UC Davis School of Veterinary Medicine Veterinary Genetics Laboratory

Genetic Diversity Testing for Flat-Coated Retrievers

Overview

The Veterinary Genetics Laboratory (VGL), in collaboration with Dr. Niels C. Pedersen and staff, has developed a panel of short tandem repeat (STR) markers that will determine genetic diversity across the genome and in the Dog Leukocyte Antigen (DLA) class I and II regions. This test panel will be useful to breeders who wish to track and increase genetic diversity of their breed as a long term goal.

Genetic diversity testing of Flat-Coated Retrievers is now in the development phase -please see Enrolling a Breed. During this phase, we continue to test Flat-Coated Retrievers to build genetic data necessary to provide breeders with an accurate assessment of genetic diversity in their breed. We have currently tested 190 dogs, and the results are listed below. Allele and allele frequencies, and DLA class I and II haplotype frequencies may change somewhat as more dogs are tested. The goal is to keep testing dogs until no new genomic alleles or DLA haplotypes are recognized.

Price: $80.

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Results reported as:
Short tandem repeat (STR) loci: A total of 33 STR loci from across the genome were used to gauge genetic diversity within an individual and across the breed. The alleles inherited from each parent are displayed graphically to highlight heterozygosity, and breed-wide allele frequency is provided.

DLA haplotypes: STR loci linked to the DLA class I and II genes were used to identify genetic differences in regions regulating immune responses and self/non-self recognition. Problems with self/non-self recognition, along with non-genetic factors in the environment, are responsible for autoimmune disease.

Internal Relatedness: The IR value is a measure of genetic diversity within an individual that takes into consideration both heterozygosity of alleles at each STR loci and their relative frequency in the population. Therefore, IR values heterozygosity over homozygosity and uncommon alleles over common alleles. IR values are unique to each dog and cannot be compared between dogs. Two dogs may have identical IR values but with very different genetic makeups.

I. Introduction

A. Breed history

The history of the Flat-Coated Retriever is typical of many pure breeds. It usually starts with a kennel that produced a small number of outstanding dogs and a key person or persons that recognized their exceptional nature and decided to use them as a foundation for a new breed. The prototypic Flat-Coated Retriever was widely used on English estates for hunting game birds. These early dogs were “mongrels” that were purportedly bred from stock imported from North America that included breeds such as the now extinct St. John's water dog and the Newfoundland. Introgressions with native Collie-type dogs may have been used to increase the breed's trainability and Setter blood for enhanced scenting ability. Notable examples of the prototypic breed were kept by gamekeeper John Hull in 1860 and include a bitch named “Old Bouncy” and her daughter “Young Bouncy.” However, the man most credited with the breed's ultimate development was S.E. Shirley, who standardized the desired type through careful selection. H. R. Cooke, whose Riverside Kennel produced many fine field and show Flat-Coats, also helped bring public attention to the breed.

After its introduction into the U.S., the Flat-Coated Retriever began to quickly gain in popularity as a gun dog from 1873 until 1915, when it was officially recognized as a breed. However, soon after, the breed’s popularity began to decrease - eclipsed by the Golden Retriever, which was actually bred in part from the Flat-Coated Retriever and other breeds. Only a small number of Flat-Coated Retrievers remained at the end of WWII, and the breed's survival was uncertain. Fortunately, proponents of the breed were able to bring it back to reasonable numbers by the mid-1960’s, and the breed has steadily gained in popularity ever since for sport, conformation showing, and companionship. Although its popularity has never again achieved the level of the Labrador and Golden Retriever, the Flat-Coated Retriever is increasingly recognized for its comparatively good health and success in agility, hunting, retrieving, and tracking. It has also been increasingly used for drug-sniffing and as guide dog for the blind, and similar to the Golden Retriever, it is often crossed with Labrador Retrievers for these roles.

The breed has also become popular in shows in recent decades, which has increased its visibility and popularity around the world. “In 2011, 'Sh Ch. Vbos The Kentuckian' (aka Jet), a 9.5-year-old Flat-Coated Retriever from South Queensferry, near Edinburgh, Scotland, won Best in Show at Crufts. ‘Almanza Far and Flyg’ (a.k.a. Simon), from Oslo, Norway, won the Gundog Group at Crufts in 2007. Before that in 2003, a Swedish dog 'Inkwells Named Shadow' had also won the Gundog Group. The last UK dog to win the Gundog Group at Crufts was ‘Sh Ch Gayplume Dream-maker’ in 2002. The only other Flat-Coated Retriever to win Best in Show at Crufts was 'Ch. Shargleam Blackcap' in 1980.” (https://en.wikipedia.org/wiki/Flat-Coated_Retriever, 7/19/2016)

