Genotyping-by-sequencing to unlock genetic diversity and population structure in white yam (dioscorea rotundata poir.)
White yam (Dioscorearotundata Poir.) is one of the most important tuber crops in West Africa, where it is indigenous and represents the largest repository of biodiversity through several years of domestication, production, consumption, and trade. In this study, the genotyping-by-sequencing (GBS) app...
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Journal Article |
| Language: | Inglés |
| Published: |
MDPI
2020
|
| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/110236 |
| _version_ | 1855535359958450176 |
|---|---|
| author | Bhattacharjee, Ranjana Agre, A.P. Bauchet, Guillaume J. Koeyer, D. de López Montes, Antonio José Kumar, P. Lava Abberton, Michael T. Adebola, P.O. Asfaw, A. Asiedu, R. |
| author_browse | Abberton, Michael T. Adebola, P.O. Agre, A.P. Asfaw, A. Asiedu, R. Bauchet, Guillaume J. Bhattacharjee, Ranjana Koeyer, D. de Kumar, P. Lava López Montes, Antonio José |
| author_facet | Bhattacharjee, Ranjana Agre, A.P. Bauchet, Guillaume J. Koeyer, D. de López Montes, Antonio José Kumar, P. Lava Abberton, Michael T. Adebola, P.O. Asfaw, A. Asiedu, R. |
| author_sort | Bhattacharjee, Ranjana |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | White yam (Dioscorearotundata Poir.) is one of the most important tuber crops in West Africa, where it is indigenous and represents the largest repository of biodiversity through several years of domestication, production, consumption, and trade. In this study, the genotyping-by-sequencing (GBS) approach was used to sequence 814 genotypes consisting of genebank landraces, breeding lines, and market varieties to understand the level of genetic diversity and pattern of the population structure among them. The genetic diversity among different genotypes was assessed using three complementary clustering methods, the model-based admixture, discriminant analysis of principal components (DAPC), and phylogenetic tree. ADMIXTURE analysis revealed an optimum number of four groups that matched with the number of clusters obtained through phylogenetic tree. Clustering results obtained from ADMIXTURE analysis were further validated using DAPC-based clustering. Analysis of molecular variance (AMOVA) revealed high genetic diversity (96%) within each genetic group. A network analysis was further carried out to depict the genetic relationships among the three genetic groups (breeding lines, genebank landraces, and market varieties) used in the study. This study showed that the use of advanced sequencing techniques such as GBS coupled with statistical analysis is a robust method for assessing genetic diversity and population structure in a complex crop such as white yam. |
| format | Journal Article |
| id | CGSpace110236 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2020 |
| publishDateRange | 2020 |
| publishDateSort | 2020 |
| publisher | MDPI |
| publisherStr | MDPI |
| record_format | dspace |
| spelling | CGSpace1102362025-12-08T09:54:28Z Genotyping-by-sequencing to unlock genetic diversity and population structure in white yam (dioscorea rotundata poir.) Bhattacharjee, Ranjana Agre, A.P. Bauchet, Guillaume J. Koeyer, D. de López Montes, Antonio José Kumar, P. Lava Abberton, Michael T. Adebola, P.O. Asfaw, A. Asiedu, R. yams dioscorea rotundata food security genetics single nucleotide polymorphism genetic variation population structure White yam (Dioscorearotundata Poir.) is one of the most important tuber crops in West Africa, where it is indigenous and represents the largest repository of biodiversity through several years of domestication, production, consumption, and trade. In this study, the genotyping-by-sequencing (GBS) approach was used to sequence 814 genotypes consisting of genebank landraces, breeding lines, and market varieties to understand the level of genetic diversity and pattern of the population structure among them. The