Theoretical and Applied Genetics

, Volume 118, Issue 2, pp 327–338

Informative genomic microsatellite markers for efficient genotyping applications in sugarcane

  • Swarup K. Parida
  • Sanjay K. Kalia
  • Sunita Kaul
  • Vivek Dalal
  • G. Hemaprabha
  • Athiappan Selvi
  • Awadhesh Pandit
  • Archana Singh
  • Kishor Gaikwad
  • Tilak R. Sharma
  • Prem Shankar Srivastava
  • Nagendra K. Singh
  • Trilochan Mohapatra
Original Paper

DOI: 10.1007/s00122-008-0902-4

Cite this article as:
Parida, S.K., Kalia, S.K., Kaul, S. et al. Theor Appl Genet (2009) 118: 327. doi:10.1007/s00122-008-0902-4

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.

Supplementary material

122_2008_902_MOESM1_ESM.doc (117 kb)
Supplementary figures (DOC 117 kb)
122_2008_902_MOESM2_ESM.doc (1.9 mb)
Supplementary tables (DOC 1910 kb)

Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • Swarup K. Parida
    • 1
    • 3
  • Sanjay K. Kalia
    • 1
  • Sunita Kaul
    • 1
  • Vivek Dalal
    • 1
  • G. Hemaprabha
    • 2
  • Athiappan Selvi
    • 2
  • Awadhesh Pandit
    • 1
  • Archana Singh
    • 1
  • Kishor Gaikwad
    • 1
  • Tilak R. Sharma
    • 1
  • Prem Shankar Srivastava
    • 3
  • Nagendra K. Singh
    • 1
  • Trilochan Mohapatra
    • 1
  1. 1.National Research Centre on Plant BiotechnologyIndian Agricultural Research InstituteNew DelhiIndia
  2. 2.Sugarcane Breeding InstituteCoimbatoreIndia
  3. 3.Department of BiotechnologyJamia Hamdard UniversityNew DelhiIndia

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