Capillary array electrophoresis single-strand conformation polymorphism (CAE-SSCP) analysis provides a reliable high-throughput method to genotype plant germplasm collections. Primers designed for highly conserved regions of candidate genes can be used to amplify DNA from plants in the collection. These amplified DNA fragments of identical length are turned into useful markers by assaying sequence differences by CAE-SSCP analysis. Sequence differences affect the electrophoretic mobility of single-stranded DNA under non-denaturing conditions. By collecting the mobility data for both strands assayed at two temperatures, alleles can be defined by mobility alone. For a germplasm collection with an unknown number of alleles at a locus, such mobility data of homozygotes can be used to determine the number of unique alleles without the necessity of cloning and sequencing each allele.