Genetic Diversity of Yuca (Manihot esculenta esculenta; Cassava, Manioc), an Indigenous Crop in the Peruvian Amazon

Yuca (Manihot esculenta esculenta; cassava, manioc) is a native Amazonian crop represented by myriad landraces. To investigate human influences on its diversification, we conducted field observations and analyzed 13 short tandem repeat (STR) loci in 43 landraces in the Peruvian Amazon. We found a different multilocus genotype (MLG) in every landrace. However, tests for Hardy-Weinberg equilibrium found a deficit of heterozygosity at every locus (p < 0.001 for 12 of 13 loci). Further, the fraction of genetic variance due to landrace differences was greater than expected (38.84%; p = 0.001). This suggested that landrace hybridization is restricted, a finding consistent with our field observations. However, we found an excess of within-landrace heterozygosity (p < 0.001) in 39 of 43 landraces, suggesting they originated through hybridization. Mantel tests identified associations between genetic and geographic distances (p < 0.001), but their correlation coefficients were low (Mantel's r < 0.21). In addition, AMOVA analyses revealed that differences between landraces collected from five sampled rivers accounted for just 3.05% of observed genetic variance (p < 0.001). Neighbor joining and principal components analyses also revealed little evidence of differentiation between rivers. Finally, in a comparison with a secondary sample, we found that the closest relative of 27 of 28 specimens had a landrace name different from their own, suggesting that traditional nomenclature is a poor indicator of genetic relatedness.