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better bred ...REALLY ???
#1
The Possible Detrimental Effect Of Using Haplotypes alone for Canine Breeding Programmes.
You CANNOT Breed “Better” if You have NO idea what you are breeding AWAY from and to use such a term could denote that YOUR lines carry diseases you are attempting to hide from the buying public…..
Dog breeds are required to conform to a breed standard, the pursuit of which often involves intensive inbreeding: The latest technology to assist breeders is the genetic mapping of the dog. Research that started with the Poodle and has now seen its way into very much smaller gene pool breeds like Havanese is Haplotypes diversity studies.  However as with all new ideas there will be those amongst the breeding fraternity that will attempt to usurp this for their own needs and in the process create poorer breeding rather than better. By poorer I need to clarify here, if a University is looking for participants then samples and pedigree information should only be sent directly to those, pedigree databases are not there to allow new breeders to retain information that could be used at a later date against any breeder whose pedigree they look at and discuss with their exceptionally small circle of friends and breeding partners in a hope to find founders of a disease. This IS being done by a new Havanese breeder and it shows poor practice.
In addition to dog breeds, extensive pedigree records that can inform gene-mapping studies are available for a number of economically important species, such as cattle. Several human populations—many of them the focus of interest for gene-mapping efforts—have detailed pedigree information available, ranging from isolated religious groups, such as the Amish (Hurd 1983Agarwala et al. 1998) and the Hutterites (Chapman et al. 2001), to 2.2 million living and deceased residents of Utah (Maul et al. 2006). Several European populations have extensive pedigrees recorded in the marriage certificates of parish churches and have already been used for demographic studies (Boattini et al. 2006). Our population structure index Ψ could be useful in rapidly assessing population structure in advance of genotyping in such populations, as well as to help select individuals for genotyping.( https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2390636/)
The old saying “don’t throw out the baby with the bathwater” warns us not to lose track of what’s important by overemphasizing a negative detail. Anyone who achieves lasting success in the dog game learns that it is the totality of an individual dog that must be considered. While there are specific faults and defects that are deal-killers for any responsible breeder, most need to be evaluated in the larger context of the breed, a breeding program, or the dog’s collection of vaults and virtues. However, in recent years a technological advancement has sometimes made the bathwater so murky for some of us that we forget there is a baby in there somewhere If some is good, more is better… …is another oft-cited truism. This phrase might even be hardwired into the human brain. We are endlessly fascinated by extremes of all types which we often view as ‘better” than the normal run of things. DNA screening tests are proving to be one of those things. Until very recently, the only way we knew to prevent producing something unwanted was to avoid it. If a particular thing was very bad, avoidance might mean eliminating a whole group of related dogs from a breeding program or even an entire breed. Not every one of those dogs would have the potential to produce the unwanted trait, but there was no way to tell who did and who didn’t. The risk of breeding those individuals and possibly producing the bad thing wasn’t worth it despite whatever good traits the dog might possess. Since the completion of the canine genome in 2005, science has been able to pinpoint individual genes responsible for particular traits. When those traits are diseases, a DNA screening test is soon developed and made available to the public. These tests are of tremendous benefit: For the first time in dog breeding history, a breeder can know with absolute certainty what every one of her breeding dogs’ genotype is for various inherited diseases, as well as a few physical traits like coat color. Since dog breeds’ genetic backgrounds differ, the diseases common in one will vary from those common in another. Therefore, each breed has its own set of tests. In Australian Shepherds, we commonly do DNA tests for MDR1, a drug reaction mutation; HSF4, a gene with mutations that cause cataracts, one of which causes most of the cataracts I Aussies; as well as Collie Eye Anomaly and the progressive rod-cone degeneration form of Progressive Retinal Atrophy. About a half dozen other tests are offered for the breed, but the diseases are sufficiently rare that they are used only by those whose lines have those diseases in or because a related individual has been diagnosed. All this testing is a good thing: With it we can prevent producing puppies that have those diseases. But sometimes our pursuit of best practices can lead to overkill. In a classic example of more is better, there are people in dogs who decided that mutations ought not to be tolerated at all, even when carrier dogs are healthy. This viewpoint appears to be especially prevalent in Europe, but there are breeders in North America who also subscribe to the philosophy. Perfect is the enemy of good Anyone who’s been in