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

Kpatenon Mariano Joly, Salako Kolawolé Valère, Santoni Sylvain, Zekraoui Leïla, Latreille Muriel, Tollon-Cordet Christine, Mariac Cédric, Jaligot Estelle, Beulé Thierry, Adeoti Adéola Zouri-Kifouli. 2020. 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, 21:145, 23 p.

https://doi.org/10.1186/s12863-020-00955-y

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Url - jeu de données - Entrepôt autre : https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA576413 / Url - jeu de données - Entrepôt autre : https://bmcgenomdata.biomedcentral.com/articles?searchType=journalSearch&sort=PubDate&page=5

Quartile : Q3, Sujet : GENETICS & HEREDITY

Liste HCERES des revues (en SHS) : oui

Thème(s) HCERES des revues (en SHS) : Anthropologie-Ethnologie

Résumé : 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.

Mots-clés Agrovoc : Borassus aethiopum, microsatellite, variation génétique, structure de la population, diversité génétique (comme ressource)

Mots-clés géographiques Agrovoc : Bénin

Mots-clés libres : Borassus aethiopum, Genetic diversity, High-throughput sequencing, Microsatellite, Simple sequence repeat, Marker transferability, Under-studied species

Classification Agris : F30 - Génétique et amélioration des plantes

Champ stratégique Cirad : CTS 1 (2019-) - Biodiversité

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