Deciphering the mosaic genome of sugarcane cultivars through polyploid admixture inference with AdmixPoly
Abstract
Background: Characterizing population structure and admixture events between ancestral groups plays a key role in understanding the evolutionary history of species and crops. Most tools for inferring admixture have been developed for diploids and are not suitable for polyploids, in particular those with high and mixed ploidy such as Saccharum. Results: Here we present AdmixPoly, an R-package designed to infer admixture in polyploid species both at the genome-wide scale and locally along chromosomes. We compare AdmixPoly with state-of-the-art methods using simulations, demonstrating its precision and computational efficiency. Notably, local admixture inference in complex scenarios, such as high ploidy levels, large numbers of ancestral groups and alleles per marker is enabled through efficient approximations of emission and transition probabilities within a hidden Markov model framework. We apply this approach to characterize the contributions of wild Saccharum species to the complex polyploid genome of modern sugarcane cultivars. A panel of wild and cultivated Saccharum accessions is genotyped for 80K genomic regions, each revealing approximately 50 read-scale haplotypes. Conclusions: The results reveal that most of the approximately 12 copies of each basic chromosome in modern cultivars are derived from the domesticated species Saccharum officinarum, with one to four copies typically contributed by distinct subgroups of the wild species Saccharum spontaneum. In addition, contributions from an unknown wild Saccharum group originating from the Pacific were identified in most cultivars. The conserved pattern of these introgressions suggests that they can be traced back to the early stages of sugarcane breeding approximately a century ago.
Related
- Genetic diversity within and between polyploid sugarcane (Saccharum spp.) families obtained via caryopsis using microsatellite markers and multicategory model
- Genetic architecture of sugarcane traits in a polyploid genomics framework
- STAVelo: deciphering spatiotemporal cellular dynamics via spatial RNA velocity inference from spatial transcriptomics data
- Snow carps as an emerging model for polyploid genome evolution
- SPLATCHE2: a spatially explicit simulation framework for complex demography, genetic admixture and recombination
BibTeX
@article{rio2026deciphering,
title = {{Deciphering the mosaic genome of sugarcane cultivars through polyploid admixture inference with AdmixPoly}},
author = {Simon Rio and Franck Gauthier and Olivier Garsmeur and George Piperidis and Jean-Yves Hoarau and German Serino and Raul Castillo Torres and Shailesh Vinay Joshi and Yoshifumi Terajima and Jershon Lopez-Gerena and María Francisca Perera and Andrew Stoute and Goolam Badaloo and Dongliang Huang and Kerrie Barry and Jeremy Schmutz and Tristan Mary-Huard and Angélique D'Hont},
journal = {Genome Biology},
year = {2026},
month = jun,
doi = {10.1186/s13059-026-04162-3},
url = {https://hal.science/hal-05751271v1},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Deciphering the mosaic genome of sugarcane cultivars through polyploid admixture inference with AdmixPoly
AU - Simon Rio
AU - Franck Gauthier
AU - Olivier Garsmeur
AU - George Piperidis
AU - Jean-Yves Hoarau
AU - German Serino
AU - Raul Castillo Torres
AU - Shailesh Vinay Joshi
AU - Yoshifumi Terajima
AU - Jershon Lopez-Gerena
AU - María Francisca Perera
AU - Andrew Stoute
AU - Goolam Badaloo
AU - Dongliang Huang
AU - Kerrie Barry
AU - Jeremy Schmutz
AU - Tristan Mary-Huard
AU - Angélique D'Hont
PY - 2026
DA - 2026/06/19
JO - Genome Biology
DO - 10.1186/s13059-026-04162-3
UR - https://hal.science/hal-05751271v1
AB - Background: Characterizing population structure and admixture events between ancestral groups plays a key role in understanding the evolutionary history of species and crops. Most tools for inferring admixture have been developed for diploids and are not suitable for polyploids, in particular those with high and mixed ploidy such as Saccharum. Results: Here we present AdmixPoly, an R-package designed to infer admixture in polyploid species both at the genome-wide scale and locally along chromosomes. We compare AdmixPoly with state-of-the-art methods using simulations, demonstrating its precision and computational efficiency. Notably, local admixture inference in complex scenarios, such as high ploidy levels, large numbers of ancestral groups and alleles per marker is enabled through efficient approximations of emission and transition probabilities within a hidden Markov model framework. We apply this approach to characterize the contributions of wild Saccharum species to the complex polyploid genome of modern sugarcane cultivars. A panel of wild and cultivated Saccharum accessions is genotyped for 80K genomic regions, each revealing approximately 50 read-scale haplotypes. Conclusions: The results reveal that most of the approximately 12 copies of each basic chromosome in modern cultivars are derived from the domesticated species Saccharum officinarum, with one to four copies typically contributed by distinct subgroups of the wild species Saccharum spontaneum. In addition, contributions from an unknown wild Saccharum group originating from the Pacific were identified in most cultivars. The conserved pattern of these introgressions suggests that they can be traced back to the early stages of sugarcane breeding approximately a century ago.
SN - 1474-7596
ER -