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Informative genomic microsatellite markers for efficient genotyping applications in sugarcane

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Abstract

Genomic microsatellite markers are capable of revealing high degree of polymorphism. Sugarcane (Saccharum sp.), having a complex polyploid genome requires more number of such informative markers for various applications in genetics and breeding. With the objective of generating a large set of microsatellite markers designated as Sugarcane Enriched Genomic MicroSatellite (SEGMS), 6,318 clones from genomic libraries of two hybrid sugarcane cultivars enriched with 18 different microsatellite repeat-motifs were sequenced to generate 4.16 Mb high-quality sequences. Microsatellites were identified in 1,261 of the 5,742 non-redundant clones that accounted for 22% enrichment of the libraries. Retro-transposon association was observed for 23.1% of the identified microsatellites. The utility of the microsatellite containing genomic sequences were demonstrated by higher primer designing potential (90%) and PCR amplification efficiency (87.4%). A total of 1,315 markers including 567 class I microsatellite markers were designed and placed in the public domain for unrestricted use. The level of polymorphism detected by these markers among sugarcane species, genera, and varieties was 88.6%, while cross-transferability rate was 93.2% within Saccharum complex and 25% to cereals. Cloning and sequencing of size variant amplicons revealed that the variation in the number of repeat-units was the main source of SEGMS fragment length polymorphism. High level of polymorphism and wide range of genetic diversity (0.16–0.82 with an average of 0.44) assayed with the SEGMS markers suggested their usefulness in various genotyping applications in sugarcane.

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Acknowledgments

The work presented in the manuscript was funded by the Department of Biotechnology (DBT), Government of India. The authors thank the Institute of Plant Genetics and Crop Research (IPK) for the availability of microsatellite search tool MISA.

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Authors and Affiliations

  1. National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India

    Swarup K. Parida, Sanjay K. Kalia, Sunita Kaul, Vivek Dalal, Awadhesh Pandit, Archana Singh, Kishor Gaikwad, Tilak R. Sharma, Nagendra K. Singh & Trilochan Mohapatra

  2. Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, 641007, India

    G. Hemaprabha & Athiappan Selvi

  3. Department of Biotechnology, Jamia Hamdard University, New Delhi, 110062, India

    Swarup K. Parida & Prem Shankar Srivastava

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  1. Swarup K. Parida
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  2. Sanjay K. Kalia
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  3. Sunita Kaul
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  4. Vivek Dalal
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  5. G. Hemaprabha
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  7. Awadhesh Pandit
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  8. Archana Singh
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  9. Kishor Gaikwad
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  11. Prem Shankar Srivastava
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  12. Nagendra K. Singh
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  13. Trilochan Mohapatra
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Corresponding author

Correspondence to Trilochan Mohapatra.

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Communicated by A. Kilian.

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Parida, S.K., Kalia, S.K., Kaul, S. et al. Informative genomic microsatellite markers for efficient genotyping applications in sugarcane. Theor Appl Genet 118, 327–338 (2009). https://doi.org/10.1007/s00122-008-0902-4

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  • DOI: https://doi.org/10.1007/s00122-008-0902-4

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