dogs for any length of time will have encountered someone, usually very new to the game, who proudly declares that she would never, ever breed anything with any sort of fault. Experience soon teaches us, if we didn’t know already, that there are no perfect dogs any more than there are perfect people or anything else. Living beings have flaws. It is the breeder’s task to evaluate those flaws and decide how she will minimize their effect in her breeding program. In most cases this means, among other things, breeding away from any unwanted traits a dog may have. If the dog’s faults are sufficiently numerous or especially bad it may not be bred at all. DNA tests have provided yet another factor for breeders to consider. All of them will tell you what variants of a specific gene a dog has. If it is clear, so is the “bathwater” and nothing need be thrown out. But the presence of a mutation sends some people running to dump not only the water but the baby and the bathtub, too. When DNA test results indicate the presence of one or even two copies of a mutation, the breeder must consider what the presence of that mutation actually means for the dog and her breeding program. Striving for perfection – in this case no mutation – is a lofty goal, but only if eradication of the mutation does not also cause major harm to a breeding program or, worse yet, the breed. This does not mean the breeder can simply shrug off the results and do whatever she wanted to do anyway. She must give serious consideration to test results, but within a wider context than the test result alone. When it comes to health issues, the point is to produce healthy puppies. The removal of affected dogs from the breeding pool has long been and remains an important form of prevention; the affected dog necessarily has genes for whatever disease it has and will pass them to its offspring. DNA tests allow breeders to make use of healthy carriers with no risk of producing affected pups. People tend to use the term “carrier” loosely and some testing labs use it incorrectly. The mode of inheritance for a particular mutation determines whether there are – or are not – carriers:  Dominant – even a single copy of the mutation will lead to disease, there are NO carriers with this type of inheritance.  Recessive – a dog must have two copies of the mutation to develop disease, those with only one are carriers and will remain healthy.  Polygenic – specific variants of multiple genes, which individually may be any mode of inheritance, are required for the dog to develop disease. The specific collection of gene variants a dog has will determine whether it is affected or not. (There are no DNA tests at present for this type of disease.)  Incomplete penetrance – the mutation may be dominant or recessive, but not every dog with the disease genotype will actually develop the disease, probably due to environmental factors or the actions of other genes. These genes are often said to confer a “risk factor.” Caveat Foecunduque Canes (Let the dog breeder beware.) The presence of a mutation, in and of itself, is not a reason to eliminate a dog from breeding: Every dog has mutations. The only way to get rid of them all is to cease breeding dogs. If a mutation is common in a breed, excessive culling may narrow the breed’s gene pool. Heavy-handed culling can also lead to problems far worse than the one being culled. The Basenji offers an example of how this can happen. Before there were DNA tests breeders were occasionally lucky enough to have a blood test for a disease that revealed carriers. Such was the case with the lethal recessively inherited disease, pyruvate kinase hemolytic anemia (PKHA.)
Road maps tell you where you’ve been and where you are going. If you are breeding dogs, pedigrees are your roadmap. They don’t just tell you what has been. Used properly, they can give you a good idea of where you need to go. This doesn’t mean that your goal is to make something that looks pretty on paper. You’re breeding dogs, not documents but those documents contain a wealth of data and can point you toward additional information. Analysis of pedigrees and supporting information will aid you in making informed breeding decisions. Pedigreed Dogs The use of written pedigrees is so intrinsic to the breeding of purebred dogs that the general public views them as synonymous. Recently, researchers at the University of California, Davis, asked a group of breeders what we wanted to have studied with the ultimate goal of developing screening tests. Our list consisted of diseases that are polygenic or which result from an interaction of genes and environment. Complex traits are difficult to pin down at the current state of the art; screening tests will be a long while coming. Even so, we should keep asking because someday science will be able to tackle them. In the meanwhile, we need to concentrate on issues that are genetically simple and with which the researcher can have reasonable hope of success. As with so many other aspects of life, money can be a problem. Research goals often include finding the responsible gene. Doing so bears a big price tag. A huge donation, from our point of view, might be totally inadequate. Mark Neff, of Davis’ Veterinary Genetics Laboratory, pointed out that laboratory consumables for a single researcher can cost about $2000 per month. Salaries of the people working on the project raise the monthly cost even higher. A successful research project, from initiation to publication, costs around $200,000.
 