B. Breed standard and appearance

Flat-Coated Retrievers are extremely uniform in appearance as a result of decades of adherence to the breed standard. Google search finds many fine images of individuals, young and old and at work and play, https://goo.gl/0Xeuaa. The Flat-Coated Retriever Society of America, Inc. (FCRSA) is highly active in maintaining the standards and health of the breed (http://www.fcrsainc.org). Flat-Coated Retrievers come mainly in two solid colors, black and liver (deep reddish-brown). Yellow is an uncommon color. They were recognized by the AKC in 1909 and are currently the 90th most popular pure breed in the US. The Flat-Coated Retriever is a large and athletic dog, with the familiar retriever shape and retriever abilities. Positive traits are listed as a thick coat with feathering on ears, legs and tail; athleticism, proper behavior even with strangers and other animals, and its rarity and uniqueness. Negative characteristics include the need for vigorous exercise, rowdiness and over-exuberance (especially when young or not routinely exercised), excessive chewing, the need for regular brushing to avoid excessive shedding into the environment, and high incidence of cancer that can decrease their average lifespan.

C. Heritable disorders

Glaucoma and progressive retinal atrophy (PRA) occur in about 1% of Flat-Coated Retrievers and are considered to be heritable conditions. The exact mutations are unknown and no genetic tests are available (http://www.fcrsainc.org/resources/articles/glaucoma.html; http://fcrsainc.org/health/praarticle.html). However, routine testing for both conditions should be conducted, and affected animals not used for breeding. Occasionally, epilepsy is also seen in the breed. Bloat (gastric torsion) is a life-threatening condition that is seen occasionally in all large deep-chested dogs.

Flat-Coated Retrievers have a higher risk of cancer than most dogs. Hemangiosarcoma, lymphoma, osteosarcoma, and malignant histiocytosis are particularly devastating, and occur at higher rates in Flat-Coats than in many other breeds. The first three cancers are common in dogs and are especially prevalent among Golden Retrievers, while malignant histiocytosis is a peculiar cancer shared almost exclusively with the Bernese Mountain Dog. According to studies sponsored by the Flat-Coated Retriever Society of America (FCRSA), the average lifespan of the Flat-Coated Retriever is only about eight years, with a high percentage of deaths due to cancer.

Flat-Coated Retrievers have a very low rate of hip dysplasia and luxating patellas compared to other medium-sized breeds; the Orthopedic Foundation for Animals statistics consistently show a rate of hip dysplasia in the breed of less than 3%. In the 1997 FCRSA health survey, 4.2% of males and 3.2% of females had been diagnosed with luxating patellae.

II. Baseline genetic diversity testing and what it tells about Flat-Coated Retrievers

A. Standard genetic assessments based on 33 STR loci on 25 chromosomes and allele frequencies

STR markers are highly polymorphic and have great power to determine genetic differences among individuals and breeds. The routine test panel contains 33 STRs, those recommended for universal parentage determination for domestic dogs by the International Society of Animal Genetics (ISAG) and additional markers developed by the VGL for forensic purposes. Each STR locus manifests a number of different genetic configurations known as alleles. Each individual inherits one of these alleles from the sire and the other from the dam. Table 1 lists the alleles recognized at each STR locus among 190 Flat-Coated Retrievers tested to date, as well as listing the frequency of any given allele in the population.

(link to table 1)

1. Standard genetic assessment values for individual STR loci

The allele frequencies (Table 1) can be used to do a standard genetic assessment of heterozygosity at each STR locus (Table 2). The value Na is the number of alleles that are observed at each locus for a specific breed, while Ne is the number of effective alleles observed at each locus. Effective alleles are those alleles that contribute the bulk of the diversity. The Na values for individual STR loci for this population of 190 Flat-Coated Retrievers ranged from a low of 3 to a high of 9, while the Ne ranged from 1.106 to 4.227.

