Genes are not lost but merely assembled is such a way that we can’t detect.
I'm going to disagree with this one Seed, otherwise selective breeding would not work. Say you cross parents (animal or plant) so that at one specific gene pair one contributes gene "A", a dominant gene. The other parent contributes gene "a", a recessive gene. Since A is dominant, the offspring will exhibit that trait. But when you breed the offspring to offspring when they both have Aa at that gene pair you get three possibilities. About 1/4 will get AA, 1/2 Aa, and 1/4 aa. If you elect to go forward with the "aa" offspring for your next round of breeding the "A" gene is lost. It's gone. It is not there anymore in that line. If you select an "AA" for your breeding project the "a" gene is lost. But since "A" is dominant you can't tell which offspring is AA and which is Aa. This makes it easy to eliminate dominant genes but really hard to eliminate recessive genes.
The purpose of selective breeding is to stabilize the offspring. You do that by permanently eliminating the genes whose effects you don't want. If you want a certain flower color you want to permanently eliminate all the genes that make the flowers different colors.
Most characteristics are affected by a multitude of genes not a simple dominant gene. Some things are simple to select for. Other things we may believe we are gaining on expressing something we want only to find out that we did nothing.
It's even harder than this but this is something extremely important. Some genes are dominant, some recessive. Some are partially dominant and some only act if other specific genes are present. Some are sex linked.
Some traits are a simple one gene dominant or recessive. I've read that whether a bean is a climbing bean or bush is this type of gene, dependent on one gene pair with climbing the dominant version. But some climbing beans may climb 3', some may regularly top 12'. Some bush beans are pretty low to the ground or grow fairly tall. There are a lot of other gene pairs that modify the growth habit to get that diversity.
I'm more familiar with chicken genetics. The last I heard, 13 different genes had been identified that effect the shade of brown on an egg if the egg is brown. There is one different dominant/recessive gene pair that determines basic color, blue or white. Blue is dominant. Green is just brown on top of blue. The shade of brown or green is determined by which of those 13 genes are present, that's why you get so many different shades of brown or green. One of those genes doesn't add brown, it can bleach out brown to make white. I'm not sure if that bleach acts on one specific brown gene or all of them. One of those brown gene is sex linked, if a hen has it she only gives it to her sons while if the rooster has it he gives it to both male and female offspring.
I'll use another chicken gene to demonstrate partial dominance. The B/B/S gene (Blue/Black/Splash) creates a Splash colored chicken if both genes at that gene pair are B/B/S. Splash is a white chicken with splashes of black. If one of those genes at that gene pair is B/B/S and the other is not you get a Blue chicken. If neither of those two genes are B/B/S you get a black chicken. But this only works on what would normally be a black feather. If the feather would normally be red or white then you won't see any effects of the B/B/S gene. You can get a red chicken with a blue tail. B/B/S may be lurking in the background, not because it is recessive but because conditions are not right for it to express itself.
I think that is an extremely important point, that most characteristics are controlled by a multitude of genes, not a single gene. How those genes express themselves depends on the mix of those genes you have.
Then you have the interaction between environment and genetics, making it near impossible to detect permanent changes.
In a lot of traits I totally agree. This spring has been cooler than it was last spring. Some of my beans were a lot more vigorous last spring than this year. I can typically grow two crops of dried beans down here. The ones I grow in the spring/early summer are typically much more vigorous and productive than the ones I plant in the heat of summer. On the bean thread it's often mentioned that the same stable dried bean can have different colors or patterns depending on which soil it is grown in.
The way I look at hybrid vigor is that it is genetic diversity. Breeds of horses or chickens or open pollinated varieties of plants are developed by selective breeding. You eliminate the genes you don't want to stabilize the genes you want. You do that by inbreeding. But if you inbreed too much you can lose vigor and other important stuff. There is a balance there and of course techniques have been developed to try to manage that. I think of spiral breeding or pen breeding techniques with chickens. When I'm trying to stabilize a dried bean I try to select all the beans I'll grown from one specific plant to try to eliminate the genetics I don't want. But once the bean is stabilized I collect the beans I'll grow from many different plants to maintain a certain diversity. I try not to inbreed too much once I've finished with selective breeding but I still try to eliminate any genes I don't want.
Another point. It doesn't have to be different breeds or varieties to introduce hybrid vigor/genetic diversity. If you have a flock of Barred Rock chickens that have inbred for a while you can lose genetic diversity to a point that they are less vigorous. But if you then breed them to another Barred Rock that has been genetically isolated from your flock for several generations you get a boost of hybrid vigor while keeping them Barred Rocks. You introduce a lot of the lost genetics that has nothing to do with them being Barred Rocks.
Sometimes when you cross breeds or varieties or different gene pools you get things you don't want. Instead of getting a larger tomato you may get a smaller one. The plant may be vigorous but not produce what you want. What you want is hybrid vigor in the traits you want.
I don't know why increasing genetic diversity leads to hybrid vigor. I've read different theories on that. But it is demonstrated to work.
Now my disclaimer. I have no education or credentials that make me a geneticist. All this is my own demented opinion on this stuff. For any that made it all the way through this feel free to pick it apart.
. Seed' is there also, especially with the genetic complexity and environmental factors at play.
