An Examination of Breeding Strategies
by Sean Nowicki
This article may be reproduced if is properly cited and reproduced in its full context.
Companion animals are an important part of society. For thousands of years, man has lived with dogs, cats, birds and other animals and has established emotional attachments to these creatures. This paper examines various breeding styles with a critical analysis of many considerations in the breeding of companion animals. The majority of breeding programs are random and do not consider the consequences of the breeding. The use of genetic research can result in a breeding program based on the goals and limitations of a breeder while producing a population with a lower disease occurrence and better genetic gains.
Goals of a Breeding Program
An ideal companion animal breeding program will place an emphasis on maintaining the lowest possible occurrence of disease expression while maximizing the genetic merits of the stock (Fangy, 1993). A breeder must also consider consistency of stock and genetic diversity.
Unfortunately decreasing the frequency of inheritable diseases is not an easy task. Ideally, a breeder would begin a program by obtaining disease free stock. A specimen will have little genetic importance if it will only produce disease-plagued offspring.
According to research by Sonesson, Janss, and Meuwissen, obtaining disease free stock is nearly impossible. In their study of selection against genetic defects in dogs in conservation schemes while controlling inbreeding, they state that many domesticated animal populations show heritable defects. (Sonesson et al, 2003).
Since obtaining disease free stock is not always possible, breeders must do the best they can to minimize the expression of these diseases. In the study mentioned above, Sonesson, Janss, and Meuwissen established that selecting against disease is a method of eliminating it in a population of breeding. (Sonesson et al, 2003)
Because diseases have different modes of inheritance, different approaches to eliminating disease expression may be in order.
Evidence found by Sonesson, Janss and Meuwisson lends to the idea that selection against a disease caused by a single gene is a tool breeders can use. In their dog study they found that disease that is caused by a single gene which has been previously identified screening for the disease is possible through the use of direct DNA testing. Because they are testing on a DNA level, environmental influences are of no concern (Sonesson et al, 2003).
For those diseases caused by unknown genes, selection for disease prevention may not be as obvious. Breeders working in this situation will be required to count on their record keeping and pedigree research at this point. This was addressed in the above-mentioned study. The researchers found that when dealing with unknown genes, pedigree analysis could be used to identify an affected animal (Sonesson et al, 2003).
In breeding, keeping accurate records is of the greatest importance. Breeders should do research on any animal they are thinking about breeding. Additional information can be acquired by looking at littermates, parents, parent’s littermates, grandparents, and grandparent’s littermates. An individual may not always exhibit a disease, but upon inspection of their pedigree, a high disease occurrence may become evident.
Knowing the mode of inheritance in the Sonesson, Janss, and Meuwissen study had little effect on the efficiency of the selection scheme (Sonesson et al, 2003). By avoiding disease-inflicted individuals, a breeder will reduce the rate of the expression of these diseases.
In addition to considering the frequency of disease, a breeder must work toward a desirable phenotype and consistency in a breeding program. A healthy individual that has no desirable qualities is of little use. Higher consistency of the progeny is valuable if the stock mirrors a desired look (Fangy, 1993).
Although a uniform, consistent look is ideal, as the diversity of the stock decreases it is likely to loose rare desirable traits, so both consistency and rare desirable traits should be considered.
Limitations faced by breeders
There are many limitations faced by the breeders of companion animals. These include: space availability, time, access to technology, operating costs, population size due to either closed registries or real population size, and ethical decisions which result from these limitations.
A breeder must be able to adequately house the animals. Most companion animal breeders are operating out of a home or small kennel and this limits the number of animals that can be housed. This can sometimes stand in conflict with the goals of a breeding program. Increased numbers offer a breeder better odds of obtaining a desirable trait. It is unrealistic for most breeders to own hundreds of animals. Therefore, the breeder must determine how many animals they can house and which animals to retain for breeding stock to fill those limited positions. It is advantageous for the breeder to have a cyclical program where superior individuals replace their inferior counterparts.
A breeder must consider time. Genetic gains are made from generation to generation. Time is a limited commodity. It is advantageous to maximize the genetic accomplishments in the shortest time possible. Failure to maximize the genetic gains may result in years of breeding accomplishing little while a competitors breeding program may be advancing
Operating cost is another major consideration. Most companion animal breeders participate in this activity as a hobby and are not necessarily independently wealthy. Cash limitations require a breeder to at least break even in their breeding project. Those who are full-time breeders would run their operations as a business and would not have the capitol to spend more money than they make. A breeder must maximize their use of capital on operating costs, quality of care for the animal, and money for genetic screening. Although tests may be available to potentially screen for a genetic disease, the testing may cost more than the breeder can afford.