Observed heterozygosity (Ho) is based on the actual allele frequencies at each STR locus and their distribution, while the expected heterozygosity (He) of a locus is the value that would be predicted if allele frequencies at a specific locus were in Hardy-Weinberg equilibrium (HWE). HWE is achieved when all alleles at a specific locus are segregating randomly. A Ho value of 1.0 would be observed when alleles at each locus are unique to each individual in the population. A Ho value of 0.00 would occur if there is no heterozygosity, e.g. every individual has the same alleles at a given locus. Ho ranged from 0.147 to 0.768, indicating a large range of genetic diversity from one locus to another. The He ranged from 0.142 to 0.763 across the 33 STR loci (Table 2). The Ho and He values were used to calculate the F value (1-Ho/He), a measure of deviation from HWE. F values ranged from -0.164 to +0.117. Twenty-three loci had FIS values of 0 or greater, while 10 loci had FIS scores less than 0, indicating an excess of inbred alleles in the population. One allele was virtually fixed at two loci, LE1004 and VGL1828 (92.4 and 95% of dogs, respectively) (Table 1). This near fixation of a single allele indicates that these two loci are associated with breed defining traits that have been strongly conserved throughout breed evolution.

Table 2: Genetic assessments for individual STR loci of 190 Flat-Coated Retrievers. Na= alleles/locus; Ne= effective alleles/locus; Ho=observed heterozygosity; He=expected heterozygosity; F=coefficient of inbreeding (deviation from HWE expectation).

Locus N Na Ne Ho He F
AHT121 190 5.000 2.905 0.600 0.656 0.085
AHT137 190 6.000 3.197 0.647 0.687 0.058
AHTH130 190 4.000 2.832 0.621 0.647 0.040
AHTh171-A 190 4.000 1.642 0.421 0.391 -0.076
AHTh260 190 4.000 2.139 0.526 0.532 0.011
AHTk211 190 4.000 3.090 0.621 0.676 0.082
AHTk253 190 5.000 2.346 0.532 0.574 0.073
C22.279 190 5.000 2.692 0.695 0.628 -0.105
FH2001 190 7.000 2.334 0.558 0.572 0.024
FH2054 190 7.000 1.979 0.437 0.495 0.117
FH2848 190 5.000 2.116 0.532 0.527 -0.008
INRA21 190 6.000 3.478 0.679 0.712 0.047
INU005 190 3.000 2.443 0.579 0.591 0.020
INU030 190 3.000 1.710 0.379 0.415 0.087
INU055 190 3.000 1.582 0.368 0.368 -0.001
LEI004 190 3.000 1.168 0.147 0.144 -0.024
REN105L03 190 4.000 2.436 0.621 0.589 -0.054
REN162C04 190 4.000 2.517 0.579 0.603 0.039
REN169D01 190 5.000 3.847 0.737 0.740 0.004
REN169O18 190 6.000 4.227 0.758 0.763 0.007
REN247M23 190 3.000 2.009 0.484 0.502 0.036
REN54P11 190 4.000 2.951 0.658 0.661 0.005
REN64E19 190 5.000 3.321 0.663 0.699 0.051
VGL0760 190 8.000 2.941 0.768 0.660 -0.164
VGL0910 190 9.000 4.095 0.737 0.756 0.025
VGL1063 190 9.000 3.661 0.705 0.727 0.030
VGL1165 190 8.000 3.874 0.716 0.742 0.035
VGL1828 190 4.000 1.106 0.089 0.096 0.068
VGL2009 190 4.000 1.499 0.332 0.333 0.004
VGL2409 190 4.000 1.311 0.253 0.237 -0.064
VGL2918 190 9.000 3.096 0.679 0.677 -0.003
VGL3008 190 5.000 1.828 0.442 0.453 0.024
VGL3235 190 6.000 3.159 0.700 0.683 -0.024

2. Using allele frequency data to do standard genetic assessments on the population as a whole.

Allele frequencies across all 33 STR loci taken from Table 1 can also be used to calculate a mean observed heterozygosity (Ho) and expected heterozygosity (He) for the Flat-Coated Retriever population as a whole (Table 3), as compared to 164 Golden Retrievers (Table 4). The population of 190 Flat-Coated Retrievers which were tested had a mean number of alleles (Na) of 5.182 across all 33 genomic STR loci. The average number of alleles per locus was low compared to other breeds that have been tested, indicating a low level of genome wide genetic diversity. The mean effective alleles (Ne) per locus were 2.592, also one of the lower Ne scores that we have observed. The low Ne indicates that about one half of available alleles account for most of the diversity, which is a common proportion for many pure breeds.

The mean observed heterozygosity (Ho) was 0.553, which was lower than the expected heterozygosity (He) of 0.562. This resulted in an F value (0.014) that is slightly higher than zero, indicating that breed wide heterozygosity is nearly in line with HWE, with the exception of a small proportion of dogs that are more inbred than the population as a whole. Heterozygosity values based on allele frequencies across the entire breed and 33 STR loci indicate that most Flat-Coated Retrievers are products of matings between bitches and studs that are as unrelated as possible, given the limited genetic diversity in the breed. However, Ho and He are average scores for the population and may not accurately reflect individuals that are more outbred or inbred than the population as a whole. This is better reflected by the IR scores (see below).

