Let me try to explain expression by using humans as an example. In every one of our cells, we have approximately 20,000 genes (a region of the DNA double helix). Each gene has the instructions to produce the 100,000 proteins which actually perform tasks in the body (e.g., enzymes for chemical reactions, contractile proteins in muscle, structural molecules likes collagen in tendons and ligaments). Because DNA has to last the life of the cell (which, in some cases, is the life of the organism), it is kept relatively safe in the nucleus. When a cell needs more copies of a specific protein, a copy of the gene is made in the form of RNA (a process called transcription) which travels to the cytoplasm where the nucleotides are used by a structure called the ribosome to indicate the order of the 20 amino acids that make up proteins (a process called translation). All the cells in your body have the same DNA, plus or minus a few copying errors. Any particular cell makes only a subset of those proteins and accesses (expresses) just a subset of those genes. For example, while a muscle cell has the DNA information on making the hormone insulin, it does not "express" that information. A pancreatic cells has the information to synthesize hemoglobin, but it is not expressed in these cells.
When an egg is first fertilized, it appears to be capable of expressing all of the genes in its arsenal. But as the embryo develops, cells begin to specialize into tissue types (endoderm on the inside, mesoderm in the middle, ectoderm on the outside). Specialization occurs within these major tissue types too (e.g., ectoderm into skin and into neurons). During this specialization process (also known as differentiation), chemical markers may be added to some of the genes that prevent them form being copied into RNA, essentially turning them off (a process called methylation). Others become easier to express (copy into RNA) when other chemical markers are added to structural proteins that support these gene regions (a process called acetylation). [There are other mechanisms that have these impacts too.] These kinds of changes fall into the broad category of epigenetics because they occur during the lifetime of the organism. The DNA information is still there, but its access has been changed.
In subsequent generations, these epigenetic markers (acetylation / methylation) are removed and the organism returns to its original state. In some cases, the markers last only a single generation, but in other cases, the markers persist for several generations. For example, extreme starvation in Holland near the end of the Second World War resulted in a series of epigenetic changes in fetuses that developed during that time (see
http://www.naturalhistorymag.com/features/142195/beyond-dna-epigenetics). They were born at a smaller size and stayed small throughout their lives (and had a lower risk of diabetes); these epigenetic changes for efficient use of energy were passed onto their children even though they suffered no starvation during their own development.
One way to think of these epigenetic changes in humans (and hatchery fish) is that there are teams of genes that work best under one set of environmental conditions and other teams that work best under other environmental conditions. As the world is a variable place, epigenetics allows an organism to activate the suite that will work best and silence the ones that won't as an organism adapts to its current environment.
Some speculation. From this study of hatchery vs. wild steelhead, it appears that the crowded conditions of the hatchery favor one suite of genes, while the conditions in the wild favor another suite. And it would appear that expressing the wrong suite is very bad for growth and survival. The overall DNA in the two groups (hatchery vs. wild) is probably quite similar, but the expression is different because of their different rearing environments. And these differences in expression may persist for more than one generation. This would explain the very poor survival of the offspring of hatchery fish that spawn in the wild, even when half of the genes come from a wild parent - wrong epigenetic markers for survival in the wild. However, some of these offpring do survive and the more generations they are in the wild the more their epigenetic markers revert to the wild conditions and the hatchery imprints are lost.
Steve
