Principle of CAPS and dCAPS Markers

Sequence Characterized Amplified Region or SCAR Marker or Locus Specific Marker is a PCR-agarose gel electrophoresis based on sequence specific polymorphic RAPDs fragments use cloning and sequencing techniques to synthesize specific primers (16-24) bp in length to identify specific locus that linked to interested traits, Direct SCAR Marker initiate by DNA extraction for PCR amplification of RAPDs assay and separate amplified PCR product by gel electrophoresis and cut and purify interested fragment from agarose gel for sequencing and compare sequence using BLAST tool in NCBI website to synthesize specific SCAR primers that flank regions of original RAPDs primers and re-amplify template with SCAR primers to Identify specific Bands, Indirect SCAR Marker initiate by DNA extraction for PCR amplification of RAPDs assay and separate amplified PCR product by gel electrophoresis and cut and purify interested fragment from agarose gel and clone purified interested fragment in suitable vector and transform vector to high component cells of E-coli bacteria to isolate plasmid DNA from selected transformed colonies and digest plasmid DNA by restriction enzymes to check the same size fragment that corresponding to RAPDs assay fragment for sequencing to synthesize specific SCAR primers that flank regions of original RAPDs primers and re-amplify template with SCAR primers to Identify specific Bands, SCAR Marker consider co-dominant inheritance marker with locus specific nature and stable and reproducible and informative marker, SCAR Marker require skills and efforts and expense in designing specific primer for each locus and exhibit dominance when primer partially overlap site of sequence variation, SCAR Marker use for locus specificity and gene tagging and DNA fingerprinting and genetic diversity and marker assisted selection (Watch Related Video in #geneticteacher) #geneticteacher