Access to technology is a factor that affects the operation of a companion animal breeder. Genetic level tests are becoming available to breeders on a limited basis. For example, some dog breeds are selecting against a vision problem called Progressive Retinal Atrophy. Some breed clubs offer DNA screening kits that test young puppies for the disease, before they ever express the trait. This type of testing is advantageous to a breeder because it aids in the decision of selecting which individuals to keep from the mating. This saves money, time, and the stress of an emotional attachment to inferior individuals. These types of tests are only available for very few inherited defects at this point.
Screening for genetic diseases using x-ray machines and medical equipment is routinely performed on adults before breeding. These tests help to identify individuals who may have a genetic condition, but not recognized by the naked eye. A few of the commonly used tests include screening for hip and elbow dysplasia, cardiac abnormalities, eye problems such as PRA, knee and joint problems, and thyroid abnormalities (Orthopedic Foundation of America, 2003).
The limitation in population size in companion animals that are following a particular registry is also a consideration. Most purebred dogs and cats are associated with an organization that officially records the lineage of the animals (a registry) that usually does not allow new additions. This was discussed in research by Ubbink, Knol, and Bouw when they found that purebred dog populations are closely related due to the fact that they come from closed gene pools and are derived from common ancestors. (Ubbink et al, 1992). This is a major limitation to people who choose to operate within these registries. Any breeding that is not already registered would cause the offspring to be ineligible for registration.
Because of the limited size and number of available breeding animals, attention must be paid to the consequences of over using individuals which often lead to diseases that may plague a whole population (Fangy, 1993).
Ethical considerations are a constant issue in companion animal breeding. Those breeding chickens can eat their mistakes, but society views pets much differently. A certain amount of failure is possible in any breeding program and it is important that breeders learn from those mistakes and do what they can to prevent the same errors in the future. Disease plagued companion animals cause many difficulties, both financial and emotional, to breeders and owners. This was discussed by Van Der Beek, Nielen and Schukken in their research on puppy mortality when they concluded that breeders experience emotional and financial repercussions following the death of puppies (Van Der Beek et al , 1999).
An ideal breeding program optimizes the available space to house the their most superior individuals while maximizing the genetic gains for a given period of time with a limited amount of money. New technological advancements aid us in achieving these gains, although operation cost and working population are unavoidable limitations. Breeders will often face difficult decisions regarding how aggressively a trait can be selected for because there may be ethical consequences.
Breeding Types
A breeder, as the name suggests, is responsible for choosing the mating of a companion animal. There are several types of breedings available to breeders. These will categorize the mating in the following manner- random mating, chasing the winner, out crossing, line breeding, and inbreeding. There are different merits, weaknesses, and ethical consequences to these different types of breedings.
Random Mating
Random mating refers to any cross where an animal with superior genetics would have the same chance of being bred as one with inferior genetics (Campbell, 1999). This is common with owners who are breeding their companion animal with little or no research involved. Common scenarios include: a friend or neighbor will own the same breed and be affiliated with the same registry organization, someone breeding two individuals they both own, and breeding to an animal they just happen to see and like. These decisions are based on emotion and not on any genetic research or logic.
Merits of this method are usually convenience and emotion. People involved with great amounts of research and willing to drive across the country have significantly more invested financially than to someone using a breeding pair they own. Some people also have interest in producing offspring of the pet to which they are emotionally attached. Breeding unknown genetics are a great weakness of random mating. A companion animal could have a predisposition to genetic aliments. A mating chosen at random also may fail to complement genetic components, where as a well thought out breeding may accomplish this.
One possible merit of random breeding is that there may be a greater potential for genetic diversity.
On the down side, there are many ethical consequences to random breeding. Questions that should be asked include: Who will be responsible for these animals once they leave the breeders possession? How will breeding to an animal for self-satisfaction weigh in against disease prevention? Those completing random breedings should ask these questions and weigh the consequences before making this choice. A local animal shelter is a great place to see the results of this type of breeding.
Chasing the Winner
Although the name may sound a bit ridiculous, in my experience many people perform this type of mating. Often people who are new to a breed will show up at an animal performance event and because they are not able to evaluate the quality of individuals themselves, they will look at the animal is already successful.
If an animal is successful in competition, the assumption is that this indicates superior genetics. Breeders often spend a lifetime acquiring an eye for qualities that would bring their stock success. By looking toward those who are successful, they can save themselves time reinventing the wheel.
This method can seem very logical but it has many deficiencies. The winning individuals may be a rare occurrence in their genetic pool. Although exhibiting superior quality, the animal may not be able to produce the qualities they have (Fangy, 1993).
Another consideration in a closed gene pool is the over use of an individual specimen. If the majority of people breed to the top placing animal in a competition who is also a carrier of a disease, then the whole population will become quickly affected and breeders will have no place to turn to get rid of the problem.
This method has more merit than the random mating. Breeding to superior animals offers a much better chance of acquiring desired traits than a random mating. Weaknesses of the method include a lack of research, which is necessary to prevent disease. It also follows the same consequences of disease expression as the random mating.
