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

Waxy gene is crucial for amylose biosynthesis in rice, which affects cooking and textural properties of rice grain. This study aims to elucidate the functional dynamics of the Wx gene using In-silico and gene expression analyses in four rice varieties. The Wx gene sequences were retrieved from the NCBI database, analyzed for similarity using BLAST, and subjected to multiple sequence alignments. Structural features of the Wx gene protein were predicted using ExPASy-ProtParam and SWISS-MODEL, revealing that the Wx gene protein consists of 605 amino acids, it to be a stable protein with significant regions of conservation across various Indica rice. Phylogenetic analysis demonstrated evolutionary relationships among and secondary structure predictions showed 16% disorder, 26% a-helix, and 15% ß-strand. A 3D model was generated with high confidence, covering 80% of the sequence and c3vufA was highest scoring template. The Ramachandran plot showed 85% of residues in favorable regions, with a total of 488 residues analyzed. Expression analysis via semi-quantitative PCR indicated differential Wx gene expression across four rice varieties, with Pusa Basmati-1121 variety exhibiting the highest expression level.