It's technically possible, but a pretty difficult question to answer. Firstly, your approach will depend on if you have paired DNA sequencing too, or if you want to infer genotypes from the RNA Seq data.

Secondly, you should consider if this is a worthwhile endeavour based on the number of samples you have. To reliably call eQTLs, you generally want a relatively large number of samples. Then again, it depends on how genetically diverse your organism is.

Genotypes: If you're inferring Genotypes from RNA Seq data, and it's a non-model organism, you're going to have trouble. There are approaches in the GATK best practises, but splicing makes it very very tricky, even in human samples. If you're going from DNA Sequencing, then you might have a potential shot at getting it working, using Samtools, and an assembled reference.

Reference: As you don't have a model reference to work from, then you'll have to do a denovo assembly using something like Trinity. This will be by no means perfect, but it's at least something.

RNA Seq: If you're inferring genotype from this alone, then you'll need quite a bit of depth to get away with it. This is a lot of work to take on, specifically if all you have to work with is a limited number of RNA Seq samples. You'll need to; De Novo assemble a genome to make your reference, genotype using a mix of Samtools and GATK (I'm not 100% convinced this will work at the split 'n' trim stage without a good model reference, or if GATK would work properly).

Conclusion: The more I think about it, the more you're going to hit a lot of road blocks. I doubt this will work with RNA seq data alone.