Genetic diversity in the Golden Retriever (Table 4), although considered to be relatively low compared to other breeds, was still greater than for Flat-Coated Retrievers (Table 3). The average number of alleles per locus (Na) and average number of effective alleles per locus (Ne) was also greater for Golden Retrievers as were the observed and expected heterozygosity (Ho, He). However, the inbreeding coefficient F for Golden Retrievers was higher than for Flat-Coated Retrievers (0.049 vs 0.010) indicating that the proportion of inbred dogs was higher among Golden Retrievers than Flat-coated Retrievers.

Table 3: Genetic assessment of 190 Flat-Coated Retrievers based on allele frequencies at 33 genomic STR loci on 25 chromsomes.

N Na Ne Ho He F
Mean 190 5.182 2.592 0.553 0.562 0.014
SE 0.318 0.150 0.030 0.030 0.010

Table 4: Genetic assessment of 164 Golden retrievers based on allele frequencies at 33 genomic STR loci.

N Na Ne Ho He F
Mean
164
6.42
3.36
0.649 0.682 0.049
SE
0.04
0.34
0.015 0.014 0.010

3. Using allele frequency data from 33 genomic STR to examine the genetic relationship of individuals within a population.

Principal coordinate analysis (PCoA) uses genetic distance based on allele sharing to demonstrate genetic differentiation between individuals in related or unrelated populations. The resulting data is multi-dimensional (spherical), but can be accurately portrayed in a two dimensional graph by selecting values from the two coordinates that represent the greatest proportions of individuals (coordinate 1 and 2 in this case). Figure 1 is a PCoA plot of 190 Flat-coated Retrievers. The plot shows that all 190 dogs cluster as a single breed, although the plot is somewhat diffuse with a number of more distant outliers. This suggests that there is still phenotypic, and therefore genotypic, variation in the breed.

Figure 1: PCoA plot of 190 Flat-coated Retrievers.

It is believed that Flat-coated Retrievers played an important role in the development of the Golden Retriever. Figure 2 is a PCoA plot comparing 164 Goldent Retrievers with 190 Flat-coated Retrievers. This PCoA plot shows that the 190 Flat-Coated Retrievers belong to a single breed (population) that is genetically distinct from Golden Retrievers. Although this does not mean that Golden Retrievers are unrelated to Flat-coated Retrievers, it does suggest that the relationship is not as close as assumed. Comparisons of two distinct breeds tends to accentuate the relationship of individuals with a breed. The tight clustering of the Flat-Coated Retrievers compared to Golden Retrievers in this comparative PCoA indicates that Flat-Coats are much more related (less genetically diverse) to each other than Golden Retrievers are related to each other.

Scatter plot PCoA including Flat-Coated Retrievers and Golden Retrievers

Figure 2: PCoA plot comparing 296 Flat-Coated Retriever (FR) population with 686 Golden retrievers (GR).

B. The use of genomic allele frequencies to determine internal relatedness

1. Internal relatedness of individuals and the population as a whole

Genetic assessments such as those presented in Table 3 are indicators of population-wide heterozygosity and do not reflect the genetic diversity of individuals within the population. The genetic diversity of an individual dog is largely determined by the diversity inherited from each of its parents. Internal Relatedness (IR) is a calculation that has been used to determine the relative genetic contributions of both parents to an individual. The IR calculation evaluates homozygosity and uses allele frequencies to give more importance to rare and uncommon alleles. IR scores of all individuals in a population can be graphed to form a curve ranging from -1.0 to +1.0. A dog with a value of -1.0 would have parents that were totally unrelated at all 33 STR loci), while a dog with an IR value of +1.0 has parents that were genetically identical at all loci. An IR value of +0.25 would equivalent to offspring of full sibling parents from a random breeding population. IR values >0.25 occur when the parents of the full sibling parents were themselves highly inbred.

