Even though both methods are PCR-based molecular markers, there is a number of differences between them. RAPD relies on the amplification of genomic DNA using short primers (10 nucleotides) with a random sequence, whereas ISSR is based on the amplification of regions flanked by repeating sequences (microsatellites or SSR), so the primers used contain those 2-6 nucleotides repeats with usually 2 varying nucleotides to the 3' end. RAPD markers are considered to be uniformly distributed along the genome, whereas ISSR are found only between microsatellite loci.
They also have some technical differences, PCR reaction in RAPD is performed using low annealing temperature (between 35-40 C), which gives them low reliability due to nonspecific amplification. Both methods produce several bands when separated in gel, so the scoring is quite similar.
You can also check:
http://d.yimg.com/kq/groups/18463231/1914912574/name/Molecular
http://www.adfg.alaska.gov/static/fishing/PDFs/research/geneconservation/snp/schlotterer2004.pdf
This book can be handy.
http://www.google.com.ni/url?sa=t&rct=j&q=ipgri%20molecular%20markers&source=web&cd=3&ved=0CD8QFjAC&url=http%3A%2F%2Fwww.vcru.wisc.edu%2Fspoonerlab%2Fpdf%2FIPGRI%2520Molecular%2520Markers.pdf&ei=GVFRUZqTHIyG9QTBx4GoDg&usg=AFQjCNEXaDRA-sutll5OwrMr9ylF548cZw
supplement,
i think in RAPD, it can recognize many whole genome site by "Random", but if in ISSR, it is more spesific...
Hello, everyone
I have a question about ISSR markers, and it's quite difficult to find someone that works on ISSR. Most scientists haven't used this marker in the recent decade. Why are ISSR markers being avoided by scientists?
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