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Carotenoids are part of a larger family. That family includes alpha-carotene, beta-carotene, carotene and Vitamin A. Those carotenes are found in vegetables like carrots, beets and bell peppers. Worth noting, too much Vitamin A is toxic, many carotenes and carotenoids are not.
In salmon, that carotenoid is called astaxanthin. It is an antioxident that is 10 time more powerful than other carotenoids. To be fair, wild salmons have eight (8) times more astaxanthin than farm raised. This seems to be a nutritional and husbandary issue, not the salmon or species. In addition, the amount of Omega-3 fatty acids seem to be about the same. The Omega-3 fatty acids is the reason most people eat salmon.
Read more about astaxanthin and some notes
on canthaxanthin.
In 2003, the legal firm of Smith & Lowney instigated, for their clients, a lawsuit for the improper labeling of salmon against three corporate supermarket chains. Technically, the FDA has ruled that astaxanthin is a color additive. As such, although astaxanthin works as a powerful antioxident, because it provides color to "food stuffs" it is to be labeled as a "color additive". The supermarkets quickly followed up with labeling - to moot this lawsuit.
In the interest of full disclosure, astaxanthin is also used to color egg yolks by feeding it to egg-laying chicken. As of this writing, astaxanthin has limited use - mostly as an animal feed supplement. Part of the reason is it's high price, about $2000/kg for synthetic and $7000/kg from natural sources. Synthetic astaxanthin is made from petroleum. Natural is made from yeast, alge and to a lesser extent from (endangered) shrimp heads and shells.
Next is the infamous Salmo-fan(tm). Some writers have driven this item forward in their writings - perhaps to imply some sort of conspiracy. The turth be told a similar device is used in the marketing of wild salmon. It is well known within the (wild salmon) industry that consumers will pay more for certain colors based on perceived notions or tastes. For instance, albino salmons (1 in 6000) receive an appreciable premium. It stands to reason that farm-raised salmon will undergo similar pricing means. To this, the producer of synthetic astaxanthin established the Salmo-fan(tm) to demonstrate the color prefered by survey, and to assist farmers and vendors communicate the color prefered by survey. In other words, in a survey taken consumers beleive that certain colors are worth more, so producers deliver that color.
The next point is the allegation that farmers and vendors conspired to arrange for a color based on the Salmo-fan(tm). I'm not sure of this point. If you ask a consumer for their preferrence and they tell you, then it would be expected that that would be communicated - industry-wide. However, with new legislation in place requiring the labeling of farm-raised salmon it is hoped consumers will become educated in their own self interest.
Should any of this information be cause for concern, be assured farmers are well on their way in the production of organic salmon. Canada, Austraila, Japan and much of Europe are certifying organics. Petitions have been filed with the USDA and FDA, but investigations are still under way. Lastly to add confusion, in April 2003 as part of the Emerency Wartime Supplemental Appropriations Act the Secretary of the USDA was instructed to "allow (...) wild seafood to be certified or labeled as organic."