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Journal of Plant Biology

, Volume 48, Issue 1, pp 96–105 | Cite as

Genome constitution and classification using retrotransposon-based markers in the orphan crop banana

  • Chee How Teo
  • Siang Hee TanEmail author
  • Chai Ling Ho
  • Qamaruz Zaman Faridah
  • Yasmin Rofina Othman
  • John Seymour Heslop-Harrison
  • Ruslan Kalendar
  • Alan Howard Schulman
Article

Abstract

We have exploited the repetitive and dispersed nature of many long terminal repeat (LTR)-retrotransposon families for characterizing genome constitutions and classifying cultivars of the genusMusa. Insertional polymorphisms of the elements were studied using seven published and two newly designed primers facing outwards from the LTRs and reverse transcriptase (RT) domain of the retrotransposon. The primers generated specific amplification patterns showing the universal applicability of this marker type. The Inter-Retrotransposon Amplified Polymorphism (IRAP) markers distinguished the A and B genomes of the banana species (Musa acuminata Col la andMusa balbisiana Colla) and between banana cultivars. The IRAP markers enabled phylogenetic analysis of 16 Malaysian banana cultivars and determination of the genome constitution of hybrid banana (AAB, ABB, AABB, and AAAB), and gave information about ancestral genotypes of the hybrids. In addition, the IRAP detected new retrotransposon insertions into the genome of tissue culture regenerants. This PCR-based IRAP assay is amenable to large-scale throughput demands in screening breeding populations and is applicable for any crop.

Keywords

genome constitution Inter-Retrotransposon Amplified Polymorphism long terminal repeat Musa phylogenetic analysis retrotransposon 

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Copyright information

© The Botanical Society of Korea 2005

Authors and Affiliations

  • Chee How Teo
    • 1
    • 5
  • Siang Hee Tan
    • 2
    Email author
  • Chai Ling Ho
    • 1
  • Qamaruz Zaman Faridah
    • 3
  • Yasmin Rofina Othman
    • 4
  • John Seymour Heslop-Harrison
    • 5
  • Ruslan Kalendar
    • 6
  • Alan Howard Schulman
    • 6
    • 7
  1. 1.Department of Biotechnology, Faculty of Food Science and BiotechnologyUniversiti Putra MalaysiaSerdangMalaysia
  2. 2.Molecular Biology DepartmentSime Darby Technology Centre Sdn BhdPetaling JayaMalaysia
  3. 3.Department of Biology, Faculty of Science and Environmental StudiesUniversiti Putra MalaysiaSerdangMalaysia
  4. 4.Institute of Biological SciencesUniversiti MalayaKuala LumpurMalaysia
  5. 5.Department of BiologyUniversity of LeicesterLeicesterUnited Kingdom
  6. 6.MTT/BI Plant Genomics Laboratory, Institute of BiotechnologyUniversity of HelsinkiHelsinkiFinland
  7. 7.Plant Breeding BiotechnologyMTT Agrifood Research FinlandJokioinenFinland

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