My approaches to developing DNA sequence markers for non-model organisms have been diverse, including PCR-based methods that involve mining GenBank and aligning accessions to design broad-use primers (e.g., plant introns, Garrick et al. 2008 Conserv. Genet. [Supplementary Material]), as well as trialing next-generation DNA (Illumina) sequencing approaches.
We have started a project focused on generating and screening a different class of molecular markers (haplotype STRs) in non-model invertebrates.