Genomics is central to modern breeding efforts. High-throughput genotyping can be used to construct genetic maps. These are key components of molecular assisted breeding. The most powerful genetic maps should be capable of various applications and should integrate information from different populations and species. In cowpea (Vigna unguiculata), a 1536 SNP assay was applied to thirteen breeding populations (1,293 individuals) and used to construct population-specific genetic maps using JoinMap 4. These maps were then integrated, using MergeMap, to develop a robust consensus genetic map with 1107 EST-derived SNP markers (856 bins). Here some applications of the consensus genetic map are demonstrated including comparative genomics, quantitative trait characterization, and map-based cloning. Syntenic relationships with soybean (Glycine max) are clarified and translate a wealth of annotated loci from the model crop to cowpea. Regions controlling the quantitative inheritance of heat tolerance during reproductive development, thrip (Thysanoptera: Thripidae) resistance, and maturity were identified through Bayesian and Interval Mapping methods using PROC QTL and MapQTL respectively. Map-based cloning and candidate gene analysis of cowpea pigmentation genes demonstrate the utility of the consensus map in functional genomics. Additionally, this consensus genetic map is of use to whole genome assembly, marker-assisted selection, and association mapping. These advances are being used to develop pest resistant and enhanced horticultural lines of cowpea. Please explore the HarvEST database (http://harvest.ucr.edu) for a plethora of open access information concerning this work among others.