In Silico identification and characterization of candidate genes in Quantitive Trait Loci (QTL) regions associated with hundred-seed weight of rice (Oryza sativa L.).

Date

4-2006

Degree

Bachelor of Science in Biology

College

College of Arts and Sciences (CAS)

Adviser/Committee Chair

Netzie N. Bebing

Abstract

Fourteen quantitative trait loci (QTL) or genomic regions associated with hundred seed weight of rice (Oryza saliva) were identified and characterized in silico. These QTLs are found on chromosomes 2(AQE049), 3(AQE050 and AQE051), 4(AQE052, AQE053 and AQE0021), 5(AQE054 and AQE055), 7(AQE056), 8(AQE057 and AQE0022) and 11(AQE046, AQE047 and AQE048). Genetic maps were retrieved from the web-accessible Gramene. BLASTN analysis was done to anchor the coordinates of the QTLs. Physical maps were anchored through the BLASTN results. On the other hand, BLASTP was done to annotate the genes in the QTL regions against the Arabidopsis thaliana. BLASTP analysis showed significant similarities with the A. thaliana genome. Gene Ontology analysis suggests that genes for hundred-seed weight in rice have high similarities with the genes of Arabidopsis responsible for the enzyme kinase — the most frequent GO term in most of the chromosomes associated with the trait. Comparison of inside QTL regions with outside regions showed no similarities suggesting that these GO terms are unique in the QTL regions and not found on any part of the chromosomes. This suggests that hundred-seed weight may probably be affected by the kinase activity in the endomembrane system during protein amino acid phosphorylation. Other enzymes such as monooxygenases, phosphoric diester hydrolases, oxidoreductases and catalases were also found and believed to have an effect on the yield of rice.

Language

English

Location

UPLB Main Library Special Collections Section (USCS)

Call Number

Thesis

Document Type

Thesis

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