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

In-silico characterization and expression analysis of the Waxy gene in rice (Oryza sativa L.). Abstract 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. Formats available You can view the full content in the following formats: Indexing Terms Descriptors Identifiers Organism Descriptors Broader Terms Information & Authors Information Published In 2024 Copyright Open Access This preprint is distributed under the terms of the Creative Commons CC0 Public Domain Dedication waiver (https://creativecommons.org/publicdomain/zero/1.0/), which permits unrestricted use, distribution, and reproduction in any medium, without asking permission. History Issue publication date: 2024 Submitted: 8 July 2024 Published online: 8 July 2024 Language English Authors Metrics & Citations Metrics SCITE_ Citations Export citation Select the format you want to export the citations of this publication. EXPORT CITATIONSExport Citation Citing Literature - Yuanbo Pan, Kuiju Niu, Fangming Shen, Guiqin Zhao, Yuehua Zhang, Jikuan Chai, Zeliang Ju, Genome-wide analysis of the COMT gene family in Avena sativa: insights into lignin biosynthesis and disease defense mechanisms, Frontiers in Plant Science, 10.3389/fpls.2025.1609698, 16, (2025). - Miaomiao Huang, Yuanbo Pan, Zeliang Ju, Kuiju Niu, Genome-Wide Analysis of the POD Gene Family in Avena sativa: Insights into Lignin Biosynthesis and Responding to Powdery Mildew, Agronomy, 10.3390/agronomy15040852, 15, 4, (852), (2025). View Options View options Login Options Check if you access through your login credentials or your institution to get full access on this article.