MOF, Alm.del - 2018-19 (1. samling) - Endeligt svar på spørgsmål 654: Spm. om Københavns Universitets undersøgelse af MARS testen konkluderer, at testen må bruges til juridiske formål, til miljø- og fødevareministeren

Miljø- og Fødevareudvalget 2018-19 (1. samling)
MOF Alm.del
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U N I V ER SI TY O F C O P EN H AGEN

FACULTY OF HEALTH AND MEDICAL SCIENCES

Master’s thesis

2018

Laura Pedersen (mgs780)

Maria Gravgaard Laursen (kcv698)

DNA Test as a Basis of Identifying Illegal Dogs in

Denmark

Supervisor:

Co-supervisor:

P rofessor Merete Fredholm

P rofessor P eter Sandøe

Submitted:

February 11

t h

2018

MOF, Alm.del - 2018-19 (1. samling) - Endeligt svar på spørgsmål 654: Spm. om Københavns Universitets undersøgelse af MARS testen konkluderer, at testen må bruges til juridiske formål, til miljø- og fødevareministeren

Name of department:

Department of Veterinary and Animal Sciences

University of Copenhagen

Laura Pedersen (mgs780)

Maria Gravgaard Laursen (kcv698)

DNA Test as a Basis of Identifying Illegal Dogs in Denmark

An investigation of the use of a DNA test, in this study Wisdom Panel, for

identification of American Staffordshire Terrier (Amstaff) and mixed -

breed dogs containing Amstaff in Denmark in relation to the breed-specific

legislation.

Professor Merete Fredholm,

Section of Animal Genetics, Bioinformatics and Breeding

Department of Veterinary and Animal Sciences

University of Copenhagen

Professor Peter Sandøe

Section of Animal Welfare and Disease Control

Department of Veterinary and Animal Sciences

University of Copenhagen

Authors:

Title:

Topic description:

Supervisors:

Submitted on:

Grade:

Number of pages:

Front page photo:

February 11

2018

30 ECTS

Daisy, a Swedish American Staffordshire Terrier

Photo by Tina Olsen

Abstract

In 2010, possession and breeding of American Staffordshire Terrier (Amstaff) and 12 other dog

breeds became illegal in Denmark when the Danish breed specific legislation was introduced. If the

police suspect a dog to be included by this law because of its phenotypical appearance, the owner is

required to prove that the dog is legal. Presently, the owner can meet the burden of proof by

documenting the dog to be an offspring of legal breeds. Today, this is not possible by the use of a

DNA test

to identify a dog’s breed. The current study investigates the possibility to use such DNA

test in Denmark to detect purebred Amstaff and mixed-breeds containing Amstaff. An American

company has developed a DNA test, Wisdom Panel, based on breed specific SNP markers and used

to identify the composition of dog breeds to a limit of 12.5% in a dog. The test is mainly based on

American DNA samples and therefore, the usability in Denmark is uncertain.

To investigate if Wisdom Panel is usable in Denmark, DNA material from 20 Swedish Amstaffs

(representing the Danish population) and six American Amstaffs were analyzed with Wisdom Panel

4.0. In addition, DNA material from 192 Danish dogs was analyzed. In total, 55 different dog breeds

were represented in the study.

The results revealed that Wisdom Panel was able to correctly detect all samples from 46 out of the

55 analyzed dog breeds including Amstaff. The 46 detected dog breeds are all included in the Wisdom

Panel database whereas the remaining nine are not included. It is concluded that a DNA test is usable

in Denmark as Wisdom Panel is able to detect Amstaff and other breeds included in the database to

a limit of 12.5%. Regarding the breed-specific legislation the implementation of a DNA test could

improve the legal rights, as the test improve the ability to prove a dog’s breed composition and is

more accurate compared to visual breed identification.

Resume

I 2010 blev besiddelse og avl af Amerikansk Staffordshire Terrier (Amstaff) og 12 andre hunderacer

ulovliggjort i Danmark, da hundelovens forbudsordning trådte i kraft. Formoder politiet på baggrund

af en hunds udseende, at der kan være tale om en hund der er omfattet af forbuddet, stilles der krav

om, at ejeren kan bevise, at hunden er lovlig. I dag kan denne omvendte bevisbyrde kun løftes såfremt

ejeren kan bevise, at hunden stammer fra lovlige racer, og det er ikke muligt at identificere hundens

racemæssige sammensætning ved hjælp af en DNA- test. Dette studie undersøger muligheden for

brug af en sådan DNA-test i Danmark til at identificere renracede Amstaff og blandingshunde, hvor

Amstaff indgår. Et amerikansk firma har udviklet en DNA-test, Wisdom Panel, der er baseret på

racespecifikke SNP markører som kan bruges til at identificere tilstedeværelsen af hunderacer i en

hund ned til 12,5%. Testen er hovedsageligt baseret på DNA-prøver fra amerikanske hunde, og det

er derfor usikkert, om testen kan bruges i Danmark.

For at undersøge om Wisdom Panel kan bruges i Danmark, blev DNA-materiale fra 20 svenske

Amstaffere (repræsentative for den danske population) og 6 amerikanske Amstaffere testet med

Wisdom Panel 4.0. Yderligere blev DNA-materiale fra 192 danske hunde testet. I alt er 55 forskellige

racer repræsenterede i dette studie.

Resultaterne viste, at Wisdom Panel kunne detektere alle prøver fra 46 ud af de 55 indsendte

hunderacer, heriblandt Amstaff, korrekt. De 46 hunderacer optræder alle i Wisdom Panels database,

hvorimod de resterende ni ikke gør. Det konkluderes, at en DNA-test kan bruges i Danmark, da

Wisdom Panel kan detektere racen Amstaff og andre hunderacer, som er registrerede i databasen, ned

til 12,5%. I relation til hundeloven vil implementering af en DNA-test øge retssikkerheden, da denne

test forbedrer mulighederne for at bevise en hunds racesammensætning og er mere præcis end visuel

bedømmelse.

Foreword and Acknowledgement

This veterinary master's thesis was written as a part of the Veterinary Medicine master program at the

Faculty of Health and Medical Sciences at the University of Copenhagen. The project was carried out

as the genetic part of a project supported by the Ministry of Environment and Food of Denmark. This

thesis targets the politicians of Denmark, veterinarians, dog owners, shelters and people with special

interest in the breed-specific legislation.

We appreciate the financial support from the Ministry of Environment and Food of Denmark and the

opportunity to work with this subject.

We would like to thank our main academic supervisor Professor Merete Fredholm, Section of Anima l

Genetics, Bioinformatics and Breeding, Department of Veterinary and Animal Sciences at the

University of Copenhagen, and our co-supervisor Professor Peter Sandøe, Section of Animal Welfare

and Disease Control, Department of Veterinary and Animal Sciences at the University of

Copenhagen, for expert knowledge, great discussions, support and guidance as well as for their

patience and time during the writing process.

We would also like to thank the laboratory technicians at the Section of Animal Genetics,

Bioinformatics and Breeding at Department of Veterinary and Animal Sciences at the University of

Copenhagen for their help with the DNA samples and supervision in the laboratory. A great thanks

to our fellow students Frederikke Krøll and Ida Marie Tommerup for superb teamwork regarding the

organization of the project and the sample collection in Sweden.

We would also like to thank the Danish Kennel Club for establishing contact to the Swedish Kennel

Club, and lastly, a special thanks to the 20 Swedish American Staffordshire Terriers and their owners.

List of Abbreviations

Amstaff:

bp:

F1:

FCI:

LD:

PCA:

PCR:

SNP:

U.S.:

USDA:

American Staffordshire Terrier

Base pair

First filial (offspring as a result of breeding of two purebred dogs)

Fédération

Cynologique Internationale

Linkage Disequilibrium

Principal Component Analysis

Polymerase Chain Reaction

Single Nucleotide Polymorphism

United States

United States Department of Agriculture

Table of Contents

Abstract ............................................................................................................................................. 3

Resume ............................................................................................................................................... 4

Foreword and Acknowledgement ................................................................................................ 5

List of Abbreviations ...................................................................................................................... 6

Table of Contents ............................................................................................................................. 7

1. Background .................................................................................................................................. 9

1.1 The Danish Breed-Specific Legislation................................................................................ 9

1.2 Visual Breed Detection.........................................................................................................10

1.3 History of Dog Breed Formation.........................................................................................11

1.4 History of American Staffordshire Terrier.........................................................................12

1.5 Dog Breed Genetics ..............................................................................................................13

1.5.1 Microsatellites ....................................................................................................................14

1.5.2 Single Nucleotide Polymorphism (SNP) ........................................................................15

1.6 Wisdom Panel ........................................................................................................................16

1.7 Genetic Differences Between American and European Dog Populations .....................18

1.8 Study Purpose ........................................................................................................................18

2. Materials and Methods ............................................................................................................19

2.1 Study Design ..........................................................................................................................19

2.1.1 Animal Material .................................................................................................................19

2.1.2 Sample Collection ..............................................................................................................19

2.1.3 DNA Extraction..................................................................................................................20

