SNPs are the most abundant in a genome and suitable for analysis on a wide range of genomic scales (Rafalski, 2002; Zhu et al., 2003). However, the development of high-throughput genotyping platforms for large numbers (thousands to millions) of SNPs has proved to be relatively time-consuming and costly. Typically, a fairly large sequencing effort is devoted to identify polymorphic sites in a genome among a set of breeding lines.