Out crossing
An out cross is a mating where the breeding occurs between two individuals with a large genetic distance (Uno et al, 2001).
The advantages of this method relate to both disease prevention and hybrid vigor (Uno et al, 2001). Because the individuals have a low genetic relationship, the diseases they carry are usually different. Because of this, the chance of obtaining an allele which is associated with the same disease from both parents is low. Progeny of this type have the chance to acquire they best traits from both parents – often referred to as hybrid vigor (Klug et al, 2000). The theory of out crossing is typically accepted by the public as compared to inbreeding (which is discussed in the next section).
Out crossing has some of the same disadvantages as chasing the winner. Whole populations can become carriers of diseases in a closed gene pool. A breeder who has a desired look may also dilute the look of his stock as the genetic diversity increases (Fangy, 1993). A breeder may also have an animal which contains recessive diseases that express themselves randomly when bred to animals with similar deficiencies.
Ethically this method has the immediate effect of lower disease expression. Progeny also have the chance to exhibit hybrid vigor.
Inbreeding
Inbreeding is the mating of closely related individuals like littermates, fathers and daughters, or other very closely related animals (Klug, 2000). Inbreeding brings out the best of the best and the worst of the worst.
There are several strengths that can justify the use of inbreeding. When selecting for a trait, referred to as making genetic gains, you can increase your chance of inheriting a trait if both mating pairs are both carriers of an allele. This often is the case when they share common ancestors who have the desirable traits. This was evidenced in Damgaard’s study on evolution of advantageous alleles affecting population ecological characteristics in partially inbred populations and found that the average time for an allele to become consistent in a population decreases with inbreeding, regardless of the level of dominance. (Damgaard, 2003). Because of a lower fixation time, breeders will often use inbreeding techniques to obtain a desired trait, and increase the traits homozogity in their stock.
Inbreeding is also useful in purging breeding stock of lethal and semi-lethal disease alleles, according to research by Fernandez, Rodriganez, Toro, Rodriguez, and Silio. Purging through inbreeding may compromise the current generations health by expressing recessively inherited diseases, but doing so allows a breeder to select against them.
In both simulation and empirical studies, it has been shown that by tightly inbreeding, recessive genes that are either lethal and semi-lethal can be quickly eliminated from the gene pool. However, it is important to note that recessively inherited diseases with milder consequences are not as effectively removed, and in the process of trying to remove diseases of less severe consequences by tightly inbreeding it reduces the genetic variation of other non-harmful genes (Fernandez et al, 2002).
Weaknesses of inbreeding include inbreeding depression, an increased chance of offspring exhibiting genetically transmitted diseases, and the possibility of reduced reproductive fitness.
Inbreeding depression is dependant on the previous level of inbreeding. Fernandez, Rodriganez, Toro, Rodriguez and Silio examined this phenomena of inbreeding effects when they studied the parameters of the growth function on three strains of Iberian pigs. They found inbreeding depression varies between populations and the severity may be less in lines that have been subject prior inbreeding. (Fernandez et al, 2002)
Inbreeding depression in natural populations is an undeniable consequence proven by a variety of research, although the intensity depends on the amount of deleterious alleles present in the population. (Haag et al, 2002)
Inbreeding does not always increase frequency of a disease, as researchers found when examining mammary tumors in dogs. (Ubbink, G.J.; Knol, B.W.; Bouw, J. 1992)
Many people are reluctant to inbreed. Inbreeding, while increasing the chance of inheriting desirable alleles, also increases the chance of inheriting genetically transmitted diseases, severity of expressed diseases and is associated with lower reproductive fitness.
In a study examining cryptorchids in miniature schnauzers and cross bred dogs, the authors saw a direct link to increased inbreeding coefficients and the severity of the defect. (Cox et al, 1978). The researchers found a greater incidence of cryptorchids over unilateral cryptorchids and an increased severity of the condition associated with inbreeding. The increased severity of the defect is suggested by four criteria: (1) Increased proportion of bilateral cryptorchids, (2) More primitive structure of the epididymis in the bilateral cryptorchids, (3) More cranial location of the testes in the bilateral cryptorchids, and (4) Abdominal retention rather than inguinal or prescrotal location as documented in the anatomic and genetic study of canine cryptorchidism. (Cox et al, 1978.)
In a study of several diseases in Bouvier de Flanders, a breed of dog, several diseases were expressed at higher inbreeding coefficients while they were not exhibited at low inbreeding coefficients. In graph 1.1 inbreeding coefficients of randomly selected populations of Bouvier de Flanders (controls) were compared to inbreeding coefficients of Bouvier who were diagnosed with diseases. Although most diseases followed this trend, flea allergy and laryngeal paralysis are examples of diseases which were not effected by inbreeding.
Most breeds have ancestors which are unique to the breed. Because of different ancestry and disease carried in by their population, inbreeding may effect breeds differently. (Ubbink et al,1992).
