Data from: 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. senegalensis. The eleven novel microsatellites, together with one previously published, were used to assess 73 accessions belonging to the Australian K. senegalensis domestication program, sampled from across the natural range of the species. STRUCTURE analysis shows two major clusters, one comprising mainly accessions from west Africa (Senegal to Benin) and the second based in the far eastern limits of the range in Sudan and Uganda. Higher levels of genetic diversity were found in material from western Africa. This suggests that new seed collections from this region may yield more diverse genotypes than those originating from Sudan and Uganda in eastern Africa.塞内加尔桃花心木（Khaya senegalensis，俗称非洲桃花心木、干带桃花心木）是一种高价值硬木用材树种，在澳大利亚北部人工林培育中极具应用潜力。该树种自然分布于撒哈拉以南从塞内加尔至苏丹、乌干达的带状区域。由于过度采伐，加之自然更新与可持续种植受到限制，目前该物种已被列为易危物种。本研究描述了利用下一代测序（next generation sequencing）开发该物种微卫星标记（microsatellite markers）的过程，旨在评估其天然分布区内的种内遗传多样性，这对该物种的良种繁育计划与有效保护管理至关重要。下一代测序共获得93943条序列，平均读长为234 bp。组装后的序列中共包含1030个简单序列重复（simple sequence repeats，SSR）位点，针对其中522个微卫星位点设计了扩增引物。对21个微卫星位点进行验证后，有11个位点在塞内加尔桃花心木中表现出稳定扩增与多态性。将这11个新开发的微卫星标记与1个已发表的标记联合使用，对来自澳大利亚塞内加尔桃花心木驯化项目的73份种质材料进行了遗传分析，这些材料均采自该物种的天然分布区。STRUCTURE聚类分析结果显示存在两个主要遗传类群：一类主要包含来自西非（塞内加尔至贝宁）的种质材料，另一类则分布于该物种分布区的最东部，即苏丹与乌干达境内。西非来源的材料具有更高的遗传多样性水平，这表明从该区域采集的新种子样本所获得的基因型多样性，将高于来自东非苏丹与乌干达的材料。