2.2 DNA Analysis…………………………………………………………………….…. 20

2.2.1 Microsatellite Genotyping ................................................................................................20

2.2.2 DNA Test ............................................................................................................................20

3. Results ..........................................................................................................................................21

3.1 Wisdom Panel Reports .........................................................................................................21

3.2 Wisdom Panel Results ..........................................................................................................22

3.2.1 DNA Sample Results .........................................................................................................22

3.2.2 Purebred Amstaff Results .................................................................................................25

3.2.3 Amstaff Mixed-Breeds Results ........................................................................................26

3.3 Microsatellite Genotyping....................................................................................................26

4. Discussion....................................................................................................................................28

4.1 Results from the DNA Test ..................................................................................................28

4.2 Use of Wisdom Panel in Denmark ......................................................................................31

5. Conclusion...................................................................................................................................33

6. Limitations and Future Research ..........................................................................................33

7. References ...................................................................................................................................34

8. Appendixes..................................................................................................................................38

Appendix 1....................................................................................................................................38

Appendix 2....................................................................................................................................46

Appendix 3....................................................................................................................................47

Appendix 4....................................................................................................................................55

Appendix 5....................................................................................................................................65

1. Background

1.1 The Danish Breed-Specific Legislation

After several reports of episodes with Pit Bull Terriers attacking humans in the late 1980's, the Danish

Ministry of Justice passed in 1991 a breed-specific legislation prohibiting the two dog breeds Pit Bull

Terrier and Tosa Inu, along the same lines as seen in United Kingdom at that time (Parliament of the

United Kingdom, 1991; Betænkning om farlige hunde, 2010). However, the implementation of the

breed-specific legislation did not stop the discussion about dangerous dogs in Denmark as an increase

in acquiring dogs from legal breeds with some of the same characteristics as the Pit Bull Terriers was

seen in the following years (Betænkning om farlige hunde, 2010). In 2009, the Danish Kennel Club

estimated that there were around 20,000 dogs in Denmark, which could be referred to as muscle or

fighting dogs. A committee was set to investigate the need for additions to the law from 1991

regarding dangerous dogs (Betænkning om farlige hunde, 2010). In June 2010, the Danish

Government introduced a new breed-specific legislation (§1a and §1b in the Danish Dogs Act

“Bekendtgørelse af lov om hunde”)

prohibiting an additional 11 dog breeds giving a total of 13

prohibited dog breeds and mixed-breed dogs where one or more of these breeds were included. These

dogs were all classified as "dangerous dogs" (Bekendtgørelse af lov om hunde, 2017). The American

Staffordshire Terrier (Amstaff) was one of the prohibited breeds and was in 2009, with 6,769

registrations in the Danish Dog Register, by far the most popular breed of the 13 prohibited breeds

(Betænkning om farlige hunde, 2010).

The breed-specific legislation relies on reversed burden of proof (Bekendtgørelse af lov om hunde,

2017). This means that when the police suspect a dog to be of one of the illegal dog breeds or a mixed -

breed including at least one of these breeds, based on its phenotypical appearance, it is the dog owner's

responsibility to present evidence that their dog is of a legal breed. Currently, the ways to prove a

dog's origin are through trustworthy pedigrees, statements from breeders or a paternity test that proves

a dog to be offspring from parents of legal breeds. According to the breed-specific legislation it is not

possible to prove a dog's breed from the phenotypic appearance or behavior of the dog. At present, it

is not even possible in Denmark to identify a dog's breed from a DNA sample, which makes it diffic ult

for dog owners of dogs without a studbook to provide sufficient documentation proving that the dog

consists of legal breeds (Vejledning om hundelovens forbudsordning, 2016). According to the Danish

Dog Registry Denmark has approximately 580,000 registered dogs (personal communication, Dansk

Hunderegister 2017). Of these, 18% are registered as mixed-breeds and 82% are registered as

purebreds. The purebreds can be further divided into two groups: 33% registered as purebred dogs

with a pedigree in Danish Kennel Club and 49% registered as purebreds with only verification of

breed by owner and vet and no pedigree (Proschowsky, 2017). In the Danish breed-specific legislatio n

the definition of a cross- or a mixed-breed dog is not specified and there is no percentage limit of how

much of an illegal dog breed is allowed to be present before a dog is included by this law

(Bekendtgørelse af lov om hunde, 2017).

If the dog owner fails to prove the dog's legality, euthanasia of the dog can be demanded by the police

(Bekendtgørelse af lov om hunde, 2017). Dog owners can appeal the decision and one of the most

recent cases concerning illegal dogs in Denmark were brought to the Supreme Court in October 2017

as a matter of principle. The case concerned two dogs who in 2014 were suspected to be of the breed

Amstaff or a mixed-breed including this breed and were placed in a shelter for three years while the

case was being processed. Based on visual assessment by the police and a veterinarian and the fact

that the owners could not prove the dogs' descent, the Supreme Court upheld the decision from the

High Court to euthanize the dogs (Højesteret 2017; DR, Emil Søndergård Ingvorsen, 2017).

A recently published record from the Danish Ministry of Environment and Food shows that in the

period from June 2010, when the law was passed, to August 2017, 552 dogs have been euthanized

due to the Danish breed-specific legislation. This number only includes the cases that have been

reported to the Danish National Police (Miljø-og Fødevareministeriet, 2017). A report from a

committee formed by the former Danish Ministry of Food, Agriculture and Fisheries shows that the

majority of these dogs were suspected of being an Amstaff or a mixed-breed including this breed

(Udvalget for Fødevarer Landbrug og Fiskeri, 2013).

1.2 Visual Breed Detection

According to the legislation a dog may be suspected of being illegal based on its phenotypic

appearance and the police is not obligated to obtain a secondary opinion (Vejledning om hundelo ve ns

forbudsordning, 2016). This practice is problematic because studies show that visual identification of

a dog's breeds in mixed-breed dogs is difficult: when people working with dogs, e.g. in shelters, were

asked to decide which breeds a mixed-breed dog consisted of, there was great discrepancy between

the visual identification and results from DNA testing, which was used as control (Voith

et al.,

2009,

2013). In a study by Voith et. al (2013), for 14 of the 20 mixed-breed dogs investigated, fewer than

50% of the respondents identified the breeds of the dogs that were found by DNA identification. The

study also revealed the level of inter-observer reliability as very poor, as for only seven of the 20 dogs

more than 50% of the respondents agreed on the most predominant breed of a mixed-breed dog. A

study by Olson et al. (2015) concerning Pit Bull-type dogs is consistent with the poor level of inter-

observer reliability and illustrates that reliable inclusion or exclusion of dogs as Pit Bull-type dogs

are not possible. It is also demonstrated in their study how one in five mixed-breed dogs containing

Pit Bull-type breeds (American Staffordshire Terrier and Staffordshire Bull Terrier) were not labeled

as such; and one in three mixed-breed dogs lacking any of these breeds were labeled as a Pit Bull-

type by the participants. The overall mean sensitivity and mean specificity of visual identification of

Pit Bull-type dogs were 50% and 83% respectively (Olson

et al.,

2015).

1.3 History of Dog Breed Formation

The breed-specific legislation prohibits 13 individual dog breeds which is possible because of the fact

that today’s population of dogs is divided into well-defined

subpopulations called breeds, which are

possible to distinguish from each other.

The present population of domesticated dogs stems from a common ancestor, the grey wolf, and no

other canid species have contributed to the genetic makeup. The domestication and co-living with

humans began over 15,000 years ago, however, many details in the dog's geographical origin,

evolution, history and domestication remain unclear (Ostrander

et al.,

2017). It was not until nearly

two centuries ago that the majority of dog breeds, as we know them today, were established. In the

middle of the nineteenths century a new tendency was seen. People started to control dog breeding

with the purpose to improve their animals. This new interest was combined with a sporting element

in dog shows and field trials, where dog owners were rewarded for their work. In the beginning, dogs

competed in both dog shows and field trials but later these activities became more specialized and

most dogs were bred for the purpose of joining only one of the competitions. These specialized dogs

became the first purebreds and they all had a documented pedigree stating their ancestors. Pedigrees

or studbooks were established by including particularly good representative dogs of each breed, and

after choosing these original animals, the studbooks were closed. After closure of the studbooks, only

offspring from these chosen dogs were regarded as purebreds. To avoid conflicts regarding which

dogs were accepted as purebreds and which were not, kennel clubs like American Kennel Club, The

Kennel Club and Danish Kennel Club were in the late 1800's established to manage this (Sandøe,

Corr and Palmer, 2016; The Kennel Club, 2017b; American Kennel Club, 2018b; Dansk Kennel

Klub, 2018). The controlled selection by man has led to the development of closed intraspec ies

groups, where each dog breed represents an isolated breeding population with relatively unifor m

physical characteristics defining each breed (Irion

et al.,

2003; Parker, Shearin and Ostrander, 2010).

The first kennel club, The Kennel Club, recognized 40 breeds (Sandøe, Corr and Palmer, 2016). At

present, 344 different dog breeds are recognized by the Fédération

Cynologique Internationale (FCI),

who organizes kennel clubs worldwide (Fédération Cynologique Internationale, 2018b).

