Breeding for Genetic Diversity

The following breeding considerations have been adapted from the Populations Genetics in Practice by J. Jeffrey Bragg, to support breeding philosophies that preserve as much genetic diversity within populations as possible. These considerations were developed by Mr. Bragg during his work on the Seppala Siberian Sled-dog Project, a Canadian bloodline conservation and breed development initiative under Ministry of Agriculture charter. It should be noted here again, that none of the following considerations should infer that line breeding or inbreeding strategies are not viable, useful or even necessary in some cases, simply that the following considerations are important in evaluating breeding populations to design breeding strategies that maintain as broad a pool as possible as the breed continues to evolve in the United States.

Encourage breeders to maintain balance of sires and dams – Efforts should be made to balance the number of sires and dams within breeding populations. Heavy reliance on popular sires in which small numbers of selected males sire grossly disproportionate numbers in the breed population should be avoided. This typically occurs when the “best” ram is bred to all females within a breeder’s flock. Any significant restriction immediately effectively restricts the breeding population.

Efforts should be made to use as many male individuals as possible, both for a breed population as a whole, as well as within individual flock systems. Given the large number of ewes that can be covered with a limited number of rams, it is sometimes more practical keeping several members of specific sire lines to preserve some outcross genetics within each family.  

Monitor incestuous matings – Virtually all purebred populations demonstrate serious and sustained inbreeding when the full pedigree is evaluated. While inbreeding in and of itself may not be detrimental if the underlying genetic contributions are free from defect, this is virtually never the case. As inbreeding depression is subtle, incremental and in limited populations seriously widespread, it is important to track and publish as much genetic information as available to assist breeders in tracking potential genetic profiles and to help avoid unintended additional inbreeding resulting from a lack of pedigree history.

The American Teeswater population is susceptible to these issues. Of the 7 sires that were originally imported, Royal Prince, Endsmoor Majic and Rimington Playboy are directly related, and share more distant relationships with both Rimington Crusader and Patley Prince Charming. Much is not known about Lakeland Majestic, but anecdotal accounts indicate common ancestry with the others.  Grey Green Star represented a more diverse pedigree, but the heavy line breeding used by American breeders to achieve higher blood percentages as well as the very low number of surviving progeny of several sires have led to extensive loss of what genetic information was available.    

Understand and monitor coefficient of inbreeding – Simply avoiding incestuous matings within the first three generations of breeding is not a reliable index of the level of inbreeding of a particular pedigree. The Coefficient of Inbreeding (COI) should be monitored, preferably over 10 generations in conjunction with a reliable breed database. Additionally, many breeders conflate a different farm name with dissimilar pedigrees, when in fact ancestry may be almost exactly the same between two individuals, that have just been born at two different farms, therefor it is critically important that breeders carefully study pedigree information to clearly understand relationships.

Wright's Coefficient of Inbreeding represents the statistical probability that the alleles contributed by sire and dam at any given gene locus will be identical by descent. It may also be regarded as the percentage of multi-allele genes that are likely to be homozygous by descent for a particular mating. Therefore, COI is the principle measure of the degree of inbreeding and its effects on the genome.

It should be noted here that a fundamental concern in arbitrary blood percentage restrictions is the necessity of culling animals that are “unregisterable”. In practice, what is the difference between a 87.5% and a 91% animal? Any why is it reasonable to have to cull an outstanding animal that exhibits better type and performance that a higher percentage animal simply as a result of mathematical calculation. Such rules inevitably lead to issues with pedigree integrity, and absent intensive genetic certification, which presents its own set of issues, especially in larger breeding enterprises, it is counter productive to deprive breeders of the ability to work with such animals. Further, such restrictions were most certainly not adhered to by the foundational breeders of these animals such as Bakewell an others, and it seems a more reasonable strategy to encourage high quality and accurate record keeping and track additional information to inform pedigree selection rather than the other way around.

Pay attention to the trend in COI – because it is impossible to avoid inbreeding in upgrading programs by virtue of the highly restricted nature of available imported genetic material, the fact that a high COI exists in and of itself is likely not avoidable, however consideration should be given to the longer term trend of the COI. Failure to leverage genetic diversity resulting from matings with younger generational age or different base genetics represents a significant loss of genetic information that currently is considered less valuable as it is “lower percentage”

Calculate number of unique ancestors – Genetic diversity is available on both the sire and dam side, and while familial lines can be used to preserve specific characteristics, there is value in using multiple individual ancestors both within a flock and in the context of the larger breeding population.

