This is another interesting question.
There is a project that Simon Fraser University is leading and UBC is a partner, where we are looking at coho salmon, in particular, for exactly what you said. The cultures of coho have gone down to about 5% of what they used to be, only a few decades ago, and they have become endangered in some parts of the B.C. waters. This project is using genome technology to try to see how we can enhance the wild population, but also how we can help the local, sustainable, containment aquaculture of coho to help supplement the supply.
So, yes, there is. My group is there to do the economics, while they do the genome science, and we combine the two to do exactly what you're saying for coho, in particular. This can be expanded to other species, of course.