However,

the overall number of breeds is in reality higher, as different breeds are accepted by different kennel

clubs. Most modern dog breeds are a closed population and breed membership requires that both

parents are registered members of the same breed before mating (Dansk Kennel Klub, 2017).

FCI classifies dog breeds in ten different groups

(Fédération Cynologique Internationale, 2018a).

The Danish Kennel Club is a member of FCI and organizes dogs after FCI's internatio na l

classification system. The American Kennel Club and The Kennel Club are not members of FCI, and

upholds their own systems when it comes to classification

(The Kennel Club, 2017a; America n

Kennel Club, 2018a).

1.4 History of American Staffordshire Terrier

As earlier described, the Amstaff was the most popular of the 13 prohibited dog breeds in Denmark

(Betænkning om farlige hunde, 2010). The history of the American Staffordshire Terrier, often called

Amstaff, exists in slightly different versions, but there is great agreement on the fact that the Amstaff

has a British ancestor in a dog type bred by crossing the Bulldog, which until the mid-19

century

was primarily used for the purpose of acting in staged fights with bull or bear, with the White Englis h

Terrier or the Black-and-Tan Terrier, or any other game terrier. This new dog type was bred to

1: sheepdogs and cattledogs 2: pinscher and schnauzer

–

molossoids, swiss mountain and cattledog 3: terriers 4:

dachshunds 5: spitz and primitive types 6: scent hounds and related breeds 7: pointing dogs 8: retrievers, flushing dogs

and water dogs 9: companion and toy dogs 10: sighthounds.

American Kennel Club: Sporting group, hound group, working group, terrier group, toy group, non -sporting group,

herding group, miscellanous class, and foundation stock service.

The Kennel Club: Gundog, hound, pastoral, terrier, toy, utility and working.

combine the spirit and agility from the terrier and courage and tenacity from the bulldog for the

purpose of dog fighting. These types of dogs were in the beginning called Half and Half, Bull-a nd-

Terrier, Pit Dog or Pit Bullterrier. When brought to the United States of America around 1870 by

immigrants from United Kingdom, they were known as Pit Dogs, Pit Bull Terriers, American Bull

Terriers or Yankee Terriers. After being imported to the United States (U.S.) the breed developed

into a heavier type of dog and was adjusted to general farm work, to hunt wild animals, to guard the

farm and for general companionship. In 1936, the dog type was registered in American

Kennel Club’s

studbook as its own breed, called Staffordshire Terrier. In 1972, the name was changed to American

Staffordshire Terrier to distinguish these dogs from the British version of the Staffordshire Terrier

now called Staffordshire Bull Terrier which had recently been recognized by the American Kennel

Club (American Kennel Club, 2018c). Currently, the Amstaff is recognized by American Kennel

Club but not by The Kennel Club in United Kingdom.

In the late 1980’s the Amstaff came to

Scandinavia and in 1990 the first Swedish Amstaff litter was born (Svenska Amstaffklubben, 2018).

The Amstaff became a popular dog in Denmark where the media drew special attention to the uptake

of Amstaffs among a special segment of unexperienced owners, who used the dog as a part of their

image; as a tool of power and as a "weapon" to frighten the public (Nyhedsavisen, Rene Fredensborg,

2007; Politikken, Morten Sørensen, 2009; Information, Lærke Cramon, 2017). It should be

underlined that it is not known how many of the former Amstaff owners in Denmark fitted this

stereotype view and how many were caring owners of Amstaffs as a family dog.

Today, the Amstaff is illegal in Denmark and Norway but not in Sweden where they are found in

relatively great numbers, as 8,650 dogs were registered as Amstaff in 2017 (Forskrift om hunder,

2004; Bekendtgørelse af lov om hunde, 2017; Jordbruksverket, 2017).

1.5 Dog Breed Genetics

If dog breeds are to be distinguished on another basis than their phenotypical appearance, the

underlying genetic structure must be studied. The present population of dogs express long range

linkage disequilibrium (LD), long haplotype-blocks and great homozygosity within breeds in contrast

to the great phenotypic diversity seen between breeds (Parker

et al.,

2004; Sutter

et al.,

2004;

Lindblad-Toh

et al.,

2005; Dreger

et al.,

2016). This is the result of intense breeding, closing of

subpopulations and several bottlenecks throughout the dog's history. The first bottleneck came with

the divergence from the wolf. Another at the breed formation, which introduced breed-specific

bottlenecks due to closing the populations, popular sires and restricted breeding, which caused a

decreased geneflow between breeds and an increase in the level of inbreeding. More recent events,

such as the two World Wars, have left few founding animals in several breeds e.g. the Leonberger

and the Cavalier King Charles and have contributed to new bottlenecks. This further limited the

genetic pool (Ostrander and Kruglyak, 2000; Lindblad-Toh

et al.,

2005; Dreger

et al.,

2016). It has

been suggested that only a 5% reduction in the genetic diversity was seen due to domestication, while

a 35% loss of diversity occurred due to breed formation (Gray

et al.,

2009).

1.5.1 Microsatellites

Because of the unique population structure and close interaction with humans, the dog has been used

widely in genetic studies over the years (Ostrander and Kruglyak, 2000; Parker, 2012). Some of the

previous analyses of the dog's genome were based on microsatellite markers that were used to

differentiate breeds and to look at the canine genetic make-up. Microsatellites are repeated sequences

of 1-6 base pairs (bp) and are also known as short tandem repeats or simple sequence repeats.

Several studies have examined the variation of microsatellites within and between dog breeds

(Fredholm and Winterø, 1995; Koskinen and Bredbacka, 2000; Irion

et al.,

2003). Microsatellite loci

vary in a population because of different length of the repeated sequence in a given allele. The length

depends on the number of repeats (Zajc

et al.,

1994). Microsatellites are highly polymorphic, and this

is demonstrated by the fact that different loci in different breeds have been analyzed finding wide

variations in allele size. Breed specific alleles exist, but most of all, the difference in breeds is caused

by different allele frequencies and allele distribution, and not in the allele length at a specific locus

(Fredholm and Winterø, 1995; Koskinen and Bredbacka, 2000). There is a relative high level of allele

heterozygosity between breeds, but the degree differs within the individual microsatellite. A lower

degree of heterozygosity within breeds can be ascribed to a limited gene pool and non-random

mating. Heterozygosity decreases concurrently with decrease in population size within a breed

(Fredholm and Winterø, 1995; Irion

et al.,

2003). In 2004, Parker et al. demonstrated that a genetic

difference exists between dog breeds and that dogs can correctly be assigned to their individual breed

based on their genotype using microsatellites. In this study, 414 dogs representing 85 different breeds

were genotyped with 96 microsatellite loci revealing a genetic difference between breeds. More than

one quarter (27%) of the genetic variation in a dog is the result of variation between breeds rather

than variation between individual dogs in contrast to a 5-10% of variation observed between human

populations (Parker

et al.,

2004).

In Denmark, one way to prove whether a dog is legal is through parentage testing. This is only

possible if DNA from both parents is available (Vejledning om hundelovens forbudsordning, 2016).

Paternity testing is based on microsatellite sequences, which are used because of their highly

polymorphic nature and the fact that they show Mendelian codominant heritage. Microsatellites can

be easily read with multiplexing Polymerase Chain Reaction (PCR) and the amplified PCR products

pooled for electrophoresis. This makes microsatellites an efficient parentage testing assay (Zajc

al.,

1994; Koskinen and Bredbacka, 1999).

With the canine genome characterized partly in 2003 and fully in 2005, more genetic information has

become available. Kirkness et al. (2003) established a partial reference genome by sequencing

the canine genome to a sequence depth of 1.5X sequence coverage (Kirkness

et al.,

2003). In 2005,

Lindblad-Toh et al. (2005) succeeded with a full characterization of the canine genome by

compiling data from the partially sequenced

genome from 2003 with

their

own sequence

information of a 7.5X sequence coverage of a female boxer's genome. As an increasing number of

sequence information became available

new genotyping tools based on single

nucleotide

polymorphism (SNP) have been established. Since a large number of SNPs can be genotyped together

using SNP-chip this methodology has now to a large extend replaced microsatellites as a research and

practical tool (Vaysse

et al.,

2011).

1.5.2 Single Nucleotide Polymorphism (SNP)

A SNP-marker is a change in a single bp in a DNA sequence at a unique locus in the genome. SNP's

are thereby responsible for some of the genetic variation existing among individuals. SNPs represent

a unique genomic pattern for each dog breed and the SNP allele frequency differs between breeds

(Mars Veterinary, 2007).