The IR curve calculated from the 190 Flat-Coated Retrievers ranged from around -0.279 for the most outbred dog to +0.385 for the most inbred, with a mean value for the population of +0.021 (Table 5, Fig. 3). Therefore, one half of the dogs had IR values over +0.021 and one quarter over +0.096. However, the IR curve was bimodal, with one quarter of dogs having a peak value nearer to +0.25 and a range from +0.096 to 0.385. A value of +0.25 is comparable to the genetic diversity of offspring of a full-sibling mating. This highly inbred subpopulation is balanced by the one quarter of outbred dogs with IR values of -0.058 to -0.279. This balancing of highly outbred and inbred dogs is why the Ho, He and FIS values calculated for the whole population using allele frequencies of the 33 genomic STR loci gave the impression that the 190 dogs tested were all in Hardy-Weinberg equilibrium.

Fig. 3: Distribution of IR estimates in 190 Flat-coated Retrievers based on intra-breed diversity (Red line), compared with IR adjusted for diversity lost during breed development (Blue line). Diversity lost as a result of breed development was determined by comparing allele frequencies at the same loci between Flat-coated Retriever and randomly breeding village dogs from the Middle East, SE Asia, and the Pacific Islands.

Table 5: Statistical breakdown of IR and IRVD values used to create population curve shown in Figure 3.

IR IRVD
Min. -0.27884 0.0334
1st Qu -0.05769 0.2378
Median -0.0023 0.3038
Mean 0.020774 0.3133
3rd Qu 0.095531 0.3985
Max. 0.385474 0.6327

2. IRVD values as a measure of genetic diversity lost during the entire period of breed evolution from earliest ancestors to present

The IR values can be adjusted in such a way as to provide an estimate of the amount of genetic diversity that has been during breed evolution. This is done by using allele frequencies obtained from DNA of present day village dogs from the Middle East, SE Asia and Island Pacific nations, which closely reflect the ancestors of dogs before extensive pure breeding. Village dogs are the most random bred and genetically diverse population that has been studied to date. The adjusted IR value is known as IR-village dogs or IRVD. The IRVD curve was shifted well to the right, reflecting a considerable loss of genetic diversity during breed development (Fig. 3, Table 5). One half of the dogs, when adjusted for diversity lost since their progeny evolved from village dogs, had IRVD values from +0.304 to +0.633. The relative lack of overlap between the IR and IRVD curves was another indicator that Flat-coated Retrievers have retained only a small portion of the genetic diversity that existed in their village dog ancestors.

C. DLA Class I and II Haplotype frequencies and genetic diversity

The DLA consists of four gene rich regions making up a small part of canine chromosome 12. Two of these regions contain genes that help regulate normal cell- (Class I) and antibody-mediated (Class II) immunity. Polymorphisms in these regions have also been associated with abnormal immune responses responsible for autoimmune diseases. The Class I region contains several genes, but only one, DLA-88, is highly polymorphic (with many allelic forms) and is therefore most important for immune regulation. Specific alleles at the four STR loci associated with the DLA88 are linked together in various combinations, forming specific haplotypes (Table 4). Groups of genes and their alleles inherited as a block, rather than singly, are called haplotypes. The class II region also contains several genes, three of which are highly polymorphic, DLA-DRB1, DLA-DQB1 and DLA-DQA1. Specific alleles at STR loci associated with each of the three Class II genes are strongly linked and also inherited as a single block or haplotype (Table 5). One haplotype comes from each of the parents.

The STR-based haplotype nomenclature used in this breed diversity analysis is based on numerical ranking with the first haplotypes identified in Standard Poodles being named 1001, 1002, ... for class I haplotypes and 2001, 2002, ... for class II haplotypes. It is common for various dog breeds to share common and even rare haplotypes, depending on common ancestry.

We have identified eight STR-associated DLA Class I and 10 DLA Class II haplotypes among 199 Flat-Coated Retrievers we tested (Table 5). This was an increase of three DLA class I and four DLA class II haplotypes from the initial study of 139 Flat-coated Retrievers. With the exception of 1017 and 2005, which are over-represented among the haplotypes that exist in the breed, the remaining haplotypes are relatively random in distribution. The DLA class II 1142 and 1143 haplotypes are unique to the breed and most likely goes back to one of the original founders, while the remaining haplotypes are common in other breeds such as the Standard poodle (1017), Italian greyhound (1054) and Golden retriever (1066, 1068). All of the DLA class II haplotypes are also found in breeds such as the Standard poodle (2003, 2005, 2014, 2022) and Golden retriever (2046, 2053). The sharing of haplotypes between Standard poodle, Golden retriever and Flat-Coated Retrievers is understandable given that they were all originally developed as retrievers of fowl in Western Europe. Since DLA haplotypes are inherited largely intact and by descent, the low number of DLA class I and II haplotypes suggests either a small founder population, or a subsequent loss of genetic diversity due to artificial genetic bottlenecks such as geographic isolation, popular sire effects, popular bloodline effects, catastrophic events such as world wars, etc.

