What turkeys and cows can teach us about selective breeding

By Carol Beuchat PhD

There are some astonishing examples of what you can accomplish with selective breeding of domestic animals. The humble turkey has nearly doubled in size, from about 13 pounds in the 1920s to about 30 pounds 90 years later, and it's still gaining. This bird more than doubled its size through selective breeding over many generations.

This was accomplished simply by selective breeding of animals in the breeding population. No genes for faster growth or bigger size were added to the mix in the gene pool. So how, then, without adding new genes, can you produce such dramatic changes in phenotype?

Scheltens 2015, Turkeys have gotten ridiculously large since the 1940s; https://bit.ly/3ZqbEcn

Dairy farmers have also produced spectacular increases in milk cows. Over the last 50 years, production has doubled through generations of selective breeding.

​Again, how can you start with the gene pool contributed by founder animals of unremarkable quality, and through a few generations of selective breeding transform the descendents into super-producers?
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Brito et al 2021

​Let me tell you first what won't work to produce animals that are better than their ancestors. Grabbing the top one or two outstanding animals of each generation (the so-called "pick of the litter") might produce better animals in the next generation, but not generation after generation. Over the longer term, this strategy will not  ultimately produce the kind of spectacular increases in production quality that have been accomplished in animals like poultry and cattle. 

The rub is that while production might increase, the health of the animals declines. Here's how it was described in a recent review of genetic selection for milk production in dairy cattle.

"Despite the great betterment in production efficiency, strong drawbacks have occurred along the way. First, across-breed genetic diversity reduced dramatically, with the worldwide use of few common dairy breeds, as well as a substantial reduction in within-breed genetic diversity. Intensive selection for milk yield has also resulted in unfavorable genetic responses for traits related to fertility, health, longevity, and environmental sensitivity."  (Brito et al 2021)

The livestock breeders were using the latest breeding and genetic technologies to improve breeding success. What went wrong?

They learned the hard way that choosing only the best animals to breed (i.e., best-to-best) comes up against the hard reality of genetics. They didn't pay attention to inbreeding, which was eroding their gene pool generation by generation, until they finally realized the impact when the cows were unable to reproduce. You're not a useful cow if you produce lots of milk but can't get pregnant - one being related to the other, eh? Note that we're not talking here about breathtaking levels of inbreeding. Inbreeding was less than 10% in 2020 in a variety of milk cow breeds (figure), and the industry was facing catastrophe if they didn't solve the problem of viability. 
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Brito et al 2021

​Livestock breeders have now realized that highly trait-specific selective breeding might improve one feature to the detriment of others that are critical to animal health. 

Moving forward, the dairy industry needs to continue refining the current selection indexes and breeding goals to put greater emphasis on traits related to animal welfare, health, longevity, environmental efficiency (e.g., methane emission and feed efficiency), and overall resilience. This needs to be done through the definition of criteria (traits) that (a) represent well the biological mechanisms underlying the respective phenotypes, (b) are heritable, and (c) can be cost-effectively measured in a large number of animals and as early in life as possible. (Brito et al 2021)

What seemed like a sensible way to breed to dramatically increase production traits, by restricting breeding to only the best animals in a population, resulted in inbreeding depression that would eventually sink the ship. But this is how we breed purebred dogs. Most have inbreeding greater than 10%, and in more than half of breeds tested, inbreeding exceeds 30%, with some exceeding even 40%.

Are dogs less sensitive to inbreeding than cows? No. Dog breeders are just less sensitive to the consequences of inbreeding than livestock breeders, no doubt because a commercial livestock breeder won't stay in business if the quality of the herd declines.

In milk cows,

"Intensive selection for milk yield has also resulted in unfavorable genetic responses for traits related to fertility, health, longevity, and environmental sensitivity" (Brito et al 2021).

But what we want to know is how, despite significant inbreeding depression, breeders were able to achieve such remarkable improvements in production traits? ​

In fact, commercial breeders do in fact choose the best offspring of each generation to breed to, but not just the top few animals. They select all of the best performing animals, perhaps 10-20% of the best animals. The goal is to capture the genetic variation present in the best animals. They know thatt each animal is a mix of genes from two good quality parents, and from the same parents this mix will be more fortuitous in some animals than others. The result is a collection of offspring that carry the genes of good producers, and when bred together in the next generation the new mixes of genes will once again produce some animals that are better than others. By selecting many of the top animals in each generation, the gene pool of the popualtion is gradually shifted in the direction of higher productivity as each new generation produces animals with a different mix of genes.
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This assumes that genes are at least partly responsible for the traits of interest. If not, or if the influence is very small, you will not see imprrovement in performance with seletive breeding. But as in this example of selection for a trait like speed, selection of the 10% fastest animals in each generation will move the average performance of the animals in the population to higher speed. 

Of course, not only must the trait have some genetic basis, but for this to work you need enough genetic variation to produce many new combinations of genes in the next generation of offspring, some of which can perform better than their parents. The key here is genetic varaiation. If you only keep the top animal in each generation, you will lose the genetic variation needed to improve anything. The genes associated with the best performance will become fixed in the population, ending your genetic improvement program.

​Inbreeding and strong selection eliminates the raw material - genetic variation - that is necessary for improvement of traits in animals. Because of Inbreeding in each generation of dogs, genetic variation is lost and homozygosity increases, which can drive traits to unwanted extremes. Most breeders realize that breeding together two outstanding but closely related dogs doesn't guaranted outstanding puppies. This is because loci that were heterozygous in the parents can be homozygous in the offspring, which then lose the genetic advantage of heterozygosity. This is called "overdominance", where the phenotype of the heterozygous combination is superior to the phenotypes of either allele when homozygous. For traits that depend on overdominance for the best phenotype, inbreeding will destroy the advantage of heterozygosity. 

What's the lesson here?

One of the "pearls of wisdom" often offered by long-time breeders is that you should "breed the best to the best". This suggests that the secret to success is the consistent application of this simple rule of thumb. But what we know about genetics makes clear that, while this might produce nice puppies from a pair of parents, selecting the pick of that litter and doing the same in the next generation will leave a trail discarded genetic variation that might include the raw material you need to produce something better than either parents. It's the shuffling of this variation in each generation that provides the opportunity for fortuitious combinations that can create animals that are superior to their ancestors, generation after generation. This is how we got those massive turkeys and the amazing milkers. 

Dog breeders, the value of your dogs is in their genes; it's your money in the bank that will pay dividends generation after generation. Don't toss out the lesser dogs that happened to get the perfect mix of the available variation. 

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