Several studies have worked with identification of canine SNPs and the establishment of a canine

marker library to be used in canine mapping projects. When Lindblad-Toh et al. in 2005 sequenced

the entire genome of a female boxer the study also reported an initial compilation of SNP markers

covering the population of dogs. A comprehensive set of SNP markers (2.5 million in total) were

identified by comparing

the boxer’s genome to the previously sequenced poodle genome,

to nine

diverse dog breeds, to four grey wolves and to one coyote (Lindblad-Toh

et al.,

2005). Since this

original SNP map contained gaps, further development of the SNP markers has been done by targeted

resequencing in order to ensure that the entire dog genome is covered. The combined efforts to

identify SNP markers have let to the establishment of the CanineHD SNP array panel comprising a

total of 170,000 SNPs (Vaysse

et al.,

2011). The use of SNP chip in canine genetics is now widely

known. In 2016 Dreger et al., used the CanineHD SNP array to evaluate genomic breed-specific

homozygosity in 800 purebred dogs representing 80 different breeds. By comparing shared (between

individuals of a breed) and individual homozygous regions in ten dogs from each breed, it was

demonstrated that each dog breed has a unique profile of genome diversity caused by varying numbers

and sizes of homozygous regions (Dreger

et al.,

2016).

SNPs can be used in genetic studies because of their high density across the genome, their high

polymorphism and the fact that they are evenly distributed across the genome. By comparing the

genotypes of ten different breeds, a SNP-rate at one SNP pr. 900 bp were found to be reflecting

of the polymorphism and variation among breeds. Reduced polymorphism was seen within breeds

and was reflected by a SNP-rate at one SNP pr. 1600 bp. SNP genotyping has confirmed that dog

genomes within breeds consist of large LD blocks and that homozygous regions extend over large

regions (Lindblad-Toh

et al.,

2005). This reflects the limited haplotype diversity seen in dog breeds.

Long-range haplotypes are typical for most dog breeds, but the exact haplotypes vary between breeds

and the location of homozygosity differs between individual dogs (Lindblad-Toh

et al.,

2005; Dreger

et al.,

2016). Haplotype frequencies differ between breeds and only 2-4 haplotypes accounts for a

frequency of 80% of the chromosomes within each breed, thereby causing homozygosity (Sutter

al.,

2004; Lindblad-Toh

et al.,

2005).

1.6 Wisdom Panel

By using the presence of breed specific genetic profiles and SNP markers, several breed-detector

DNA tests have been developed. One of these products is Wisdom Panel developed by Wisdom

Health, a business unit of Mars Petcare which is a part of Mars Incorporated (Wisdom Panel, 2017c).

Wisdom Panel is a commercial, patented product and the first edition, Wisdom Panel MX, was

presented in 2007. By analyzing DNA extracted from a blood sample, Wisdom Panel MX was able

to identify the different breeds combined in a specific dog's recent ancestry - mixed or purebred - to

the great-grandparent levels. The first Wisdom Panel consisted of more than 300 SNP markers

selected after analyzing 4,608 SNPs out of the total 2.5+ million existing SNP markers. The test made

use of breed specific SNP allele frequencies to discriminate between different breeds. By analyzing

the genome and comparing hundreds of SNPs across the chromosomes, the test was able to find

various breed signatures and define the breed background in the dog being tested (Mars Veterinar y,

2007).

Wisdom Panel has been improved over the last ten years and the latest version of the product is called

Wisdom Panel 4.0. This is a cheek swab-based DNA test and the genotyping is now conducted on a

canine Illumina® Infinium® chip consisting of 1,800 SNP markers created specifically for the test.

Wisdom Panel 4.0. consists of a computer algorithm and a database containing more than 12,000

DNA samples covering over 250 different breeds, types and varieties (including all American Kennel

Club recognized breeds). Based on the results received from examining DNA samples with the 1,800

SNP-markers, the algorithm finds over 18,000,000 different combinations of ancestry trees and gives

each of them a score based on how well they match the specific dog's data. The pedigree tree with the

best score is considered the best possible match and illustrates the dog's ancestry up to three

generations (Wisdom Panel, 2017f, 2018a). The SNPs used in the genotyping are not chosen to cover

the genes responsible for the breed specific traits, as many of the markers are found in the part of the

genome that does not link to a phenotypic trait. Therefore, the pedigree tree result of a mixed-breed

dog could show ancestors where only a very few evident traits are inherited (Wisdom Panel, 2018c).

The database is based on DNA samples mostly from American dogs but dogs from United Kingdom,

Canada, Australia and Germany have also been included during the recent years and therefore, the

test is useable in these countries. According to Wisdom Health, differences in the genetic breed

signature across geographical areas have been found during the development of Wisdom Panel, and

the use of the test on Scandinavian dogs can therefore be questionable (Wisdom Panel, 2017a).

In 2007, when the first panel (Wisdom Panel MX) was developed, the company promised an accuracy

of 84% (Mars Veterinary, 2007). At the present moment, it is not possible to find exact data indicating

how accurate the DNA test is, as this depends on the quality of the DNA samples. However, to

maintain a high quality, Wisdom Health ensures that tests are run in an USDA-accredited laboratory

(quality controlled), that repeated tests of a dog's data are run and that independent third parties review

the test (Wisdom Panel, 2017d).

1.7 Genetic Differences Between American and European Dog Populations

The differences in the genetic breed signature between American and European dog breed populatio ns

found by Wisdom Health have also been demonstrated in a study by Quignon et al. (2007) who

showed how the Golden Retriever shared 70.1% of its haplotypes between the breed populations in

U.S. and Europe. This displays a higher diversity in the Golden Retriever compared to the other

breeds included in the study, such as the Bernese Mountain Dog who shared 76.2 % of its haplotypes

between the populations in U.S. and Europe. At the same time, the Golden Retriever shows a higher

number of total haplotype blocks compared to the Bernese Mountain Dog, Rottweiler and Flat-coated

Retriever. This correlates well with the popularity and size of the Golden Retriever populatio n

(Quignon

et al.,

2007).

A recent study has shown that when importing a dog breed to a new country, genetic differences

between the breed in its original country and in the new country, can occur (Parker

et al.,

2017). This

was seen in the Cane Corso, a breed of Italian origin. When analyzing haplotypes in the Cane Corso

the U.S. population significantly shared haplotypes with the Rottweiler and the Mastiff. This was not

seen in the Italian population. The study also implies that when a breed is introduced to a new country

the genetic pool is decreased compared to the origin population. This contributes to a possible genetic

difference between breeds in different geographical regions (Parker

et al.,

2017).

1.8 Study Purpose

This project was established in light of the ban of the so called dangerous dog breeds which is a

legislation that presently relies on the reversed burden of proof using visual judgment of phenotypes.

The aim of the present study was to establish if a DNA test can be used in Denmark for identificatio n

of American Staffordshire Terrier (Amstaff) and mixed-breed dogs containing Amstaff.

2. Materials and Methods

2.1 Study Design

The study was designed to establish if a DNA test, in this study Wisdom Panel 4.0, could be used to

identify the genetic profile of Amstaffs sampled in Sweden. To validate the use of the test in Denmark,

samples from other dog breeds were analyzed as well.

2.1.1 Animal Material

The DNA material used for this study consists of purified DNA from 192 Danish dogs distributed on

174 dogs representing 58 different specific breeds and 18 samples from Danish mixed-breed dogs.

Furthermore, purified DNA material from six American Staffordshire Terriers born and raised in the

United States of America and DNA samples from 20 American Staffordshire Terriers born and raised

in Sweden, were included. See appendix 1 for a complete list of samples.

2.1.2 Sample Collection

DNA samples from the 192 Danish dogs were selected from a Biobank established at Section of

Animal Genetics, Bioinformatics and Breeding, Department of Veterinary and Animal Sciences at

the University of Copenhagen. Selection of the specific DNA samples was a result of dog breeds

available in the Biobank and an estimation of dog breeds that would be informative for the sake of

establishing info on Amstaffs and mixed-breeds. The final list included samples from dog breeds with

phenotypic similarities to the Amstaff (e.g. Mastiff, Rottweiler, Staffordshire Bullterrier), worldwide

popular dog breeds (e.g. Labrador Retriever, Golden Retriever, German Shepherd), dog breeds with

origin in Denmark (e.g. Broholmer, Danish-Swedish Farmdog, Old Danish Pointing Dog), randomly

selected breeds from the Biobank (e.g. Saluki, Xoloitzc uintli, Wippet) and some samples registered

as mixed-breeds. Two of the Biobank samples represents DNA from Danish Amstaffs. Eight of the

mixed-breed samples derived from the same litter of puppies, which had been confiscated by the

Danish police under the suspicion of being illegal regarding the breed-specific legislation.

DNA material from the six American Amstaffs was kindly provided by Professor Kerstin Lindblad -

Toh, Broad Institute, Harvard, United States of America.

DNA material from the 20 Swedish purebred Amstaffs was collected in November 2017. Since

Sweden does not have a breed-specific legislation and the Amstaff is a common breed in Swedish

households, it was ideal to collect samples in our neighboring country. Because of the small

geographic distance between Denmark and Sweden, the population of Swedish Amstaffs is a good

representative for the Danish population of Amstaffs. The animals were recruited via the Swedish

Kennel Club. DNA from the Swedish dogs was obtained by buccal swabs. Two swabs per dog were

collected with Wisdom Panel 4.0 Canine DNA Test Kit and one swab per dog was collected with a

gyno brush to use in the laboratory at Section of Animal Genetics, Bioinformatics and Breeding,

Department of Veterinary and Animal Sciences at the University of Copenhagen. The dogs did not

eat food or shared toys or water bowls with any other dog an hour before sample collection as this

could disturb the test results.

