When we run the amplified SSR product in an agarose gel, how heterozygous and homozygous conditions are differentiated ? Can anyone illustrate the scenario with a gel picture ?
Hi Binoy,
Heterozygote will essentially give you amplification of SSR alleles from both the parents, while a homozygous SSR allele will either look like parent 1 or parent 2.
SSR allele from F1 will always give you a heterozygous pattern, while fixed lines (RIL or DH) will be homozygous.
Attached image will give you an idea about homozygote (AA or aa) and heterozygote (Aa).
I would suggest you to refer Collard et al. Euphytica (2005) 142: 169–196,
DOI: 10.1007/s10681-005-1681-5.
I would further suggest you to use acrylamide gel electrophoresis for resolving SSR variation. Agarose gel may not resolve SSR allele differ by 2 bases.
Cheers,
Hi
These images are of SSR product resolved on agarose gel clearly differentiating maize inbreds and their F1 hybrids.
These images will give you clear idea about homozygote and heterozygote on gel image.
Hi Ravindra,
Jay is right. You will need hihger resolution power than common agarose gels. Even with high resolution agarose gels use to be difficult to distignguish 6bp differentiated alleles. And just to add that two you should be careful with the presence of null alleles.
It is easy to identify F1 on PAGE rather than agarose gel. Agarose can be used for dominant markers where band either present or absent. '
here PAGE pic showing clear banding pattern
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