Dogs have diversifi ed in size, shape, and behavior perhaps more than any other mammal ( Figure 8.2 ). This diversifi cation recently accelerated as dog breeders established closed populations for various breeds and deliberately selected some lines for novel or exaggerated phenotypes according to the distinctive standards of each breed. Depending on one’s viewpoint, the 400 or so modern breeds of dog persisting today represent either the perfection or the perversion of the canine form, drastically expanding the range of phenotypic diversity present in the dog’s wild progenitor, the gray wolf. Genetic analysis of purebred dogs and wild canids shows that most breeds trace back relatively recently with only a few breeds—the Basenji and a smattering of Asian, Middle Eastern, and Nordic breeds—showing more ancient roots or unique signatures of wolf admixture ( Larson et al., 2012 ; Parker et al., 2004 ; vonHoldt et al., 2010 ). Certainly, distinct ‘kinds’ of dogs were present in ancient times, but most of these either died out (e.g., the English Turnspit dog, Morris, 2002 ; the Salish Wool dog of the Pacifi c Northwest, Crockford, 1997 ) or admixed with other dogs suffi ciently to destroy much of their ancient or localized heritage (e.g., Rhodesian Ridgebacks and Pharaoh Hounds; Boyko et al., 2009 ; Parker et al., 2004 , 2007 ). Neolithic dogs likely had similar relationships to the humans that lived with them as present-day village dogs do, having fulfi lled varied roles in the human communities they associated with. It seems unlikely that they were bred in the same manner as current breed dogs, with closed breed books orsimilar strict protocols guarding the line’s purity. Ancient dog populations or breeds that could not be kept isolated from the emerging ‘modern’ European breeds lost their genetic distinctiveness, a process accelerated in populations with close proximity to populations of modern breeds or with attributes such as small body size that made them easy to transport ( Larson et al., 2012 ; Pires et al., 2009 ). Deliberate interbreeding of ancient breeds with modern stock also occurred in some lineages, particularly those with breed-defi ning dominant mutations like the Rhodesian Ridgeback or the Mexican Xoloitzcuintli ( Fox, 2003 ), or those facing dwindling numbers as their utility waned (e.g., Irish Wolfhounds and Finnish Spitzes). Yet, most dogs throughout history and even today are not breed dogs in any sense, but are freebreeding human commensals ( Coppinger and Coppinger, 2001 ). The population history of these village dogs is potentially much richer than that of modern breeds, which largely refl ect genetic variation present in a few dogs in Europe several centuries ago. Village dogs have a nearly global distribution, with most continental populations fi rst established millennia ago. Notably, these village dogs refl ect the ancestral stock for all dog breeds, and may represent an important genetic resource for reinvigorating some purebred lineages using outbred individuals related to the breed founders. Like many modern breeds, some populations of village dogs are also genetic mixtures of several modern European breed dogs that were relatively recently imported to those areas (e.g., Puerto Rican and central Namibian village dogs; Boyko et al., 2009 ). These dogs resumed a scavenging, free-breeding existence (they are ‘secondarily free- breeding’), but they retain little or no localizable genetic signature and do not contain unique genes resulting from local adaptation over millennia. We refer to these dogs as admixed village dogs. Other village dog populations, however, have much more ancient roots and are likely to be very informative for deciphering the origin of dogs and the movement of early dog populations across the globe (e.g., Ugandan village dogs; Boyko et al., 2009 ). These indigenous village dogs also represent unique genetic resources for understanding local adaptation and may provide unique services to the humans that live with them. In many ways, indigenous village dogs are intermediate between purebred dogs and wolves. Village dogs, living off human scraps, are mostly freed from the demands of needing to hunt preyand thus have reduced selective pressure on many functional traits. However, without strict breeding controlled by humans, they still must compete for mating opportunities. Even in cases where humans control breeding for some village dogs, sympatric scavenging dogs that are not under human control also contribute to the dog population. Further, these dogs are generally selected for functional traits like greater hunting aptitude, which tends to decrease genetic diversity less than breeding for conformation (Pedersen et al., 2013). Given this, village dogs exhibit more diversity in their behavior and morphology than do wolves, but nothing like what could be seen in an afternoon at the Westminster Kennel Club Dog Show (but see de Caprona and Savolainen, 2013 , who argue that a high level of phenotypic diversity co-occurs with a high level of genetic diversity in southern Chinese village dogs). Likewise, even though all dogs (village dogs and purebred dogs) descend from the same ancestral stock, the lack of strong artifi cial selection in most village dog populations means they have more genetic variants and genome characteristics (e.g., a high level of heterozygosity) in common with the fi rst domestic dogs (and also modern wolves) than purebred dogs, which rapidly lost their genetic diversity in the last few decades or centuries ( Calboli et al., 2008 ). Finally, whereas wolves are a keystone species and clearly an important conservation target from an ecological perspective ( Fortin et al., 2005 ) and purebred dogs are not generally ecologically important (e.g., a keystone species), free-breeding dogs, because they interact with both humans and the natural environment, present an interesting intermediate case. They can potentially mediate the interactions between humans, other domestic animals, and wildlife ( Woodroffe et al., 2007 ; Ritchie et al., Chapter 2 ; Vanak et al., Chapter 3 , Butler et al., Chapter 5 ) and, at least in some animal communities, act as an important predator species (e.g., dingoes, Johnson et al., 2007 ; Zimbabwean village dogs, Butler et al., 2004 ). Dogs are the only domesticated species that pre-dates the origin of agriculture, and rural freebreeding dog populations likely live a similar lifestyle to that of the very fi rst dogs, mostly choosing their own mating partners while relying on scavenging food from humans ( Coppinger and Coppinger, 2001 ). Whether dogs ‘pre-adapted’ humans for the Neolithic revolution or not, the fact remains that village dogs have fi lled an important niche (guard/ companion/scavenger) ever since farming communities fi rst existed. As human populations expanded and diversifi ed, so did dog populations, with dogs serving as hunters, sentries, shepherds, warriors, and food animals. Thus, genetic analysis of village dog populations could shed light on theories of dog origins and also yield unique anthropological insights and improve our understanding of the genetic basis of natural and artifi cial selection. As dogs spread across the globe, they encountered different geographical features, ecological contexts, and historical events. These led to different selection regimes and demographic histories of the dog populations in different areas. Due to this, the dogs on each continent are not equally useful for preserving the genetic diversity of dogs as a whole.
Molecular approaches to genetic diversity offer a very precise way to decide how inbred dogs are, but even molecular approaches are capable of different interpretations.Wade (2011)found that ‘Even after the formation of breeds, restrictive breeding practices in breed registries and geographical isolation, breeds have retained (on average) 87% of available domestic canine genetic diversity.’ This impressive number is based on measuring single nucleotide polymorphism (SNP) heterozygosity obtained from individuals within breeds and expressed as a percentage of the SNP heterozygosity from a large number of individuals from many different breeds, using SNP arrays. Three assumptions are made:
 