2.1.3 DNA Extraction

DNA from the 20 Swedish Amstaffs was extracted and purified from gyno brushes using the Promega

Kit with a protocol for DNA extraction from the Section of Animal Genetics, Bioinformatics and

Breeding, Department of Veterinary and Animal Sciences at the University of Copenhagen.

See appendix 2.

2.2 DNA Analysis

2.2.1 Microsatellite Genotyping

The raw data from the Wisdom Panel analyses were inaccessible for this study. Therefore, a

microsatellite genotyping of the DNA samples from the Swedish and American Amstaffs were

conducted to compare the genetic profile of the two populations. PCR-analysis was run with the

extracted DNA from the 20 Swedish and six American Amstaffs and a microsatellite assay (Canine

Genotypes

T M

Panel 1.1). The microsatellite assay is used at present for parentage testing at the

Department of Veterinary and Animal Sciences at the University of Copenhagen and is approved and

standardized by International Society for Animal Genetics (ISAG). The assay encompasses 19

different loci. The PCR product was visualized with electrophoresis using ABI PRISM 3130 XL

Genetic Analyzer and the results were read with Genemapper version 3.7.

2.2.2 DNA Test

DNA material from the 192 Danish dogs, the six American dogs and the 20 Swedish dogs were sent

to Wisdom Health. Here the DNA genotyping was conducted on a canine Illumina® Infinium® chip

and analyzed by the patented method, Wisdom Panel 4.0. For further description of the test, see

section "Wisdom Panel" in the background section.

3. Results

3.1 Wisdom Panel Reports

The results from Wisdom Panel were received as individual sample reports on email. For each dog

the report contains sections named: ancestry, ancestry tree, breed tests (for purebreds), breed

description and adult weight. For an example of a purebred and a mixed-breed report see appendix 3

and 4 respectively.

In the ancestry section, a calculated percentage of the most likely breeds in the specific dog is shown.

Figure 1 shows three illustrative examples of different ancestries.

Figure 1: Examples from the Wisdom Panel reports, showing the calculated percentage of breeds

involved in a dogs ancestry. A) illustrates the reults from a purebred Amstaff. B) illustrates the results

from a mixed-breed containing Amstaff. C) illstrates a mixed-breed dog containing DNA from breeds

not reprensented above 12.5% of the total DNA. These breeds are gatherd in a ”mixed

-breed

group”.

Note: reprinted from Wisdom Panel reports.

The lowest possible breed percentage to detect for a single specific breed is 12.5%. If the dog's DNA

consists of breeds not represented above 12.5% in the total DNA the test cannot detect those specific

breeds. Instead these percentages are gathered in a "mixed-breed group" with information on which

groups (Asian, companion, guard, herding, hound, Middle East and African, mountain dogs,

sighthound, sporting, terrier or wild canids) the DNA is most similar to. An example of this is seen

in figure 1, C.

Besides the calculated percentages of breeds in the specific dog, Wisdom Panel illustrates the dog's

most likely ancestry tree. For an example see appendix 3 or 4, page 49 and 57. Currently, the test

does not identify who the maternal and paternal ancestors are.

If the result of a dog turns out to be a purebred dog or an F1 mix of two breeds, the panel performs

several breed tests to see how consistent the sample is to the suggested breed. In the Single Breed

PCA Test and the All Breed PCA Test, Wisdom Panel uses Principal Component Analysis (PCA) to

illustrate how well the dog's DNA sample is consistent with other samples from the same breed and

to a single representative sample from every other breed in the Wisdom Panel database. A PCA is a

statistical method that reduces the numbers of variables in a dataset. It is an analysis that emphasizes

variations and illustrates strong patterns of relatedness in a dataset. Samples from the same breed or

the same subpopulation of a breed are expected to be closer together compared to other breeds and

this tends to create a cluster. If a sample falls within such a cluster, the dog is most likely a purebred

of the specific breed. PCA can be used to visualize genetic variation and relatedness in a populatio n

analysis.

Another way to compare the sample to the breed profile in the database is with a homozygos ity

profile. This profile shows to what percent a sample’s genetic markers are identical and compares

this to the breed specific range of homozygosity score found in the Wisdom Panel database.

All of these breed tests are carried out to secure the highest accuracy when deciding a dog's breed and

each analysis is performed individually.

3.2 Wisdom Panel Results

3.2.1 DNA Sample Results

The breed results from Wisdom Panel for each DNA sample appeared in the individual reports and a

complete list of the results are registered in appendix 1.

Out of a total number of 218 samples sent to Wisdom Panel only the three samples KP70, KP151,

KP153 were unable to be successfully processed (for abbreviations see appendix 1). Regarding KP70,

failure was due to not enough high-quality DNA to meet the minimum standards for analysis. The

reason for failure for KP151 and KP153 is unknown. Two samples, KP47 and KP74, were lost during

transportation and sample reports were never received.

The results of the ancestry reports from eleven dogs (KP99, KP106, KP107, KP115, KP118, KP121,

KP130, KP132, KP134, KP166, KP167) did not match the breed the samples were registered as in

the Biobank. Most of these dogs were reported to be mixed breeds and going back to the informatio n

that was registered on these dogs in the Biobank, it turned out that none of them are pedigreed dogs,

and that insufficient information had been provided on the ancestry. Thus, they should in fact have

been registered as unknown. Because KP106, KP107, KP121, KP166 and KP167 are unknown

breeds, Cavapoo, Large Münsterlander and Xoloitzcuintli are no longer represented in the samples

and the total number of breeds sent to Wisdom Panel are 55.

The results from three of the six American Amstaffs (KP87, KP88, KP89) were reported as mixed-

breeds after being analyzed by Wisdom Panel. Discussing this with Professor Kerstin Lindberg- To h,

who provided the DNA, it could not be ruled out that they were actually mixed-breeds.

In some breeds, different standards of the breed exist e.g. the Poodle, which is represented in a

miniature, a toy and a standard version. In the samples sent to Wisdom Panel it is not distinguis hed

which standard of the breed the sample represented, and the results were therefore reported as the

overall right breed but sometimes with more specific information on the standard. This is seen in the

samples representing the Poodle (KP113, KP114), the Bull Terrier (KP103, KP104) and the

Dachshund (KP116, KP117). Also, the Belgian Sheepdog covers a breed variation of four different

standards. Three samples are listed as Belgian Tervuren and one of these samples was reported back

as purebred Belgian Sheepdog (KP159) and the two other samples were reported back as a mix of

Belgian Tervuren and Belgian Sheepdog (KP160, KP161). The sample representing the Jack Russel

Terrier (KP133) was reported as a mix of Jack Russel Terrier and Parson Russel Terrier.

In a total, Wisdom Panel was able to detect 46 of the 55 represented breeds sent to analysis. These

breeds are listed in table 1.

Table 1: Breeds detected correctly by Wisdom Panel in DNA samples sent from the Biobank

Airedale Terrier

American Staffordshire Terrier

Beagle

Belgian Sheepdog

Belgian Tervuren

Bernese Mountain Dog

Boxer

Bulldog (English)

Bullmastiff

Bull Terrier

Cavalier King Charles Spaniel

Coton de Tulear

Dandie Dinmont Terrier

Dachshund

Dobermann Pinscher

Dogue de Bordeaux

English Cocker Spaniel

French Bulldog

German Shepherd Dog

German Shorthaired Pointer

Golden Retriever

Great Dane

Great Pyrenees

Greater Swiss Mountain Dog

Greyhound

Havanese

Hovawart

Irish Glen of Imaal

Irish Wolfhound

Jack Russel Terrier

Labrador Retriever

Lagotto Romagnolo

Leonberger

Maltese

Mastiff

Neapolitan Mastiff

Newfoundland

Poodle

Pug

Rottweiler

Saluki

Samoyed

Siberian Husky

Staffordshire Bull Terrier

West Highland White Terrie

Whippet

In nine out of the 55 represented breeds, Wisdom Panel was not able to detect the correct breed. These

nine breeds are listed in table 2.

Tabel 2: Breeds Wisdom Panel was unable to detect in DNA samples sent from the Biobank

Broholmer

Danish/Swedish Farmdog

Eurasier

Greenland Dog

Gross Spitz

Landseer

Old Danish Pointing Dog

Polski Owczarek Podhalanski

Scharpendos

The eight mixed-breed samples (KP58, KP59, KP60, KP101, KP102, KP171, KP185, KP186) were

reported as mixed-breeds. In all samples, multiple breeds were detected. Se appendix 1 for a complete

list of the dogs' breed composition.

3.2.2 Purebred Amstaff Results

All 20 Swedish Amstaff samples were correctly assigned to the American Staffordshire Terrier breed

by Wisdom Panel. The same was the case for the three American Amstaffs (KP85, KP86, KP90) and

the two Danish Amstaffs samples (KP91, KP92). See appendix 1.

The Single Breed PCA Test and the All Breeds PCA Test placed the samples from the Amstaffs into

three subpopulation clusters. An example from a Single Breed PCA Test is seen in figure 2. The 20

Swedish Amstaffs can be found in the light blue cluster. In this cluster the two Danish Amstaffs

(KP91, KP92) are also found. Two out of three American Amstaffs (KP85, KP86) are found in the

light purple cluster and the last one (KP90) is found in the dark purple cluster.