genetic diversity among different genotypes was assessed using three complementary clustering methods, the model-based admixture, discriminant analysis of principal components (DAPC), and phylogenetic tree. ADMIXTURE analysis revealed an optimum number of four groups that matched with the number of clusters obtained through phylogenetic tree. Clustering results obtained from ADMIXTURE analysis were further validated using DAPC-based clustering. Analysis of molecular variance (AMOVA) revealed high genetic diversity (96%) within each genetic group. A network analysis was further carried out to depict the genetic relationships among the three genetic groups (breeding lines, genebank landraces, and market varieties) used in the study. This study showed that the use of advanced sequencing techniques such as GBS coupled with statistical analysis is a robust method for assessing genetic diversity and population structure in a complex crop such as white yam. 2020 2020-11-19T11:12:41Z 2020-11-19T11:12:41Z Journal Article https://hdl.handle.net/10568/110236 en Open Access application/pdf MDPI Bhattacharjee, R., Agre, P., Bauchet, G., De Koeyer, D., Lopez-Montes, A., Kumar, P., ... & Asiedu, R. (2020). Genotyping-by-sequencing to unlock genetic diversity and population structure in white yam (Dioscorea rotundata Poir.). Agronomy, 10(9), 1437: 1-16. |
| spellingShingle | yams dioscorea rotundata food security genetics single nucleotide polymorphism genetic variation population structure Bhattacharjee, Ranjana Agre, A.P. Bauchet, Guillaume J. Koeyer, D. de López Montes, Antonio José Kumar, P. Lava Abberton, Michael T. Adebola, P.O. Asfaw, A. Asiedu, R. Genotyping-by-sequencing to unlock genetic diversity and population structure in white yam (dioscorea rotundata poir.) |
| title | Genotyping-by-sequencing to unlock genetic diversity and population structure in white yam (dioscorea rotundata poir.) |
| title_full | Genotyping-by-sequencing to unlock genetic diversity and population structure in white yam (dioscorea rotundata poir.) |
| title_fullStr | Genotyping-by-sequencing to unlock genetic diversity and population structure in white yam (dioscorea rotundata poir.) |
| title_full_unstemmed | Genotyping-by-sequencing to unlock genetic diversity and population structure in white yam (dioscorea rotundata poir.) |
| title_short | Genotyping-by-sequencing to unlock genetic diversity and population structure in white yam (dioscorea rotundata poir.) |
| title_sort | genotyping by sequencing to unlock genetic diversity and population structure in white yam dioscorea rotundata poir |
| topic | yams dioscorea rotundata food security genetics single nucleotide polymorphism genetic variation population structure |
| url | https://hdl.handle.net/10568/110236 |
| work_keys_str_mv | AT bhattacharjeeranjana genotypingbysequencingtounlockgeneticdiversityandpopulationstructureinwhiteyamdioscorearotundatapoir AT agreap genotypingbysequencingtounlockgeneticdiversityandpopulationstructureinwhiteyamdioscorearotundatapoir AT bauchetguillaumej genotypingbysequencingtounlockgeneticdiversityandpopulationstructureinwhiteyamdioscorearotundatapoir AT koeyerdde genotypingbysequencingtounlockgeneticdiversityandpopulationstructureinwhiteyamdioscorearotundatapoir AT lopezmontesantoniojose genotypingbysequencingtounlockgeneticdiversityandpopulationstructureinwhiteyamdioscorearotundatapoir AT kumarplava genotypingbysequencingtounlockgeneticdiversityandpopulationstructureinwhiteyamdioscorearotundatapoir AT abbertonmichaelt genotypingbysequencingtounlockgeneticdiversityandpopulationstructureinwhiteyamdioscorearotundatapoir AT adebolapo genotypingbysequencingtounlockgeneticdiversityandpopulationstructureinwhiteyamdioscorearotundatapoir AT asfawa genotypingbysequencingtounlockgeneticdiversityandpopulationstructureinwhiteyamdioscorearotundatapoir AT asiedur genotypingbysequencingtounlockgeneticdiversityandpopulationstructureinwhiteyamdioscorearotundatapoir |