A survey of the AA genome Oryza species through ecotilling (targeting induced local lesions in genomes)

Date

4-2007

Degree

Bachelor of Science in Biology

College

College of Arts and Sciences (CAS)

Adviser/Committee Chair

Adelina A. Barrion

Co-adviser

Kenneth L. Mcnally

Abstract

GAMALINDA, MICHAEL BIAG. 2007. A Survey of the AA Genome Oryza Species through EcoTILLING (Targeting Induced Local Lesions in Genomes) University of the Philippines Los Banos. B.S. Biology Major in Genetics.

Adviser: Dr. Adelina A Bart (UPLB) Co-adviser: Dr. Kenneth L. McNally (IRRI) ABSTRACT The potential application of the SNP-detection mechanism of EcoTILLING as well as the utility of low copy nuclear genes for biosystematic studies was demonstrated by studying the genetic relationships among the six wild species of rice having the AA genome, namely 0. barthii, 0. glumaepatula, 0. longistaminata, 0. meridionalis, 0 nivara, and 0. rufipogon. Variation among the Asian taxa (0. nivara and 0. rufipogon) was higher than that of the African (0. longistaminata and 0. barthii), South American (0. glumaepatula) and Australian (0. meridionalis) taxa. Four dendrograms were constructed (two using NTSYSpc version 2.02 and two from DARwin version 5.0) based on the similarity coefficient calculated from the single nucleotide polymorphism (SNP) patterns occurring at 7 loci putatively linked with drought tolerance (examples of low copy nuclear genes) contrasted against two reference lines, Nipponbare (japonica type) and 1864 (indica type). The dendrograms showed differentiation among the wild AA genome species of rice according to their geographical origin except for 0. glumaepatula, which occurs in Latin America, but is closely linked with the African 0. barthii. In the analysis using Nipponbare as a contrast, the Australian 0. meridionalis grouped into a single cluster distinct from the other taxa. Analysis of contrasts to both indica and japonica reference lines clearly showed that the largest group includes all 0. nivara and 0. rufipogon accessions. Concordance of the results obtained in this study with that of the existing literature reinforces the utility of EcoTILLING as a tool for biosystematics in rice. EcoTILLING the 95 AA genome accessions using primers designed from segments of the amino acid permease 6 (AAP6) gene, a putative insect tolerance gene, yielded numerous mismatch sites, making it difficult to identify specific haplotypes for candidate gene association. Brown planthopper (BPH) bioassay showed that among the 95 wild AA genome accessions used in the study, only six accessions showed resistance to BPH that included three accessions each of 0. nivara (100195, 102171, and 105343) and 0. rufipogon (80541, 80714, and 100819).

Language

English

Location

UPLB Main Library Special Collections Section (USCS)

Call Number

Thesis

Document Type

Thesis

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