Ancient and Modern DNA Reveal How Traditional Farming Preserves Manioc’s Genetic Diversity

New study shows how Indigenous farming practices have sustained one of the world’s most important crops for thousands of years

Manioc (Manihot esculenta), also known as cassava or yuca, is a staple crop feeding nearly a billion people worldwide. But unlike most crops, which are grown from seeds, manioc is cultivated almost entirely through the propagation of cuttings, an ancient method of cloning plants that theoretically limits genetic variation. However, a new study published in Science reveals that manioc has retained an extraordinarily high level of genetic diversity over thousands of years, thanks to traditional farming techniques used by Indigenous communities across the Americas.

Genetic variety within a crop species provides important protections, helping the plants develop resistance against pests and disease and enabling them to adapt to a changing climate.  Given the importance of genetic diversity, and of manioc as a dietary staple, the research team set out to explore how millennia of clonal propagation has impacted the crop’s genetic diversity, as well as the role of Indigenous farmers in shaping the crop’s genetic landscape.

The scientists analyzed 573 genomes, including historic herbarium collections, living specimens, archaeological samples, and wild relatives, and conducted interviews with indigenous farmers in Brazil. Their research uncovered several surprising results, providing key insights into traditional agricultural practices that have helped sustain manioc’s diversity.

“We weren’t exactly sure what to expect in terms of genetic diversity in a highly clonal species, but we found very high diversity across the crop grenomes as well as an unexpected enrichment of genetic variation within individual plants,” says Logan Kistler of the Smithsonian’s National Museum of Natural History and lead author of the study. In fact, the analysis of a 2,000-year-old archaeological manioc genome from Chile suggests that selection for genetic diversity has intensified in recent millennia, likely in response to the long-term shift to clonal cultivation. “The maintenance of high diversity protects cassava genomes from the harmful mutations that can arise in the long lives of genetic clones,” Kistler suggests.

The team also identified ways in which cultural networks shape the dispersal of manioc genes. Through practices such as exchanging cuttings during marriage, planting gardens for long-term sustenance, and selectively cultivating new volunteer plants from soil seed banks, Indigenous communities play a crucial role in maintaining manioc’s gene pool. These human-mediated dispersal networks have resulted in genetic kinship among manioc grown across vast geographic regions.

The new study challenges conventional wisdom about clonal crops, demonstrating that human intervention can counteract the expected loss of genetic diversity. By understanding manioc’s genetic history, researchers hope to gain new insights into crop domestication and resilience. In this way, the traditional knowledge that has sustained its genetic diversity in manioc could inform breeding programs to improve crop resilience, ensuring food security for millions.

“This study highlights the deep connections between human culture and agricultural biodiversity,” says Yoshi Maezumi, one of the study’s authors and researcher the Max Planck Institute of Geoanthropology, “emphasizing that traditional knowledge remains invaluable for the future of food security.”