Know the genetic load but don't obsess about it - Breeders are told that to produce animals with genetic defects marks them as "bad breeders," so they tend not to share information about such defects. They are also told that their objective should be to "eliminate" these genes, which is used as justification for inbreeding and expensive screening programs. This kind of advice builds up an obsessive attitude towards genetic load. People spend endless time discussing specific defects, individual animals, screening programs and the like, whilst ignoring the true causes of genetic disease.

It is unlikely that ovine genetic load can be effectively eliminated, at least at the present stage of genetic knowledge. Not until the functions and interactions of all genes in the sheep genome are fully known, and gene surgery commonplace, would that become a real possibility. It is therefore important that breeders share knowledge about genetic load within their breeds, so that they can avoid unfortunate breeding combinations. The fact that inbreeding "exposes" recessives is not necessarily helpful, because in most cases it is impractical to remove or "eliminate" the "defect" genes, and further often leads to a fail to report and track it adequately. Additionally, knee-jerk reactions to misunderstood data can lead to premature or incorrect decisions regarding the root cause of genetic load. Rather, breeding should be guided in such a way as to avoid reinforcement of known recessives whilst maintaining genetic diversity in the population. Screening and selection can never succeed as a strategy for the "elimination" of genetic disease. As one defect is eliminated, others will be reinforced, and the latter state of the breed will be worse than the former. The genetic load must be known, tolerated and managed; to obsess about its elimination will lead only to disaster.

It is important to note that obsessive culling in upgrading programs can be particularly problematic as the benefits of heterosis from foundation animals frequently mask issues for several generations. In practice, this appears to express itself significantly between the F3 and F4 generation. As the effects of heterosis begin to wane, animals that previously performed well become more unproductive or inconsistent, and excessive culling in the foundation lines as the next “upgraded generation” is placed in production may make it impossible to revive certain genetic information to correct these issues. Maintaining generational diversity is important as more is learned and shared about genetic performance of individuals and bloodlines.

Use pedigree analysis - Every breeder should also carry out in-depth pedigree analysis for prospective matings, listing the major ancestors on which inbreeding occurs in that mating, noting the number of occurrences and the generation number of each occurrence. This analysis should be carried back for at least six ancestral generations, ideally for eight. This practice will alert the breeder to undesirable "pile-ups" on key animals and therefore to potential genetic problems (where these are known to be associated with such individuals) in the planned mating. This can be done entirely without computer software. An alternative or supplementary approach is to use the "percentage blood" function of pedigree software. The percentage blood function, in contrast to COI, illustrates just where in the pedigree major inbreeding problems may be occurring, whether just in a handful of key animals, or more broadly throughout the entire pedigree. The percentage blood in this example is differentiated from theoretical blood percentage as used as a common designation of “percent purity” in breed up programs.

Conserve sire and dam-line diversity – The sire line and the dam line represent unique genetic content, held by the mitochondrial DNA and the sex chromosomes, much of which is transmitted only by those pedigree lineages. Diversity in the sire and dam lines is very restricted in the Teeswater population. These lines are important, particularly the dam-line with its association with mitochondrial DNA. This kind of DNA is held outside the cell's nucleus, in the cell mitochondria within the cytoplasm. Since the spermatozoon has no mitochondria it plays no part in the transmission of mitochondrial DNA, which is inherited only from the dam. Given the distant genetic commonalities of American populations of foundations breeds that have been recently used to reinforce the existing British Teeswater population (defined as within the last 100 years) additional consideration and evaluation should be given to the performance of Teeswater sires in these matings, as rapid expression of specific desirable phenotype is frequently experienced on those foundation breeds that were previously involved in development of the native (British)  population.

Practice assortative mating to fix greatly desired traits- A breeder should consider the use of assortative mating (mating unrelated parents who are phenotypically similar for the desired traits) instead of inbreeding if possible. Assortative mating is much less dangerous than inbreeding and will accomplish much the same ends. It should be obvious that to breed "like to like" for given desired traits will tend to yield more of what is desired, but if the parents are not closely related, there is a greatly reduced chance that other unconsidered traits will be unknowingly reinforced by such matings.