That SNPs used in the analyses are representative of all SNPs in the dog genome. The SNPs used in these array-based analyses were selected by position, but also as showing polymorphism in a small number of breeds on which they were originally tested. They are likely to come from regions of the genome in which diversity has been maintained in these breeds and may not be representative of regions placed under purifying selection in multiple dog breeds. Hence it is possible that some areas of the genome have lost a higher proportion of original variation than the arrays reveal.
That estimates of total genetic diversity based on individuals drawn from many different, but largely Western and purebred breeds, represent the whole of domestic dog genetic diversity, including that of feral and mixed breed dogs. If total diversity is underestimated, then the proportion of diversity already lost within current breeds will also be underestimated.
That the average heterozygosity measured in a limited sample of (usually) unrelated individuals is representative of heterozygosity in all individual dogs within a purebred breed. Line breeding and popular sire effects may mean that some individuals within breeds have much reduced heterozygosity.
 
As noted byWade (2011), complete loss of SNP alleles within breeds is up to 30% compared with the entire population, even when this is defined using arrays as above(Karlsson et al., 2007). A different method, comparing full sequence information in a small region of a single chromosome, ledGray et al. (2009)to estimate that loss of nucleotide diversity with breed formation averaged 35%. Whilst heterozygosity is a good measure of short term capacity to respond to selection, loss of allelic diversity restricts the likelihood of being able to respond to selection over the long term(Allendorf, 1986)and, in particular, reduces retention of useful alleles to reverse long term directional selection.
 
