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<p>Research focused on understanding the mechanisms of ethylene signalling in response to deep flooding in traditional tall rice varieties using in silico methods is scarce. This study aimed to explore the function of seven previously uncharacterized ethylene-responsive genetic loci (ERGL), identified through RNA-sequencing, in the promising but understudied rice variety Kumrogarh, which shows tolerance to extended deep flooding due to two distinct flood-tolerant quantitative trait loci (QTLs), known as <i>Sub1</i> and <i>SNORKEL</i>. To investigate their evolutionary origins, a sequence alignment was conducted among the seven ERGLs. Notably, LOC_Os05g06320.2 showed an exceptional 100% similarity with the previously documented ethylene receptor <i>OsERS2</i> (sharing the same locus ID), while LOC_Os02g36510.1 exhibited a 34.30% match with another known factor, <i>OsEIL1a</i>. In contrast, the remaining five loci had less than 10% sequence similarity with other recognised conserved regulators, <i>OsETR2</i> and <i>OsEIN2,</i> identified in the conventional ethylene signalling model. As a result, these elements were deemed clearly distinct, prompting us to examine them closely and to reveal their contributions to the deep flood response of var. Kumrogarh. This research involved comprehensive analyses that included phylogenetic links, secondary structures, physicochemical characteristics, and three-dimensional configurations. Furthermore, for detailed functional characterisation, advanced tools such as MEME 5.5.5 and InterProScan were utilised to identify any functional motifs and domains present in these proteins, followed by extensive protein–protein interaction studies employing STRING tools to further clarify molecular interactions. Considering their roles in flood-triggered ethylene signalling, a model was developed to illustrate the connections among these ERGL and to contrast them with the traditional model of ethylene signalling. This research represents a pioneering effort to identify the regulatory factors associated with the deep submergence response in the <i>Sub1-SK</i> allele-bearing rice genotype, utilising advanced bioinformatics tools. The study is expected to provide critical insights for developing rice cultivars that are resistant to multiple floods, thereby enhancing our understanding of plant adaptation in challenging environments.</p>

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Decoding Ethylene-driven Molecular Mechanism in Deepwater Rice Carrying Sub1 and SK Genes Together: an In-Silico Perspective

  • 期刊论文

  • 发表日期：

    2026年5月11日

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  • Pratyasha Samanta,
  • Narottam Dey

摘要

Research focused on understanding the mechanisms of ethylene signalling in response to deep flooding in traditional tall rice varieties using in silico methods is scarce. This study aimed to explore the function of seven previously uncharacterized ethylene-responsive genetic loci (ERGL), identified through RNA-sequencing, in the promising but understudied rice variety Kumrogarh, which shows tolerance to extended deep flooding due to two distinct flood-tolerant quantitative trait loci (QTLs), known as Sub1 and SNORKEL. To investigate their evolutionary origins, a sequence alignment was conducted among the seven ERGLs. Notably, LOC_Os05g06320.2 showed an exceptional 100% similarity with the previously documented ethylene receptor OsERS2 (sharing the same locus ID), while LOC_Os02g36510.1 exhibited a 34.30% match with another known factor, OsEIL1a. In contrast, the remaining five loci had less than 10% sequence similarity with other recognised conserved regulators, OsETR2 and OsEIN2, identified in the conventional ethylene signalling model. As a result, these elements were deemed clearly distinct, prompting us to examine them closely and to reveal their contributions to the deep flood response of var. Kumrogarh. This research involved comprehensive analyses that included phylogenetic links, secondary structures, physicochemical characteristics, and three-dimensional configurations. Furthermore, for detailed functional characterisation, advanced tools such as MEME 5.5.5 and InterProScan were utilised to identify any functional motifs and domains present in these proteins, followed by extensive protein–protein interaction studies employing STRING tools to further clarify molecular interactions. Considering their roles in flood-triggered ethylene signalling, a model was developed to illustrate the connections among these ERGL and to contrast them with the traditional model of ethylene signalling. This research represents a pioneering effort to identify the regulatory factors associated with the deep submergence response in the Sub1-SK allele-bearing rice genotype, utilising advanced bioinformatics tools. The study is expected to provide critical insights for developing rice cultivars that are resistant to multiple floods, thereby enhancing our understanding of plant adaptation in challenging environments.