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Species-specific abundant retrotransposons elucidate the genomic composition of modern sugarcane cultivars

Abstract

Modern sugarcane cultivars are highly polyploid and derived from the hybridization of Saccharum officinarum and S. spontaneum, thus leading to singularly complex genomes. The complex genome has hindered the study of genomic structures. Here, we adopted a computational strategy to isolate highly repetitive and abundant sequences in either S. officinarum or S. spontaneum and isolated four S. spontaneum-enriched retrotransposons. Fluorescence in situ hybridization (FISH) assays with these repetitive DNA sequences generated whole-genome painting signals for S. spontaneum but not for S. officinarum. We demonstrated that these repetitive sequence-based probes distinguish the parental S. spontaneum genome in hybrids derived from crosses between it and S. officinarum. A cytological analysis of 14 modern sugarcane cultivars revealed that the percentages of chromosomes with introgressive S. spontaneum fragments ranged from 11.9 to 40.9% and substantially exceeded those determined for previously investigated cultivars (5–13%). The comparatively higher percentages of introgressive S. spontaneum fragments detected in the aforementioned cultivars indicate frequent recombination between parental genomes. Here, we present the application of our strategy to isolate species-specific cytological markers. This information may help to elucidate complex plant genomic structures and trace their evolutionary histories.

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Funding

This research was supported by the National Natural Science Foundation of China (31771862) and International cooperation project of Fujian Agriculture and Forestry University (KXGH17002).

Author information

KW and ZW acquired financial support and provided overall direction of the project. KW, ZW, and YH designed the research. YH, HC, SM, and GY performed the experiments. JH and YZ conducted the bioinformatic analysis. KW, ZW, and YH analyzed the data and wrote the manuscript.

Correspondence to Zonghua Wang or Kai Wang.

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The authors declare that they have no competing interests.

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Huang, Y., Chen, H., Han, J. et al. Species-specific abundant retrotransposons elucidate the genomic composition of modern sugarcane cultivars. Chromosoma 129, 45–55 (2020). https://doi.org/10.1007/s00412-019-00729-1

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Keywords

  • Sugarcane
  • Species-specific abundant
  • Retrotransposons
  • Genome structure
  • Fluorescence in situ hybridization