In this proposal we present a systematic approach to gene mapping and genotyping based on the simultaneous analysis of multiple Amplified Sequence Polymorphisms (ASPs). The proposal has three broad features: the development of a technology suitable for the automation of gene mapping and genotyping, the application of this technology to the development of markers for the X chromosome and then for the entire genome, and the development of a computer tool for the management of gene mapping experiments. The main concept associated with ASP technology is that a DNA segment containing the sequence variation of a polymorphic locus can be amplified in such a way that it has a unique physical property. This unique property will allow individual loci to be distinguished from one another such that multiple loci can be analyzed simultaneously. In this application, we are proposing to use the length of the DNA segment as this distinguishing physical property and the polymerase chain reaction (PCR) as the method of amplification. Two alternative approaches for the generation of ASP markers are to be explored. The first is allele specific PCR (AS-PCR) in which the length of the PCR amplified fragment is different for different loci producing the marker directly. The second is allele specific primer extension (AS-PE) in which the PCR products are analyzed with oligonucleotide primers which produce allele specific fragments of different lengths for different loci. Specifically we plan to 1) refine ASP technology, 2) develop ASPs for the X chromosome and the genome and 3) create appropriate software for aiding the scientist in concerning ASP based mapping experiments, including an expert system.
