I want to design species specific primers and probes for porcine, bovine, ovine, chicken etc, as mitochondrial genome is really conserved it's really difficult to design assays from MT genomes. can anyone suggest any other region for such kind of assays?
Before being able to provide a full answer two other aspects have to be highlighted:
1) do you need an abundant target (or in other words, you are not looking for a target present at low copy number per haploid genome)?
2) Is it important that the target makes the distinction between pig and wild boar.
If answer on 1) is yes and on 2) is no, then mitochondrial DNA is certainly still fit for designing a target for 'specific' detection of DNA from pig or pig-related material (so including wild boar).
it is not important to distinguish between pig and wild boar, however the target could be highly fragmented and degraded.
If you want a single primer pair that will allow you to distinguish all of these then that may be impossible. It would be difficult to find primers that might work on all of these species even in highly conserved regions and then you would have the problem of classifying the products reliably using TaqMan probes or melting profiles or restriction enzyme digest pattern. On the other hand if you want to design a series of species-specific primers with one or more pairs for each species that will only work on that particular species, then that is much easier. You can just pick genes or segments that are unique to that species and design primers for them. If you are starting with genomic DNA, then any unique segment will work.
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