The proposal is to identify and develop a new type of polymorphic DNA marker that will allow simplification and acceleration of genetic analyses. These multiplex- compatible amplifiable markers will have the advantage of simplified analysis versus current PCR-based marker systems, allowing detection in a new agarose gel format rather than requiring denaturing polyacrylamide gels. The markers will also be amenable to fluorescent analysis rather than requiring radioactive detection. In phase l, the plan is to describe a method to identify large-numbers of the new markers and to isolate and characterize several examples. In addition, the basic expectations that they will produce precise amplification products and that their allelic content can be determined more efficiently, safely, and cheaply than other systems will be demonstrated. This will establish the superiority of this marker class and support the work of phase Il which includes isolation of a large number of the markers, more thorough characterization of their polymorphic content, and application in generation of linkage maps. In phase I, fluorescent detection methods will be surveyed and selected to demonstrate that the improved """"""""allele quality"""""""" simplifies detection enhancing the process of automated data retrieval and analysis using a new fluorescent imaging reader. The result will establish the feasibility of the phase ill goal of development of a fully integrated system of amplification, simplified electrophoretic separations, fluorescent detection, and automated data analysis.