Table 6: DLA class I and class II haplotypes and their frequency in Flat-coated Retriever (n=199)

DLA Class I Haplotype Frequencies (Updated Sep 20, 2017)
Flat Coated Retriever (n=301)
1017386 373 289 1780.465
1035386 373 277 1840.003
1054382 379 277 1840.115
1065380 371 277 1810.002
1066376 375 277 1780.002
1067376 373 277 1780.002
1068380 373 287 1810.264
1142376 379 277 1800.143
1143386 373 287 1810.003
1170386 373 277 1800.002
DLA Class II Haplotype Frequencies (Updated Sep 20, 2017)
Flat Coated Retriever (n=301)
2003343 324 2820.125
2005339 322 2800.430
2014339 322 2840.035
2017343 322 2800.002
2018339 324 2840.145
2022339 327 2820.118
2046339 329 2800.002
2048339 331 2820.002
2053343 324 2800.141
2083339 324 2820.002

F. Using standard genetic assessment parameters and DLA class I and II STR allele frequencies to gauge diversity in the entire DLA region.

It is important to maintain as much genetic diversity in the DLA region as possible and to select mates in a random manner to maintain that diversity. The frequency of haplotypes can be misleading, especially when they are few in number and certain haplotypes predominate. Genetic diversity in the DLA regions can be more accurately assessed by studying the alleles and allele frequency at the four DLA class I and three DLA class II STR loci. The calculations listed in Table 7 provided one measurement of how the individual alleles that define the DLA class I and II haplotypes are distributed (Table 7). The proportion of DLA class I and II STR associated alleles that are homozygous are similar except for DLA class I loci 4ACA and class II loci 5ACA. About one third of the 190 dogs are homozygous at one or more DLA class I haplotypes and 26.8% for class II haplotypes. About one fourth (26.3%) of class I and class II haplotypes are both in linkage and homozygous at all 7 STR loci. This degree of homozygosity is understandable given the low numbers of haplotypes with high frequency that exist in the breed. The chances of breeding two dogs that share one or two copies of the same common DLA haplotype becomes greater as the number of available haplotypes decreases.

Genetic diversity in the DLA region can be also be assessed by studying the frequency of the DLA class I and II alleles of the four DLA class I and three DLA class II STR loci (Tables 7, 8), in the same manner as employed with the 33 genomic STR loci. Although these STRs are associated only with the DLA class I and II regions on chromosome 12, the numerous genes and their alleles that make the entire DLA is in strong linkage disequilibrium, meaning that it is inherited as a large block of genes that are less subject to recombination. Therefore, genetic diversity in the DLA region reflects genetic diversity in the genome as a whole, but not to the same extent as the 33 genomic STR markers.

Table 7: Standard genetic assessment of the DLA regions using 7 STRs associated with the DLA class I and II regions.

Locus N Na Ne Ho He F
DLA I-3CCA 139 4.000 3.022 0.669 0.669 0.000
DLA I-4ACA 139 3.000 1.655 0.417 0.396 -0.054
DLA I-4BCT 139 3.000 2.727 0.633 0.633 0.000
DLA1131 139 4.000 3.001 0.669 0.667 -0.003
5ACA 139 2.000 1.595 0.353 0.373 0.055
5ACT 139 4.000 2.481 0.576 0.597 0.036
5BCA 139 3.000 2.362 0.626 0.577 -0.086
Mean 139 3.286 2.406 0.563 0.559 -0.007
SE 0.286 0.103 0.048 0.047 0.018

Flat-Coated Retrievers have a mean of 3.29 DLA class I and II associated alleles at each of the 7 STR loci and 2.41 of these alleles contribute to the bulk of an individual dog’s DLA diversity (Table 7). The low number of alleles at each of the DLA loci reflects the low number of DLA class I and II haplotypes in the breed. The Ho for the DLA alleles is similar to that of the 33 genomic STRs (0.553 vs. 0.555) as is the He (0.562 vs 0.561) (Tables 2, 7). The F value is lower (-0.007 vs 0.014) (Tables 2, 7) but both are close to zero. Therefore, both DLA and genomic markers as a whole are in HWE.