Inbreeding depression after initial development has routinely been documented. The agriculture industry has many studies on this subject. In a study of cattle Cassell, Adamec, and Pearson found animals with coefficients of inbreeding about 10% were more likely to be culled as compared to animals with coefficient of inbreeding less than 5%. (Cassell et al, 2003).
Another study examined the chances of survival in inbred animals. They found that cows with inbreeding coefficients greater than 8% were 1.05 to 1.1 times more likely to be removed from breeding stock than compared to cows with coefficients of inbreeding less than 7%.(Caraviello et al, 2003). In this study, length of survival time was measured from first calving until selection for butchering. The author did not consider animals with severe inbreeding depression that did not reach the age of first calving.
“Inbreeding effects on conception rate, embryonic loss, abortion, stillbirth, calf mortality, and heifer fertility were ignored in this study, although one or more of these traits could be significantly impaired in highly inbred animals” (Caraviello et al, 2003).
Inbreeding also lowers the reproductive fitness of animals, according to studies of common flies. Research demonstrated this in female flies. They found the inbred flies exhibited reproductive problems at a higher frequency than outbred ones. This study examined both laboratory produced strains and field samples. (Haag et al, 2002).
Although companion animals are often much more complex than flies, research in more closely related animals has yielded similar results.
A study of quail further supports decreased reproductive fitness. The authors find that fitness which was evaluated by “fertility, hatchability, and viability was reduced by about 4.3 to 7.5% for each 10% increment in breeding.” (Maeda et al, 1981).
A study of reproductive fitness in dogs found puppy mortality increase in dogs which were over 15% inbreed. The average trend was a 1% increase in puppy mortality for each 2% increase of inbreeding, although when inbreeding went below the 15% threshold no difference was observed.
For example, a dog which has an inbreeding coefficient of 40% would have a 20% increase in puppy mortality (Van Der Beek et al,1999). This figure is very similar to the estimates provided by the study of quail.
In a study of pig reproduction authors found inbreeding suppresses litter size, birth weight, vitality and fertility. Selection based on fertility was not able to overcome the loss of vigor. Lower fertility was the main cause of losing inbred strains. (Ubbink et al, 1992)
Ethical consequences can be severe when inbreeding. Although a breeder may be able to have higher genetic gains, they will also have an increase in disease expression. To those in the agriculture market this may be of little concern. To those selling people a companion for their family, it can have severe consequences in used inappropriately.
Line breeding
Line breeding is the breeding of individuals who share some type of genetic relationship. This can vary from distantly related ancestors to those very closely related. Line breeding concentrates the genes of a specific ancestor or ancestors through their appearance multiple times in a pedigree (Klug et al 2000).
When a specific ancestor appears more than once behind both the father’s side and the mother’s side of the mating, homozygosity for the ancestor’s traits greatly increases in their offspring. Having several genetic paths to a specific ancestor gives the breeder an even a greater chance of inheriting the desired traits, and for the trait to breed true.
The increased frequency of an allele greatly improves the chances that the resulting offspring will in turn pass on the desired traits of the ancestor to their offspring. With line breeding one often observes more uniformity within a litter. When the number of offspring exhibiting a desired trait increases, this also increases the likelihood that the trait will be preserved and breed true to the line (Fangy, 1993).
Line breeding, like inbreeding, will increase the probability of a recessive gene being passed from a common ancestor on both the sire and the dam's side, creating offspring homozygous for the recessive trait. This allows the recessive trait to become expressed. The resulting offspring displays a phenotype neither of their parents displayed. However, the inbreeding does not create these undesirable genes, it simply increases the chance that traits which are already present in a heterozygous state within the breed to be displayed.
Some breeders choose to operate a breeding program based on just one line. They breed only animals which share some predetermined standard on common ancestry. These breeders only mate animals who share the same ancestors.
If the line has great qualities, the breeder of one line will enjoy having these traits passed along from generation to generation . Because no breedings are done outside of the breeding stock, new disease can not be introduced, with the exception of a genetic mutation (Fangy 1993). A breeder who keeps careful records is aware of most genetic problems in their line and is able to select against them, and avoid using individuals which exhibit any traits which plague their stock.
While a closed line has the advantage of not introducing new undesirable genes and improved consistency, it does have several disadvantages. These include population size, genetic bottle neck effects, and loss of vigor as seen with inbreeding.
A breeder practicing closed population line breeding must be conscious of his working population size. They must house all of the animals required to maintain the desirable traits of the line in addition to extra individuals which may be lost to due some sort of bad luck. These breeders often work with other breeders who share a common interest in the line. This allows a greater safety margin with regard to the population size, it reduces the risk of losing a breeding program in unfortunate accident like a fire, and allows the breeder to retain a lower number of animals while still maintaining their line.
