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
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 developmen...
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| Format: | Article |
| Language: | English |
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BMC
2020-12-01
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| Series: | BMC Genetics |
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| Online Access: | https://doi.org/10.1186/s12863-020-00955-y |
| _version_ | 1818006663930576896 |
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| author | Mariano Joly Kpatènon Kolawolé Valère Salako Sylvain Santoni Leila Zekraoui Muriel Latreille Christine Tollon-Cordet Cédric Mariac Estelle Jaligot Thierry Beulé Kifouli Adéoti |
| author_facet | Mariano Joly Kpatènon Kolawolé Valère Salako Sylvain Santoni Leila Zekraoui Muriel Latreille Christine Tollon-Cordet Cédric Mariac Estelle Jaligot Thierry Beulé Kifouli Adéoti |
| author_sort | Mariano Joly Kpatènon |
| collection | DOAJ |
| description | 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 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. |
| first_indexed | 2024-04-14T05:04:22Z |
| format | Article |
| id | doaj.art-304c8e645f874a5192d99884cd0f770c |
| institution | Directory Open Access Journal |
| issn | 1471-2156 |
| language | English |
| last_indexed | 2024-04-14T05:04:22Z |
| publishDate | 2020-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genetics |
| spelling | doaj.art-304c8e645f874a5192d99884cd0f770c2022-12-22T02:10:46ZengBMCBMC Genetics1471-21562020-12-0121112310.1186/s12863-020-00955-yTransferability, 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 BeninMariano Joly Kpatènon0Kolawolé Valère Salako1Sylvain Santoni2Leila Zekraoui3Muriel Latreille4Christine Tollon-Cordet5Cédric Mariac6Estelle Jaligot7Thierry Beulé8Kifouli Adéoti9Laboratoire de Microbiologie et de Technologie Alimentaire (LAMITA), Faculté des Sciences et Techniques, Université d’Abomey-CalaviBiodiversité et Ecologie des Plantes (BDEP), Faculté des Sciences et Techniques, Université d’Abomey-CalaviAGAP, Univ Montpellier, CIRAD, INRAE, Montpellier SupAgroDIADE, Univ Montpellier, IRDAGAP, Univ Montpellier, CIRAD, INRAE, Montpellier SupAgroAGAP, Univ Montpellier, CIRAD, INRAE, Montpellier SupAgroDIADE, Univ Montpellier, IRDDIADE, Univ Montpellier, IRDDIADE, Univ Montpellier, IRDLaboratoire de Microbiologie et de Technologie Alimentaire (LAMITA), Faculté des Sciences et Techniques, Université d’Abomey-CalaviAbstract 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.https://doi.org/10.1186/s12863-020-00955-yBorassus aethiopumGenetic diversityMicrosatelliteMarker transferabilityHigh-throughput sequencingSimple sequence repeat |
| spellingShingle | Mariano Joly Kpatènon Kolawolé Valère Salako Sylvain Santoni Leila Zekraoui Muriel Latreille Christine Tollon-Cordet Cédric Mariac Estelle Jaligot Thierry Beulé Kifouli Adéoti 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 Borassus aethiopum Genetic diversity Microsatellite Marker transferability High-throughput sequencing Simple sequence repeat |
| 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_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_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_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 |
| topic | Borassus aethiopum Genetic diversity Microsatellite Marker transferability High-throughput sequencing Simple sequence repeat |
| url | https://doi.org/10.1186/s12863-020-00955-y |
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