Theoretical and Applied Genetics

, Volume 102, Issue 2, pp 296–306

A rapid PCR-based method for genetically mapping ESTs

  • S. A. Cato
  • R. C. Gardner
  • J. Kent
  • T. E. Richardson
Original Paper

DOI: 10.1007/s001220051646

Cite this article as:
Cato, S., Gardner, R., Kent, J. et al. Theor Appl Genet (2001) 102: 296. doi:10.1007/s001220051646

Abstract 

A simple, semi-automatable procedure was developed for converting expressed sequence tags (ESTs) into mappable genetic markers. The polymerase chain reaction is used to amplify regions immediately 5′ or 3′ to the coding regions of genes in order to maximise sequence variability between alleles. Fragment length and nucleotide substitution polymorphisms among amplified alleles can be detected using either ethidium bromide staining or automated laser-based fluorescence. A 6% non-denaturing acrylamide gel, analysed with an ABI 377 DNA sequencer, proved capable of resolving homoduplexes and heteroduplexes formed between amplified alleles containing nucleotide substitutions as well as resolving allelic length differences. With this approach 75% of 60 ESTs from a range of Pinus species could be genetically mapped in each of three pedigrees from P. radiata and P. taeda. Furthermore, three or four alleles were detected in each pedigree for 42% of the EST markers.

Keywords Expressed sequence tagPolymerase chain reactionFragment length polymorphismSingle nucleotide polymorphismHeteroduplexPinus radiataPinus taeda

Copyright information

© Springer-Verlag Berlin Heidelberg 2001

Authors and Affiliations

  • S. A. Cato
    • 1
  • R. C. Gardner
    • 2
  • J. Kent
    • 1
  • T. E. Richardson
    • 1
  1. 1.Forest Research, Private Bag 3020, Rotorua, New Zealand Fax: +64-7-3435444 e-mail: sheree.cato@forestresearch.co.nzNZ
  2. 2.School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New ZealandNZ