Rapid microsatellite marker development for African mahogany (Khaya senegalensis, Meliaceae) using next-generation sequencing and assessment of its intra-specific genetic diversity.

Khaya senegalensis (African mahogany or dry-zone mahogany) is a high-value hardwood timber species with great potential for forest plantations in northern Australia. The species is distributed across the sub-Saharan belt from Senegal to Sudan and Uganda. Due to heavy exploitation and constraints on natural regeneration and sustainable planting, it is now classified as a vulnerable species. Here we describe the development of microsatellite markers for K. senegalensis using next generation sequencing in order to assess its intra-specific diversity across its natural range, which is a key for successful breeding programs and effective conservation management of the species. Next generation sequencing yielded 93 943 sequences with an average read length of 234 bp. The assembled sequences contained 1030 simple sequence repeats, with primers designed for 522 microsatellite loci. Twenty one microsatellite loci were tested with eleven showing reliable amplification and polymorphism in K. seneg...