Résumé
Sugarcane is a major crop of unclear origins due to its complex polyploid interspecific genome. We analyzed genome ancestries using whole-genome sequence data from 390 representative accessions based on repeated k-mers and chloroplast phylogeny. The results provided evidence that Saccharum officinarum was domesticated in the New Guinea region from the S. robustum wild species and revealed that its genome is a mosaic involving different S. robustum subgroups. We discovered a wild Saccharum contributor to most modern cultivars, likely originating from East Melanesia. We highlighted two early centers of sugarcane diversification associated with human transport, one in continental Asia through hybridization with different S. spontaneum subgroups and one in the Melanesian and Polynesian islands via hybridization with the discovered ancestor and Miscanthus. Finally, we revealed the genome ancestry of modern cultivars, highlighting untapped wild Saccharum diversity as a source of alleles for breeding programs.
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•Repeated k-mers allow tracing of admixture in complex polyploids such as sugarcane•Sugarcane domestication involved hybrids between distinct groups of wild S. robustum•Diversification involved hybridization with wild Saccharum species and Miscanthus•An unknown Saccharum contributor to modern cultivars was discovered
Genomic analyses of 390 accessions reveal the domestication history of highly polyploid sugarcane and the wild contributors to its diversification and to modern cultivars.