upregulated under drought stress, particularly in MR 219. Expression of selected sORFs (OsisORF_0050, OsisORF_3394, and OsisORF_3007) was confirmed under drought conditions. This study reveals sORFs as previously overlooked contributors to drought stress responses in O. sativa subsp. indica rice and provides a foundation for their functional characterization and potential application in crop improvement.