In silico identification and characterization of candidate genes in genomic regions associated with drought tolerance in 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

Candidate genes in genomic regions associated with drought tolerance in rice (Oryza saliva L.) were identified and characterized in silico by bioinformatic methods. Six quantitative trait loci (QTLs) were found to be associated with drought tolerance; two of which are highly associated on chromosome 5 (AQAN001) and on chromosome 12 (AQAN002) and four are interacting loci on chromosomes 1 (AQAN003), 4 (AQAN004), 8 (AQAN005) and 3 (AQAN006). The genomic regions associated with drought tolerance were translated to physical map location on the IRGSP rice pseudomolecule 3.0 using BLASTN. Gene predictions within each translated regions were then characterized through homology with Arabidopsis thaliana proteome using BLASTP. Functional assignment of each annotated gene was done through Gene Ontology (GO) search. The most frequent biological themes underlying each QTL differ from one another. The 971 annotated genes in six QTL regions could be classified into seven functional groups. The biological themes inside and outside two interesting QTL regions (AQAN001 and AQAN002) differ from one another which suggest "enrichment" of drought-tolerant associated biological themes inside the region. Eighteen interesting genes were nominated to be used for the further breeding studies of drought-tolerant rice varieties. Their functional descriptions were also discussed. Bioinformatics have been useful in the identification and characterization of candidate genes in genomic regions associated with drought tolerance.

Language

English

Location

UPLB Main Library Special Collections Section (USCS)

Call Number

Thesis

Document Type

Thesis

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