Molecular markers from the transcribed region of the genome can offer potential for various applications in plant genotyping as they reveal polymorphisms that might be directly related to gene function. A novel marker system called Start Codon Targeted Polymorphism (SCoT) was described by Collard & Mackill (2009b), based on the observation that the short conserved regions of plant genes are surrounded by the ATG translation start codon (Sawant et al., 1999). The technique uses single primers designed to anneal to the flanking regions of the ATG initiation codon on both DNA strands. The generated amplicons are possibly distributed within gene regions that contain genes on both plus.