Figure 2: Wisdom Panel results from the Single Breed PCA test for the Swedish

Amstaff Maya, showing three different clusters in the Amstaff populatio n.

Maya is placed in the light blue cluster.

Note: reprinted from

Maya’s Wisdom Panel report.

3.2.3 Amstaff Mixed-Breeds Results

In the mixed-breed litter, confiscated by the Danish police, the ancestry results differed between the

puppies - both in ancestry percentage and in presence of breeds in the ancestry. However, all eight

samples included Amstaff. The results are listed in table 3.

Table 3: Wisdom Panel results from the mixed-breed litter confiscated by the Danish police.

Sample name of the

puppy

KP172

Breeds detected by Wisdom Panel in the samples

25% American Staffordshire Terrier, 25% American Bulldog, 12,5%

Boxer, 12,5% Cane Corso, 12,5% Golden Retriever, 12,5% Labrador

Retriever

25% American Staffordshire Terrier, 25% Cane Corso, 12,5% Boxer,

12,5% American Bulldog, 12,5% Bullmastiff, 12,5% Labrador Retriever

37,5% American Staffordshire Terrier, 25% Cane Corso, 12,5% Boxer,

12,5% American Bulldog, 12,5% Labrador Retriever

37,5% American Staffordshire Terrier, 25% Cane Corso, 12,5% American

Bulldog, 12,5% Bullmastiff, 12,5% Labrador Retriever

25% American Staffordshire Terrier, 25% American Bulldog, 25% Cane

Corso, 12,5% Labrador Retriever, 12,5% Mixed-breed Groups (sporting,

guard, terrier)

37,5% American Staffordshire Terrier, 25% American Bulldog,12,5 %

Labrador Retriever, 25% Mixed-breed Groups (guard, herding)

25% American Staffordshire Terrier, 12,5% Boxer, 12,5% American

Bulldog, 12,5% Golden Retriever, 12,5% Labrador Retriever, 25% Mixed-

breed Groups (guard, herding, sporting)

25% American Staffordshire Terrier, 25% American Bulldog, 25% Cane

Corso, 12,5% Golden Retriever, 12,5% Labrador Retriever

KP173

KP174

KP175

KP176

KP177

KP178

KP179

3.3 Microsatellite Genotyping

To compare the genetic profile of the American and Swedish populations of Amstaffs, a microsatellite

genotyping assay was conducted. The results consist of alleles found in each dog in the 19 loci. For

a complete list of the alleles see appendix 5.

When looking at the results from the microsatellite panel, some differences in the alleles present in

the American Amstaff population and the Swedish Amstaff populations are seen, as some alleles are

found in only one of the populations. We analyzed how the American samples differentiate from the

Swedish samples and not the reverse because three American dogs are not sufficient to represent the

American population of Amstaffs. The results of the genotyping show that of a total of 54 different

alleles found in the American dogs in the 19 loci of the panel, 19 alleles were not represented in the

Swedish population. The size and locus of the alleles are listed in table 4.

Two of the Swedish dogs, Santos and Bruno, did not run properly in test and therefore, the results are

not included. Also, the three American Amstaffs (KP187, KP188, KP189) which were determined as

mixed-breeds by Wisdom Panel were excluded.

The results from the loci on the sex chromosomes, Amelogenin, are not included in our analysis as it

is not relevant for this study.

Table 4: alleles found with the microsatellite analysis only in the American Amstaff population compared to the Swedish

population.

*The results from the loci on the sex chromosomes, Amelogenin, are not included in our analysis .

Locus name

AHT121

AHT137

AHTh171

AHTh260

AHTk211

AHTk253

Amelogenin*

CXX279

FH254

FH2848

INRA21

INU005

INU030

INU055

REN162C04

REN169D01

REN169O18

REN247M23

REN54P11

Allele size of alleles found only in the American dogs

102

143, 149, 151

239

250, 252

91, 95

116, 120

176

242, 244

101

130

164

222, 234

4. Discussion

4.1 Results from the DNA Test

This study reveals that a DNA test, in this study Wisdom Panel 4.0, can be used to detect purebred

and mixed-bred Amstaff in the Danish dog population.

Because Wisdom Panel is mainly based on DNA material from U.S. and dog breed populatio ns

from different geographical areas might have different genetic profiles, it was expected that the test

could have difficulties detecting all the breeds in the Danish and Swedish samples correctly. Also,

during development of the test, Wisdom Health observed that certain breeds sometimes have different

genetic breed signatures in different countries (Wisdom Panel, 2017a). Nevertheless, all samples from

Amstaffs in this study were correctly assigned to their breed, however the samples from different

geographical origins were found in different clusters in the PCA tests (see figure 2). The PCA results

and the results from the microsatellite panel assay, where some alleles in the American populatio n

are not found in the Swedish population (see table 4), might indicate a minor difference in the genetic

profile across geographical origin.

There seem to be a ‘continent’ specific DNA

profile, however this

can be overcome by Wisdom Panel 4.0.

Also, when looking at the results from the samples registered as Golden Retriever in the Biobank,

Wisdom Panel seems to overcome the genetic difference in the European and U.S. populatio n

previously described by Quignon et al. (2007). The fact that Wisdom Panel is able to determine the

Golden Retriever correctly could indicate that including DNA material from United Kingdom and

Germany in the database has increased the reliability of the breed test in the European samples, and

therefore also in the Danish samples.

To evaluate the use of Wisdom Panel to identify Amstaff in the Danish dog population, this study

also demonstrated Wisdom Panel’s accuracy in Danish samples from other dog breeds. In

the current

study Wisdom Panel was able to detect 46 out of 55 different breeds in the samples from the Biobank.

These 46 breeds are all listed on www.wisdompanel.com as detectable breeds included in the test

(Wisdom Panel, 2018b). The nine undetectable breeds are not mentioned on this list and were

therefore not expected to be detected correctly. Based on the results of this study, it is suggested that

the genetic difference between geographical distinct breed populations does not determine whether

Wisdom Panel is able to detect the correct breeds in Denmark or not. More likely, this is determined

by the fact that some breeds are not yet included in the Wisdom Panel database.

Included in the nine undetectable breeds are four dog breeds with origin in Denmark

–

Broholmer,

Danish/Swedish Farm Dog, Old Danish Pointing Dog and Greenland Dog. If these breeds and other

breeds of relevance in Denmark, such as the 13 banned dog breeds (except American Staffordshire

Terrier, Boerboel and American Bulldog, which are already recognized by Wisdom Panel), should

be included in the Wisdom Panel database, Wisdom Panel needs to be provided with DNA from a

large number of dogs of these breeds.

The results for the eight puppies from the Amstaff mixed-breed litter, revealed a difference in ancestry

between the puppies. This difference is to be expected as a result of crossover events where maternal

and paternal homologues chromosomes exchange random pieces of DNA during meiosis and every

puppy inherits a unique combination of DNA with a new assortment of genes (Hartwell

et al.,

2011).

The final genetic make-up depends on which part of the chromosomes the puppy inherits. If some of

the great-grandparents were mixed-breeds, it is possible that some of the puppies inherited DNA from

one breed involved in the ancestors and not from another breed. Since an offspring inherits different

breed-specific alleles from its ancestors the ancestor tree can be different for each puppy even though

the same ancestors are shared in real life, as seen for the Amstaff mixed-breed puppies in the current

study (Wisdom Panel, 2018c). Another reason that may result in different ancestry in a litter is the

fact that a litter of puppies can have more than one father (Wisdom Panel, 2017e). Both reasons to

different ancestry in litter mates demonstrate the importance of testing an entire litter, as one puppy's

genetic profile does not necessarily represent the rest.

Since doubts about ancestry often arise regarding mixed-breed dogs, like the litter with the eight

puppies, it would be optimal to establish Wisdom Panel's accuracy in breed determination in such

mixed-breed samples. In order to estimate this accuracy, it would have been ideal to include samples

from several mixed-breeds with known descent. We tried to recruit such dogs, but this turned out to

be very difficult within the time frame of this study since owners of mixed-breeds rarely know the

entire ancestry of their dogs. We are therefore not able to document the accuracy of Wisdom Panel

in mixed-breeds, but it seems reasonable to think that the received results regarding mixed-breeds are

reliable. This is due to the high accuracy reported in purebred dogs, demonstrated with the fact that

Wisdom Panel was able to detect 46 out of the 55 represented breeds in Danish dogs.