These lines are closed populations and are usually derived from a few common ancestors. While they offer a greater chance of inheriting desirable characteristics, they will also have an increased chance of inheriting an undesirable trait. Occasionally the breeding stock becomes uniform carriers of an undesirable gene and go through what breeders call a genetic bottleneck. This term is used to describe what happens to the gene pool as many individuals are not used for mating as a result of being identified as carriers or affected by the undesirable trait (or the use of only a few superior individuals) . Only a small percentage of the population survives and is able to pass along the stock’s desirable qualities while being free of the bottleneck causing trait. Rare desirable qualities can be lost due to this bottleneck effect and preexisting diseases may increase in frequency.
Sonesson and colleagues examine the frequency of heritable diseases due to genetic drift. They found that genetic drift increases the occurrence of heritable diseases. Breeding programs with limited population sizes should be conscious of increasing rates of inbreeding when selecting against a disease or for a non-disease. (Sonesson et al, 2003)
Line breeding only one line will have the same negative qualities as inbreeding. Diseases that are recessive and already in the line will appear more often due to the increased homozygosity.
Line breeding multiple lines
Another approach to line breeding is using a few separate distinct lines. This approach is often seen in agricultural breeding. Each line is maintained separately, choosing matings that would exemplify the qualities of their line. When these separate lines are crossed by the breeder, hybrid vigor is often observed (Campbell, 1999). Because the lines have unique ancestry, they are rarely carriers of similar recessive diseases. The resulting offspring being heterozygous will not express the disease. These hybrid offspring which are from lines that complement each others weakness are often healthier and more robust than either line could produce separately. The breeder may also choose to merge lines if severe bottle necks occur and populations size becomes to small to maintain the line independently.
Although these hybrids are of little use to the breeder, they may exemplify the best of both lines. If a breeder is able to maintain these separate lines they offer the ability to consistently produce healthier and more robust individuals will a lower occurrence of diseases in the hybrid offspring whenever they choose.
One possible weakness of this is that the hybrids may be carriers of genetic problems that are not expressed and therefore may not be removed from the breeding program.
Successful line breeding is a long and arduous task- one that often requires a lifetime commitment to a particular line. The product of this effort can be great and hybrid vigor can allow a breed to make great genetic gains.
Improving Genetic Gains
Breeders are usually working toward improvement in their line - also know as making genetic gains. This can be done by breeding to individuals which carry a desired genotype. The section examines the effectiveness of different selection based on family, individuals, and inbreeding coefficients and ways to improve genetic gains while limiting inbreeding coefficients
Inbreeding to increase genetic gains
Because inbreeding and line breeding increase the chance of obtaining a desirable characteristic, both are reasonable methods to increase genetic gains. This is perhaps one of the most routinely used procedures. In a study by David, Pike and Stine, genetic gains were evaluated using four different selections methods. In the first method, [FS], family selection ranked families based on family means and retained all individuals in the selected families regardless of their individual performance. Another method [IS], individual selection, ranks each individual and rogues those below a minimum threshold. The third method [FWFS], family within family selection, retains a specific number of individuals in the best families. The last method [CS], combined selection, creates an index value for each individual based on that individual and family performance weighed according to individual and family heritabilities respectively. The authors ranked these methods. The ranked order of the selection methods examined for genetic gain are CS > FWFS > IS > FS (David et al, 2003). Combined selection was the optimum selection method, and the least effective was family selection which retains all individuals in selected families.
DNA identified traits
Perhaps the most effective way of increase gene frequency is the use of DNA testing which directly identifies a trait. This method allows for screening for the traits at birth minimizing operation costs and time involved with keeping an animal until adulthood. Unfortunately, these types of tests are not readily available at this time. Some tests are available (as mentioned earlier with Progressive Retinal Atrophy in specific breeds of dogs), but not enough to make this a viable alternative at this time.
Health screening
Another technological method for increasing genetic gains falls under this health screening category. Hip dysplasia is an example of a commonly inherited polygenetic defect that plagues many breeds of dogs. Breeders are able to x-ray the hips of prospective breeding stock to aid in the evaluation of the hips before these animals are bred. By breeding individuals with high scoring hips to mates with high scoring hips, hips improvements in the breed’s statistics are being observed. If it were not for this type of screening, breeders would only be able to avoid animals which exhibited the genetic defect. With the use of X-rays, a breeder not only can avoid affected individuals, they are able to produce better hips on average than otherwise possible
Genetic gain with a limit on inbreeding
Genetic gains increase with inbreeding on a desired trait. When inbreeding is practiced this also increases the probability of inheriting other genetic diseases which are not desired. Breeding plans frequently are designed to maximize the gains from selection and place limits the rate of inbreeding (Meuwissen et al,1998).
Artificial insemination and reciprocal breeding of individuals
By using an animal multiple times, but over different generations genetic gains are possible with lower inbreeding coefficients than if the individual was heavily inbred. This method can be performed on live animals, or the use of frozen semen. Breeders are now able to freeze semen on superior individuals within their breed. While this simplifies the breeding of animals which are geographically distant, it also allows breeders to use semen for a mating which other wise may not be possible due to lifespan.
