Major change, minor change....I don't think anyone really has the answers to that. But are broodstock fish one generation removed from wild fish genetically different than their wild counterparts? Yes. Whether its enough to cause some of the problems believed to be caused by traditional hatchery stocks interacting with wild stocks is not clear.
Mark Chilcote, an Oregon Fish and Wildlife biologist has a draft paper that looks at population trends in OR rivers with and without hatchery supplementation. His conclusions were that population declines of wild steelhead unexplained by other factors occurred in rivers supplemented by hatchery stocks. He also didn't find a difference in the type of hatchery stock, whether it be traditional hatchery fish bred to different timing, or brood stock programs--population declines in wild steelhead were found when interactions occurred with both types of hatchery fish.
What he also found was that there appeared to be a threshold of interaction, below which there were no apparent effects to wild steelhead populations. This threshold appeared to be around 10 percent--below this, hatchery fish had no effect on wild populations. I don't have the paper with me right now; what immediately comes to mind is how one defines interaction as a percentile. I'll have to dig it up and review it again.
Now, he used a lot of statistics and there are datagaps in his assessment, but I don't believe there's an agenda here. The paper's not an ODFW report, but one that I believe he wants to publish in the refereed scientific literature.
I don't know what kind of guidelines Oregon uses to maintain genetic diversity and fitness in their broodstock programs, but the Chilcote paper seems to indicate that wild and brood stock fish are different enough such that the production of wild fish may be affected if they interact too much.
Certainly more study is necessary; I'm not a geneticist, maybe Carl O. can provide some input here. Despite these preliminary findings, I 'm still a proponent of brood stock programs because I believe many are not run with an objective of genetic diversity (and not just lip service). And if there is a threshold of interaction below which there are no effects to wild fish, it could be a management goal to have such programs in watersheds where you can remain below it.
My opinion of todays hatchery programs will firm up in the next few seasons, I think. Last years summer and winter runs in Puget Sound streams were the worst in my recollection. Something is going on in Puget Sound that is not conducive to either hatchery or wild steelhead, but the hatchery fish got clobbered. If it keeps up a few more years, than the fish have likely lost the fitness to survive except during the most optimal of conditions (and everybody knows how unimpressive those Chambers Creek brats are, as well).
The alternative of severely curtailing hatchery production I feel would invite either the eventual stressing of wild stocks by overfishing, or a reduction of overall recreational fishing effort for steelhead if there were no fish to keep. The anti-hatchery folks would argue against the latter, but this isn't what happened in BC. During the transition between C&K and C&R, total fishing effort declined, and it is believed that a subsequent rebound in fishing occured because of substantial increases in hatchery production.