I have amplified the rpl32-trnL spacer region for five different grass species (trnL (UAG) and rpl32-F primers). Instead of seeing one consistent amplicon size, I have some fragments that differ by about 150 bp. Has anyone seen something similar in plants or grasses in particular? Could there be a microsatellite region that is being amplified that is causing this size difference?
Hi Clarke,
I dont know anything about the locus you amplified, but I think it is not unusual that you get diverse fragments for different species.
I would say they have a simple length polymorphisms. Did you blast your primers to compare the sequences between the primers for these species ?
Regards
Stephan
Stephan Schie , thank you for your answer! I did blast the primers, and it seems that the product size for Eragrostis species ranges between 550 and 580 bp, and about 730 for Phragmites australis. So there is definitely quite a large difference between species! It must be something along the lines of simple length polymorphisms, SSRs or ISSRs. I will have them sequenced and have a look. I'll keep this post updated :)
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