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.

塞内加尔非洲桃花心木（Khaya senegalensis，又名非洲桃花心木或旱区桃花心木）是一种高价值阔叶用材树种，在澳大利亚北部人工林培育中具有极高应用潜力。该物种自然分布于撒哈拉以南地带，西起塞内加尔，东至苏丹与乌干达。由于过度采伐、自然更新受限以及可持续种植瓶颈，目前该物种已被列为易危物种。本研究阐述了利用下一代测序（next generation sequencing）技术开发塞内加尔非洲桃花心木微卫星标记（microsatellite markers）的过程，旨在评估其天然分布范围内的种内遗传多样性——这是该物种成功实施育种计划与开展有效保护管理的核心前提。下一代测序共获得93943条序列，平均读长为234 bp。组装得到的序列中包含1030个简单序列重复（simple sequence repeats）位点，共为522个微卫星位点设计了扩增引物。随后对21个微卫星位点进行验证，其中11个在塞内加尔非洲桃花心木中表现出稳定扩增与多态性。本研究利用这11个新开发的微卫星标记，结合1个已发表的微卫星标记，对澳大利亚塞内加尔非洲桃花心木驯化项目中的73份种质资源开展遗传分析，这些种质均采自该物种的天然分布范围。STRUCTURE群体结构分析结果显示存在两个主要遗传集群：其一主要包含来自西非（塞内加尔至贝宁）的种质，其二则分布于该物种分布范围的最东部区域，即苏丹与乌干达。研究发现西非地区的种质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可获得比东非苏丹、乌干达来源种质更为多样的基因型。