One genomic structure associated with loss of allelic diversity is the presence of long runs of homozygosity(Kirin et al., 2010). In the human data, these long runs correlate highly with coefficients of inbreeding obtained from pedigrees stretching back many generations(McQuillan et al., 2008). Long regions of homozygosity have already been detected in dogs, although these may be the results of selective sweeps around desirable alleles, as well as of the contributions of breed founder and popular sire effects and line breeding to consanguinity(Karlsson et al., 2007;Sutter et al., 2007;Boyko et al., 2010;Vaysse et al., 2011). Small effective population sizes, such as those found in pedigree breeds in the UK(Calboli et al., 2008)and probably elsewhere, will reduce recombination around loci experiencing selection and increase the presence and length of these tracts.
 
Whatever the cause, Karlsson et al. (2007) showed that, for seven breeds, 25% of the genome on average was found in homozygous tracts above 100 kilobase in length, whilst Boyko et al. (2010) showed that for, 10 individuals from each of 59 American Kennel Club (AKC) recognised breeds, between an average of 7.5% of the genome (in the Jack Russell terrier) and an average of 51% (in the Boxer) existed in homozygous tracts >1 megabase in length, considered likely to be autozygous (It is notable that Jack Russell terriers are not a pedigree breed in the UK and show substantial variation in type). In agreement with Karlsson et al. (2007), and as might be predicted from the reduced numbers of long haplotypes seen byVonholdt et al. (2010), Boyko et al. (2010) found that average individuals from most breeds examined had 25-30% of their genomes in these long homozygous tracts.
 
Implications of loss of heterozygosity and of the presence of homozygous tracts
Many monogenic recessive diseases are considered to be relatively rare, but quoted allele frequencies based on DNA testing of samples collected deliberately as representative of the whole population have varied from a few per cent to >50% (Jobling et al., 2003;Lee et al., 2007;Davis et al., 2008;Mellersh et al., 2009;Karmi et al., 2010;Gentilini et al., 2011;Gould et al., 2011;Minor et al., 2011;Mizukami et al., 2011;Gavazza et al., 2012;Vidgren et al., 2012). If monogenic recessive disease alleles are present in the population at a frequency of 10% (giving a disease frequency of 1% in an outbred population), then in a population with 13% loss of heterozygosity the frequency of disease will increase by <1.2%. However, many such recessive diseases are reported for each canine breed. In the database ‘Inherited Diseases in Dogs’[1]1552 disease types are associated with 273 breeds(Sargan, 2004). This database relies on the peer reviewed literature and so is necessarily incomplete, with more numerous and better surveyed breeds suffering much larger numbers of diseases.
 
Assuming that there are six independently segregating inherited monogenic diseases per breed, with the same (10%) allele frequency for each disease allele, 5.85% of an outbred population would suffer one or more of these diseases. However, with 13% loss of heterozygosity, the disease proportion will more than double to 12.34%; this represents a substantial additional welfare burden for individual affected animals, as well as presenting emotional, ethical and potentially financial responsibilities for owners of affected dogs. As can be seen from Fig. 1, for breeds with higher than average levels of homozygosity, this problem is more severe, and even disease allele frequencies of 0.1 for six alleles could imply that inbreeding is causing an additional 15% or more of individuals of these breeds to suffer reduced genetic health, based only on monogenic recessive disorders.
 
In some common breeds, much rarer disease alleles are circulating, but for larger numbers of different monogenic diseases. Some common breeds have 15 or more such disorders reported. Excess morbidity is not negligible when these larger numbers of alleles are involved even at low disease alleles frequencies: for example, P = 0.02 (giving disease frequency 1 in 2,500 for each allele, or less than 0.6% of individuals suffering morbidity in total across all these diseases in the outbred population), will give 7-10 fold higher frequency of morbidity at levels of inbreeding seen in most pedigree breeds.
 
The very presence of homozygous tracts might suggest that they are not highly detrimental to the health of most of the dogs that carry them. However, even if they do not contain monogenic recessive lethal alleles or other monogenic disease alleles, they do contain alleles that may be involved in more complex diseases, such as those associated with exaggerated conformation, and reduce the diversity available to cope with environmental challenges. If homozygous regions are shared by all individuals of a breed, then clearly back selection against an undesired characteristic, or even against an adventitiously fixed gene, will only be possible through outcrossing. A good example of this problem is the fixation of an allele of the SLC2A9 gene causing hyperuricosuria in Dalmatian dogs(Bannasch et al., 2008), where outcrossing to German pointer dogs, followed by backcrossing, has provided the diversity needed to select against the defect.
 
