Project Number: 1275-21000-164-09
Project Type: Specific C/A

Start Date: Aug 01, 2002
End Date: Jul 31, 2007

Objective:
The objectives of this research are to develop a cost effective and high throughput system for the detection of single nucleotide polymorphisms (SNPs) in plant DNA. A major problem associated with the detection of SNPs is the need to perform a separate polymerase chain reaction (PCR) amplification for each DNA fragment in which a SNP is being assayed. This may require hundreds or even thousands of amplification reactions. The specific objectives of the proposed research are 1) to develop a system whereby many SNP containing DNA fragments can be amplified at the same time and 2) to demonstrate the use of this system for the detection of SNPs.

Approach:
Our cooperative approach will be to digest plant genomic DNA with two restriction endonucleases followed by the ligation of DNA linkers to the ends of the resulting restriction fragments. The DNA linkers will serve as the target for PCR primers that can amplify subsets of the total pool of genomic DNA fragments much as is done when amplification fragment length polymorphism (AFLP) DNA markers are amplified. The various subsets of PCR fragments will contain DNA sequences in which we have previously determined the presence of SNPs. These specific DNA fragments will become the targets that will be assayed for the presence of SNPs. Two approaches will be evaluated for the SNP detection assay. One involves the use of the single base extension (SBE) technique for SNP detection and the other uses allele specific hybridization (ASH). We will determine which of these approaches is most amenable to the detection of multiple SNPs in a large and diverse mixture of DNA fragments.

Project Team

Cregan, Perry Jose Costa - Associate Professor 301-504-5070

Project Annual Reports

FY 2003

Related National Programs

Plant, Microbial & Insect Genetic Res., Genomics, & Genetic Improv. I (301)   Plant Biological and Molecular Processes (302)