Development and Evaluation of SSR Markers Based on Large Scale Full-Length Transcriptome Sequencing in Sugarcane

Naiyan Xiao, Hengbo Wang, Wei Yao, Muqing Zhang, Ray Ming, Jisen Zhang

Research output: Contribution to journalArticlepeer-review


Sugarcane generates the vast majority of sugar consumed worldwide. The large-scale development of EST-SSR markers are crucial for the analysis of genetic mechanisms important in agronomic traits of sugarcane. In this study, based on published 107,598 full-length expressed sequence tags (ESTs) from 22 sugarcane cultivars, we identified a total of 46,043 loci of simple repeat sequences. The SSRs with di-nucleotide (8175 loci) and tri-nucleotide (10,709 loci) repeat motifs account for 40.96% (18,884) of the total SSR loci, with (AT/TA)n and (ACA/TGT)n being found to be the major repeat motifs. A total of 1070 pairs of primers were randomly selected to verify using 12 accessions including S. officinarum, S. robustum, S. spontaneum and cultivars. The results showed that 847 (79.1%) were successfully amplified, of which 349 (32.60%) were polymorphic in the analyzed samples. The polymorphic rates of EST-SSR markers with di-nucleotide, tri-nucleotide, tetra-nucleotide, penta-nucleotide and hexa-nucleotide repeat motifs were 36.82% (81), 49.40% (165), 43.04% (34), 30.19% (32) and 34.26% (37), respectively. Among them, the EST-SSRs comprising five types of repeat motifs (CA)n, (CCG)n, (CCGC)n, (CGGCG)n and (GCCGGC)n presented high degrees of polymorphism. Finally, 20 EST-SSR markers with polymorphisms were selected to perform a cluster analysis of 48 accessions from Saccharum and Erianthus genera. These results demonstrated that Chinese sugarcane cultivars from group IV (25/39) had a lower genetic divergence than cultivars from other countries and EST-SSR markers can also be used in determining the genetic diversity of Erianthus genus. This set of EST-SSR markers is an important molecular resource for analyzing genetic diversity, molecular fingerprinting and genetic mapping.

Original languageEnglish (US)
Pages (from-to)343-352
Number of pages10
JournalTropical Plant Biology
Issue number4
StatePublished - Dec 2020


  • Polymorphic analysis
  • Sugarcane
  • Transcriptome

ASJC Scopus subject areas

  • Genetics
  • Plant Science


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