Start Codon Targeted (SCoT) Polymorphism: A Simple, Novel DNA Marker Technique for Generating Gene-Targeted Markers in Plants

  • Bertrand C. Y. CollardEmail author
  • David J. Mackill


Random amplified polymorphic DNA (RAPD) markers have been used for numerous applications in plant molecular genetics research despite having disadvantages of poor reproducibility and not generally being associated with gene regions. A novel method for generating plant DNA markers was developed based on the short conserved region flanking the ATG start codon in plant genes. This method uses single 18-mer primers in single primer polymerase chain reaction (PCR) and an annealing temperature of 50°C. PCR amplicons are resolved using standard agarose gel electrophoresis. This method was validated in rice using a genetically diverse set of genotypes and a backcross population. Reproducibility was evaluated by using duplicate samples and conducting PCR on different days. Start codon targeted (SCoT) markers were generally reproducible but exceptions indicated that primer length and annealing temperature are not the sole factors determining reproducibility. SCoT marker PCR amplification profiles indicated dominant marker like RAPD markers. We propose that this method could be used in conjunction with these markers for applications such as genetic analysis, bulked segregant analysis, and quantitative trait loci mapping, especially in laboratories with a preference for agarose gel electrophoresis.


Gene-targeted markers Start codon Genetic diversity QTL mapping 



Technical assistance for gel electrophoresis by Ms. Miladie Penarubia is gratefully acknowledged. We also thank Dr. C. Raghavan and two anonymous reviewers for valuable comments on the manuscript.


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Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  1. 1.Plant Breeding, Genetics and Biotechnology DivisionInternational Rice Research Institute (IRRI)Metro ManilaPhilippines
  2. 2.Department of Primary IndustriesBundooraAustralia

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