Throwing in another couple of cents - (Not a geneticist, but grew up on a dairy, studied animal science, and now am raising backyard livestock.) Linecrosses & line breeding are used to some degree in most animal breeding situations. Ideally, in any situation, a breeder fully assesses each individual and pairs males and females based on their relative strengths and weaknesses. For instance, if one had a female with good body shape but only moderate egg laying ability, one would cross that female with a male from a dam who was an excellent egg layer and who had sired other ducks that were also excellent egg layers. But! If both the female and the male were on the upper limit of desireable size, one would expect the offspring to also be large/perhaps too big. So perhaps a breeder would only keep those offspring that were slightly smaller than average. (This holds for all breeding, and in fact, even dedicated line breeders will frequently bring in a selected individual to correct a deficiency that is spread throughout the herd/flock/pack.) The problem is that one can't, even in this day of gene sequencing, know 100% all the good and bad traits carried by each individual. By using linebreeding, after a few generations, one has a better idea of what sort of 'genejunk' is floating around in the chromosomes, and so better assess an individual because one knows their parents and grandparents - and also nieces, nephews, etc. So. Breeding good to better and not breeding bad to worse is actually the easy part - the hard part is picking out the bad, the poor, the fair, and (eventually) the average, and NOT using them for breeding. EVERY SINGLE BREEDING CAN PRODUCE POOR QUALITY ANIMALS. Furthermore, in litters and clutches, at best half of the offspring are going to be average (as good as the parents) or better - the rest will be, for whatever reason, slightly to significantly worse in quality. It's very tempting, esp in an age of 'papered' animals, to breed whichever female is ready, and sell ALL offspring as 'purebreds'. Rare breeds, esp, run into this. This is bad. It's bad for the animals, as it leads to breeding animals with bad traits & physical conditions, it's bad for the new owners who get a sub-par animal that can't be use for breeding, and it's bad for the breed because poor quality animals are passing on their genes. Take away points: Good breeders breed for better animals than the ones they start with, by pairing animals to strengthen weaknesses. Linebreeding can help assess the total animal. Improving the breed depends on culling sub-par individuals (neutering or selling as pets = culling...you don't have to kill or eat all your culls). If you're just breeding whatever animals you happen to have, and are not carefully selecting the best overall offspring to keep, then you run into the dangers that Kansas mentioned. It's a common enough problem that I feel very justified telling new breeders to not start by breeding 1 degree relations, until the breeders are good at selecting quality. Genes are like paint - in the hands of some, we end up with the Mona Lisa. In the hands of others, we end up with graffiti on the sides of railcars. Depends on what you do with it.