The calculations listed in Table 7 provided one measurement of how the individual alleles that define the DLA class I and II haplotypes are distributed and suggest that diversity in this important region is being maintained in a random fashion. However, the low number of haplotypes and the high frequency of an even smaller number of them increases the chance that even random breeding may lead to a high frequency of homozygosity in DLA haplotypes, something that is generally seen as more likely to be deleterious than beneficial. It is possible to measure the proportion of the population that have inherited the same DLA class I or II haplotype from each parent (i.e., homozygous) (Table 8). About one third of Flat-Coated Retrievers have inherited the same DLA class I haplotype from each parent, one-fourth for the same class II haplotype, and one-fourth for the same linked class I/II haplotypes. This degree of homozygosity is understandable given the low numbers of DLA haplotypes that exist in the breed, as well as the high degree of allele sharing among 33 genomic STR markers.

Table 8: Homozygosity vs. heterozygosity for alleles at each of the 4 DLA class I and three DLA class II associated STR loci for 190 Flat-coated Retrievers

#homozygous #heterozygous %homozygous
DLA class I loci
3CCA 62 128 32.60%
4ACA 108 82 56.80%
4BCT 70 120 36.80%
1131 63 127 33.20%
DLA class II loci
5ACA 125 65 65.80%
5ACT 80 110 42.10%
5BCA 72 117 38.40%
Class I haplotype 62 128 32.60%
Class II haplotype 51 139 26.80%
Class I/II haplotype 50 140 26.30%

III. Interpretation of genetic diversity test data for Flat-Coated Retrievers

A. Implications of low genetic diversity

Flat-Coated Retrievers have a low level of breed-wide genetic diversity comparable to breeds such as the Bulldog, Black Russian Terrier and Doberman Pinscher. This is understandable given that the breed descended from a small number of founders that were heavily influenced by a famous mother and daughter. Aspects of these first “flat-coats” were greatly admired by S. E. Shirley, who standardized the desired type and created the ultimate founder population. Such “standardization” usually involves inbreeding to obtain a uniform physical appearance and behavior, after which the founder population is closed to further genetic introgressions. A lack of genetic diversity is also reflected by the great uniformity between individual Flat-Coated Retrievers. Phenotypic differences, even when small, are associated with genotypic differences, and the more genotypic differences, the greater the genetic diversity.

Although the history of Flat-Coated Retrievers mentions the use of a several breeds in its origin, it must be assumed that either not as many breeds were used as believed or that the diversity provided by many of the initial founders has been subsequently lost. The breed undoubtedly lost some of its diversity during WWII, as did many other European breeds, or from the loss of popularity after the war and until the 1960’s when a decision was made to rescue remnants of the breed.

A loss of genetic diversity is often associated with a decline in breed health, but this does not seem to be the case with the Flat-Coated Retriever, as it has been for other breeds. If the foundation stock of a breed possesses good genetic health at the onset, it remains closed to the deliberate or inadvertent introgression of deliterious genes from outside of the breed, good health will usually be maintained over numerous generations, providing that the population remains continuously in what is called Hardy-Weinberg equilibrium. Spontaneous mutations can always occur, and some can be deliterious, but they will remain at low frequency as long as they are not inadvertently amplified by positive selection of a linked beneficial trait. Popular sire or line effects are most likely to cause deliterious mutations to rise to a level of importance. Championships in the show ring over the last decade has definitely increased the popularity of Flat-coated Retrievers, and there is no doubt that the fastest way to attain a certain appearance is to mate dogs of the same desired type. Phenotype is determined by the genotype, and if the phenotypic appearance is similar, the genotypes will be similar. Therefore, even if the pedigrees show two dogs to be unrelated, if they have the same desired traits, they are apt to share the same DNA encoding those traits.

The greatest problem faced by any breed is the loss of health and longevity resulting from the accumulation of numerous complex and simple deleterious genetic traits. Although the Flat-Coated Retriever has a relatively low amount of genetic diversity, founders of the breed and subsequent breeders were wisely chosen to maintain the basic appearance of the normal ancestral dog. The fact that this form was tested in actual performance venues also favored selection for soundness. Form and function are intimately associated, and when form is changed, so is function. An example would be the Bulldog, which is actually somewhat more genetically diverse than the Flat-Coated Retriever, but nonetheless suffers numerous serious health problems due to an over exuberance towards chondrodysplasia, brachycephaly, and skin wrinkles.

