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Mining EST-Derived SSR Markers to Assess Genetic Diversity in Cassava (Manihot esculenta Crantz)

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Abstract

Cassava (Manihot esculenta Crantz) is a very important staple and industrial crop in tropical and subtropical regions of the world. The paucity of markers is a serious limitation in marker-assisted breeding. A total of 35,992 expressed sequence tags (ESTs) from cassava, which were clustered in 13,173 unigenes, were used in this study. A total of 1,889 microsatellites were identified, with an average density of one simple sequence repeats (SSRs) every 4.40 kb. Of the 1,058 designed EST-SSRs from cultivars SC06, TMS60444, and W14, 431 were polymorphic. Then, 31 randomly selected EST-SSRs from the 431 polymorphic EST-SSRs were used to evaluate the genetic diversity of 76 cassava accessions. A total of 93 alleles were identified, and the number detected for each EST-SSR ranged from one to four. Based on the 93 alleles, the 76 cassava accessions could be classified into six groups, and the genetic similarity coefficient ranged from 0.55 to 0.94. This study demonstrated the potential of EST-derived SSRs in cassava. The resources developed in this study enriched the available molecular markers for cassava.

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Acknowledgments

This work was supported by the National Key Technology R & D Program (Pre 973) No. 2006CB708204. The authors wish to thank M. Ishitani, J. Tohme, M. Fregene, and other researchers from GeneTrop for their involvement in the development of the cassava EST database. We also thank Dr Bin Liu and F. Claude for their valuable comments on the manuscript.

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Authors and Affiliations

  1. The Institute of Tropical Biosciences and Biotechnology (ITBB), Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, 571101, People’s Republic of China

    Meiling Zou, Zhiqiang Xia, Yang Zhang, Xin Chen, Weiping Bo & Wenquan Wang

  2. Citrus Research and Education Center (CREC), University of Florida (UF), Gainesville, FL, USA

    Peng Ling

  3. Tropical Crops Genetic Resources Institute (TCGRI), Chinese Academy of Tropical Agricultural Sciences (CATAS), Danzhou, 571737, People’s Republic of China

    Zusheng Wei

  4. Hainan University, Haikou, 571101, People’s Republic of China

    Meiling Zou, Zhiqiang Xia, Yang Zhang & Weiping Bo

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  1. Meiling Zou
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  2. Zhiqiang Xia
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  3. Peng Ling
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  4. Yang Zhang
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  5. Xin Chen
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  6. Zusheng Wei
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  7. Weiping Bo
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  8. Wenquan Wang
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Correspondence to Wenquan Wang.

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Meiling Zou and Zhiqiang Xia contributed equally to this paper.

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Appendix 1

Features of new set of polymorphic EST-SSR markers developed. The data provided represent detail of the new SSR markers, e.g., marker name, repeat type, primer sequence, annealing temperature, and expected product size (DOC 1,042 kb)

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Zou, M., Xia, Z., Ling, P. et al. Mining EST-Derived SSR Markers to Assess Genetic Diversity in Cassava (Manihot esculenta Crantz). Plant Mol Biol Rep 29, 961–971 (2011). https://doi.org/10.1007/s11105-011-0299-0

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