The health of a dog may also be adversely affected by inbreeding if the genes used in generating an immune response become homozygous. As noted by Wade (2011), breeds or species can survive within a limited habitat with reduced major histocompatibility complex (MHC) polymorphism(Angles et al., 2005; Castro-Prieto et al., 2011). However, the ability of an individual to cope with pathogens in one habitat is no guarantee that the same individual will be able to survive in another habitat where the pathogens are different(Wilbe et al., 2009; Maki, 2010). Furthermore, Angles et al. (2005) state that ‘inbreeding can have profound effects on the immune system, predisposing to increased immunodeficiency, autoimmune disease and cancer.’ Direct evidence for heterozygote advantage at the MHC and significant associations between MHC and production, disease and fertility traits have been noted in cattle(Codner et al., 2012).
 
In considering recessive monogenic disease traits, MHC polymorphism, and polygenic disease associated with conformation, to equate breed survival with individual health provides an incomplete picture. Any breeding practice that increases genetic diversity in the MHC up to a given optimum is likely to increase the proportion of healthy individuals and hence to improve the overall health of a breed.
 
Conclusions
Inbreeding can have the effect of purging (removing from the gene pool) a proportion of alleles with seriously damaging effects, with obvious fitness and health benefits. However, in the process of inbreeding, other alleles with less serious effects can become homozygous and can be retained in the population. Outcrossing to introduce fresh ‘blood’ can mitigate such effects by introducing greater variability into the gene pool, but outcrossing does carry the possibility that the benefits of purging are undone by introducing new deleterious recessive alleles. Whilst inbreeding is generally seen as being undesirable, the debate has become more nuanced in recent years. By no means all inherited diseases are carried by single pairs of genes. Many inherited diseases arise from the interaction of the products of several genes. If one or more of these genes contributing to the inherited disease are eliminated by genetic drift or by skilful breeding, it is possible, although still hypothetical, that the disease may no longer be seen in the offspring.Leroy (2011)took the view that purging has been relatively unimportant in dogs. The ratio of non-synonymous to synonymous polymorphisms, d(N)/d(S), is about 50% greater for SNPs found in dogs than SNPs in wolves, suggesting a relaxation of centralising selection at many loci(Cruz et al., 2008).
 
We have examined the evidence relating to genetic diversity in dog breeds and its relationship to disease because breeders could be tempted into complacency by suggestions that inbreeding is slight or does not matter concerning their own current practices, leading to denial about the health problems in the dogs they breed. Any thoughtful breeder of dogs should worry about the potentially adverse effects of inbreeding, but breeders are typically faced with a dilemma. They are aware of the effect of closed breeding in excluding or even purging undesirable alleles, and in fixing desirable qualities, so that in considering matings of closely related animals this desire for ‘purity’ often wins over any fears about inbreeding too much. The conflict between preserving desirable characteristics and avoiding the potentially unfavourable outcomes that may accompany inbreeding is real.
 
Notwithstanding the dilemma, the concern about the effects of inbreeding should be taken seriously. We note that the effective population sizes of 6/10 popular UK dog breeds (Calboli et al., 2008), already fall below the ‘short term minimum’ rule of thumb of Ne = 50 suggested by(Franklin, 1980)as being necessary to ensure against inbreeding depression. Aside from the arguable danger to whole breeds, genetic diseases can lead to suffering and distress in affected animals. It is the responsibility of scientists and dog breeders alike to encourage breeding choices directed at reducing the burden of genetic disease on individual animals - a duty that in our opinion overrides that of preserving the rather nebulous notion of breed purity. Tools such as the UK Kennel Club’s Mate Select website, 2012[2]are helpful in empowering breeders with knowledge to make mating decisions, even though based on pedigree information of varying completeness. It is to be hoped that, in the future, rapid molecular techniques may further guide these decisions. In the meantime, it is important that scientists consider the issue of inbreeding from the point of view of individual as well as whole breed consequences and therefore every effort should be made to encourage the retention of genetic diversity within breeds.
 
