I am working on marker assisted backcross breeding in rice and during the foreground selection I can see the band in donor as well as recipient parent although it is of different band size. The donor parent is showing the amplification of target allele which is justified but why my recipient parent is showing the amplification in different position? which I am assuming it should not show any amplification.
May be both of the parents are carried the same gene, but one parent has WT form and another parent the mutated form. I guess the mutation involved InDel, therefore same primer give bands for both parents but in different position. You can evaluate your progenies considering band size comparison.
Yes, I agree with Ujjal Kumar Nath. I am assuming that you were using PCR-based co-dominant marker systems, such as microsatellites/SSRs. As a good marker, primer pairs are usually conserved across individuals (can be across taxa too). The mutation variants in between the flanking primers is our main interest. For SSRs, we are measuring the number of repeat motives (e.g. (TC)n) on an amplicon sequence. Hence, this can be determined by fragment sizes, either in bp using a sequencing machine, or in band position on electrophoresis gel. An diploid example, you would get Band 1/Band 1 in donor and Band 1/Band 2 in recipient for a same marker. However, you would have absent/present band if you used dominant markers, such as RAPD. Hope this would help.
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