The term DNA sequencing refers to methods for determining the order of the nucleotides
bases adenine,guanine,cytosine and thymine in a molecule of DNA. The first DNA sequence
were obtained by academic researchers,using laboratories methods based on 2- dimensional
chromatography in the early 1970s. By the development of dye based sequencing method
with automated analysis,DNA sequencing has become easier and faster.
Automated DNA sequencing is a core research tool used by almost every research biochemistry lab. It is used to determine the sequence of DNA, or the genetic code, that serves as the blueprint of life for every organism on Earth.
The utility of primer pairs in SCoTs was advocated by Gorji et al. (2011). SCoT
markers are generally reproducible, and it is suggested that primer length and annealing
temperature are not the sole factors determining reproducibility (Gorji et al., 2011). They are
dominant markers, however, while a number of co-dominant markers are also generated
during amplification, and thus they could be used for genetic diversity analysis (Collard &
Mackill, 2009b). This has been validated through study of genetic diversity among rice
varieties (Collard & Mackill, 2009b).
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.