Individuals differ in the exact nucleotide sequence of their genomes. These differences can be utilized to track the inheritance of chromosomal regions, allowing mutations produced by genetic screens or disease-causing gene alleles to be rapidly mapped. Approaches for identifying these changes, called single nucleotide polymorphisms or SNPs are rapidly improving, and yet both the discovery and genotyping of SNPs in all organisms, but particularly ones without known genome sequences, remains a major undertaking. The long-term objectives of this application are to develop techniques for SNP discovery and genotyping that are inexpensive, high-throughput, and are applicable to a variety of organisms. As sequence information becomes inexpensive and custom high-density tiling microarrays become readily available, Restriction site Associated DNA (RAD) tags provide superior characteristics for genotyping. Thousands of RAD tag markers are assayable with a single hybridization, the polymorphism is converted into a simple binary presence or absence of a DNA fragment several hundred nucleotides long, and the marker allows the rapid genotyping of large populations on a marker by marker basis, speeding fine-scale mapping.
The specific aims are to 1) Optimize protocols for the discovery of RAD markers on tiling arrays and characterizing the design parameters of RAD markers when genetic mapping with pooled populations. 2) Develop methods for the high-throughput isolation of RAD tags, which will allow the genotyping of many individuals in a population. The RAD marker approach allows inexpensive, high- throughput screening of high-density genetic markers in any organism, a significant benefit for researchers wishing to understand the genetic basis of phenotype.Project narrative Identifying the genetic changes that cause disease in humans, or affect a biological process in a model organism, has been difficult. This application develops methods to allow genetic changes to be rapidly and inexpensively mapped to a small region of the genome.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Exploratory/Developmental Grants (R21)
Project #
5R21HG003834-02
Application #
7597070
Study Section
Genomics, Computational Biology and Technology Study Section (GCAT)
Program Officer
Ozenberger, Bradley
Project Start
2008-04-01
Project End
2011-03-31
Budget Start
2009-04-01
Budget End
2011-03-31
Support Year
2
Fiscal Year
2009
Total Cost
$185,000
Indirect Cost
Name
University of Oregon
Department
Biochemistry
Type
Organized Research Units
DUNS #
948117312
City
Eugene
State
OR
Country
United States
Zip Code
97403
Etter, Paul D; Johnson, Eric (2012) RAD paired-end sequencing for local de novo assembly and SNP discovery in non-model organisms. Methods Mol Biol 888:135-51
Davey, John W; Hohenlohe, Paul A; Etter, Paul D et al. (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet 12:499-510
Etter, Paul D; Preston, Jessica L; Bassham, Susan et al. (2011) Local de novo assembly of RAD paired-end contigs using short sequencing reads. PLoS One 6:e18561
Baird, Nathan A; Etter, Paul D; Atwood, Tressa S et al. (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One 3:e3376