Genotyping-by-sequencing to unlock genetic diversity and population structure in white yam (dioscorea rotundata poir.)
Bhattacharjee, R., Agre, P., Bauchet, G., de Koeyer, D., Lopez-Montes, A., Lava Kumar, P., Abberton, M., Adebola, P., Asfaw, A., Asiedu, R. (2020). Genotyping-by-sequencing to unlock genetic diversity and population structure in white yam (dioscorea rotundata poir.). Agronomy, [online] 10(9), http://dx.doi.org/10.3390/AGRONOMY10091437
Plain language summary
White yam (Dioscorea rotundata Poir.) is indigenous to West Africa and one of the most important crops in the region. In the present study, genotyping-by-sequencing (GBS) was used to characterize white yam landraces, breeding lines, and market varieties to
understand the genetic relationships and population structure for further improvement of this very important species in West and Central Africa. This study confirmed the reliability and accuracy of high-density SNP markers generated from next-generation sequencing-based genotyping coupled with complementary statistical analyses for genetic diversity and population structure. The genetic relationships identified among different genetic groups in this study could be further explored in white yam improvement programs by identifying diverse parents for breeding and genetic research.
White yam (Dioscorea rotundata 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.