Beyond domestication: The unexpected contribution of native Musa wild relatives to cultivated banana diversity in Mainland Southeast Asia

The diversity of cultivated bananas remains partially unknown, whereas cultivars with suitable adaptive traits could address the drastically increasing biotic and abiotic constraints on banana production. This partial knowledge also impacts our understanding of domestication processes, although replicating these processes is an endorsed strategy for banana varietal improvement. To address this gap, 91 specimens were collected during a collecting mission across northern Vietnam, northern Laos, and China’s Yunnan region, an underexplored area at the northern limit of the Musa natural range. Native wild relatives were also collected (Musa acuminata subsp. burmannica, M. balbisiana, M. itinerans, M. yunnanensis) to assess their potential contributions to cultivated crops. SNP polymorphisms revealed that, beyond the globally cultivated sweet or starchy cultivars, farmers cultivate numerous previously undescribed landraces. SNP-based chromosome paintings further showed that all these landraces carry genomic signatures from endemic wild Musa relatives. Notably, Musa acuminata subsp. burmannica, typically regarded as a minor contributor to cultivated bananas, was detected in several M. acuminata derived diploids (AA) and triploids (AAA) as well as M. acuminata × M. balbisiana derived AAB and ABB landraces. Remarkably, we also report here for the first time polyploid landraces containing a complete haplotype of the local M. itinerans. Crucially, we showed that these landraces were not directly domesticated from the endemic wild Musa. They appear to result from local hybridizations of endemic wilds with exogenous AA diploids introduced into Mainland Southeast Asia from distant regions and originating from earlier domestication farther south. In addition, the various M. acuminata subspecies contributing to these exogenous diploids, provide arguments for an alternative eastern route of introduction via southern China or Taiwan and through the Philippines, distinct from the previously described western route via the Malay Peninsula, through Java, and Sumatra. We highlight an accumulation of genomic introgressions from native wild relatives, suggesting that banana diversity was shaped by an atypical process of cumulative diversification. This ‘post-domestication’ process is thought to enhance local adaptation through genes pyramiding. This multi-level genetic stacking is strengthened in bananas by polyploidy and vegetative propagation fixing any valuable combinations.