Fig 1.
Distribution of 4,957 SNPs across 20 Dioscorea rotundata chromosomes.
Fig 2.
Frequency of heterozygous genotypes and heterozygosity of 4,957 SNP markers generated using DArTseq platform across 207 yam genotypes.
Fig 3.
Heat map plot of kinship matrix using average linkage clustering based on SNP markers.
Table 1.
Analysis of molecular variance within and among the 207 genotypes assessed with 4,957 SNP markers.
Fig 4.
Hierarchical clustering of 207 yam genotypes based on 4,957 SNPs.
Fig 5.
Population structure in the yam germplasm.
(A) Likelihood of ΔK showing the best K value (K = 2); (B) Population structure obtained for 207 yam genotypes based on 4,957 SNPs.
Table 2.
Pairwise comparison (Fst) and expected heterozygosity among the two subpopulations using the model-based clusters.
Fig 6.
Discriminant analysis of principal components (DAPC).
(A) The graph of Bayesian information criterion (BIC) vs. the number of clusters indicates the optimum number of clusters inferred in the yam diversity panel; (B) Discriminant analysis of principal components with K = 2; (C) Discriminant analysis of principal components with K = 3; (D) Discriminant analysis of principal components with K = 4. The axes represent the first two linear discriminants. Each colour represents a cluster and each does represent an individual.
Table 3.
Genetic variability among (net nucleotide distance) and proportion of individuals, Major allele frequency, gene diversity, and PIC.