Abstract
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.
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Acknowledgements
This project was supported by the Science and Technology Planting Project of Guangdong Province (2019B020238001), NSFC (31201260, 31760413 and 31660420), Science and Technology Major Project of Guangxi (AA17202025). The Science and Technology Major Project of Fujian Province [2016NZ0001] and Program for New Century Excellent Talents in Fujian Province [KLa17073A] in China.
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Jisen Zhang and Hengbo Wang designed the experiments. Naiyan Xiao performed the experiments and analyzed the data. Hengbo Wang drafted the manuscript and Jisen Zhang revised critically the paper. Wei Yao, Muqing Zhang, Ray Ming participated in revising the manuscript. All authors read and approved the final article.
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Communicated by: Hongwei Cai
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Xiao, N., Wang, H., Yao, W. et al. Development and Evaluation of SSR Markers Based on Large Scale Full-Length Transcriptome Sequencing in Sugarcane. Tropical Plant Biol. 13, 343–352 (2020). https://doi.org/10.1007/s12042-020-09260-5
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DOI: https://doi.org/10.1007/s12042-020-09260-5