Acknowledgements
We thank Dr Elizabeth P. Murchison for helpful discussions.
 
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[1]See: www.vet.cam.ac.uk/idid/ (accessed 13 August 2012).
[2]See: www.the-kennel-club.org.uk/services/public/mateselect/Default.aspx (accessed 17 August 2012).
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#2
http://journals.plos.org/plosone/article...ne.0001324
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#3
Concerns of Genetic Diversity
Jerold S. Bell, DVM

 
There is a tendency for breeders to breed to the male who is the top-winning dog. This can also occur with a popular dog that has OFA excellent hip conformation, or has produced no epileptic offspring in matings to epileptic dams. Regardless of the popularity of the breed, if a large portion are breeding to a single stud dog, (the popular-sire syndrome), the gene pool will drift in that dog's direction and there will be a loss of genetic diversity. Too much breeding to one dog will give the gene pool an extraordinary dose of his genes, and this will include whatever detrimental recessives he may carry, to be uncovered in later generations. This can cause future breed-related genetic disease through what is known as the founder's effect.
Along with the thrill of owning a popular sire, comes your responsibility to the breed. Over time, you will find out what detrimental genes he carries. Hopefully these will cause minor faults, but occasionally they may cause genetic disorders. The true measure of a conscientious breeder is how this knowledge is disseminated to the owners of the next generation.
Purebred dog breeds have closed studbooks. No new genes are available to the breed, except from infrequent mutations that are usually not desirable. Considering a breed as a whole, genes cannot be gained through selective
breeding; they can only be lost. This has lead breeders to question whether a pure breed can go though hundreds of years of selective breeding and still maintain its health and viability.
All genes come in pairs: one from the sire and one from the dam. If both genes are of the same type, the gene pair is homozygous. If the two are different, the gene pair is heterozygous. While each dog can have a maximum of two different genes in a pair, many different genes are potentially available to be part of the pair. The greater the number of genes that are available to each pair, the greater the breed diversity.
Breeders underestimate the amount of diversity that can be present in a breed; even one with a limited group of founders. A molecular genetic study of the Chinook dog breed, which was reduced to four dogs in the 1970s,
showed that there was significant gene diversity and heterozygosity in the breed.
The studbook for the Thoroughbred horse has been closed for more than 300 years. However, researchers have found that on average 63 percent of the variable gene pairs are heterozygous and that 4.7 genes are potentially available to each pair. This diversity is present in spite of the fact that 95 percent of the breed traces back to a single founder male.
Some breeders express concern that inbreeding depression may affect the viability of their breed. The consequence of inbreeding depression is not due to a general effect from a high level of homozygous gene pairs. The problem that inbreeding depression causes in purebred populations, stems from the effects of deleterious recessive genes. When homozygous, they cause impaired health.
Lethal recessives place a drain on the gene pool, through smaller litter size or neonatal death. Other deleterious genes can cause disease or impair immunity. If there is no breed diversity in a gene pair, but the particular homozygote that is present is not detrimental, there is no negative effect on health. The characteristics that make a breed reproduce true to its standard are based on non-variable (homozygous) gene pairs.
The Doberman Pincher breed has a problem with von Willebrand's disease; an autosomal recessive bleeding disorder. Genetic testing has found that the defective gene is present in 77 percent of Dobermans. Doberman
breeders can test and identify carrier and affected dogs. They can decrease the defective gene's frequency by breeding carriers to normal-testing dogs and selecting quality, normal-testing offspring for breeding. By not just eliminating carriers, but replacing them with their normal-testing offspring, genetic diversity will be preserved.
The perceived problem of a limited gene pool has caused some breeders to discourage linebreeding and promote outbreeding in an attempt to protect genetic diversity. However, it is a fallacy that each dog must carry the diversity of the breed. Studies in genetic conservation and rare breeds have shown that this practice actually contributes to the loss of genetic diversity.
By uniformly crossing all "lines," or families of dogs in a breed, you eliminate the differences between them, and therefore the diversity between individuals. This practice in livestock breeding has significantly reduced diversity and caused the loss of unique rare breeds. The process of maintaining separate lines, with many breeders crossing between lines and breeding back as they see fit, maintains diversity in the gene pool. It is the varied opinion of breeders as to what constitutes the ideal dog, and their selection of breeding stock that maintains breed diversity.
A basic tenet of population genetics is that gene frequencies do not change from the parental generation to the offspring. The gene frequencies will remain the same regardless of the homozygosity or heterozygosity of
the parents, or whether the mating represents an instance of outbreeding, linebreeding, or inbreeding. If some breeders outbreed, and some linebreed to certain dogs that they favor while others linebreed to other dogs that they favor, then breedwide genetic diversity is maintained.
The loss of genes from a breed's gene pool occurs through selection: the use and non-use of offspring. If a popular sire is used extensively, gene frequencies, and the gene pool can shift towards his genes, limiting the breed's genetic diversity. On the other hand, dogs that are poor examples of a breed should not be used simply to maintain diversity. Related dogs with desirable qualities will maintain diversity and improve the breed.
Breeders should concentrate on selecting toward the breed standard, based on ideal temperament, performance, and conformation, and should select against the significant breed related health issues. If breeders continually breed healthy, superior examples of their breed and avoid the popular-sire syndrome, the genetic health of the breed can be maintained.
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#4
The perceived problem of a limited gene pool has caused some breeders to discourage linebreeding and promote outbreeding in an attempt to protect genetic diversity. However, it is a fallacy that each dog must carry the diversity of the breed. Studies in genetic conservation and rare breeds have shown that this practice actually contributes to the loss of genetic diversity.
By uniformly crossing all "lines," or families of dogs in a breed, you eliminate the differences between them, and therefore the diversity between individuals. This practice in livestock breeding has significantly reduced diversity and caused the loss of unique rare breeds. The process of maintaining separate lines, with many breeders crossing between lines and breeding back as they see fit, maintains diversity in the gene pool. It is the varied opinion of breeders as to what constitutes the ideal dog, and their selection of breeding stock that maintains breed diversity.
A basic tenet of population genetics is that gene frequencies do not change from the parental generation to the offspring. The gene frequencies will remain the same regardless of the homozygosity or heterozygosity of
the parents, or whether the mating represents an instance of outbreeding, linebreeding, or inbreeding. If some breeders outbreed, and some linebreed to certain dogs that they favor while others linebreed to other dogs that they favor, then breedwide genetic diversity is maintained.
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#5
Decisions to linebreed, inbreed or outbreed should be made based on the knowledge of an individual dog's traits and those of its ancestors. Inbreeding will quickly identify the good and bad recessive genes the parents share in the offspring. Unless you have prior knowledge of what the pups of milder linebreedings on the common ancestors were like, you may be exposing your puppies (and puppy buyers) to extraordinary risk of genetic defects. In your matings, the inbreeding coefficient should only increase because you are specifically linebreeding (increasing the percentage of blood) to selected ancestors.

