Date of Publication

2023

Document Type

Bachelor's Thesis

Degree Name

Bachelor of Science in Biology major in Molecular Biology and Biotechnology

Subject Categories

Biology

College

College of Science

Department/Unit

Biology

Thesis Advisor

Mark Christian Felipe R. Redillas

Defense Panel Chair

Llewelyn S. Moron-Espiritu

Defense Panel Member

Chona Camille V. Abeledo
Yokimiko D. Torrejos

Abstract/Summary

Nitrogen (N) is one of the essential elements required by plants for growth and various metabolic processes, where it is used in biosynthesizing vital macromolecules. Sufficient nitrogen is thus vital for optimal crop growth, but its availability in the environment is highly variable. To address this, the process of loop-mediated isothermal amplification (LAMP) may be employed in producing a molecular-based nitrogen sensing system for Oryza sativa L. A literature search was conducted to identify a study from which candidate target genes could be selected for primer design. Thirteen candidate genes were then identified from the chosen study as those that responded to N starvation in rice plant roots, particularly those involved in N transport and assimilation. Data from the online database RiceXPro were gathered in order to visually characterize these candidate genes’ role in N deficiency in roots. Graphs were constructed to show the genes’ upregulation or downregulation response to N starvation. This data was then compared to the findings of the base study, where it was observed that all genes except OsNAR2.2 and OsNR2 had consistent responses between both sources. PrimerExplorer v5 was then used to generate potential primer sets. Five sets were generated for all thirteen candidate genes, which were run through an automated scoring system programmed through R. Grading was based on the criteria for optimal primer design, where the values for changes in free energy, Tm, and GC rate were judged against. Scores ranged between 37 points for OsNR2 to 28 points for OsNAR2.2 out of a possible maximum 39 points. These were then ranked by total score in descending order, and the highest-scoring primer set of each gene was selected for further use. These chosen primers were subjected to specificity checks using NCBI BLASTN, which determined that all but one primer set (OsAMT2.2) were specific to their respective target genes. With the findings of this study, it may be possible to create a LAMP-based sensing system to determine real-time N concentration in rice roots. However, it would still be necessary to test these selected primer sets in a laboratory setting before employment in a field setting.

Abstract Format

html

Language

English

Format

Electronic

Physical Description

ix, 130 leaves

Keywords

Rice

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Embargo Period

8-15-2023

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