locating the ghost bands

Brad A Didion t80bad1 at CORN.CSO.NIU.EDU
Mon Apr 17 12:11:13 EST 1995

I would like feedback on a conundrum encountered in using RAPDs.  There is 
a gel band which is associated with a trait of interest but the 
association is negative.  Ergo, the band is genotyped as negative and 
when there is no band, it is genotyped as positive.  So, how best to 
ferret out what the ghost band (positive genotype).  We have cloned the 
negative band, designed PCR primers and amplify up the same band as 
expected. What's unexpected is that these primers amplify up the same 
band size in the animals previously genotyped as positive (i.e. having 
the ghost band). My hope is that this is not too confusing for your 
pondering. We'll begin doing rest enzym digests on this pcr product to 
see if differences exist across the two genotypes. any help is 

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