In silico analysis of single nucleotide polymorphisms (SNPs) in loci of rice (Oryza sativa L.) othologous to maize (Zea mays L.) C4 photosynthetic pathway genes

Date

4-2008

Degree

Bachelor of Science in Biology

College

College of Arts and Sciences (CAS)

Adviser/Committee Chair

Ivan Marcelo A. Duka

Abstract

Thirty four genes in rice (Oryza sativa L.) coding for C4 photosynthesis enzymes were curated from online accessible journals and databases. Phylogenetic trees based from protein sequences showed ten of these curated rice genes were orthologous to maize (Zea mays L.) C4 specific genes. These genes were LOC_Os08g44810 for NADP-malate dehydrogenase (NADP-MDH), LOC_os01g09320 for NADP-malic enzyme (NADP-ME), LOC_Os08g27840, LOCos09g14670, and LOC_Os0g14770 for phosphoenoloyruvate carboxylase (PEPC), LOC_Os05g33570 for pyruvate orthophosphate dikinase (PPDK), and LOC_Os12g19470, LOC_Os12g17600, LOC_Os1219381, and LOC_Os12g19394 for ribulose 1.5-bisphosphate carboxylase / oxygenase (RuBisCO). Only two genes were found to contain SNPs LOC_Os08g44810 and LOC_Os12g19394: RuBisCO). In these two genes, there were 10 specific coordinated that contain SNPs, three were found in exons and seven were in introns. All SNPs in exons were discovered to be fully conserved in the twenty varieties of rice. These results revealed that rice genes othologous to maize C4 photosynthesis genes are conserved in twenty varieties of rice.

Language

English

Location

UPLB Main Library Special Collections Section (USCS)

Call Number

Thesis

Document Type

Thesis

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