Genetic Management of Small Closed Populations – Maintaining a Broad Genetic Base and Managing Inbreeding

 D. Phillip Sponenberg DVM, PhD

Virginia-Maryland Regional College of Veterinary Medicine
Virginia Tech
Blacksburg, VA24061

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Management of small populations must be tailored to consider and reduce inbreeding, and this is unfortunately a very technical subject. A few definitions are essential to help in understanding the details. “Inbreeding” is any mating of related animals – animals that have an ancestor (or more) in common. “Linebreeding” is essentially the same as inbreeding, but usually designated as only concentrating a specific ancestor, and is generally defined as the mating of animals less closely related than in the case of inbreeding. “Linecrossing” occurs when two animals of different linebred lines are mated. “Linecrossing” is therefore a specific type of “outbreeding” or “outcrossing,” both of which describe the mating of unrelated animals.

Managing small populations of animals for genetic vigor and production is a challenge for breeders of rare breeds as well as for those with specific color goals that require closed or nearly closed populations. Maintaining isolated closed populations makes at least some level of inbreeding inevitable, yet it is well known that prolonged inbreeding brings with it the likelihood of some depression of reproduction and general vitality. This is called “inbreeding depression,” and is a major drawback of mating systems involving related individuals.

The fine points behind the biology of inbreeding depression are intricate, but inbreeding depression appears to be the result of animals being homozygous at many loci. As inbreeding proceeds over several generations, more and more of the genome becomes homozygous, and the result is a general decrease in vitality and especially in reproductive performance. The other side of the coin, hybrid vigor, is the result of heterozygosity at most loci in the genome. In regards to inbreeding depression, it is the relative level of homozygosity that is leading to the degree of depression, so that more homozygosity leads to worse depression. This is the reason that prolonged inbreeding is likely to be more deleterious than is inbreeding that is managed over fewer generations, as it results in animals that are increasingly homozygous over more and more loci.

Playing inbreeding depression and hybrid vigor off of one another is, at the most basic level, playing homozygosity against heterozygosity. Some level of homozygosity is needed, though, for an animal to be predictable genetically – which is the whole goal of purebred animal breeding. And, likewise, predictability is the usual goal for sheep breeders interested in certain (generally recessive) colors. Balancing the level of homozygosity needed for predictability against higher levels that lead to inbreeding depression is a balancing act.

Circumventing the problems of inbreeding depression while maintaining relatively closed small populations is a special challenge for breeders needing a closed population. This challenge is of special interest to breeders working with colored purebreds, as these usually come in a range of recessive colors that are easily lost on initial outcrosses so that a closed population makes the most sense as a strategy for color production.

Breeders interested in maintaining a small, closed population must make the goal of population vitality the top goal, and it and and the philosophies that underlie it must become primary in the decision making process that guides the breeding program. The goal of maintaining a vital, closed population is fundamentally different than the more common goals of maximizing production or conformation, and must take precedence over those other goals if success is to be achieved. To adopt too many goals for a single population is to risk attaining none of them.

The main risk to small populations is inbreeding, as it is nearly impossible to avoid mating relatives after a decade or so of maintaining a closed population of sheep. While some examples of very inbred and productive sheep can be found, these are always identified after the success instead of before it – and therefore these do not answer the question of what proportion of populations can withstand inbreeding depression. The successes are interesting, but tell very little about the populations that succumbed to depression by diminished reproductive or other performance. Inbreeding is documented to diminish performance and vigor, so it is always wisest to manage populations so that inbreeding does not become obligatory.

One strategy for maintaining genetic health in a closed population is to try to manage it so that a reasonably distantly related mate is available to every animal in the population. This has the practical implication of requiring more males than are needed for populations that do not need to worry about the risk of inbreeding because they are more able or willing to use outcrosses. In populations that are not closed, a quick outcross can quickly manage any depression that may arise. In closed populations (whether for genetic or biosecurity reasons) going outside the population is not an option, and so inbreeding must be strategically managed if it is not to diminish performance and vigor.

One strategy that can successfully manage inbreeding in small populations is to subdivide the flock into different genetic lines based on ancestry. The goal is to manage the flock based on the separate families within the flock. The different family lines within the flock can be managed to always provide for a reasonably unrelated outcross to every individual animal in the population. The key with this strategy is to manage inbreeding/linebreeding rather than avoiding it altogether because avoiding it altogether in small populations is eventually impossible. Inbreeding can be managed at acceptable levels, and can be kept at levels low enough to avoid much concern for depression. One useful way to accomplish this on a population basis is to use linebred males on a variety of females to generate both linebred and linecross replacements.

