Novel Polymorphic Markers for Genetic Analyses

Our research will identify and develop a new type of polymorphic DNA marker that will allowsimplification and acceleration of genetic analyses. These multiplex-compatible amplifiable markers willhave the advantage of simplified analysis versus current PCR-based marker systems, allowing detectionin a new agarose gel format rather than requiring denaturing polyacrylamide gels. The markers will alsobe amenable to fluorescent analysis rather than requiring radioactive detection. In phase l, the plan isto describe a method to identify large-numbers of the new markers and to isolate and characterizeseveral examples. In addition, the basic expectations that they will produce precise amplificationproducts and that their allelic content can be determined more efficiently, safely, and cheaply than othersystems will be demonstrated. This will establish the superiority of this marker class and support thework of phase Il which includes isolation of a large number of the markers, more thorough characteriza-tion of their polymorphic content, and application in generation of linkage maps. In phase I, fluorescentdetection 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 newfluorescent imaging reader. The result will establish the feasibility of the phase ill goal of developmentof a fully integrated system of amplification, simplified electrophoretic separations, fluorescent detection,and automated data analysis.