Proc. Assoc. Advmt. Anim. Breed. Genet. Vol 14 103 TIPS: A PROCESS FOR RAPID FINE MAPPING OF QTLS USING ESTS AND COMPARATIVE MAPPING J.C. McEwan 1 , K.A. Paterson 2 , A. Zadissa 2 , T. Van Stijn 2 , C. Diez-Tascon 2 , A.M. Crawford 2 1 AgResearch, Invermay Research Station, PB 50034, Mosgiel, New Zealand 2 AgResearch Molecular Biology Unit, Biochemistry Department, University of Otago, PO Box 56, Dunedin, New Zealand SUMMARY Targeted Intronic Polymorphic Sequence identification (TIPS) is a procedure, which allows rapid identification of novel SNPs in ruminant species, targeted to an area of interest. Normally, this region would be a QTL and the markers would aid in its fine mapping. An advantage of TIPS is that it can be used for cross species SNP identification within expressed genes, and therefore allows rapid development of Type 1 markers across species. Current results suggest that the process is both rapid and cost effective relative to previous alternatives. The process is dependent on the availability of draft human genomic sequence, and ESTs, the latter derived either from the species of interest or from a closely related genus. Results to date suggest that for an average 10 Mbp human region, around 50% of unique genes will have a bovine contig. Of the primers developed using bovine sequence, approximately 72% work in ovine DNA, and SNPs have been be identified in 64% of cases. This results in an overall success rate of 46% per primer pair designed. Approximately 9 SNPs per 10Mbp can be identified with the bovine ESTs available in February 2001. The costs per targeted SNP marker developed are likely to be less than NZ$1000. This is approximately an order of magnitude cheaper than previous alternatives. Keywords: SNP, DNA, ruminant, introns, comparative mapping. INTRODUCTION In recent years there has been an upsurge of reports where QTL affecting production traits have been detected in ruminant livestock species. Many more have been unreported because of commercial considerations. While there have been a few reports of subsequent successful identification of the genetic polymorphisms underlying these traits (e.g. Kambadur et al. 1997; Galloway et al. 2000; Wilson et al. 2001), the present methods are expensive in time and personel. The key problems have been the lack of sufficient polymorphisms in farmed ruminant livestock in a given region of interest, and also the lack of detailed comparative maps of type 1 markers. For example the latest (3rd generation) sheep map contains 1061 markers of which only 120 are type 1 markers (Maddox et al. 2001). Previous work (Zadissa 2000) has described the level of homology required for successful automated design of PCR primers and suggested that while orthology comparisons could be made in silico between humans and ruminants, successful PCR primer design required ruminant sequence. Fortunately, the number of public and private bovine ESTs has increased rapidly and as at February 2001 there were more than 160,000 sequences in Genbank (http://www.ncbi.nlm.nih.gov/). Single nucleotide polymorphisms (SNPs) are the most common DNA variant, but unfortunately few SNPs are conserved across species (Hacia et al. 1999). However, it is possible to detect SNPs across closely related species using ESTs, because of the high level of conservation of the length and position of