Many superior individuals in a breed may be over bred causing a founder effect. A smart breeder may identify and use the superior animal, and then use frozen semen several generations later. This individual can make contributions to their line, and minimize the possibility of doubling up on a undesirable recessive trait that may be carried by the animal whose semen was frozen. T. Meuwissen suggests maximizing the genetic merit of an individual by placing a constraint on inbreeding coefficients which would only allow mating of individuals which are under the predermined level of inbreeding. (Meuwissen,1998)
Suggested method of breeding
After reviewing different concepts of mating and examining their strengths and weaknesses, I have conclude there is not one correct method. The ideal breeding strategy will use the strengths of each style and minimize the weaknesses. This will consist of initial stock selection, purging the breeding stock of lethal and semi-lethal diseases, and developing separate distinct lines with an emphasis on maximizing genetic gains while minimizing the occurrence of diseases. Finally we will cross the lines to produce the finest specimens are lines can produce.
Researching initial stock selection.
While breeding countless litters could produce some ideal specimens, a more logical approach would be to work smarter, not harder. When in the initial stock selecting phase a breeder should begin a methodical practice of record keeping by obtaining as much information as possible about perspective breeding animals. A thorough examination of littermates, parents and their littermates, grandparents and their littermates is required. If an animal has been bred before, this is another great source of information about the genetics of an animal.
A breeder should begin to assemble a list of possible stock by rating each specimen for low disease occurrence and overall quality. Breeders may notice some dogs are dramatically superior to others in the breed. These ideal specimens will be great assets to a breeding program. Any information obtained by asking questions of those who have previous experience with these animals will save time and money in unnecessary breedings and the possible the production more unhealthy animals. When selecting initial stock it is important that a breeder obtain the highest quality animal possible. Money is not always a predictor of quality. Breeders must use good judgment and the advice of experts in the field.
As a general rule the more times a desirable trait appears in a pedigree, the more likely the trait will be seen in the offspring. For example, if a breeder selecting for trait B, and the father exhibits trait B but the mother and other ancestors do not, it is unlikely many of the offspring will carry the trait B. In a more ideal mating this trait B would be in the mother, father, in many ancestors and ideally in the offspring if they have been bred previously.
Usually a breeder picks females to start a breeding program. A breeding program is only as good as its’ females. A breeder usually has many males to pick from when selecting a sire.
After doing all of the research possible, a breeder can be confident that they are off to a great start and will hopefully have an animal with great qualities to offer, produced by a family known for a low genetic disease load.
Purging stock lethal and semi-lethal diseases
In a perfect world, breeding stock would come from a breeder who has worked most of their lifetime optimizing a line. In the event that a breeder begins with unknown stock, or if the stock exhibits lethal, or semi-lethal diseases it is logical to first remove these severe diseases from the stock.
This was verified in research by Fernandez, Rodriganez, Toro and Rodriguez. Their research supports the idea of purging deleterious recessive genes in a long term process of inbreeding and selection (Fernandez et al, 2002).
A suggested method of removing lethal or semi-lethal genes is the breeding of littermates. A breeder can take healthy offspring out of the 2nd generation and breed those littermates together, and finally take healthy littermates from that breeding and breed those together (Fangy, 1993).
While doing this may cause individuals to express diseases initially, removing these traits from the gene pool will avoid the trait expressing itself sporadically, and in the end, purging these diseases will dramatically lower the overall number of affected individuals when breeding for a lifetime.
An addition to removing the lethal and semi-lethal diseases, the remaining population will be less susceptible to effects of inbreeding. This may be used to increase genetic gains in the breeding stock. This idea is supported by current research. Fernandez and fellow researchers found that following purging future inbreeding has a “small phenotypic consequences” (Fernandez et al, 2002).
The use of inbred breedings followed by selectino can decrease the disease frequency of the population within a line of animals.
Identify and remove high disease load individuals
When the three generations of purging is complete, not only are the lethal genes removed, there is now reliable information about the new stock. If a breeder started this project with several individuals, they can compare quality of stock that remains, as well as the overall health. It is to the breeder’s advantage to choose among the stock which exhibits the overall lowest occurrence of non-lethal diseases and the most genetic merit.
When evaluating the stock, it is necessary to have them in similar conditions where they would function. This is especially true if the population size is low, and inbreeding coefficients are high. This is due to the possible loss of genetic diversity. Reed, Lowe, Briscoe, and Frankham examined Drosophila melanogaster (a strain of fly) and determined that populations adapted to laboratory conditions are less adaptable to stressful environments (Reed et al, 2003).
