Single-strand conformation polymorphism analysis coupled with stratified DNA sequencing reveals reduced sequence variation in the su(s) and su(wa) regions of the Drosophila melanogaster X chromosome.

Single-strand conformation polymorphism (SSCP) analysis followed by DNA sequencing of stratified sub-samples was used to survey DNA polymorphism in the su(s) and su(wa) regions in a natural population of Drosophila melanogaster. su(s) and su(wa) are located near the telomere of the X chromosome, where the rate of crossing over per kilobase of DNA monotonically decreases toward the tip. SSCP was assessed in 12 noncoding segments amplified from the su(s) region (3213 bp) and in 8 noncoding segments amplified from the su(wa) region (1955 bp). Sets of segments were multiplexed in a single electrophoretic lane to increase the number of base pairs assayed per lane. Eight segments were monomorphic, and the other 12 segments exhibited two to four SSCP classes. Only four within-SSCP-class DNA sequence differences (a single nucleotide substitution) were observed among 24,360 bp compared within classes. The between-SSCP-class DNA sequence comparisons revealed 27 substitutions and 9 insertion/deletion polymorphisms. The average numbers of substitutional differences per site were 0.0010 and 0.0021 for su(s) and su(wa), respectively. These values are intermediate between those reported for the more distal y-ASC region (0.0004) and the more proximal Pgd locus (0.0024). This observation is consistent with the prediction of the hitchhiking-effect model-i.e., a monotonic increase in polymorphism as a function of crossing over per kilobase.