The degree of unrelatedness may be limited given the original relatedness of the genetic pools, however, using this practice to set general trends or goals within a breeding program can yield results over time, that will help to reduce genetic drift in a population.

Maintain high generation time - Genetic losses occur infallibly with almost every generation of purebred animals. This happens through a variety of causes -- random drift, from too few progeny contributing to the next generation, from the inbreeding/selection cycle, bottlenecking, etc. For that reason, the fewer the intervening generations between foundation stock and current stock, the less genetic diversity is lost. Breeders should therefore maintain a high average generation time (age of the sire at mating plus the age of the dam at mating, divided by two) for each generation produced: four years should be considered an appropriate minimum. To maintain a high average generation time gives the breeder a distinct advantage when it comes to producing healthy stock, and makes breeding results more predictable, as well as minimizing generational losses of genetic diversity.

This represents a fairly significant shift in conventional upgrading wisdom, which tends to favor short generational ages, replacing existing productive stock with the next generation of “higher purity” stock. The inherent problem with this approach is the loss of genetic information and the failure to adequately determine if the replacement stock has significant underlying issues that cannot be corrected once preceding generations are culled. While this can create challenges with the number of animals retained, sharing of genetics, and deliberate retention and testing of progeny are sound strategies to support selection for subsequent generations.

Avoid repeat breeding - Many breeders make a routine practice of repeating favorite breeding over and over again. Do not always use the same sire for a particular ewe (or vice-versa)! Take care to maintain diversity in your matings. Endless repetitions of the same matings greatly reduce the available breeding combinations both within the individual flock as well as for the breed at large. This principle would seem obvious on the face of it, yet how many people ignore it as soon as they find a "nick". Many show winners can’t repeat themselves and it remains critically important to small populations to preserve as many combinations as possible

Ensure sibling contribution – Sometimes phenotypic expression may not align in a specific individual, however the latent genetics of siblings may be able to pass along or out produce others, and provide additional genetic outcross to the pool. 

Monitor fitness indicators - Breeders should not fail to monitor key indicators of survival fitness in their stock. These are lambing, absence of stillbirths, birth weights, fertility (percentage of successful matings), fecundity (average litter size compared to the norm for the breed), survival to adulthood, and longevity; be sure that your breeding program does not trend toward the reduction of any of these. Complete production records are critically important to these tracking efforts, and record keeping is intended to provide a complete historical production record for as many individuals as possible. Additionally, care should be given to not propagating issues that required excessive intervention, simply because we can save an animal, does not mean that it should be perpetuated in the gene pool.  

Attempt founder balancing -  It may be valuable to attempt to balance the relative contributions of founders (where possible and appropriate), particularly subsequent to founder events or genetic bottlenecks. This is routine practice in zoological park captive-breeding programs, yet virtually unheard of in a ovine context. "Founder" is a not an absolute, but rather a relative term. If a breed has a long pedigree history with original breed foundation stock at thirty or more generations removed from current stock, it may well prove impossible to balance the contributions of the original breed founders, whose relative contributions may already be set in stone for all practical purposes. But founder events tend to occur repeatedly within the history of a breed, not only when the book is first opened. Bottlenecks occur with dismal regularity. At least the breeder can pay attention to the most recent founder set that is clearly identifiable, attempt to prevent the loss of individual bloodlines that are seriously under-represented, and seek to balance the relative contributions. Clearly this is no simple matter and to suggest that it be applied consistently may be a counsel of perfection. At least it is one more possible tool in the breeder's armory against diversity losses

Monitor population growth - Growth by fits and starts, with periods of rapid overexpansion followed by sudden cutbacks or population collapse, is very bad for genetic health. It is difficult to impossible wholly to avoid population bottlenecking, but its existence and ever-present threat should be recognized. To whatever extent may be possible, breed clubs and individual breeders should do what they can to ensure smooth, steady population expansion and to minimize cutbacks and consequent genetic bottlenecking.

