Primer was designed from the gene responsible disease resistance in Vigna sp.
That primer was used to amplify the DNA samples of different genotypes of Vigna radiata.
All the samples were run in 3% agarose gel.
All the samples were found to have similar size of band.
What should be concluded?
two possibilities:
1. Most likely, contamination of all the samples with the resistant strain. Use newly opened reactives and clean completely all the working space with DNAse between each sample preparation
2. Poor primer design. Does the molecular weight of the band matches with that of the gene you are looking for?, if it does check for contamination first, if it doesnt, you can blast with the genome and filter by size of the band to see what is being amplified.
two possibilities:
1. Most likely, contamination of all the samples with the resistant strain. Use newly opened reactives and clean completely all the working space with DNAse between each sample preparation
2. Poor primer design. Does the molecular weight of the band matches with that of the gene you are looking for?, if it does check for contamination first, if it doesnt, you can blast with the genome and filter by size of the band to see what is being amplified.
the primer might be amplifying the genomic DNA of host rather than the target gene.
you can eliminate the possibility of contamination (with the resistant strain ) by including one susceptible check in your reaction.
Good luck
When you say the primers were designed to hit all the different genotypes, do you mean with different sized products? If your primers amplify the different genotypes to equally-sized products, you can't really conclude anything.
- Badges
- Science topic
- Similar topics
- Biological Science
- Molecular Biology
- Molecular Biological Techniques