While it is necessary to expose breeding stock to the same conditions in which they will function, it has been documented that exposing breeding stock to conditions that are not normal to their environment in an effort to maintain genetic diversity and health is not realistic. In the same article the authors noted that subjecting stock to stressful environments to increase resilience is considered unrealistically stringent by the majority of theoreticians as a method of maintaining genetic diversity (Reed et al, 2003)
Selecting individuals after initial screening
Up to this point, only breedings of unknown genetics or high disease load individuals were completed. Now with reliable information, either from test breedings or from the work of previous breeders, a breeder can begin to weed out inferior animals. Each breeder must choose how many females to begin with. Some may only have the space and time for one individual, while others will choose to have several. This is an ethical question each must answer for themselves. From a statistical stand point, higher numbers will give a breeder better odds of achieving their goals, but numbers are worthless if quality is inferior.
Another point to consider is the age of foundation stock. Adults who have been genetically screened and perhaps already have proven their ability to produce, are much less risk than obtaining a juvenile who has not been bred or even aged to the point where diseases would be expressed. This is another ethical question one must answer for themselves. Emotions aside, the adult is less risky.
Many people will opt for a kitten or puppy- one which has just been weaned from their mother. In this case, you must use juvenile predictors to judge quality even though the litter was from the stock with the highest genetic potential. Advice from experts of the breed may supply a novice with opinions of juvenile predictors to judge which animal to keep for breeding.
Establishing the lines
When the initial foundation stock has matured and has proven to be free from any genetic aliments, it is time establish our initial breeding scheme. If space permits, a breeder should try to plan on having at least 2 lines, although 3 would be better. Each line should be genetically distant from the other. Each line should represent the animals with the highest genetic merit in our initial test breedings or the best of proven lines if they were adopted by experienced breeders.
Optimize each line independently
The suggested method that I am proposing will work on each line independently. Although each line will have unique strengths and weaknesses, the goal will be to optimize each line independently. To do this we must consider a few basic concepts. First is the need to maintain a large enough working population size in the breeding stock. While working toward improving specific traits in the breeding stock by the application of selection and inbreeding, it will be a necessary limit the rate of inbreeding. It will also be necessary to also optimize the environmental conditions to avoid losing breeding stock to non-genetic causes.
Population size
A line must have a certain number of individuals to avoid extinction. If all individuals in the line become closely related, reproductive fitness will decline as discussed in the inbreeding study listed above. Extremely tight inbreeding can have ethical consequences. When an entire line exhibits high coefficients of inbreeding compared to others in the line, the risk of extinction becomes a major concern.
The problem of balancing genetic diversity, genetic merit and population viability was documented in the Journal of Animal Breeding and Genetics. Piyasatian and Kinghorn found low population size due subject to genetic drift and inbreeding are causes of lowered reproductive fitness and increased risk of extinction (Piyasatian et al, 2003).
Reed, Lowe, Briscoe and Frankham also investigated the effects of low population size. They concluded that population size has significant effects on genetic variation for fitness and on overall fitness. Smaller populations encounter lower fitness due to three main reasons: an increase in inbreeding depression, less efficient selection for eliminating deleterious alleles, and beneficial mutations that are less likely to occur and more likely to be lost due to drift (Reed et al, 2003).
The article also examined inbreeding effects on the population. The authors found that inbred populations had lower fitness than the non-inbred populations from which they were derived. This was documented in both before and after selection in a unique environment. As a result of these findings, populations with size as a concern should be kept as large as possible to reduce inbreeding and loss of genetic variation” (Reed et al, 2003).
When selecting for traits in a population, rare and important traits can be lost if they are not being selected for. Selection of desired traits leads to smaller populations having less genetic variation than larger populations (Reed et al, 2003). If a stock already exhibits every trait desired, this may not be of a concern. If the line does not exhibit every trait needed, this would suggest the need for a larger population size.
Population size is an obstacle which must be monitored. Many computer programs are now available to quickly determine inbreeding coefficients. Pedsys, a genetic management software, is available on line free of charge at http://www.sfbr. org/sfbr/ public/software/ software. html
One nice feature of this program is that it allows the evaluation of kinship. You can quickly figure inbreeding coefficients of every mating possible within your line. With this information a breeder is able to plan matings which would maximize the genetic distance of individuals within the line.
Selecting for traits
Rather than have a quality specimen in our line periodically, the method proposed will be built on consistency. Progress will be fairly steady, offering quality specimens improving generation to generation.
A method proposed by Dr. Roy Fangy, a geneticist who lectures for national breed clubs, proposed the idea of working on the 3 worst traits in the line. When one of the traits are no longer a concern the next weakest trait will be selected for improvment.
When a breeder considers which male to use on a female, they would pick a male who improves the three traits being selected for. Sometimes more than one male will could improve the three traits. The breeder should then use the male who offers the improvement of the three traits along with the overall highest genetic merit.
To reiterate the conclusion of this research paper on improving genetic gains, the optimum method to increase genetic gains involves creating an index value based on individual and family performance and weighted according to individual and family heritabilities.
