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(SSR) Markers and Application to the Analysis of Genetic Transferability, development of simple sequence repeat (SSR) markers and application to the analysis of genetic diversity and population structure of the African fan palm (Borassus aethiopum Mart.) in Benin Mariano Joly Kpatènon, Kolawolé Valère Salako, Sylvain Santoni, Leila Zekraoui, Muriel Latreille, Christine Tollon-Cordet, Cédric Mariac, Estelle Jaligot, Thierry Beulé, Kifouli Adéoti To cite this version: Mariano Joly Kpatènon, Kolawolé Valère Salako, Sylvain Santoni, Leila Zekraoui, Muriel Latreille, et al.. Transferability, development of simple sequence repeat (SSR) markers and application to the analysis of genetic diversity and population structure of the African fan palm (Borassus aethiopum Mart.) in Benin. BMC Genetics, 2020, 21 (1), 10.1186/s12863-020-00955-y. hal-03105540 HAL Id: hal-03105540 https://hal.inrae.fr/hal-03105540 Submitted on 11 Jan 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License Kpatènon et al. BMC Genetics (2020) 21:145 https://doi.org/10.1186/s12863-020-00955-y RESEARCH ARTICLE Open Access Transferability, development of simple sequence repeat (SSR) markers and application to the analysis of genetic diversity and population structure of the African fan palm (Borassus aethiopum Mart.) in Benin Mariano Joly Kpatènon1,2,3, Kolawolé Valère Salako2,4, Sylvain Santoni5, Leila Zekraoui3, Muriel Latreille5, Christine Tollon-Cordet5, Cédric Mariac3, Estelle Jaligot3,6†, Thierry Beulé3,6† and Kifouli Adéoti1,2*† Abstract 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 (Continued on next page) * Correspondence: [email protected] Estelle Jaligot, Thierry Beulé and Kifouli Adéoti are equal contributors as last authors. 1Laboratoire de Microbiologie et de Technologie Alimentaire (LAMITA), Faculté des Sciences et Techniques, Université d’Abomey-Calavi, Cotonou, Bénin 2Biodiversité et Ecologie des Plantes (BDEP), Faculté des Sciences et Techniques, Université d’Abomey-Calavi, Cotonou, Bénin Full list of author information is available at the end of the article © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Kpatènon et al. BMC Genetics (2020) 21:145 Page 2 of 23 (Continued from previous page) 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. Keywords: Borassus aethiopum, Genetic diversity, Microsatellite, Marker transferability, High-throughput sequencing, Simple sequence repeat, Under-studied species Background amplification/polymorphism detection, require some Many plant species remain under-studied due to their prior knowledge of the genome of the target species low economic importance, complicated biology and/or and may prove to be expensive and time-consuming the absence of available genome sequence information. [11, 13]. In order to overcome this difficulty, ap- Upon initiating a research project aimed at characteriz- proaches relying on the transfer of SSR markers be- ing the genetic diversity of such a species, researchers tween species or genera have therefore been may be confronted with the situation that some re- implemented. They have been successful in many in- sources can be found in related taxa. In such cases, the stances, as documented across Prunus species and first step is often to assess whether some of these re- among members of the Rosaceae family [14, 15]; be- sources, such as molecular markers, can be used to study tween species of the Hevea genus and to other Euphor- the new species. Provided that the “source” species dis- biaceae [16]; among Lamiaceae [17]; among Legumes play enough genetic similarities to the “target” species belonging to the Vicia genus [18] and from the Phaseo- and that marker transferability has been previously lus genus to Vigna [19]. In other cases, the ever- assessed, this first step may lead to quick progress in a increasing affordability of high-throughput sequencing cost-effective manner. Often, transferring markers be- technologies and the development of dedicated bio- tween species is seen as a smarter investment than de- informatics data mining tools have enabled the identifi- veloping and testing new markers, especially if limited cation of microsatellite loci and the development of funding is available [1, 2]. SSR markers, including in non-model plant species with Over the last three decades, molecular markers have limited or no background genetic information [20–23]. been widely used to study genetic variation among and Borassus aethiopum Mart., also known as ron palm, within populations of various plant species [3–7]. toddy palm or African fan palm, is a dioecious species be- Among the different types of markers that are available, longing to the Arecaceae family. It is widely distributed microsatellites or simple sequence repeats (SSRs) are across West and Central Africa, where it is present as wild often selected due to their high mutation frequency, populations [24]. The species is classified as a non-timber − − which ranges from 10 2 to 10 6 nucleotides per locus forest products (NTFPs)-providing plant, since different per generation [2, 8] and generates multiple allelic parts of the plant are used for various purposes by local forms, and their co-dominant nature. The combination populations [24, 25]. In Benin (West Africa) for instance, of both characteristics makes them sensitive tools for 121 different uses distributed in seven categories (medi- the assessment of genetic diversity among species, de- cinal, handicrafts, food, construction, firewood, cere- termination of population structure, phylogenetic re- monies and rituals) have been reported for the species construction, genetic mapping, evolutionary analyses, [26]. Among these, the consumption of ripe fruits (fresh and molecular breeding [9–12]. From a practical
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