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Molecular Breeding

, 39:25 | Cite as

LTR retrotransposons and highly informative ISSRs in combination are potential markers for genetic fidelity testing of tissue culture-raised plants in sugarcane

  • Prashant R. Shingote
  • S. V. Amitha Mithra
  • Pratima Sharma
  • Navadagi B. Devanna
  • Kirti Arora
  • Somnath K. Holkar
  • Suhail Khan
  • J. Singh
  • Sanjeev Kumar
  • T. R. Sharma
  • Amolkumar U. SolankeEmail author
Article
  • 6 Downloads

Abstract

Testing the genetic fidelity of micropropagated clones with DNA markers could curtail the losses caused by somaclonal variation in sugarcane tissue culture industry. Evaluation of 32 inter-retrotransposon amplified polymorphism (IRAP) markers and 100 inter-simple sequence repeats (ISSRs) in 47 sugarcane accessions identified 20 (8 IRAPs and 12 ISSRs) polymorphic markers representing 98 loci. IRAP system was superior to ISSR in terms of marker index (2.68 as against 1.76), resolving power (2.85 as against 1.98), and polymorphic loci per assay (6 compared to 4.1), except mean polymorphic information content (0.31 and 0.34). Further evaluation of the 20 polymorphic markers in testing the genetic fidelity of micropropagated sugarcane clones identified a variant clone by three primers of ISSR and one IRAP marker (UBC810, UBC813, UBC840, and LTR6149 + 3′LTR). The unique amplicons from the somaclonal variant were validated by sequencing. Based on the number of bands amplified and proportion of polymorphic loci, a set of six ISSR and four IRAP markers has been recommended to test clonal fidelity for sugarcane tissue culture industry.

Keywords

Genetic fidelity testing IRAP ISSR Phylogeny Somaclonal variation Sugarcane 

Notes

Acknowledgements

Our thanks are due for ICAR-NRCPB, New Delhi for extending all the facilities to carry out this work.

Funding information

The Department of Biotechnology (DBT), Govt. of India through Biotech Consortium India Limited (BCIL), New Delhi funded the project on National Certification System for Tissue Culture-raised Plants (NCS-TCP).

Supplementary material

11032_2019_931_MOESM1_ESM.docx (24 kb)
ESM 1 (DOCX 24 kb)

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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  • Prashant R. Shingote
    • 1
  • S. V. Amitha Mithra
    • 1
  • Pratima Sharma
    • 1
  • Navadagi B. Devanna
    • 1
  • Kirti Arora
    • 1
  • Somnath K. Holkar
    • 2
  • Suhail Khan
    • 2
  • J. Singh
    • 2
  • Sanjeev Kumar
    • 2
  • T. R. Sharma
    • 1
    • 3
  • Amolkumar U. Solanke
    • 1
    Email author
  1. 1.ICAR-National Research Centre on Plant BiotechnologyNew DelhiIndia
  2. 2.ICAR-Indian Institute of Sugarcane ResearchLucknowIndia
  3. 3.National Agri-Food Biotechnology InstituteMohaliIndia

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