A well-constructed linkage map that places genetic markers in position relative to one another is critical in quantitative trait locus (QTL) analysis in many plant and animal species. Relating DNA markers to genetically inherited traits improves the efficiency of agronomic crop research by permitting marker assisted breeding approaches to be used to select plants with desirable traits, such as improved disease resistance and increased yield. A linkage map is constructed using DNA marker genotypes for samples from an experimental population of known pedigree. Markers are assigned to linkage groups based on how closely they are linked, as measured by their recombination rates. The optimal order of markers within groups is determined to calculate the shortest genetic distance map. New features in JMP Genomics 5.1 compute linkage groups and determine an optimally ordered marker map using optimization routines in PROC OPTMODEL from SAS/OR. We highlight these new features in the analysis of DNA markers from oat plants derived from recombinant inbred lines as part of ongoing research by the Collaborative Oat Research Enterprise (CORE).