Fig 1.
Genetic origin, diversity and structure.
(A) Geographical distribution of the wild genetic groups in West and Central Africa (adapted from Mérot-L’Anthoëne et al. [7]). Genetic structure of all individuals, (B) for 127 African individuals and (C) for 126 Vietnamese individuals. The ancestry proportions of all individuals were determined via sNMF analysis with K = 6 using 261 SNPs. (D) Neighbor-joining clustering of all individuals based on the Euclidean distance.
Table 1.
Summary statistics of genetic diversity of the Vietnamese Robusta collection and the genetic groups in Africa. The African groups were classified based on the sNMF results, and the individuals with > 70% ancestry were assigned to the corresponding group. N = number of individuals; AR = average allelic richness; Ho = observed heterozygosity; He = expected heterozygosity; FIS = inbreeding coefficient.
Table 2.
Differentiation coefficient (FST) between the wild and Vietnamese groups. All the FST values are statistically significant (p = 0.000).
Fig 2.
Selection of a core set from the Vietnamese collection.
Evaluation of the core set: Histogram of (A) the expected heterozygosity and (B) allelic richness of 1,000 random sets of the same size as the core set (45 individuals). (C) Histogram of pairwise Euclidean distances between individuals in the whole collection (gray bars) and in the core set (yellow bars). (D) Individuals selected for the core set are highlighted (yellow) in a PCA projection.
Fig 3.
Genome-wide introgression in 31 admixed individuals from the core set.
(A) Local ancestry proportion (0, 50%, 100%) inferred along the chromosomes. The ancestry groups are highlighted by colors (AG – orange, OB – blue, D – red, ER – dark purple), and undetermined regions are in gray. (B) Average ancestry inference across the admixed individuals at each SNP position. The remaining 14 accessions of the core set were estimated to only have ER ancestry.