Scholarlink

Background <p>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 <i>Saccharum</i>.</p> Results <p>Here we present <Emphasis FontCategory="NonProportional">AdmixPoly</Emphasis>, an R-package designed to infer admixture in polyploid species both at the genome-wide scale and locally along chromosomes. We compare <Emphasis FontCategory="NonProportional">AdmixPoly</Emphasis> 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 <i>Saccharum</i> species to the complex polyploid genome of modern sugarcane cultivars. A panel of wild and cultivated <i>Saccharum</i> accessions is genotyped for 80K genomic regions, each revealing approximately 50 read-scale haplotypes.</p> Conclusions <p>The results reveal that most of the approximately 12 copies of each basic chromosome in modern cultivars are derived from the domesticated species <i>Saccharum officinarum</i>, with one to four copies typically contributed by distinct subgroups of the wild species <i>Saccharum spontaneum</i>. In addition, contributions from an unknown wild <i>Saccharum</i> 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.</p>

错误：搜索内容不能为空，请输入英文关键词
错误：关键词超出字数限制，请精简
高级检索

Deciphering the mosaic genome of sugarcane cultivars through polyploid admixture inference with AdmixPoly

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年6月19日

查看全文
  • Simon Rio,
  • Franck Gauthier,
  • Olivier Garsmeur,
  • George Piperidis,
  • Jean-Yves Hoarau,
  • German Serino,
  • Raul Castillo Torres,
  • Shailesh Vinay Joshi,
  • Yoshifumi Terajima,
  • Jershon Lopez-Gerena,
  • María Francisca Perera,
  • Andrew Stoute,
  • Goolam Badaloo,
  • Dongliang Huang,
  • Kerrie Barry,
  • Jeremy Schmutz,
  • Tristan Mary-Huard,
  • Angélique D’Hont

摘要

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.