Project Background: SNP Maps

a collaboration of the BDGP and Exelixis, Inc.

Project Background

Traditional strategies for meiotic recombination mapping in Drosophila rely on the use of chromosomes carrying multiple dominant or recessive marker mutations with visible phenotypes. These phenotypes are often laborious to score and may interfere with the phenotype of the mutant of interest. Most importantly, because mutations with easily scored, viable phenotypes are relatively infrequent, the mapping resolution available using this approach is limited.

A much higher degree of interstrain variation is available at the molecular level. Single nucleotide polymorphisms (SNPs) and small insertion/deletion polymorphisms are common in Drosophila. The genomic sequences of a typical pair of Drosophila strains differ by as much as 1 in 200 bp, though the rate can vary substantially across the genome. The alleles of such markers are co-dominant and usually phenotypically neutral. Modern methods for scoring molecular variants offer the advantages of high throughput and automated scoring. The high density of SNPs in the genome and the availability of rapid scoring methods make for an attractive tool to analyze recombinant chromosomes.

We have characterized SNPs by sequencing PCR products amplified from genomic DNAs of commonly used laboratory strains of Drosophila. Selected sequence tagged sites (STSs) from the P1-based genome physical map (Kimmerly et al. 1996) were amplified using oligonucleotide primers and conditions described in the Berkeley Fly Database. The same primers were used to sequence the PCR products.

In an initial study, described in Teeter et al. (2000), a set of 49 polymorphic STSs were identified and analyzed in nine Drosophila strains. These markers span the genome at an average spacing of 1 per 2.4 Mb. SNPs identified in this study are available on the world wide web site of the laboratory of Greg Gibson (North Carolina State University) at

The BDGP and Exelixis, Inc. have collaborated to identify an additional 450 biallelic markers in three commonly used laboratory strains. The majority are single nucleotide polymorphisms and sequences for the variants are presented here. The average density of the new markers is 1 per 250 kb on the autosomes. In addition, we include a set of P-element strains that provide additional utility for high-resolution mapping. This denser set of markers and a demonstration of their utility are described in Hoskins et al. (2001). These data can be downloaded in tab-delimited text format or viewed as web pages with links to the STS information, including PCR primer sequences and conditions.

General questions about this resource and specific questions about the Canton S versus Oregon R data should be directed to Roger Hoskins ( Specific questions about the w; iso2; iso3 versus P insertion strain data should be directed to Michael Cancilla (