Haplotype based methods utilizing SNPs offer a powerful approach to map polygenic traits based on the association between causal mutations and the ancestral haplotypes on which they arose. Previously we have identified a QTL on the telomeric region of SSC1q contributing to growth in pigs from birth to slaughter (Paszak et al., 1999). To maximally fine map genetic intervals containing QTL, we generated a pooled shotgun sub-library targeting the growth QTL defined by SW1301 and SW373 with an interval of 21 Mb. Nine BAC clones mapped by utilizing a radiation hybrid panel and evenly spaced in 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 HSA9. Sequences with significant BLAST hits were then used for SNP discovery. We were able to identify 145 SNP markers and 7 insertions/deletions using a panel of DNA from eight diversified pig breeds (Yorkshire, Chinese Meishan, Berkshire, Duroc, Hampshire, Landrace, Large White and Pietrain). Those SNPs that were heterozygous for the majority of the UIUC Resource Family F1 individuals are being used to genotype using a commercial population by a high-throughput SNP genotyping platform for use in linkage/linkage disequilibrium analyses.
Supported by grants from the USDA-National Research Initiative (538AG2004-35205-14187) and the USDA-Agricultural Research Service (Agreement No. 58-5438-2-313).