Background 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. Results 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. Conclusions 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.

2 to the analysis of genetic diversity and population structure of the African fan palm 3 (Borassus aethiopum Mart.) in Benin 4 5Abstract: 34 In Sub-Saharan Africa, the fan palm Borassus aethiopum Mart. is an important non-timber 35 forest product-providing palm that faces multiple anthropogenic threats to its genetic diversity. 36 However, this species is so far under-studied, which prevents its sustainable development as a 37 resource. 38 The present work is a first attempt at characterizing the genetic diversity of this palm species 39 as well as its spatial structuration in Benin, West Africa. During a first phase we implemented 40 a microsatellite markers-based approach relying on the reported transferability of primers 41 developed in other palm species and found that, in disagreement with previously published 42 results, only 22.5% of the 80 markers tested enabled amplification of African fan palm DNA 43 and polymorphism detection was insufficient. During a second phase, we therefore generated a 44 B. aethiopum-specific genomic dataset through high-throughput sequencing and used it for the 45 de novo detection of potential microsatellite markers. Among these, 11 enabled polymorphism 46 detection and were further used for analyzing genetic diversity in nine B. aethiopum 47 populations. 48Our results show that genetic diversity of Beninese fan palm populations is low, with an overall 49 average expected heterozygosity (He) of 0.354. Moreover, the positive values of the fixation 50 index (F) in populations from both the Central (Soudano-Guinean) and the Southern (Guinean) 51 regions suggest limited gene flows. Our analysis show that sampled B. aethiopum populations 52 are clustered into two groups, one spanning populations from both the Southern and most of 53 the Central region, and the other including the Central population of Savè (which also has the 54 highest He) and populations from the North.55In light of our results, we discuss the use of inter-species transfer vs. de novo development of 56 microsatellite markers in genetic diversity analyses targeting under-studied species. We also 57 suggest future applications for the molecular resources generated through the present study. 59Many plant species remain under-studied due to their low economic importance, complicated 60 biology and/or the absence of available genome sequence information. Upon initiating a 61 research project aimed at characterizing the genetic diversity of such a species, researchers may 62 be confronted with the situation that some resources can be found in more or less distantly 63 related taxa. In such cases, the first step is often to assess whether some of these resources, such 64 as molecular markers, can be used to study the new species. Provided that the "source" species 65 display enough genetic similarities to the "target" species and that marker transferability has 66 been previously assessed, this first step may lead to quick progress in a cost-effective manner. 67In many instances, transferring markers betw...

Background: 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. Results: 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. We thus generated a B. aethiopum-specific genomic dataset through high-throughput sequencing and used it in a second phase for the de novo detection of microsatellite loci. Among the primer pairs designed to target these, 11 enabled polymorphism detection and were further used for analyzing genetic diversity. Across the nine collection sites, expected heterozygosity (He) ranges from 0.263 to 0.451 with an overall average value 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, and accordingly the low number of migrants and the 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. While we globally observe a weak correlation between genetic and geographic distances, our clustering analyses indicate that B. aethiopum palms from Savè (Center) are genetically more similar to those from the Northern sites than to samples from the other Central sites. Conclusions: 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. We also suggest future applications for the molecular resources generated through the present study.

Background: 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. Results: 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. Conclusions: 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.