Construction of a high-throughput rat genetic mapping system with 466 arbitrarily primed-representational difference analysis markers

Linkage mapping of quantitative trait loci (QTLs) requires genetic markers that can be efficiently genotyped for a large number of individuals. To iso late genetic markers suitable for this purpose, we previously established t he arbitrarily primed RDA (AP-RDA) method. Dot-blotting AP-PCR products (AP -amplicons) onto filters at a high density and hybridization of the filters with the AP-RDA markers made it possible to genotype a large number of ind ividuals simultaneously for multiple loci. In this study, by using 25 prime rs or primer combinations, we isolated a total of 419 AP-RDA markers by sub tracting the AP-amplicon of BUF rats from that of ACI rats, and vice versa. By combining 47 previously isolated markers, a rat genetic map was drawn w ith 466 AP-RDA markers. Between two given strains of rats other than ACI an d BUF, the average informativeness of the markers was 38%. As for the inter cross of ACI and BUF rats, 12 selected primers served to genotype 259 loci. In addition, the amounts and quality of genomic DNA to be used for AP-PCR were examined to guarantee reliable genotyping. Now, initial genome scannin g of the rat for linkage analysis can be performed efficiently using this m apping system with AP-RDA markers.