I am doing SSR marker screening for pod shattering in soybean. I am facing problem in SSR marker amplification in some varieties but I am getting amplification in all varieties with some other SSR primers. I think there is no problem in my PCR reaction mixture.
Hi, Komal. SSR null alleles in some varieties are common. The null alleles are usually due to failure in primer annealing to the flanking regions of a SSR. The mutations in the flanking regions is always responsible for this. To solve this, you could either redesign the primers (shifting the primer pair back and forth until you get the amplification), or just look for other markers.
Hope this will help.
Hi Komal,
I agree with Chee-Keng Teh. Just to add: if null alleles are confirmed repeatedly, consider null allele as an attribute by itself and these data can be used for estimating genetic distances. In the case where you are doing marker screening/identification, null alleles are undesirable and you need to go for another set of SSRs.
Hi, Komal. SSR null alleles in few varieties are common. The null alleles are usually due to failure in primer annealing to the flanking regions of a SSR. The mutations in the flanking regions is always responsible for this. you could either shifting the primer pair back and forth until you get the amplification, or just look for other markers.
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