High-density SNP maps for chromosomal regions containing QTL have proven successful in refining map positions. Haplotype-based SNP analysis is more informative than analysis based on individual SNPs and in analyzing associations with phenotypes. A QTL for ovulation rate has been previously located in the centromeric region of SSC8p (Wilkie et al., 1999; Brauschweig et al., 2001). To maximally refine genetic intervals containing QTL and facilitate positional cloning, we generated a pooled shotgun sub-library targeting the ovulation rate QTL defined by SW205 and SW206 with an interval of 7 Mb which corresponds to human genomic positions between 34 and 42 Mb on HSA4. Twenty-seven BAC clones representing a minimal tiling pathof this region were used to generate a pooled shotgun sub-library. Skim sequencing of the pooled BAC sub-library was performed and the shotgun sequences were masked for repetitive elements and subjected to BLAST analysis for similarity to human genome sequences of HSA4.
Sequences with significant BLAST hits between 34 and 42 Mb on HSA4 were then used for SNP discovery. We were able to isolate 340 SNP markers and 27 insertions/deletions using a panel of DNA from eight diversified pig breeds (Yorkshire, Meishan, Berkshire, Duroc, Hampshire, Landrace, Large White and Pietrain). SNPs heterozygous for the UIUC Resource Family F1 individuals are being used to genotype a commercial population using a high-throughput SNP genotyping platform for use in linkage/linkage disequilibrium analyses.
Supported by grants from the USDA National Research Initiative (Grant No. 2004-35205-14187) and the USDA Agricultural Research Service (Agreement No. 58-5438-2-313).