The current emphasis of biotechnology in animal agriculture stresses the need to integrate molecular genetics into the identification of major genes affecting growth and development, reproductive performance, lactation, and disease resistance. Thus, the identification of allelic variants which affect quantitative traits will accelerate the rate of genetic improvement of animals. Our long range objective is to construct a well anchored, saturated linkage map of the pig genome through the application of abundant, randomly distributed, highly polymorphic microsatellite (MS) markers. Analysis of the segregation of these markers in the University of Illinois and MARC resource families will facilitate defining those areas of the genome where allelic variation or coding sequences describe phenotypic differences. Markers for loci which have a major impact on quantitative (economic) traits can then be incorporated into a marker-assisted selective breeding program. To this end, we have cloned MS markers while characterizing Type I and Type II markers within both resource populations. In addition, we have begun to expand existing porcine linkage groups using a random and directed marker approach. These markers are also being analyzed with respect to economic traits within both resource populations.