Indigenous Farming Shaped Manioc's Genetic Diversity

A new genomic study reveals how Indigenous traditional farming practices have shaped the evolution of manioc – one of the world's most important staple crops – for the better. The domestication of plants and the rise of agriculture were transformative events in human history. Today, a few staple crops provide most human calories, including manioc (cassava or yuca), a vital root crop that sustains nearly a billion people across the tropics. Although it ranks as the world's seventh most significant crop, manioc is primarily cultivated on small farms. The plant's domestication traces back to the southwestern Amazon, where its wild ancestor propagated via seeds. However, human cultivation, which became widespread throughout South and Central America during the mid-Holocene (~7000 years ago), led to manioc being sustained by clonal propagation through stem cuttings. To better understand the genetic consequences of traditional manioc cultivation practices, Logan Kistler and colleagues analyzed 573 manioc genomes from across the Americas, including newly sequenced samples from herbarium specimens, archaeological sites, and wild relatives. Kistler et al. also sequenced 19 manioc lineages contributed by a Waurá Indigenous community in Brazil's Xingu region, where farmers grow manioc using ancestral methods. The findings revealed a surprising pattern in manioc – all cultivated varieties, worldwide, share vast regions of identical DNA. Using a novel molecular clock method, the authors show that these genetic segments have circulated for millennia, likely a consequence of human farming methods. Despite manioc's extensive genetic interconnectedness, it sustains an exceptionally high degree of genetic diversity, the authors also report. Individual plants harbor substantially greater genetic variation within their own genomes than is observed between separate individuals. According to Kistler et al., these patterns have been actively maintained through human selection, as farmers have historically favored robust plants with high genetic diversity, effectively counteracting the genetic decline typically associated with long-lived clones. "The unexpected pattern of diversity in manioc highlights the important role of traditional management strategies that have shielded clonal populations from risks introduced through thousands of years of propagation," say Kistler and colleagues.