The genomic footprints of wild Saccharum species trace domestication, diversification, and modern breeding of sugarcane
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.
Authors
- Catherine Hervouet (ORCID: https://orcid.org/0009-0000-5225-7244)
- Shailendra Sharma (ORCID: https://orcid.org/0000-0002-0803-5203)
- George Piperidis
- Thomas Durand (ORCID: https://orcid.org/0000-0002-5122-0746)
- Olivier Garsmeur (ORCID: https://orcid.org/0000-0001-8869-3689)
- Prakash Lakshmanan (ORCID: https://orcid.org/0000-0003-1725-0391)
- Kerrie Barry (ORCID: https://orcid.org/0000-0002-8999-6785)
- Yoshifumi Terajima (ORCID: https://orcid.org/0000-0003-3201-3183)
- Marotea Vitrac
- Mike Butterfield
- Anna Lipzen (ORCID: https://orcid.org/0000-0003-2293-9329)
- Noa Kekuewa Lincoln (ORCID: https://orcid.org/0000-0003-1070-4290)
- Chris Daum (ORCID: https://orcid.org/0000-0003-3895-5892)
- Nicolas Pompidor
- Yuko Yoshinaga (ORCID: https://orcid.org/0000-0002-4978-9394)
- Jeremy Schmutz (ORCID: https://orcid.org/0000-0001-8062-9172)
- Jean-Yves Hoarau (ORCID: https://orcid.org/0000-0001-9734-4165)
- Simon Rio (ORCID: https://orcid.org/0000-0001-7014-8789)
- Anna L. Hale (ORCID: https://orcid.org/0000-0002-0329-3430)
- Erik J. Sacks (ORCID: https://orcid.org/0000-0001-7537-4558)
- Alexander Sanchez
- Angélique D’Hont (ORCID: https://orcid.org/0000-0002-5318-921X)
Institutions
- University of Hawaiʻi at Mānoa (US)
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (FR)
- Lawrence Berkeley National Laboratory (US)
- University of Illinois Urbana-Champaign (US)
- Sugarcane Research Center (Brazil) (BR)
- Joint Genome Institute (US)
- Chaudhary Charan Singh University (IN)
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR)
- Japan International Research Center for Agricultural Sciences (JP)
- National Clonal Germplasm Repository (US)
- Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicales (FR)
- Guangxi Academy of Agricultural Science (CN)
- Institut Agro Montpelier (FR)
- HudsonAlpha Institute for Biotechnology (US)
- Sugar Research Australia (Australia) (AU)
- University of French Polynesia (PF)
Publication Details
- Journal
- Cell
- Published
- 2025-10-15
- DOI
- https://doi.org/10.1016/j.cell.2025.09.017
- Citations
- 4
- Primary Topic
- Sugarcane Cultivation and Processing
- Type
- article
- Field-Weighted Citation Impact
- 7.00