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<p>The <i>Waxy</i> (Wx) gene encodes granule-bound starch synthase I (GBSSI), a key enzyme in amylose biosynthesis that strongly influences rice grain quality and cooking characteristics. This study integrated in silico characterization and gene expression analysis to elucidate the structural and functional properties of the <i>Wx</i> gene in four rice genotypes—Malviya Basmati, Basmati370, Pusa Basmati1 and IR64. Biochemical characterization revealed significant variation in aroma, gel consistency, alkali spreading value and amylose content among the genotypes, with amylose content ranging from 13.46% to 20.68%. In silico analysis using NCBI, CLUSTAL W, and SWISS-MODEL identified high sequence conservation (99–100%) among <i>indica</i> rice varieties. The Wx protein composed of 605 amino acids with a molecular weight of 66.0&#xa0;kDa, exhibited an instability index of 30.51 and a GRAVY value of − 0.197, indicating a stable and hydrophilic nature. Phylogenetic analysis confirmed a close evolutionary relationship among <i>Oryza sativa</i> accessions. Three-dimensional structural modeling and Ramachandran plot validation confirmed the reliability of the predicted protein structure. Semi-quantitative PCR analysis showed differential <i>Wx</i> gene expression with Pusa Basmati1 displaying markedly lower expression compared to control (IR64) and other basmati varieties, correlating with its intermediate amylose content. These findings enhance understanding of the molecular dynamics of the <i>Wx</i> gene and its role in determining grain quality traits providing valuable insights for rice breeding programs aimed at improving starch composition and eating quality.</p> Graphical abstract <p></p>

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In-silico characterization and expression analysis of the Waxy gene in rice (Oryza sativa L.)

  • 期刊论文

  • 发表日期：

    2026年4月18日

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  • Ali Sina Jayhoon,
  • Pushpendra Kumar

摘要

The Waxy (Wx) gene encodes granule-bound starch synthase I (GBSSI), a key enzyme in amylose biosynthesis that strongly influences rice grain quality and cooking characteristics. This study integrated in silico characterization and gene expression analysis to elucidate the structural and functional properties of the Wx gene in four rice genotypes—Malviya Basmati, Basmati370, Pusa Basmati1 and IR64. Biochemical characterization revealed significant variation in aroma, gel consistency, alkali spreading value and amylose content among the genotypes, with amylose content ranging from 13.46% to 20.68%. In silico analysis using NCBI, CLUSTAL W, and SWISS-MODEL identified high sequence conservation (99–100%) among indica rice varieties. The Wx protein composed of 605 amino acids with a molecular weight of 66.0 kDa, exhibited an instability index of 30.51 and a GRAVY value of − 0.197, indicating a stable and hydrophilic nature. Phylogenetic analysis confirmed a close evolutionary relationship among Oryza sativa accessions. Three-dimensional structural modeling and Ramachandran plot validation confirmed the reliability of the predicted protein structure. Semi-quantitative PCR analysis showed differential Wx gene expression with Pusa Basmati1 displaying markedly lower expression compared to control (IR64) and other basmati varieties, correlating with its intermediate amylose content. These findings enhance understanding of the molecular dynamics of the Wx gene and its role in determining grain quality traits providing valuable insights for rice breeding programs aimed at improving starch composition and eating quality.

Graphical abstract