[
Development & Evolution Meeting,
2008]
Recently diverged wild populations with low genetic differences coupled with strikingly distinct phenotypes offer rare opportunities to thoroughly characterize the genotype-to-phenotype relationships of natural variants. We used the massively parallel sequencing platform, the Solexa Sequence Analyzer (Illumina Inc.), to sequence the entire 169 MB genome of Pristionchus pacificus Poland RS106, a closely related strain to the reference strain California PS312. We identified between 700-6200 candidate SNPs/indels and so far validated 105 of these by traditional Sanger sequencing of PCR products from both strains. The resulting estimated true SNP frequency may be up to 10,000x less than the number of polymorphisms in the P. pacificus mapping strain Washington PS1843 (~1:26) as well as ~160x less frequent than between the C. elegans N2 and CB4858 strains (~1:1500) found in a similar Solexa study(1). Nevertheless, this estimate confirmed our expected low SNP count based on previous Sanger sequencing of randomly chosen ~30 kb genomic regions of the Poland strain. In order to map the loci responsible for the phenotypic variations in mouth dimorphism, vulva induction, egg laying, and chemoattraction to insect pheromones, we genotyped ~1000 Recombinant Inbred Lines from California/Poland crosses using ~100 confirmed SNPs distributed on all six chromosomes. Preliminary findings for loci linked to differences in mouth dimorphisms and egg laying will be discussed. Thus, the combination of the Solexa platform and QTL mapping in genetically similar but phenotypically disparate novel strains offers a rapid, powerful way to compile a nearly complete list of SNPs associated with phenotypic differences among natural variants.