Interspecific introgression patterns reveal the origins of worldwide cultivated bananas in New Guinea

Abstract

Hybridizations between Musa species and subspecies, enabled by their transport via human migration, were proposed to have played an important role in banana domestication. We exploited sequencing data of 226 Musaceae accessions, including wild and cultivated accessions, to characterize the inter(sub)specific hybridization pattern that gave rise to cultivated bananas. We identified 11 genetic pools that contributed to cultivars, including two contributors of unknown origin. Informative alleles for each of these genetic pools were pinpointed and used to obtain genome ancestry mosaics of accessions. Diploid and triploid cultivars had genome mosaics involving three up to possibly seven contributors. The simplest mosaics were found for some diploid cultivars from New Guinea, combining three contributors, i.e., banksii and zebrina representing Musa acuminata subspecies and, more unexpectedly, the New Guinean species Musa schizocarpa. Breakpoints of M. schizocarpa introgressions were found to be conserved between New Guinea cultivars and the other analyzed diploid and triploid cultivars. This suggests that plants bearing these M. schizocarpa introgressions were transported from New Guinea and gave rise to currently cultivated bananas. Many cultivars showed contrasted mosaics with predominant ancestry from their geographical origin across Southeast Asia to New Guinea. This revealed that further diversification occurred in different Southeast Asian regions through hybridization with other Musa (sub)species, including two unknown ancestors that we propose to be M. acuminata ssp. halabanensis and a yet to be characterized M. acuminata subspecies. These results highlighted a dynamic crop formation process that was initiated in New Guinea, with subsequent diversification throughout Southeast Asia.

Two haplotype-resolved genomes of highly heterozygous AAB allotriploid bananas provide insights into subgenome asymmetric evolution and banana wilt control

“…We also showed that the contribution of M. schizocarpa , previously thought to be restricted to a few M. schizocarpa × M. acuminate cultivars and suspected to be present in east African highland bananas, was present in Plantain and Silk. It is worth noting that there is a significant difference between the Silk reported in (Martin et al, 2023) and ours, so we speculate that they may not be the same Silk cultivar.…”

“…Secondly, in order to reduce false positives, the SNPs results were adjusted with the collinear block (1 kb, 10 kb and 20 kb) of the genomes. Thirdly, the results were compared with those of previous studies (accession numbers: Plantain 148 and 149, Silk 139 and 140) (Martin et al, 2023). Combining the above steps, the final results were obtained.…”

“…Thirdly, the results were compared with those of previous studies (accession numbers: Plantain 148 and 149, Silk 139 and 140) (Martin et al, 2023). Combining the above steps, the final results were obtained.…”

“…Understanding patterns of interspecific introgression can reveal the origins of cultivated bananas (Martin et al, 2023). We precisely characterized the ancestral contributions of Plantain and Silk by examining the ancestry mosaics along the genome (Extended Data Fig.…”

The Genetic Homogeneity of Uganda’s East African Highland Bananas (Mutika/Lujugira) Does Not Match the Extensive Morphological Variation Identified in this Subgroup

“…zebrina (A) [2,3]. However, sequencing data showed that the AAA-EA has large introgressions from another wild species, M. schizocarpa [4]. These bananas (Musa spp.)…”