Inbreeding/linebreeding are simply the practices of breeding closely related individuals to increase desirable traits and eliminate or reduce undesirable ones in a population. Defining and prioritizing traits to select in or out of the population varies with the species, the goals and the breeder. Inbreeding, even continually, is one tool among many that a producer can use to improve his herd. Like any practice, inbreeding/linebreeding can be done wisely or foolishly.
For example, quite a few of the Polish rabbits in our state have problems with malocclusion. We have used inbreeding/linebreeding to eliminate this trait in our herd. In culling rabbits that had or produced malocclusion, we reduced the number of both bucks and does available for breeding in the short term. However, this has produced a much healthier population. If we had continued to use all of the Polish rabbits available, to keep "genetic variation" high, this very undesirable trait would undoubtedly have remained or possibly increased in the population.
Further, inbreeding/linebreeding allowed us to identify the animals that carried the genes that produce malocclusion without expressing it. This would not have been possible without linebreeding. You can perhaps call this a shortcut, but it allowed discovery and correction in a time frame that was useful to us (and to the rabbits that were not thus born with malocclusion), rather than the trial-and-error of outcrossing that quite possibly may have
never illuminated the situation.
But inbreeding does not necessarily mean
never breeding any animal to an unrelated one. It does not necessarily mean using 2 male animals to produce most of the offspring in the next 40 years. I have never actually heard anyone suggest that a breeding program should start with two individuals and never bring any new blood into the line. We use linebreeding continually, but not exclusively. Most of us use inbreeding/linebreeding alternated with judicious outcrossing.
This is because outcrossing has its own perils. After four generations spent eliminating malocclusion, if we bring in an unrelated Polish that just happens to carry the genes that produce maloccusion, we have undone all of our work (and yet, we still benefit from the linebreeding we've done, because even now we
know which animal produced the trait). The animal may also bring in many other undesirable characteristics. Sometimes the risk is worth taking, just as at other times the risks of inbreeding are worth taking. We used first linebreeding, and then outcrossing to Mini Satins, in our Polish. Sure enough, we are now working backward (i.e. linebreeding) to eliminate unwanted traits the Mini Satins introduced to our Polish line.
See, that's the thing - in livestock, genetic variability isn't an
unqualified good thing. Genetic variation can include all sorts of undesirable genes, and reducing or eliminating them is generally a positive outcome, both short- and long-term. From an evolutionary/natural selection viewpoint, genetic variability is considered a good thing because it acts as a repository for traits that are currently maladaptive but may, in a changing environment, eventually become adaptive (note here that because the traits are currently maladaptive, the animals that carry and/or express those traits suffer and/or die). But this is a little nonsensical to argue in relation to the breeding of domestic rabbits; one breed may serve one purpose better than another, but it takes as little as a single outcross to import a new trait and inestimable genetic variation, if desired. Further, you can reduce, eliminate, or increase certain gene frequencies without reducing, eliminating, or increasing others. Ultimately, inbreeding/linebreeding doesn't
necessarily reduce important variability; that depends on how big and how variable the population is to begin with, genetic linkages, the heirarchy of selective choices, and many other factors.
If you go back to the beginning, whether you subscribe to creation or evolutionary theory or a combination of the two, you may come to the conclusion that not just all breeds, but all
species started out with very few individuals. Most genetic variation came about as a result of mutations; yet as far as geneticists know, the vast majority of mutations are not only maladaptive, but lethal...which is another thing that suggests that genetic variation, in itself, is not an unqualified good.
As far as the entire Holstein breed being wiped out, I do not share that concern. First, Holsteins are a breed of cattle selected and bred by humans for a specific reason, but I'm not sure the loss of a specific purebreed is cause for great anguish. There are numerous other breeds of cattle that can fulfill the purpose served by Holsteins (though perhaps not to the satisfaction of Big Ag). Second, there is some unknown number of small farmers, ranchers and homesteaders raising Holsteins and Holstein crosses. These animals - it is pretty much impossible to know how many are out there - are not included in the genetic analyses examining relatedness; and the crossbreeds, especially, may function as a tremendous resource for reinvigorating the breed. Finally, it takes relatively little outcrossing to restore genetic viability even in a significantly inbred population like Holsteins:
"Actually, it is easy to implement methods to maintain genetic (pedigree) diversity within a breed despite heavy use of genomic selection by simply limiting the influence of individual bulls and females that rank highest in the breed at any point in time. Spreading the pedigrees of young bulls across more bull and cow families than has been done over the past decade for Holsteins will result in very little, if any, loss of actual genetic gain over the long term." "The narrowing of the Holstein gene pool" by Les Hansen, Ph.D. in Dairy Cattle Genetics
https://www.procross.info/wp-conten...ng-of-the-Holstein-gene-pool-July-2021-v2.pdf
I think the real problem you've identified in the Holstein and cornish cross chicken examples is greed, not inbreeding itself. Greed has resulted in myopic, very short-term views regarding breeding practices in big commercial operations. Thus, inbreeding (like many, many
other practices in Big Ag) in these particular examples was done without much consideration for anything other than immediate profit. Multiple of these other unfavorable practices (e.g. excessive antibiotic use, overcrowding, unhealthy feed sources and feeding practices, to name just a few), in addition to careless inbreeding, have no doubt factored into the increase in significant health issues in Holsteins, chickens and other species farmed on an industrial scale (turkeys come immediately to mind as well). As Hansen notes in the same article linked above, "Genetic theory tells us short-term genetic gain should always be balanced alongside the potential for long-term genetic gain when developing strategies for genetic improvement of a breed." When that advice is ignored, both animals and people suffer as a result; and that argues for prudence in the practice of, rather than elimination of, linebreeding.
Big Ag's Holsteins and cornish cross chickens are good examples of inbreeding done foolishly. But I don't want to throw the baby out with the bathwater.
