Theoretical and Applied Genetics

, Volume 133, Issue 1, pp 187–199 | Cite as

Characterization of a Saccharum spontaneum with a basic chromosome number of x = 10 provides new insights on genome evolution in genus Saccharum

  • Zhuang Meng
  • Jinlei Han
  • Yujing Lin
  • Yiyong Zhao
  • Qingfang Lin
  • Xiaokai Ma
  • Jianping Wang
  • Muqing Zhang
  • Liangsheng Zhang
  • Qinghui YangEmail author
  • Kai WangEmail author
Original Article


Key message

A novel tetraploid S. spontaneum with basic chromosome x = 10 was discovered, providing us insights in the origin and evolution in Saccharum species.


Sugarcane (Saccharum spp., Poaceae) is a leading crop for sugar production providing 80% of the world’s sugar. However, the genetic and genomic complexities of this crop such as its high polyploidy level and highly variable chromosome numbers have significantly hindered the studies in deciphering the genomic structure and evolution of sugarcane. Here, we developed the first set of oligonucleotide (oligo)-based probes based on the S. spontaneum genome (x = 8), which can be used to simultaneously distinguish each of the 64 chromosomes of octaploid S. spontaneum SES208 (2n = 8x = 64) through fluorescence in situ hybridization (FISH). By comparative FISH assay, we confirmed the chromosomal rearrangements of S. spontaneum (x = 8) and S. officinarum (2n = 8x = 80), the main contributors of modern sugarcane cultivars. In addition, we examined a S. spontaneum accession, Np-X, with 2n = 40 chromosomes, and we found that it was a tetraploid with the unusual basic chromosome number of x = 10. Assays at the cytological and DNA levels demonstrated its close relationship with S. spontaneum with basic chromosome number x = 8 (the most common accessions in S. spontaneum), confirming its S. spontaneum identity. Population genetic structure and phylogenetic relationship analyses between Np-X and 64 S. spontaneum accessions revealed that Np-X belongs to the ancient Pan-Malaysia group, indicating a close relationship to S. spontaneum with basic chromosome number of x = 8. This finding of a tetraploid S. spontaneum with basic chromosome number of x = 10 suggested a parallel evolution path of genomes and polyploid series in S. spontaneum with different basic chromosome numbers.



This work was supported by the National Natural Science Foundation of China (31771862), National Engineering Research Center of Sugarcane Open Fund (2017.1.5, NER2018.1.5) and State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources (SKLCUSA-b201808). We would like to thank National Field Genebank of Sugarcane Germplasm of China and National Infrastructure for Crop Germplasm Resources–Sugarcane platform of China for supplying us the S. spontaneum plants.

Author contributions

KW and QY designed the research and drafted manuscript. ZM, YL, YZ, QL, JH, and XM conducted the experiments. ZM, KW and JH designed chromosome-specific oligo probes. KW, QY, YZ, LZ, JW, and MZ participated in the data analysis and manuscript preparation. All authors read and approved the final manuscript.

Compliance with ethical standards

Conflict of interest

On behalf of all authors, the corresponding author states that there is no conflict of interest.

Ethical approval

This article does not contain any studies that were performed with human participants or animals by any of the authors.

Supplementary material

122_2019_3450_MOESM1_ESM.docx (16 kb)
Supplementary material 1 (DOCX 15 kb)
122_2019_3450_MOESM2_ESM.docx (14 kb)
Supplementary material 2 (DOCX 13 kb)
122_2019_3450_MOESM3_ESM.pdf (915 kb)
Supplementary material 3 (PDF 914 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyFujian Agriculture and Forestry UniversityFuzhouChina
  2. 2.State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab for Sugarcane BiologyGuangxi UniversityNanningChina
  3. 3.Sugarcane Research InstitutionYunnan Agricultural UniversityKunmingChina
  4. 4.State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, School of Life SciencesFudan UniversityShanghaiChina
  5. 5.Department of AgronomyUniversity of FloridaGainesvilleUSA

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