BREEDING BY PHENOTYPE
Many breeders plan matings solely on the appearance (phenotype) of a dog and not on its pedigree or the relatedness of the prospective parents. Matings based on appearance are called "assortative matings". There are positive assortative matings (like-to-like) and negative assortative matings (like-to-unlike) for individual traits. Breeders use positive assortative matings when they wish to fix traits, and negative assortative matings when they wish to correct traits or bring in traits the breeding stock may lack.
Some individuals may share desirable characteristics, but they inherit them differently. This is especially true of polygenetic traits, such as ear set, bite or length of forearm. Breeding two phenotypically similar but geno-typically unrelated dogs together would not necessarily reproduce these traits.
Conversely, each individual with the same pedigree will not necessarily look or breed alike. Therefore, breedings should not be planned solely on the basis of the pedigree or appearance alone. Matings should be based on a combination of appearance and ancestry. If you are trying to fix a certain trait - like topline - and it is one you can observe in the parents and the linebred ancestors of two related dogs, then you can be more confident that you will attain your goal.
If a linebreeding produces a puppy with magnificent qualities, but those qualities are not present in any of the ancestors the pup has been linebred on, then the dog may have a wonderful show career, but it may not breed true. Therefore, careful selection of mates is important, but careful selection of puppies from the resultant litter is also important to fulfill your genetic goals.
Outcrossing (matings with a lower inbreeding coefficient than the average for the breed) tends to increase heterozygosity, matching pairs of unrelated genes from different ancestors. Most outcrossing tends to produce non-uniform litters. The exception would be if the parents are so dissimilar that they create a uniformity of heterozygosity. This is what usually occurs in a mismating of two breeds. The resultant litter tends to be uniform, but demonstrates "half-way points" between the dissimilar traits of the parents. Such litters may be phenotypically uniform, but will rarely breed true due to the mix of dissimilar genes.
Outcrossing can be a useful tool to bring in traits that you do not have in your breeding stock. While the parents may be genotypically dissimilar, you should choose a mate that corrects your dog's faults but phenotypically complements your dog's good traits.
It is not unusual to produce an excellent quality dog from an outcrossed litter. The abundance of genetic variability can place all the right pieces in one individual. Many top-winning show dogs are outcrosses. Consequently, however, they may have low inbreeding coefficients and may lack the ability to uniformly pass on their good traits to their offspring. After breeding an outcross, breeders should breed back to their original stock to increase homozygosity and attempt to fix newly acquired traits.
PUTTING IT ALL TOGETHER
Decisions to linebreed, inbreed or outcross should be made based on the knowledge of an individual dog's traits and those of its ancestors.
Inbreeding will quickly identify the good and bad recessive genes the parents share in the offspring. Unless you have prior knowledge of what the pups of milder linebreedings on the common ancestors were like, you may be exposing your puppies (and puppy buyers) to extraordinary risk of genetic defects.
As a geneticist, I am a proponent of linebreeding and occasional, prudent inbreeding. To breed dogs for more than one or two generations, type has to be established. In your matings, the inbreeding coefficient should only increase because you are specifically linebreeding (increasing the relationship coefficient) to selected ancestors.
If your breeding program is stagnating after several outcrosses, there is really no concrete direction you can go with it. You will have an abundance of heterozygosity, little uniformity and a diminished response to selection. Conversely, if you run into trouble with a linebreeding program, you can always outcross in one generation, which will bring in new genes and allow you to immediately change direction toward more specific goals.
Don't set too many goals in each generation, or your selective pressure for each goal will necessarily become weaker. Genetically complex or dominant traits should be addressed early in a long-range breeding plan, as they may take several generations to fix. Traits with major dominant genes become fixed more slowly, as the heterozygous (Aa) individuals in a breed will not be readily differentiated from the homozygous-dominant (AA) individuals. Desirable recessive traits can be fixed in one generation because individuals that show such characteristics are homozygous for the recessive genes. Dogs that breed true for numerous matings and generations should be preferentially selected for breeding stock. This prepotency is due to homozygosity of dominant (AA) and recessive (aa) genes.
Trying to develop your breeding program scientifically can be an arduous, but rewarding, endeavor. By taking the time to understand why you wish to linebreed on selected ancestors, you can then concentrate on those particular traits and produce a better dog.