Flat-Coated Retrievers suffer from a low incidence of genetic disorders that are potentially of a simple recessive nature, such as PRA and glaucoma. However, breeders appear to have limited these disorders to a low level by testing their dogs for the earliest signs of these diseases and avoiding using affected dogs for breeding. Orthopedic problems such as hip and elbow dysplasia are also comparatively uncommon, again due to the avoidance of chondrodysplasia and selection for a gait more compatible with performance. The most significant problem in the breed is cancer. Except for malignant histiocytosis, the major cancers of the breed are closely linked to those of the Golden Retriever, a breed sharing ancestral history. Malignant histiocytosis is also a significant cancer in the Bernese Mountain Dog, which indicates the genetic influence of a common ancestor(s) and inheritance by descent.

Should Flat-Coated Retriever breeders be worried about the small amount of genetic diversity that exists in the breed? If they are pleased with the appearance and health of their breed, they can accept the status quo. However, they must be careful to avoid any further loss of diversity caused by artificial genetic bottlenecks that might involve certain sires, dams, and bloodlines. Inbreeding for a particular show-winning form may greatly increase the incidence of diseases like PRA and glaucoma and bring other genetic defects to the forefront. Additional genetic diversity can be brought into the breed by outcrossing, but outcrossing is often followed by a period of inbreeding, backcrossing, and an eventual return to random breeding. Therefore, extreme care must be taken in choosing dogs for outcrossing that are free of simple and complex genetic traits, while most closely matching the breed standard. For instance, Flat-Coated Retrievers do not suffer very much from autoimmune diseases, which is a common occurrence with inbreeding into specific sires and blood lines in breeds such as the Standard Poodle and Italian Greyhound. Because the breed lacks diversity, deleterious traits would be manifested much earlier and it would also be more difficult eliminate them after they are introduced.

B. How will you be given the results of DNA-based genetic diversity testing on your dog?

After a sample is submitted for genetic testing, the identity of the dog and owner will be replaced by a laboratory barcode identifier. This identifier will be used for all subsequent activities and each owner will be provided with a certificate that reports the internal relatedness, genomic STR genotypes and DLA class I and II haplotypes for the dog(s) tested. The internal relatedness value for the dog being tested is related to the population as a whole.

Example Diversity Certificate 1Example Diversity Certificate 2

C. What should you do with this information?

The goal for Flat-Coated Retriever breeders should be to continue to produce puppies with IR scores less than 0, and with time even lower scores. Although most of the individuals tested were randomly bred, there were small subpopulations of dogs that were much more inbred or outbred than the rest of the population. Therefore, there is a possibility to better balance genetic diversity in the breed. Mates should be selected to avoid homozygosity at any genomic loci or DLA class I and II haplotype and encourage the use of dogs with less common genomic alleles or DLA haplotypes. Maintaining existing genomic diversity will require using IR values of potential mates based on the 33 STR loci to assure puppies of equal or greater overall diversity, similar to what is being done by many Standard Poodle breeders. However, IR values, because they reflect the unique genetics of each individual, cannot be used as the criteria for selecting ideal mates. Mates with identical IR values may produce puppies significantly more or less diverse than their parents. Conversely, a mating between dogs with high IR values, providing they are genetically different, may produce puppies having much lower IR scores than either parent. A mating between a dog with a high IR value and a low IR value, providing the latter has few alleles and DLA haplotypes in common, will produce puppies much more diverse than the highly inbred parent. Breeders should also realize that a litter of puppies may have a wide range of IR values, depending on the comparative contributions of each of the parents. The more genetically diverse and different the parents, the greater the range of IR values in their offspring.

The next step is to compare the DLA class I and II haplotypes. You want to avoid breeding pairs that will produce puppies that will be homozygous for the same haplotypes, and once again, less common haplotypes may offer more diversity than common ones.

Breeders who do not have access to computer programs to predict the outcome of matings based on IR values of sire and dam can also compare values by manual screening. Potential sires and dams should be first screened for genetic differences in alleles and allele frequencies for the 33 genomic STR loci. Some extra weight should be given to rare vs common alleles. This information is included on all certificates and on the breed-wide data on the VGL website.

Puppies, once born, should be tested for their actual IR values, which will reflect the actual genetic impact of each parent on internal diversity. Considerations of mate choices for genetic diversity should be balanced with other breeding goals, but maintaining and/or improving genetic diversity in puppies should be paramount.

An additional goal of this study is to contribute this genetic information to a web repository, hopefully under the control of the registry. The best format for such a repository and testing has been provided by Standard Poodle breeders. This information could be incorporated into a mate selection service that will allow a breeder to identify, among all of the dogs tested, potential mates that would be most ideal for increasing genetic diversity in their litters- https://www.betterbred.com/.

Veterinary Genetics Laboratory, Tel 530-752-2211, Email VGL