Start Codon Targeted (SCoT) Polymorphism: A Simple,Novel DNA Marker Technique for Generating Gene-Targeted Markers in Plants |
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Authors: | Bertrand C Y Collard David J Mackill |
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Institution: | (1) Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines;(2) Present address: Department of Primary Industries, Bundoora, Victoria, 3083, Australia |
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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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Keywords: | Gene-targeted markers Start codon Genetic diversity QTL mapping |
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