Genome-wide genetic diversity and population structure of Garcinia kola (Heckel) in Benin using DArT-Seq technology
Garcinia kola (Heckel) is a versatile tree indigenous to West and Central Africa. All parts of the tree have value in traditional medicine. Natural populations of the species have declined over the years due to overexploitation. Assessment of genetic diversity and population structure of G. kola is...
| Autores principales: | , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
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Public Library of Science
2020
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| Acceso en línea: | https://hdl.handle.net/10568/110021 |
| _version_ | 1855536474649264128 |
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| author | Dadjo, C. Nyende, A.B. Yao, Nasser Kiplangat, N. Assogbadjo, A.E. |
| author_browse | Assogbadjo, A.E. Dadjo, C. Kiplangat, N. Nyende, A.B. Yao, Nasser |
| author_facet | Dadjo, C. Nyende, A.B. Yao, Nasser Kiplangat, N. Assogbadjo, A.E. |
| author_sort | Dadjo, C. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Garcinia kola (Heckel) is a versatile tree indigenous to West and Central Africa. All parts of the tree have value in traditional medicine. Natural populations of the species have declined over the years due to overexploitation. Assessment of genetic diversity and population structure of G. kola is important for its management and conservation. The present study investigates the genetic diversity and population structure of G. kola populations in Benin using ultra-high-throughput diversity array technology (DArT) single nucleotide polymorphism (SNP) markers. From the 102 accessions sampled, two were excluded from the final dataset owing to poor genotyping coverage. A total of 43,736 SNPs were reported, of which 12,585 were used for analyses after screening with quality control parameters including Minor allele frequency (≥ 0.05), call rate (≥ 80%), reproducibility (≥ 95%), and polymorphic information content (≥ 1%). Analysis revealed low genetic diversity with expected heterozygosity per population ranging from 0.196 to 0.228. Pairwise F-statistics (FST) revealed low levels of genetic differentiation between populations while an Analysis of molecular variance (AMOVA) indicated that the majority of variation (97.86%) was within populations. Population structure analysis through clustering and discriminant analysis on principal component revealed two admixed clusters, implying little genetic structure. However, the model-based maximum likelihood in Admixture indicated only one genetic cluster. The present study indicated low genetic diversity of G. kola, and interventions are needed to be tailored towards its conservation. |
| format | Journal Article |
| id | CGSpace110021 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2020 |
| publishDateRange | 2020 |
| publishDateSort | 2020 |
| publisher | Public Library of Science |
| publisherStr | Public Library of Science |
| record_format | dspace |
| spelling | CGSpace1100212025-12-08T09:54:28Z Genome-wide genetic diversity and population structure of Garcinia kola (Heckel) in Benin using DArT-Seq technology Dadjo, C. Nyende, A.B. Yao, Nasser Kiplangat, N. Assogbadjo, A.E. genomes crops primary forests garcinia Garcinia kola (Heckel) is a versatile tree indigenous to West and Central Africa. All parts of the tree have value in traditional medicine. Natural populations of the species have declined over the years due to overexploitation. Assessment of genetic diversity and population structure of G. kola is important for its management and conservation. The present study investigates the genetic diversity and population structure of G. kola populations in Benin using ultra-high-throughput diversity array technology (DArT) single nucleotide polymorphism (SNP) markers. From the 102 accessions sampled, two were excluded from the final dataset owing to poor genotyping coverage. A total of 43,736 SNPs were reported, of which 12,585 were used for analyses after screening with quality control parameters including Minor allele frequency (≥ 0.05), call rate (≥ 80%), reproducibility (≥ 95%), and polymorphic information content (≥ 1%). Analysis revealed low genetic diversity with expected heterozygosity per population ranging from 0.196 to 0.228. Pairwise F-statistics (FST) revealed low levels of genetic differentiation between populations while an Analysis of molecular variance (AMOVA) indicated that the majority of variation (97.86%) was within populations. Population structure analysis through clustering and discriminant analysis on principal component revealed two admixed clusters, implying little genetic structure. However, the model-based maximum likelihood in Admixture indicated only one genetic cluster. The present study indicated low genetic diversity of G. kola, and interventions are needed to be tailored towards its conservation. 2020-09-23 2020-10-30T08:24:38Z 2020-10-30T08:24:38Z Journal Article https://hdl.handle.net/10568/110021 en Open Access Public Library of Science Dadjo, C., Nyende, A.B., Yao, N., Kiplangat, N. and Assogbadjo, A.E. 2020. Genome-wide genetic diversity and population structure of Garcinia kola (Heckel) in Benin using DArT-Seq technology. PLoS ONE 15(9):e0238984. |
| spellingShingle | genomes crops primary forests garcinia Dadjo, C. Nyende, A.B. Yao, Nasser Kiplangat, N. Assogbadjo, A.E. Genome-wide genetic diversity and population structure of Garcinia kola (Heckel) in Benin using DArT-Seq technology |
| title | Genome-wide genetic diversity and population structure of Garcinia kola (Heckel) in Benin using DArT-Seq technology |
| title_full | Genome-wide genetic diversity and population structure of Garcinia kola (Heckel) in Benin using DArT-Seq technology |
| title_fullStr | Genome-wide genetic diversity and population structure of Garcinia kola (Heckel) in Benin using DArT-Seq technology |
| title_full_unstemmed | Genome-wide genetic diversity and population structure of Garcinia kola (Heckel) in Benin using DArT-Seq technology |
| title_short | Genome-wide genetic diversity and population structure of Garcinia kola (Heckel) in Benin using DArT-Seq technology |
| title_sort | genome wide genetic diversity and population structure of garcinia kola heckel in benin using dart seq technology |
| topic | genomes crops primary forests garcinia |
| url | https://hdl.handle.net/10568/110021 |
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