Often only a select few closely related individuals offer the desired traits. Inbreeding does increase the chances of obtaining the trait, especially if the trait is recessive or polygenetic. Dr. Fangy, along with staticians, concluded that genetic gains and consistency will improve until inbreeding coefficients reach 40%. Further inbreeding will result in less progeny with the desired traits because of lower reproductive fitness and an increase in disease occurrence (Fangy 1993)
Obviously if the trait being select for is available in more distantly related individuals within the line, it would be beneficial to use the less related individual if everything else is equal. From the research available at this time, inbreeding levels lower than 10% resulted in the lowest disease expression.
When selecting from a line breeding the breeder must choose offspring that display the desired traits of the specific ancestor or they have accomplished little.
Every generation has the possibility of being superior to the preceding generation. Increased genetic gains from generation to generation often lead to younger animals which produce better quality compared to the older animals they were founded on (Meuwissen, 1998).
Although new generations may have higher genetic gains, caution must be taken in the use of animals that are not mature. Many diseases are not expressed until maturation and breeding juveniles who may carry a disease could commit a line to genetic suicide if bred extensively.
When an undesirable trait is expressed, the breeder who does his breed a real service is the one that stays with his line long enough to rid it of the undesirable trait. By controlling which specimens within their line are used for breeding in succeeding generations they can eliminate the undesirable trait. Once the recessive gene is removed it can never again affect the breeder's line.
In summation of the method of selecting for traits, it is ideal to keep inbreeding coefficients lower than 10% to avoid unneeded disease expression. Genetic gains increase as inbreeding coefficients rise until 40% at which point further inbreeding becomes counterproductive.
Limit the rate of inbreeding
Genetic gains accomplished by inbreeding can lead to a higher disease expression. Because of this dilemma, breeding programs generally attempt to maximize genetic accomplishments and limits the rate of inbreeding (Meuwissen et al, 1998).
One method used to limit the rate of inbreeding is to make the best use of the genetic merit of the animal while placing thresholds on the kinship (Meuwissen, 1998). This idea would not encourage the breeding of superior individuals which are going to be used extensively to those who are inferior or will not complement the mating. This will help to avoid the founder effect.
Another approach to increasing expression of a rare desirable trait is referred to as back crossing. Back crossing involves using an individual several times, but each injection happens after several generations. This method is proposed by Meuwissen and Sonesson as a way to limit the effects of inbreeding. They suggest that breeders use individuals over several overlapping generations as a method to decrease inbreeding coefficients. (Meuwissen et al, 1998).
Another extension of the backcross is possible if artificial insemination is used. Frozen semen may allow innumerable generations before the backcross, effectively lowering inbreeding coefficients.
In summary, I recommend maintaining at least 2 lines. An additional 3rd line would be ideal. Selection should be made in each line to optimize genetic gains with a limit on inbreeding.
Cross lines to help limit expression of any recessive diseases
Another possibility which is not related to maintaining the breeding stock is crossing the lines to produce hybrids. These hybrids may be of little use for maintaining the lines . My recommendation is to maintain a breeding stock of independent lines. In the event of a population size which faces extinction or a homozygous condition for a serious disease, crossing the lines you have established can be useful in preserving a lifetime of work. Another advantage to the breeder is that the quality from these hybrid offspring will have a masking effect of recessive alleles. The offspring will often be healthier than each line from which they were bred. The hybrids can also merge the strengths of both lines, exemplifying the work a breeder has put into their line. By maintaining the separate lines a breeder can produce these hybrids time and time again.
Conclusion
The majority of companion animal breeding programs breed at random and do not consider the consequences of the breeding. A superior program would be based on producing a population with low disease occurrence while optimizing genetic gains and considering the limitations faced by the breeder.
Inbreeding, out crossing, and line breeding all have strengths and weakness, and a program which combines the benefits of each is suggested. Researching stock can save time and heartache. Inbreeding stock to purge lethal and semi-lethal disease will lower disease frequency on a long-term basis. Unfortunately, disease expression will be higher during the test breedings. Information collected on the test breedings will aid in identifying high disease load individuals that should be culled from the line.
The remaining stock should be evaluated for identification of superior individuals which will be used to form foundation stock. These genetically superior individuals will be used to form separate lines based on their family ancestry.
Breeders should optimize each line independently. Each line should be monitored for population size and inbreeding coefficients while a breeder is selecting for traits. Ideal inbreeding coefficients should be limited to under 10% to reduce disease frequency, although a breeder may make the choice to breed litters as high as 40%, which is found to be the highest value achieving genetic gains, if they feel the value of the trait warrants higher disease expression.
A breeder also has the option to cross their lines to produce hybrids. These individuals will often be superior to either of the original lines, offering the possibility of combining each line’s great qualities, and limiting expression of recessively inherited diseases. While hybrids are usually not used in preserving the breeder’s stock, they typically exemplify the best of what the breeder can offer.
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