Don't set too many goals in each generation, or your selective pressure for each goal will necessarily become weaker. Genetically complex or dominant traits should be addressed early in a long-range breeding plan, as they may take several generations to fix. Traits with major dominant genes become fixed more slowly, as the heterozygous (Aa) individuals in a breed will not be readily differentiated from the homozygous-dominant (AA) individuals. Desirable recessive traits can be fixed in one generation because individuals that show such characteristics are homozygous for the recessive genes. Dogs that breed true for numerous matings and generations should be preferentially selected for breeding stock. This prepotency is due to homozygosity of dominant (AA) and recessive (aa) genes.

If you linebreed and are not happy with what you have produced, breeding to a less related line immediately creates an outbred line and brings in new traits. Repeated outbreeding to attempt to dilute detrimental recessive genes is not a desirable method of genetic disease control. Recessive genes cannot be diluted; they are either present or not. Outbreeding carriers multiplies and further spreads the defective gene(s) in the gene pool. If a dog is a known carrier or has high carrier risk through pedigree analysis, it can be retired from breeding, and replaced with one or two quality offspring. Those offspring should be bred, and replaced with quality offspring of their own, with the hope of losing the defective gene.

Trying to develop your breeding program scientifically can be an arduous, but rewarding, endeavor. By taking the time to understand the types of breeding schemes available, you can concentrate on your goals towards producing a better dog.
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#6
https://oup.silverchair-cdn.com/oup/back...A4LVPAVW3Q
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#7
https://academic.oup.com/jhered/article/...elopmental
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