The details will be illustrated below, but the overall strategy is to assure that some moderate level of linebreeding is occurring within the flock, but linebreeding to different lines rather than to only one line. This assures that that outcrosses are available, as the different lines remain genetically distinct from one another. Rather than a complete avoidance of inbreeding, this strategy manages the inbreeding so that it becomes optional rather than obligatory.

The strategy, for sheep, can develop along different methods because the overall flock can either be divided by time or by space. Most usual is to divide the flock by space into different breeding groups each year, with a different line of ram in each group. Somewhat more elegant, and with other advantages, is to divide the flock by time, and each year use a two-year-old ram so that in sequential years a different line of ram is used. By using three different lines through the ewe flock, inbreeding can be managed.

Any breeding program must be tailored to specific properties and situations, but a general approach can be outlined. The strategy outlined here does not work well with fewer than three lines in the flock, although it will always work better with a greater number of lines as these reduce the overall relatedness within the flock. Regardless of the approach taken (multiple or single rams per year), the program depends upon dividing the ewe flock by pedigree into separate bloodlines. By using three as the model, these are lines A, B, and C.

It is important to understand what happens with the various animals in the flock depending on which way they are mated. When a line A ram is used, the line A ewes produce linebred line A lambs. The line B ewes produce linecross lambs that are A from the sire and B from the dam, or AB. The line C ewes produce linecross lambs that are AC.

The key is that the line A ram has sired both linebred (A) and linecross (AB and AC) lambs. If a linebred A line ram is maintained as a replacement, then he will be reasonably unrelated to both linebred B and linebred C animals. This is the value of the linebred ram - he is unrelated to more of the ewes in the flock than would be a linecross ram. For example, a linecross AB ram is related to all ewes that have either line A or line B in them, and is only unrelated to linebred C line ewes. So, he is unrelated to fewer animals in the flock than is a linebred individual.

Ewe lambs, in contrast, can and should include both linebred and linecross individuals. The system works best if some ewes are linebred, and others are linecross. As an example, a ewe that is linebred A will produce linebred lambs to an A ram, but linecross lambs to a B or C ram. If an AC ewe is retained, then she has the advantage of being linecrossed herself, but able to contribute a linebred replacement to either an A or a C ram, as the relationship to that line increases. The value of retaining linecross ewes is that they are not inbred themselves, but can contribute back to the linebred lines with the appropriate ram. By this method the genetic material can vary from generation to generation as linebred or linecrossed, and this helps to diminish inbreeding depression.

The eventual outcome is a ewe flock that is of mixed lines. Some ewes are linebred back to A, some to B, some to C, and some are varying combinations of these different lines. It is important when saving ewe replacements to realize that they need to be evaluated not only for their type and production, but also for how they fit into the population structure. Each ewe should ideally be able to contribute back to a linebred line, as well as to linecrossing within the flock. The rams are basically pulling the flock back into three different founding bloodlines, and the ewe flock needs to be managed to assure that this can happen by retaining a variety of linebred and linecross options.

Over long periods of time it is unlikely that any animal is purebred back to any of the founding lines, but instead the ewe flock has the following makeup: linebred A with contributions of B, C, or both, Linebred B with contributions from the other lines, linebred C with contributions of the other lines, and also a variety of linecross animals with contributions from one or two other lines. The lambs of the various types of ewes will fall into these basic classes:

The key is to notice that each type of ewe has a different role in the flock. For example, a linebred A line ewe can contribute linebred A replacements for rams, and also for ewes. She can also contribute linecross offspring to B and C line rams, but in this case only ewe lambs should be retained. The reason for this is that a linecross ram, if used in the flock, will generate linebred offspring back into two lines instead of just one. After a few generations of that strategy the entire flock is related to itself and no unrelated linecrosses are available. A linecross A and B ewe can contribute to linebred A and B offspring to either A or B rams, but only linecross offspring to a C ram.

Ram replacements are at least potentially problematic, for a variety of reasons. Due to the biology of inbreeding depression and hybrid vigor, it is very likely that the linecross rams will be superior to the linebred rams. This is a problem, because if linecross rams are kept and the flock remains closed, then eventually every animal becomes closely related to every other animal and inbreeding cannot be avoided or managed. By constraining ram replacements to linebred individuals the constraint is put into place that each ram will have a greater number of ewes in the flock to which he is distantly related. That provides for the linecrossing boost each year, but requires that the flock manager make decisions based on this strategy.

This strategy can and does work, but attention to animal identification and a willingness to turn over male generations rapidly is a key to its success. Most traditionally-minded breeders may find this less satisfying than developing a truly superior male and then using him for several years. Using a male for several years, however, assures a rapid build-up of inbreeding within the flock, and can eventually result in its lowered performance unless an outside animal is introduced to counteract inbreeding. In order for a flock to remain closed, it is vital that the breeder pay attention to managing inbreeding as a top priority.