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.

塞内加尔非洲楝（Khaya senegalensis，俗称非洲红木或干旱区红木）是一种高价值硬木用材树种，在澳大利亚北部人工林营造中具备广阔应用潜力。该物种自然分布于撒哈拉以南带状区域，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面临瓶颈，该物种目前已被列为易危物种。本研究通过下一代测序（next generation sequencing）技术开发塞内加尔非洲楝的微卫星标记（microsatellite markers），以评估其在自然分布区内的种内遗传多样性——这是该物种高效育种计划与有效保护管理的核心关键。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）位点，研究人员为其中522个微卫星位点设计了特异性引物。本研究对21个微卫星位点进行了验证，其中11个位点在塞内加尔非洲楝中表现出稳定的扩增效果与多态性。本研究将这11个新开发的微卫星标记，加上1个已发表的同源标记，用于评估源自澳大利亚塞内加尔非洲楝驯化项目的73份种质材料，这些材料采自该物种的整个自然分布区。群体结构分析软件STRUCTURE（STRUCTURE）的分析结果显示，受试材料可分为两个主要类群：第一类群主要包含来自西非（塞内加尔至贝宁）的材料，第二类群则对应分布区最东部的苏丹与乌干达群体。西非群体的遗传多样性水平显著高于东部群体。这表明从西非地区采集的新种子，相较于来自东非苏丹与乌干达的种子，能够产生遗传多样性更为丰富的子代基因型。