Comparative assessment of genetic diversity matrices and clustering methods in white Guinea yam (Dioscorea rotundata) based on morphological and molecular markers
Understanding the diversity and genetic relationships among and within crop germplasm is invaluable for genetic improvement. This study assessed genetic diversity in a panel of 173 D. rotundata accessions using joint analysis for 23 morphological traits and 136,429 SNP markers from the whole-genome...
| Main Authors: | , , , , , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
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Springer
2020
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| Online Access: | https://hdl.handle.net/10568/117516 |
| _version_ | 1855528724003291136 |
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| author | Darkwa, K. Agre, P. Olasanmi, B. Iseki, K. Matsumoto, R. Powell, A. Bauchet, Guillaume J. Koeyer, D. de Muranaka, S. Adebola, P.O. Asiedu, R. Terauchi, R. Asfaw, A. |
| author_browse | Adebola, P.O. Agre, P. Asfaw, A. Asiedu, R. Bauchet, Guillaume J. Darkwa, K. Iseki, K. Koeyer, D. de Matsumoto, R. Muranaka, S. Olasanmi, B. Powell, A. Terauchi, R. |
| author_facet | Darkwa, K. Agre, P. Olasanmi, B. Iseki, K. Matsumoto, R. Powell, A. Bauchet, Guillaume J. Koeyer, D. de Muranaka, S. Adebola, P.O. Asiedu, R. Terauchi, R. Asfaw, A. |
| author_sort | Darkwa, K. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Understanding the diversity and genetic relationships among and within crop germplasm is invaluable for genetic improvement. This study assessed genetic diversity in a panel of 173 D. rotundata accessions using joint analysis for 23 morphological traits and 136,429 SNP markers from the whole-genome resequencing platform. Various diversity matrices and clustering methods were evaluated for a comprehensive characterization of genetic diversity in white Guinea yam from West Africa at phenotypic and molecular levels. The translation of the different diversity matrices from the phenotypic and genomic information into distinct groups varied with the hierarchal clustering methods used. Gower distance matrix based on phenotypic data and identity by state (IBS) distance matrix based on SNP data with the UPGMA clustering method found the best fit to dissect the genetic relationship in current set materials. However, the grouping pattern was inconsistent (r = − 0.05) between the morphological and molecular distance matrices due to the non-overlapping information between the two data types. Joint analysis for the phenotypic and molecular information maximized a comprehensive estimate of the actual diversity in the evaluated materials. The results from our study provide valuable insights for measuring quantitative genetic variability for breeding and genetic studies in yam and other root and tuber crops. |
| format | Journal Article |
| id | CGSpace117516 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2020 |
| publishDateRange | 2020 |
| publishDateSort | 2020 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1175162025-11-11T10:32:24Z Comparative assessment of genetic diversity matrices and clustering methods in white Guinea yam (Dioscorea rotundata) based on morphological and molecular markers Darkwa, K. Agre, P. Olasanmi, B. Iseki, K. Matsumoto, R. Powell, A. Bauchet, Guillaume J. Koeyer, D. de Muranaka, S. Adebola, P.O. Asiedu, R. Terauchi, R. Asfaw, A. genetic improvement yams dioscorea rotundata genetic markers west africa guinea yam morphology Understanding the diversity and genetic relationships among and within crop germplasm is invaluable for genetic improvement. This study assessed genetic diversity in a panel of 173 D. rotundata accessions using joint analysis for 23 morphological traits and 136,429 SNP markers from the whole-genome resequencing platform. Various diversity matrices and clustering methods were evaluated for a comprehensive characterization of genetic diversity in white Guinea yam from West Africa at phenotypic and molecular levels. The translation of the different diversity matrices from the phenotypic and genomic information into distinct groups varied with the hierarchal clustering methods used. Gower distance matrix based on phenotypic data and identity by state (IBS) distance matrix based on SNP data with the UPGMA clustering method found the best fit to dissect the genetic relationship in current set materials. However, the grouping pattern was inconsistent (r = − 0.05) between the morphological and molecular distance matrices due to the non-overlapping information between the two data types. Joint analysis for the phenotypic and molecular information maximized a comprehensive estimate of the actual diversity in the evaluated materials. The results from our study provide valuable insights for measuring quantitative genetic variability for breeding and genetic studies in yam and other root and tuber crops. 2020 2022-01-14T14:59:24Z 2022-01-14T14:59:24Z Journal Article https://hdl.handle.net/10568/117516 en Open Access application/pdf Springer Darkwa, K., Agre, P., Olasanmi, B., Iseki, K., Matsumoto, R., Powell, A., ... & Asfaw, A. (2020). Comparative assessment of genetic diversity matrices and clustering methods in white Guinea yam (Dioscorea rotundata) based on morphological and molecular markers. Scientific Reports, 10(1), 1-14. |
| spellingShingle | genetic improvement yams dioscorea rotundata genetic markers west africa guinea yam morphology Darkwa, K. Agre, P. Olasanmi, B. Iseki, K. Matsumoto, R. Powell, A. Bauchet, Guillaume J. Koeyer, D. de Muranaka, S. Adebola, P.O. Asiedu, R. Terauchi, R. Asfaw, A. Comparative assessment of genetic diversity matrices and clustering methods in white Guinea yam (Dioscorea rotundata) based on morphological and molecular markers |
| title | Comparative assessment of genetic diversity matrices and clustering methods in white Guinea yam (Dioscorea rotundata) based on morphological and molecular markers |
| title_full | Comparative assessment of genetic diversity matrices and clustering methods in white Guinea yam (Dioscorea rotundata) based on morphological and molecular markers |
| title_fullStr | Comparative assessment of genetic diversity matrices and clustering methods in white Guinea yam (Dioscorea rotundata) based on morphological and molecular markers |
| title_full_unstemmed | Comparative assessment of genetic diversity matrices and clustering methods in white Guinea yam (Dioscorea rotundata) based on morphological and molecular markers |
| title_short | Comparative assessment of genetic diversity matrices and clustering methods in white Guinea yam (Dioscorea rotundata) based on morphological and molecular markers |
| title_sort | comparative assessment of genetic diversity matrices and clustering methods in white guinea yam dioscorea rotundata based on morphological and molecular markers |
| topic | genetic improvement yams dioscorea rotundata genetic markers west africa guinea yam morphology |
| url | https://hdl.handle.net/10568/117516 |
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