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
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.
Main Authors: | , , , , , , , , , |
---|---|
Format: | article biblioteca |
Language: | eng |
Subjects: | F30 - Génétique et amélioration des plantes, Borassus aethiopum, microsatellite, variation génétique, structure de la population, diversité génétique (comme ressource), http://aims.fao.org/aos/agrovoc/c_1009, http://aims.fao.org/aos/agrovoc/c_36574, http://aims.fao.org/aos/agrovoc/c_15975, http://aims.fao.org/aos/agrovoc/c_6115, http://aims.fao.org/aos/agrovoc/c_33952, http://aims.fao.org/aos/agrovoc/c_875, |
Online Access: | http://agritrop.cirad.fr/597129/ http://agritrop.cirad.fr/597129/1/s12863-020-00955-y.pdf |
Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
id |
dig-cirad-fr-597129 |
---|---|
record_format |
koha |
institution |
CIRAD FR |
collection |
DSpace |
country |
Francia |
countrycode |
FR |
component |
Bibliográfico |
access |
En linea |
databasecode |
dig-cirad-fr |
tag |
biblioteca |
region |
Europa del Oeste |
libraryname |
Biblioteca del CIRAD Francia |
language |
eng |
topic |
F30 - Génétique et amélioration des plantes Borassus aethiopum microsatellite variation génétique structure de la population diversité génétique (comme ressource) http://aims.fao.org/aos/agrovoc/c_1009 http://aims.fao.org/aos/agrovoc/c_36574 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_6115 http://aims.fao.org/aos/agrovoc/c_33952 http://aims.fao.org/aos/agrovoc/c_875 F30 - Génétique et amélioration des plantes Borassus aethiopum microsatellite variation génétique structure de la population diversité génétique (comme ressource) http://aims.fao.org/aos/agrovoc/c_1009 http://aims.fao.org/aos/agrovoc/c_36574 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_6115 http://aims.fao.org/aos/agrovoc/c_33952 http://aims.fao.org/aos/agrovoc/c_875 |
spellingShingle |
F30 - Génétique et amélioration des plantes Borassus aethiopum microsatellite variation génétique structure de la population diversité génétique (comme ressource) http://aims.fao.org/aos/agrovoc/c_1009 http://aims.fao.org/aos/agrovoc/c_36574 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_6115 http://aims.fao.org/aos/agrovoc/c_33952 http://aims.fao.org/aos/agrovoc/c_875 F30 - Génétique et amélioration des plantes Borassus aethiopum microsatellite variation génétique structure de la population diversité génétique (comme ressource) http://aims.fao.org/aos/agrovoc/c_1009 http://aims.fao.org/aos/agrovoc/c_36574 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_6115 http://aims.fao.org/aos/agrovoc/c_33952 http://aims.fao.org/aos/agrovoc/c_875 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 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 |
description |
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. |
format |
article |
topic_facet |
F30 - Génétique et amélioration des plantes Borassus aethiopum microsatellite variation génétique structure de la population diversité génétique (comme ressource) http://aims.fao.org/aos/agrovoc/c_1009 http://aims.fao.org/aos/agrovoc/c_36574 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_6115 http://aims.fao.org/aos/agrovoc/c_33952 http://aims.fao.org/aos/agrovoc/c_875 |
author |
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 |
author_facet |
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 |
author_sort |
Kpatenon, Mariano Joly |
title |
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 |
title_short |
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 |
title_full |
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 |
title_fullStr |
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 |
title_full_unstemmed |
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 |
title_sort |
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 |
url |
http://agritrop.cirad.fr/597129/ http://agritrop.cirad.fr/597129/1/s12863-020-00955-y.pdf |
work_keys_str_mv |
AT kpatenonmarianojoly transferabilitydevelopmentofsimplesequencerepeatssrmarkersandapplicationtotheanalysisofgeneticdiversityandpopulationstructureoftheafricanfanpalmborassusaethiopummartinbenin AT salakokolawolevalere transferabilitydevelopmentofsimplesequencerepeatssrmarkersandapplicationtotheanalysisofgeneticdiversityandpopulationstructureoftheafricanfanpalmborassusaethiopummartinbenin AT santonisylvain transferabilitydevelopmentofsimplesequencerepeatssrmarkersandapplicationtotheanalysisofgeneticdiversityandpopulationstructureoftheafricanfanpalmborassusaethiopummartinbenin AT zekraouileila transferabilitydevelopmentofsimplesequencerepeatssrmarkersandapplicationtotheanalysisofgeneticdiversityandpopulationstructureoftheafricanfanpalmborassusaethiopummartinbenin AT latreillemuriel transferabilitydevelopmentofsimplesequencerepeatssrmarkersandapplicationtotheanalysisofgeneticdiversityandpopulationstructureoftheafricanfanpalmborassusaethiopummartinbenin AT tolloncordetchristine transferabilitydevelopmentofsimplesequencerepeatssrmarkersandapplicationtotheanalysisofgeneticdiversityandpopulationstructureoftheafricanfanpalmborassusaethiopummartinbenin AT mariaccedric transferabilitydevelopmentofsimplesequencerepeatssrmarkersandapplicationtotheanalysisofgeneticdiversityandpopulationstructureoftheafricanfanpalmborassusaethiopummartinbenin AT jaligotestelle transferabilitydevelopmentofsimplesequencerepeatssrmarkersandapplicationtotheanalysisofgeneticdiversityandpopulationstructureoftheafricanfanpalmborassusaethiopummartinbenin AT beulethierry transferabilitydevelopmentofsimplesequencerepeatssrmarkersandapplicationtotheanalysisofgeneticdiversityandpopulationstructureoftheafricanfanpalmborassusaethiopummartinbenin AT adeotiadeolazourikifouli transferabilitydevelopmentofsimplesequencerepeatssrmarkersandapplicationtotheanalysisofgeneticdiversityandpopulationstructureoftheafricanfanpalmborassusaethiopummartinbenin |
_version_ |
1792500069930369024 |
spelling |
dig-cirad-fr-5971292024-01-29T03:12:26Z http://agritrop.cirad.fr/597129/ http://agritrop.cirad.fr/597129/ 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. BMC Genetics, 21:145, 23 p.https://doi.org/10.1186/s12863-020-00955-y <https://doi.org/10.1186/s12863-020-00955-y> 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 eng 2020 BMC Genetics F30 - Génétique et amélioration des plantes Borassus aethiopum microsatellite variation génétique structure de la population diversité génétique (comme ressource) http://aims.fao.org/aos/agrovoc/c_1009 http://aims.fao.org/aos/agrovoc/c_36574 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_6115 http://aims.fao.org/aos/agrovoc/c_33952 Bénin http://aims.fao.org/aos/agrovoc/c_875 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. article info:eu-repo/semantics/article Journal Article info:eu-repo/semantics/publishedVersion http://agritrop.cirad.fr/597129/1/s12863-020-00955-y.pdf text cc_by info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/ https://doi.org/10.1186/s12863-020-00955-y 10.1186/s12863-020-00955-y info:eu-repo/semantics/altIdentifier/doi/10.1186/s12863-020-00955-y info:eu-repo/semantics/altIdentifier/purl/https://doi.org/10.1186/s12863-020-00955-y info:eu-repo/semantics/dataset/purl/https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA576413 info:eu-repo/semantics/dataset/purl/https://bmcgenomdata.biomedcentral.com/articles?searchType=journalSearch&sort=PubDate&page=5 |