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

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Abstract

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.

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Acknowledgements

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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  1. Bertrand C. Y. Collard

    Present address: Department of Primary Industries, Bundoora, Victoria, 3083, Australia

Authors and Affiliations

  1. Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines

    Bertrand C. Y. Collard & David J. Mackill

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  2. David J. Mackill
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Correspondence to Bertrand C. Y. Collard.

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Collard, B.C.Y., Mackill, D.J. Start Codon Targeted (SCoT) Polymorphism: A Simple, Novel DNA Marker Technique for Generating Gene-Targeted Markers in Plants. Plant Mol Biol Rep 27, 86–93 (2009). https://doi.org/10.1007/s11105-008-0060-5

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