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Article

Genotyping-by-Sequencing to Unlock Genetic Diversity and Population Structure in White Yam (Dioscorea rotundata Poir.)

1
International Institute of Tropical Agriculture, PMB 5320, Ibadan 200001, Nigeria
2
Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
3
Agriculture and Agri-Food Canada, Fredericton, NB E3B 4Z7, Canada
4
International Trade Center, 29 Independence Avenue, Accra 00233, Ghana
5
International Institute of Tropical Agriculture, PMB 82, Kubuwa, Abuja 901101, Nigeria
*
Author to whom correspondence should be addressed.
Agronomy 2020, 10(9), 1437; https://doi.org/10.3390/agronomy10091437
Received: 7 August 2020 / Revised: 12 September 2020 / Accepted: 14 September 2020 / Published: 22 September 2020
(This article belongs to the Section Crop Breeding and Genetics)
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. View Full-Text
Keywords: white yam; West Africa; SNP markers; genetic diversity; population structure white yam; West Africa; SNP markers; genetic diversity; population structure
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MDPI and ACS Style

Bhattacharjee, R.; Agre, P.; Bauchet, G.; De Koeyer, D.; Lopez-Montes, A.; Kumar, P.L.; Abberton, M.; Adebola, P.; Asfaw, A.; Asiedu, R. Genotyping-by-Sequencing to Unlock Genetic Diversity and Population Structure in White Yam (Dioscorea rotundata Poir.). Agronomy 2020, 10, 1437. https://doi.org/10.3390/agronomy10091437

AMA Style

Bhattacharjee R, Agre P, Bauchet G, De Koeyer D, Lopez-Montes A, Kumar PL, Abberton M, Adebola P, Asfaw A, Asiedu R. Genotyping-by-Sequencing to Unlock Genetic Diversity and Population Structure in White Yam (Dioscorea rotundata Poir.). Agronomy. 2020; 10(9):1437. https://doi.org/10.3390/agronomy10091437

Chicago/Turabian Style

Bhattacharjee, Ranjana; Agre, Paterne; Bauchet, Guillaume; De Koeyer, David; Lopez-Montes, Antonio; Kumar, P. L.; Abberton, Michael; Adebola, Patrick; Asfaw, Asrat; Asiedu, Robert. 2020. "Genotyping-by-Sequencing to Unlock Genetic Diversity and Population Structure in White Yam (Dioscorea rotundata Poir.)" Agronomy 10, no. 9: 1437. https://doi.org/10.3390/agronomy10091437

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