In dog breeds where different standards (size, color, coat etc.) are detected by Wisdom Panel, the

results might be considered incorrect when reported back as mixes of these standards. This applies

for the samples representing the Poodle (KP113, KP114), the Dachshund (KP116, KP117), the Bull

Terrier (KP103, KP104), the Belgian Tervuren (KP160, KP161) and the Jack Russel Terrier (KP133),

see appendix 1. It is not registered in the Biobank what specific standards are involved in these

samples and since some mating between the different standards is allowed it is possible that a dog's

genetic profile contains DNA from more than one standard and therefore is reported as a mix of

standards. For example the Belgian Sheepdog consists of four different types and in Denmark mating

between specific types are allowed (Belgiske Hyrdehunde, 2015). The breed registered as Belgia n

Sheepdog in Wisdom Panel is known as the Groenendael in Denmark and since mating between

Tervuren and Groenendael is allowed the results reported for KP160 and KP161 might illustrate such

mating. Regarding the Jack Russel Terrier, sample KP133 was reported as 50% Jack Russel Terrier

and 50% Parson Russel Terrier. These two breeds rise from the same ancestor and according to

Wisdom Panel, the Parson Russel Terrier is a show variant of the Jack Russel Terrier. Therefore, it is

possible that Wisdom Panel will detect some ancestral contribution from both dog types in a single

dog depending on the dog's ancestry and report it as a mix of the two breeds, even though it is

registered as only one of the breeds (Wisdom Panel, 2018d). Despite this, the sample is still correctly

assigned to the "Russel Terrier" type breed and no other breeds are involved.

It is not possible to evaluate the accuracy of the Wisdom Panel test regarding the standard

determinations, since the standards and types of the dogs in the samples are not registered in the

Biobank and the pedigrees are not available. However, the main focus of this study is Wisdom Panel' s

ability to assign a dog to the correct breed and in this case more specific information regarding the

breed is not necessary. In all the samples reported as mixed standard breeds, the correct overall breed

has been determined.

Since Wisdom Panel is a commercial product, the raw data from the analyses was not accessible to

us, and it was therefore not possible to perform a more thorough analysis of the method used by

Wisdom Panel. Therefore, the only way to estimate the accuracy and value of Wisdom Panel in

Danish dogs was to send anonymized DNA samples from purebred dogs to Wisdom Panel, where the

specific breeds were known by us, and then compare the results from Wisdom Panel to the samples'

registered breed. It would have been interesting to review which breed specific SNPs that were used,

how these were selected and how they are used to calculate the pedigrees. Wisdom Health has been

contacted several times regarding this, but it is not possible to receive the data from the analysis. This

makes it difficult to evaluate the method and the results on a scientific basis. Nonetheless, our results

based on microsatellite genotyping support the PCA results on Amstaff reported by Wisdom Panel.

4.2 Use of Wisdom Panel in Denmark

Based on our results, Wisdom Panel can be expected to detect the breed of a dog as long as the breed

is included on the list of detectable breeds at www.wisdompanel.com. The Amstaff is included on

this list and as it is seen in this study Wisdom Panel had no problems assigning the Swedish populatio n

of Amstaffs as purebred Amstaffs. Only two other dog breeds (American Bulldog and Boerboel) of

the 13 prohibited dogs in Denmark, are found on the list. Based on our results, it is reasonable to

believe that American Bulldog and Boerboel (both purebred and mixed-breeds) will be detected in

Danish dogs. The remaining ten prohibited dogs are not represented in Wisdom Panel's DNA database

and these breeds will not be detected by Wisdom Panel. This is a point of critique of the use of

Wisdom Panel as a tool regarding the breed-specific legislation. However, none of these ten breeds

were represented in great numbers in Denmark before 2010 and most of them do not share phenotypic

characteristics with the Amstaff (Betænkning om farlige hunde, 2010). As a result of this, a mixed-

breed containing these breeds will probably not be suspected as being illegal very frequently. If

considered necessary that the entire list of banned dogs must be represented in the Wisdom Panel

database, they can be included, as earlier mentioned, by submitting a sufficient amount of DNA

samples to Wisdom Health. However, this does not apply for the Pit Bull Terrier as the term

“Pit

Bull”, according to Wisdom Health, does not refer to a single recognized breed but rather to a

genetically diverse group of breeds, and it is therefore not possible to establish a breed-specific DNA

profile of the Pit Bull Terrier (Wisdom Panel, 2017b).

Today, there is no lower limit for illegal admixture allowed in a dog specified in the Danish breed-

specific legislation, which means that the legislation is currently being practiced with a limit of zero

per cent. If DNA testing should be implemented in the legislation, it would be reasonable to accept

the lowest limit possible with the available technology. Wisdom Panel's lower limit of detection of a

breed involved in a specific dog is 12.5% and therefore this limit needs to be accepted as the lower

limit of admixture of illegal breeds in a dog if DNA testing with Wisdom Panel should be

implemented in the Danish breed-specific legislation. Acceptance of this limit would make Wisdom

Panel a useful tool to document if a dog is illegal or not. If this limit is not accepted, Wisdom Panel

could still be used as documentation to rule out the presence of any illegal breeds in a dog if the result

shows a 100% admixture of legal breeds, e.g. 50% Rottweiler and 50% Boxer. It is important to

mention that Wisdom Panel does not distinguish between the maternal or paternal contribution of

genes. The ancestry tree of a dog is only illustrating the best possible match made by the algorithm

and not necessarily the true distribution of ancestors. Therefore, the results cannot be used to proceed

against the mother or father of a tested dog, as they will need to be tested individually.

Wisdom Panel could be a helpful tool in determination of breeds in a dog that is suspected to be

illegal regarding the breed-specific legislation in Denmark. This applies particularly to mixed-breed

dogs, which are present in relatively great numbers in Denmark. Since the accusation of a dog being

illegal is based on the phenotypic appearance, and since owners of mixed-breed dogs are often unable

to present a reliable pedigree, the cases are often based on the owners' word against the words of the

police, which may result in prolonged cases. By accepting Wisdom Panel as a tool to prove the

descent of a dog, the matter of dispute would rarely exist, which would improve legal rights of dog

owners and lower both economic and emotional costs. Even though the accuracy in mixed-breed

samples could not be established based on the samples in this study, the use of Wisdom Panel still

contributes to a higher accuracy in breed identification than the visual identification, which have been

proved insufficient in several studies (Voith

et al.,

2009, 2013; Olson

et al.,

2015).

DNA testing as a tool to prove that a dog is of a legal breed or mix, must be implemented in the

Danish breed-specific legislation, if Wisdom Panel is to be used in cases regarding this legislation in

Denmark. Accepting DNA testing would improve legal rights for dog owners in Denmark and by

demonstrating in the this study how Wisdom Panel can be used for breed identification in the Danish

dog population, it is now possible to use DNA testing and therefore, it seems reasonable to suggest

an implementation.

5. Conclusion

The aim of the present study was to establish if a DNA test can be used in Denmark for identificatio n

of American Staffordshire Terrier (Amstaff) and mixed-breed dogs containing Amstaff. Our study

demonstrates that a DNA test can be used in Denmark to breed identification of purebred and mixed -

bred Amstaff in this case to a limit of 12.5%. In light of the ban of the so called dangerous dogs this

can improve legal rights for dog owners compared to visual judgement of phenotypes.

6. Limitations and Future Research

The evaluation of Wisdom Panels' accuracy in breed identification in mixed-breed dogs were limited

by the fact that it was very difficult to recruit and collect samples from mixed-breed dogs with known

ancestry. To encourage the use of Wisdom Panel in mixed-breed dogs we recommend that future

research focus on stating the accuracy of Wisdom Panel in such samples. Another focus of future

research and improvement of the use of Wisdom Panel in Denmark is to extent the database of

Wisdom Panel to include DNA from dog breeds with Danish origin. As earlier mentioned, this can

be done by providing Wisdom Panel with DNA from these breeds. A collaboration between Section

of Animal Genetics, Bioinformatics and Breeding, Department of Veterinary and Animal Sciences at

the University of Copenhagen and Wisdom Health could provide such DNA material to establish

these breeds' genetic profiles in the Wisdom Panel database. The more genetic profiles of dog breeds

existing in Wisdom Panels' database, the better the test works, both in Denmark and worldwide.

This study investigated the use of Wisdom Panel as a breed-detector DNA test in Denmark. However,

several other breed-detector tests exist on the market and it would be interesting to evaluate the

accuracy and usability of these in Denmark.

Three of the six American Amstaffs turned out to be mixed-breeds and this limited the use of the

microsatellite genotyping in this study. To further investigate the geographical significance in relation

to genetic variation between two dog breed populations and to make a more adequate comparison of

the American and Swedish population of Amstaffs, more American samples would be required.

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8. Appendixes

Appendix 1

A complete list of the Biobank samples and the Swedish Amstaff samples sent to Wisdom Health and

analyzed by Wisdom Panel 4.0.

* represent samples from the Biobank where information of the registered breed turned out to be

insufficient.

represents

samples

from

American

Amstaffs

that

turned

out

mixed-breeds.

