Ecotilling (targeting induced local lesions in genomes) for grain quality genes in cultivated rice (Oryza sativa L.).

Date

3-2010

Degree

Bachelor of Science in Biology

College

College of Arts and Sciences (CAS)

Adviser/Committee Chair

Ivan Marcelo A. Duka

Abstract

MALABAD, JOHN CARLO MACASADDUG. 2010. EcoTILLING (Targeting Induced local Lesions in Genomes) for Grain Quality Genes in Cultivated Rice (Oryza sativa University of the Philippines Los Banos. B.S. Biology Major in Genetics.

Adviser: Ivan Marcelo A. Duka (UPLB)

Genetic diversity in cultivated rice (Oryza saliva L.) was investigated by detecting and evaluating single nucleotide polymorphisms (SNPs) in 48 representative accessions through EcoTILLING (Targeting Induced Local Lesions in Genomes). EcoTILLING is a technique to detect SNPs in natural populations through heteroduplex analysis using mismatch-specific (single-strand) endonucleases. The primers used are associated with genes for grain quality in rice, namely granule-bound starch synthase I and II (GBSSI and GBSSII), starch synthase IIC and IIIA (SSIIC and SSIIIA). One primer per gene was used, except for SSIIIA where three primers were used. 1R64 and Nipponbare DNA were used as reference lines. Banding patterns were scored based on the two contrasts and compared to identify haplotypes, or sets of SNPs in the target gene regions, and to examine genetic variations among the accessions. SSIIC recorded the least number of haplotypes, with five, while SSIIIA recorded the most, with 18. Three haplotypes for GBSSI, ten for SS1IIA, and two for SSIIC and GBSSII were singletons with only one accession each, while some other haplotypes included 10 to 26 accessions each. Sequence data of the accessions used per primer supported the banding patterns observed. Haplotypes were correlated to phenotype for association analysis, which allows for selection of important and desirable grain quality traits, specifically cooking time of rice and texture of cooked rice. Significant differences in gelatinization temperature, which determines the cooking time of the rice grains, were noted in some of the haplotypes identified. Haplotypes associated with good grain quality and low gelatinization temperature can be used for breeding and crop improvement programs that can address the growing demand for high quality rice.

Language

English

Location

UPLB Main Library Special Collections Section (USCS)

Call Number

Thesis

Document Type

Thesis

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