Laboratoire de Microbiologie et de Technologie Alimentaire (LAMITA), Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Bénin.
Biodiversité et Ecologie des Plantes (BDEP), Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Bénin.
BMC Genet. 2020 Dec 3;21(1):145. doi: 10.1186/s12863-020-00955-y.
In Sub-Saharan Africa, Borassus aethiopum Mart. (African fan palm) is an important non-timber forest product-providing palm that faces multiple anthropogenic threats to its genetic diversity. However, this species is so far under-studied, which prevents its sustainable development as a resource. The present work is a first attempt at characterizing the genetic diversity and population structure of B. aethiopum across nine collection sites spanning the three climatic regions of Benin, West Africa, through the use of microsatellite markers.
During a first phase we relied on the reported transferability of primers developed in other palm species. We find that, in disagreement with previously published results, only 22.5% of the markers tested enable amplification of B. aethiopum DNA and polymorphism detection is very low. In a second phase, we generated a B. aethiopum-specific genomic dataset through high-throughput sequencing and used it for the de novo detection of microsatellite loci. Among the primer pairs targeting these, 11 detected polymorphisms and were further used for analyzing genetic diversity. Across the nine sites, expected heterozygosity (He) ranges from 0.263 to 0.451 with an overall average of 0.354, showing a low genetic diversity. Analysis of molecular variance (AMOVA) shows that within-site variation accounts for 53% of the genetic variation. Accordingly, the low number of migrants and positive values of the fixation index (F) in sites from both the Central (Sudano-Guinean) and the Southern (Guinean) climatic regions suggest limited gene flow between sites. The global correlation between genetic and geographic distances is weak; however, our clustering analyses indicate that B. aethiopum palms from Savè (Center) are genetically more similar to those from the North than to samples from other Central sites.
In the light of our results, we discuss the use of inter-species transfer vs. de novo development of microsatellite markers in genetic diversity analyses targeting under-studied species, and suggest future applications for our molecular resources. We propose that, while prominent short-range pollen and seed dispersal in Benin explain most of our results, gene flux between the Central and Northern regions, as a result of animal and/or human migrations, might underlie the Savè discrepancy.
在撒哈拉以南非洲，Borassus aethiopum Mart.（非洲扇叶棕）是一种重要的非木材森林产品提供棕榈树，面临着对其遗传多样性的多种人为威胁。然而，迄今为止，对该物种的研究还很不足，这阻碍了其作为资源的可持续发展。本工作首次尝试利用微卫星标记物，对贝宁（西非）三个气候区的九个采集点的 B. aethiopum 进行遗传多样性和种群结构分析。
在第一阶段，我们依赖于在其他棕榈物种中报道的引物的可转移性。我们发现，与之前发表的结果不一致，只有 22.5%的测试标记能够扩增 B. aethiopum DNA，且多态性检测非常低。在第二阶段，我们通过高通量测序生成了一个 B. aethiopum 特有的基因组数据集，并利用它从头检测微卫星位点。在针对这些引物的 11 对引物中，有 11 对检测到多态性，并进一步用于分析遗传多样性。在九个地点中，预期杂合度（He）范围从 0.263 到 0.451，平均值为 0.354，显示出较低的遗传多样性。分子方差分析（AMOVA）表明，站点内的变异占遗传变异的 53%。因此，中部（苏丹-几内亚）和南部（几内亚）气候区的多个站点的低迁移率和固定指数（F）的正值表明站点间的基因流有限。遗传距离和地理距离之间的全局相关性较弱；然而，我们的聚类分析表明，来自萨维（中心）的 B. aethiopum 棕榈与北部的样本比与其他中心地点的样本更具遗传相似性。
根据我们的结果，我们讨论了在针对研究较少的物种的遗传多样性分析中使用种间转移与从头开发微卫星标记的问题，并提出了我们分子资源的未来应用。我们提出，尽管在贝宁，突出的短程花粉和种子扩散解释了我们的大部分结果，但由于动物和/或人类的迁移，中央和北部地区之间的基因流动可能是萨维差异的基础。
