Historically, linkage analysis was used to measure the genetic proximity of loci to each other, to map qualitative traits, and, more recently, to map QTL. In plants, most of these types of cosegregation analyses have been conducted in highly struc- tured populations with known pedigrees, such as F2 populations. However, these populations have two major limitations. First, the limited number of recombination events results in poor resolution for quantitative traits. Second, only two alleles at any given locus can be studied simultaneously (Figure 4). In order to increase the resolution of mapping populations, large recombinant inbred line populations that have undergone several rounds of random mating have been created for several plant species [e.g., the intermated B73 ⇥ Mo17 (IBM) population in maize (33)]. These rounds of mating increase the potential number of recombination events. Despite these efforts, the resolution for many QTL is still several centimorgans, corresponding to hundreds of genes. Additionally, the low number of alleles sam- pled per locus in each population makes it difficult to examine the full range of genetic diversity available for many plant species.