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

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

Research output: Contribution to journalArticlepeer-review

64 Citations (Scopus)


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 genus Musa. 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 Colla and Musa 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.

Original languageEnglish
Pages (from-to)96-105
Number of pages10
JournalJournal of Plant Biology
Issue number1
Publication statusPublished - Mar 31 2005
Externally publishedYes


  • Genome constitution
  • Inter-Retrotransposon Amplified Polymorphism
  • Long terminal repeat
  • Musa
  • Phylogenetic analysis
  • Retrotransposon

ASJC Scopus subject areas

  • Plant Science

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