Molecular characterization of cowpea [Vigna unguiculata (L.) Walp.] subspecies with SSR markers

Background Cowpea, Vigna unguiculata, is an important food legume in the tropics and subtropics. However, cowpea is a complex species with more than 10 subspecies which can hybridize and produce intermediate progenies. Partly because of the complex organization of the cowpea gene pool and the lack of adequate markers for these infraspecific units, cowpea breeders are not using the wild part of the cowpea gene pool. Methods Here, we report the molecular characterization of 34 representative accessions with 61 SSR markers from coding regions. Results If SSR failed to separate the closest groups, i.e. subsp. alba, subsp. tenuis and the perennial groups from subsp. unguiculata, a combination of few SSR markers can properly identify the main cowpea subspecies. Regarding the infraspecific phylogeny of cowpea, SSR markers confirm the special status of the annual subsp. unguiculata versus the different perennial subspecies. It confirms that subsp. protracta looks like the oldest subspecies, making the origin of the species in southern Africa likely. However, it unites in a single group, clearly separated from subsp. unguiculata, all the taxa of hybrid origin, i.e. subsp. alba, subsp. tenuis, subsp. pubescens and the BWA group of subsp. unguiculata. Conclusion Although a limited number of markers was tested considering that several hundred of cowpea SSR are available, the present work shows that SSR markers can be used for molecular characterization of cowpea subspecies and can be very helpful for understanding its complex evolutionnary history.