Raised baseline in Microsatellite Fragment Analysis?

[batesz]

Hi all,

Any microsatellite enthusiasts in the forum?

We have a project that uses microsatellite genotyping for variety identification in various crops. For chickpea, (Cicer arietinum L.) we are seeing a strange, raised baseline pattern across all 8 loci (see image). This raised baseline pattern is unique to this crop - we do not see this in the other crops we test. We tried different extraction kits, diluting DNA prior to PCR, and changes to PCR protocols (annealing temps, singleplex vs multiplexing). Nothing we tried reduces the baseline issue.

Thoughts?

Thanks!
Zack