I have an annotated transcriptome and would like to develop PCR primers for particular transcribed genes. My species is a non-model plant. Can I use BLAST or another tool to identify potential PCR primer sequences? Or more generally, is there a workable bioinformatics approach to identifying potential PCR primers for transcripts arising from a non-model organism? Any literature refs would be great too.
It depends if you want to amplify your target from genomic DNA or cDNA.
Depending on intron size, primers that anneal to different exons may not be able to amplify across the intron(s), and if you're unlucky enough to design a primer that spans a splice junction, you'll definitely be stuffed if you're working with genomic DNA. I would try blastn or translate to an amino acid sequence and use tblastn to see if you can identify the intron/exon structure in a related species. If you don't have a genome sequence available for anything close, I think your only option is to target as small an amplicon as possible and hope for the best.
If you are working with cDNA, any standard primer design tool should do