Genetic variation in yield-related genes: An in silico structural study of traditional Philippine rice varieties

Date of Publication

8-2026

Document Type

Bachelor's Thesis

Degree Name

Bachelor of Science in Biology major in Molecular Biology and Biotechnology

Subject Categories

Plant Sciences

College

College of Science

Department/Unit

Biology

Thesis Advisor

Mark Christian Felipe R. Redillas

Defense Panel Chair

Yokimiko D. Torrejos

Defense Panel Member

Yokimiko D. Torrejos
Paul Benedic U. Salvador
Christian Jordan O. Dela Rosa

Abstract (English)

Rice yield is a complex trait influenced by naturally occurring genetic variation that may alter the structure and function of proteins involved in growth, development, and stress responses. This study investigated the structural and functional consequences of missense variants within 27 prioritized yield-related genes among 163 traditional Philippine rice varieties using an integrated in silico structural bioinformatics approach. Genomic variation data were obtained from the 3,000 Rice Genomes (3KRG) Project through the SNP-Seek database. Missense variants were filtered based on non-conservative changes in amino acid physicochemical properties and subsequently evaluated through protein structure prediction, structural alignment, thermodynamic stability analysis, molecular docking, and Gene Ontology enrichment analysis. Correlation analyses further demonstrated that neither gene prioritization rank nor SNP density consistently predicted structural impact, highlighting the importance of evaluating mutation-specific structural and functional effects. Integrated analyses prioritized variants in Receptor-like Protein Kinase (LOC_Os10g06760), Putative Expressed Receptor-like Kinase (LOC_Os10g13970), and Leucine-Rich Repeat Receptor-Like Kinase 2 (LOC_Os10g32990) as the strongest candidates because they consistently exhibited substantial structural perturbations, altered thermodynamic stability, and pronounced changes in ligand-binding cavity geometry and protein–ligand interactions. These findings establish a computational framework for prioritizing naturally occurring missense variants for future functional validation and molecular breeding strategies aimed at improving rice productivity.

Abstract Format

html

Abstract (Filipino)

Ang ani ng palay ay isang komplikadong katangiang naiimpluwensiyahan ng likas na baryasyong henetiko na maaaring magdulot ng pagbabago sa estruktura at function ng mga protinang sangkot sa paglaki, pagdami, at pagtugon sa stress. Sinuri ng pag-aaral na ito ang mga estruktural at functional na epekto ng mga missense variants sa 27 piling gene na may kaugnayan sa ani sa 163 tradisyonal na barayti ng palay sa Pilipinas gamit ang in silico structural bioinformatics approach. Nakuha ang datos mula sa 3,000 Rice Genomes (3KRG) Project sa SNP-Seek database. Sinala ang mga missense variants batay sa mga hindi konserbatibong pagbabago sa mga katangiang pisikokemikal ng mga amino acid at sinuri gamit ang protein structure prediction, structural alignment, thermodynamic stability analysis, molecular docking, and Gene Ontology enrichment analysis. Ipinakita rin ng mga pagsusuri ng korelasyon na hindi palaging konektado ang ranggo ng gene prioritization o densidad ng SNP sa epekto sa estruktura, kaya binibigyang-diin ang kahalagahan ng pagsusuri sa partikular na epekto ng bawat mutasyon sa estruktura at function ng protina. Batay sa pinagsamang mga pagsusuri, ang mga baryanteng matatagpuan sa Receptor-like Protein Kinase (LOC_Os10g06760), Putative Expressed Receptor-like Kinase (LOC_Os10g13970), at Leucine-Rich Repeat Receptor-Like Kinase 2 (LOC_Os10g32990) ay natukoy bilang pinakamalalakas na kandidato dahil laging mayroong malaking pagbabago sa estruktura, katatagang termodinamiko, at heometriya ng ligand-binding cavity at sa mga interaksiyon ng protina at ligand. Itinatag ng mga resulta nito ang isang computational framework para sa pagbibigay-prayoridad sa mga missense variants para sa mga susunod na functional validation at mga estratehiya sa molecular breeding na naglalayong mapabuti ang produktibidad ng palay.

Abstract Format

html

Language

English

Format

Electronic

Keywords

Rice—Genetics; Rice—Varieties--Philippines

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Embargo Period

8-30-2026

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