Seek balanced traits - One ought always to evaluate breeding stock for balanced characteristics: health, vitality, temperament, production ability, intelligence, structure, type. Breeders should aim to maintain the balanced characteristics of a total sheep, not just to produce winners at shows. An all-round, balanced animal will be a much better hope for the future than a highly-selected, over-bred animal thought to be "best" due to its possessing exaggerated traits in one or two areas, whether it be a "perfect head," a showy gait, longer or finer fleece, or whatever. First, every individual needs to be a good sheep, and that should come ahead of specialized breed considerations.

Avoid unfit breeding stock - It ought not even to need saying -- but in these days in which extensive, heroic and expensive veterinary measures are routinely used to save otherwise doomed animals, it does need saying: the breeder ought never to breed from animals that would not be alive but for such interventions (excepting, of course, survivors of physical injuries). It should be obvious that if we circumvent the operation of natural selection, many of the animals that we use for breeding purposes are likely to pass on various genetic weaknesses.

In the context of long term survivability of heritage breeds, this is a fatal flaw. Many heritage breeds already exist in an economically subsidized state, as they are not managed or selected primarily for their commercial economic viability. If this tendency trends to the point that only intensely managed animals survive, the viability of the breed will be destroyed as it is impractical for many shepherds to consider taking on the challenge of supporting a population.

Avoid intervention with reproductive technology –Breeders should consider whether it is in their breed's interest routinely to use elaborate reproductive technology to produce offspring. These days various and sundry technical means are available which circumvent natural mating and lambing. Some breeds, indeed, cannot either mate or lamb without extensive shepherd or veterinary intervention.  If we use artificial insemination and hormone assay to effect mating combinations that cannot be brought about by natural mating, along with routine C-section to deliver offspring, we may rapidly find ourselves in the position of having created strains that cannot reproduce naturally without technological support.

The above should not be construed to encompass those artificial techniques necessary to introduce otherwise unavailable semen – specifically imported genetic material to provide foundation stock, rather similar to the principal of avoiding unfit breeding stock it pertains to those animals that are otherwise unable to reproduce without artificial intervention.

Restrict artificial selection - The desire for a cookie-cutter "consistency of type" causes healthy genetic diversity to be discarded intentionally at an alarming rate. The Teeswater sheep is a breed with an already alarmingly narrow genetic base, especially considering the relationships of the previously imported sire lines. As the North American breeding pool depends almost entirely on the genetic diversity of the dam line, it remains crucially important that the Associations rules do not place additional selection pressure on animals that exhibit good type and represent genetic diversity to comply with arbitrary association rules.  Specifically, the failure to recognize potential contributions from animals with calculated blood percentages below a specific minimum, use of codon status as a registration criterion, limitations of coat color and other related considerations. While these animals may not fit a longer term, broader goal, failing to allow breeders to weigh their specific genetic value can often cause damage that outweighs the potential benefit of such restriction as it only really protects the breeding pool in the short term and can result in serious and unintended consequences.

Also, it bears recognition that restrictive criteria can incentivize under or misreporting of issues by breeders, and while it is an often overlooked issue among breed associations, false reporting of pedigrees or other qualifying information is a significant problem. While it is an unpleasant truth, many pedigrees end up fudged, because the artificial selection pressure is on blood percentage or a “pedigree” rather than the animal as a whole. This is doubly dangerous as it also causes errors in data that is then used to extrapolate other decisions by membership, further cementing erroneous conclusions to the detriment of the breed. Therefore, care and consideration should be taken by any Association that its rules do not put breeders in the position of having to make breeding decisions that are detrimental to their flocks or to rely on metrics that are not really representative of anything.

Planning Breedings – One of the single most important aspects of any breeding program is the process of selecting breeding stock and planning matings. The methods and considerations used to select breeding stock and to pair individual animals together is a difficult and complex task, and is often the one most taken for granted by new and inexperienced breeders. Many new breeders fail to understand the genetic complexities involved in animal breeding and assume that simply crossing two nice looking registered individuals is all that is required to produce more viable breeding stock. However as all of us can attest, even breeding two show winners together doesn’t result in a sure thing, and often doesn’t even result in progeny as good as the parents.

There are many metrics that can and are used: from blood percentage, to conformation, to blood line evaluation, or EPDs. Any of these criteria, taken at the expense of the others can result in excessive swings and an imbalance in the overall result. It is imperative that breeders form a consistent basis of evaluation of the sum of the criteria they are working to develop, track the outcome of their matings and use that information to continually assess and refine their breeding approach.