Historic manioc genomes illuminate maintenance of diversity under long-lived clonal cultivation.

Manioc—also called cassava and yuca—is among the world’s most important crops, originating in South America in the early Holocene. Domestication for its starchy roots involved a near-total shift from sexual to clonal propagation, and almost all manioc worldwide is now grown from stem cuttings. In this work, we analyze 573 new and published genomes, focusing on traditional varieties from the Americas and wild relatives from herbaria, to reveal the effects of this shift to clonality. We observe kinship over large distances, maintenance of high genetic diversity, intergenerational heterozygosity enrichment, and genomic mosaics of identity-by-descent haploblocks that connect all manioc worldwide. Interviews with Indigenous traditional farmers in the Brazilian Cerrado illuminate how traditional management strategies for sustaining, diversifying, and sharing the gene pool have shaped manioc diversity. Despite the toxicity of many of its raw components, manioc (also known as cassava or yuca) is a prevalent staple crop. Kistler . sequenced the genomes of 200 herbarium samples, two archeological samples, and 80 modern samples of manioc to reconstruct its population history. Their analysis revealed that many lineages of manioc have been propagating for at least a century but with almost no geographical patterns of variation like their wild relatives. These patterns instead reflected local agricultural practices. By incorporating Indigenous knowledge, this study explores the impact of domestication on this crop and how this process is reflected in genetic variation. —Corinne Simonti