Use of Affymetrix re-sequencing arrays to investigate the population genetics of the Adh region in Drosophila melanogaster. D.J. Begun ¹, C.H. Langley ¹, H.A. Lindfors ¹, A.D. Kern ¹, W. Gilliland ¹, E. Scott-Bey ², A. Chakravarti ², M.E. Zwick ². 1) Evolution & Ecology, Univ California, Davis, CA; 2) Johns Hopkins University School of Medicine.

   Despite the relatively large amount of population genetic data from D. melanogaster, from a genomic perspective, descriptions of sequence variation are limited and represent a biased sampling of genomic regions. As an initial step toward our ultimate goal, the complete description of common, natural variants in the melanogaster genome, we used Affymetrix chip re-sequencing technology to measure variation in melanogaster over a 30-kb region including Adh. Re-sequencing was carried out in two-replicates for each of 30 chromosomes using hybridization of long-PCR products to arrays. Of 801,155 bases called across replicates, only 3 were discrepant, yielding a repeatibility of over 99.999%. Roughly 94% of bases were called with a quality score of at least 30. To assess accuracy and investigate alternative methods for generating templates for hybridization to arrays, we hybridized BAC DNA corresponding to the melanogaster reference sequence in two independent experiments. In the first replicate, 3 of 27,607 bases called differed from the published reference sequence. If these are incorrect calls, then this experiment suggests an accuracy of 99.989%. The second replicate of BAC hybridization yielded essentially the same result, with zero discrepancies between replicates. Overall, DNA derived from BAC vs. long PCR-products were comparable. We determined the sequence of a single allele from the homologous region of D. simulans and D. yakuba by traditional sequencing. Using these data and the population sample from melanogaster, we found that previously identified haplotype structure associated with the Adh F/S amino acid polymorphism extends several kilobases upstream and downstream of Adh. We also found interesting patterns of polymorphism and divergence of G/C vs. A/T mutations in presumably non-coding DNA in the Adh region.