Fluidigm is working really well for genotyping our low quality marine samples.

Thanks Sarah. Indeed, once you have the SNPs + flanking regions Fluidigm, VeraCode and KASP are working well. To also find earlier (lost) polymorphisms I'd rather go for a NGS sequencing approach to look at diversity and frequency change between samples. All restriction based technique are out of question unfortunately, reducing the nr of common SNP typing methods unfortunately...  I keep looking ;) Greetz to Iceland !

I ran standard GBS where some of my samples were quite degraded (but probably not as degraded as you are talking about). I just ran out the genomic on a gel, excised the largest fragments from the smear, and used that for the RL. I also amplified the individual genomics separately, then excised the same bp range from each, cleaned it up, and pooled them in equal quantities. This compensated for variable amplification strengths. This probably won't help with extreme degradation.

This is the solution

Sánchez Barreiro, F., Vieira, F. G., Martin, M. D., Haile, J., Gilbert, M. T. P., & Wales, N. (2016). Characterizing restriction enzyme‐associated loci in historic ragweed (Ambrosia artemisiifolia) voucher specimens using custom‐designed RNA probes. Molecular Ecology Resources.

Thanks Rosalia, we'll take a look at your protocol !