*** represents samples of breeds Wisdom Panel was not able to detect.

KP1

KP2

KP3

KP4

KP5

KP6

KP7

KP8

KP9

KP10

KP11

KP12

KP13

KP14

KP15

KP16

KP17

KP18

KP19

KP20

KP21

KP22

KP23

KP24

KP25

Breed

Staffordshire Bull Terrier

Bullmastiff

Pug

Mastiff

Pug

Mastiff

German Shepherd Dog

Labrador Retriever

Results from Wisdom Panel

100% Staffordshire Bull Terrier

100% Bullmastiff

100% Pug

100% Mastiff

100% Pug

100% Mastiff

100% German Shepherd Dog

100%German Shepherd Dog

100% German Shepherd Dog

100% Labrador Retriever

KP26

KP27

KP28

KP29

KP30

KP31

KP32

KP33

KP34

KP35

KP36

KP37

KP38

KP39

KP40

KP41

KP42

KP43

KP44

KP45

KP46

KP47

KP48

KP49

KP50

KP51

KP52

KP53

KP54

KP55

KP56

KP57

KP58

KP59

Labrador Retriever

Golden Retriever

French Bulldog

Great Dane

Belgian Sheepdog

Mixed

KP60

Mixed

100% Labrador Retriever

100% Golden Retriever

100% French Bulldog

Sample gone during transportation, no report received

100% French Bulldog

100% Great Dane

100% Belgian Sheepdog

50% Munsterlander (large), 12,5% Golden Retriever, 12,5% Chow

Chow, 12,5% Collie, 12,5% German Shepherd Dog

50% Havanese, 50% Shih Tzu

37,5% American Staffordshire Terrier, 12,5% Dobermann Pinscher,

12,5% Golden Retriever, 12,5% Bull Terrier (standard), 12,5%

German Shepherd Dog, 12,5% Mixed-breed Groups (guard,

sighthound, terrier)

KP61

KP62

Old Danish Pointing

Dog***

Old Danish Pointing

Dog***

Old Danish Pointing

Dog***

Old Danish Pointing

Dog***

Boxer

Old Danish Pointing

Dog***

Cocker Spaniel

Boxer

English Bulldog

Danish/Swedish

Farmdog***

Danish/Swedish

Farmdog***

Engelsk Bulldog

Dobermann

Rottweiler

American Staffordshire

Terrier (U.S)

American Staffordshire

Terrier (U.S)

American Staffordshire

Terrier (U.S)**

KP63

KP64

KP65

KP66

KP67

KP68

KP69

KP70

KP71

KP72

KP73

KP74

KP75

KP76

KP77

KP78

KP79

KP80

KP81

KP82

KP83

KP84

KP85

KP86

25% German Shorthaired Pointer, 25% Chihuahua, 12,5% Pointing

Griffon (Wire), 37,5% Mixed-breed Groups (sporting, hound,

terrier, herding)

12,5% Pointer, 25% German Shorthaired Pointer, 62,5% Mixed-

breed Groups (sporting, terrier)

12,5% Pointer, 12,5% German Shorthaired Pointer, 12,5%

Chihuahua, 12,5% Weimaraner, 50% Mixed-breed Groups

(sporting, herding)

25% German Shorthaired Pointer, 12,5% Keeshond, 12,5%

Pointer, 12,5% Poodle (miniature),

37,5% Mixed-breed Groups (terrier, sporting)

100% Boxer

25% English Setter, 25% Chihuahua, 25% German Shorthaired

Pointer, 12,5% Weimaraner,

12,5% Mixed-breed Groups (sporting, terrier)

100% English Cocker Spaniel

100% Boxer

Test failed due to low DNA quality

100% Bulldog (English)

12,5% Cocker Spaniel, 12,5% Fox Terrier (smooth), 12,5 % Parson

Russel Terrier, 62,5% Mixed-breed Groups (terrier, sporting)

50% Russel Terrier, 12,5% Parson Russel Terrier, 37,5% Mixed-

breed Groups (terrier, hound, sporting)

Sample gone during transportation, no report received

100% Dobermann Pinscher

100% Rottweiler

100% American Staffordshire Terrier

62,5% American Staffordshire Terrier, 12,5% Bullmastiff, 12,5%

Chow Chow, 12,5% Mixed-breed Groups (guard, sporting, Asian)

KP87

KP88

American Staffordshire

Terrier (U.S)**

American Staffordshire

Terrier (U.S)**

American Staffordshire

Terrier (U.S)

American Staffordshire

Terrier

American Staffordshire

Terrier

Beagle

Bernese Mountain Dog

KP89

KP90

KP91

KP92

KP93

KP94

KP95

KP96

KP97

25% American Staffordshire Terrier, 25% Rottweiler, 12,5% Bull

Terrier (miniature), 12,5% Bulldog (standard), 25% Mixed- breed

Groups (hound, sighthound, sporting, herding)

50% American Staffordshire Terrier, 12,5% Golden Retriever,

12,5% Rottweiler, 25% Mixed-breed Groups (guard, Asian,

companion)

100% American Staffordshire Terrier

100% Beagle

100% Bernese Mountain Dog

37,5% Newfoundland, 12,5% American Bulldog, 12,5% German

Wirehaired Pointer, 12,5% Vizsla, 12,5% White Swiss Shepherd,

12,5% Mixed-breed Groups (terrier, sporting, guard)

87,5% Havanese, 12,5% Maltese

100% Havanese

50% Labrador Retriever, 50% Bouvier des Flandres

50% Bull Terrier (Standard), 50% Bull Terrier (Miniature)

75% Bull Terrier (Standard), 25% Bull Terrier (Miniature)

100% Bull Terrier (Standard)

100% Cavalier King Charles Spaniel

50% Poodle (Miniature), 25% Poodle (Toy), 25% Mixed-breed

Groups (Companion, Terrier)

100% Cavalier King Charles Spaniel

100% Dogue de Bordeaux

100% Poodle (Toy)

62,5% Poodle (Miniature), 37,5% Poodle (Toy)

25% Dachshund (Miniature Shorthaired), 25% Dachshund

(Miniature Wirehaired), 25% Dachshund (Wirehaired), 12,5%

KP98

KP99

KP100

KP101

KP102

KP103

KP104

KP105

KP106

KP107

Broholmer

Havanese*

Havenese

Mixed

Bull Terrier

Cavapoo*

KP108 Cavalier King Charles

Spaniel

KP109 Cavalier King Charles

Spaniel

KP110 Cavalier King Charles

Spaniel

KP111 Dogue de Bordeaux

KP112 Dogue de Bordeaux

KP113 Poodle (toy)

KP114 Poodle (toy)

KP115 Daschhund*

KP116 Daschhund

KP117

KP118

KP119

KP120

Daschhund

Greyhound*

Greyhound

KP121 Large Münsterlander*

KP122 Gross Spitz***

KP123 Greenland Dog***

KP124 Greenland Dog***

KP125 Samoyed

KP126 Greater Swiss Mountain

Dog

KP127 Hovawart

KP128 Irish Glen of Imaal Terrier

KP129 Irish Glen of Imaal Terrier

KP130 Irish Wolfhound*

KP131 Irish Wolfhound

Dachshund (Miniature Longhaired), 12,5% Mixed-breed Groups

(sporting, companion, terrier)

37,5% Dachshund(Longhaired), 37,5% Dachshund (Miniature

Longhaired),

25% Dachshund (Miniature Shorthaired)

50% Dachshund (Longhaired), 37,5% Dachshund (Miniature

Longhaired), 12,5% Dachshund (Miniature Shorthaired)

100% Munsterlander (Large)

100% Greyhound

25% German Shepherd Dog, 25% Golden Retriever, 12,5% Chow

Chow, 12,5% Collie, 12,5% German Shorthaired Pointer, 12,5%

Mixed-breed Groups (herding, mountain dogs, sporting, Asian)

12,5% German Spitz, 12,5% Keeshond, 12,5% Rhodesian

Ridgeback, 62,5% Mixed-breed (herding, terrier, mountain dogs,

hound)

75% Canadian Eskimo Dog, 12,5% Alaskan Malamute,

12,5% Siberian Husky

75% Canadian Eskimo Dog, 12,5% Alaskan Malamute,

12,5% Siberian Husky

100% Samoyed

100% Greater Swiss Mountain Dog

100% Hovawart

100% Glen of Imaal Terrier

50% German Shepherd Dog, 50% Irish Wolfhound

100% Irish Wolfhound

37,5% Parson Russel Terrier, 25% Russel Terrier, 12,5% Fox

Terrier (smooth), 25% Mixed-breed Groups (terrier, sporting,

companion)

50% Parson Russel Terrier, 50% Russel Terrier

62,5% Russel Terrier, 12,5% Parson Russel Terrier,

25% Mixed-breed Groups (terrier, sporting, herding)

100% German Shorthaired Pointer

100% Lagotto Romagnolo

50% Newfoundland, 12,5% Poodle (standard), 12,5% Saint

Bernard, 25%, Mixed-breed Groups (sporting, guard, sighthound)

100% Leonberger

KP132 Jack Russel Terrier*

KP133 Jack Russel Terrier

KP134 Jack Russel Terrier*

KP135

KP136

KP137

KP138

KP139

German Shorthaired Pointer

Lagotto Romagnolo

KP140 Landseer***

KP141 Leonberger

KP142

KP143

KP144

KP145

KP146

KP147

KP148

Maltese

Neapolitan Mastiff

Newfoundland

Polski Owczarek

Podhalanski***

Polski Owczarek

Podhalanski***

Great Pyrenees

Samoyed

KP149

KP150

KP151

KP152

KP153

KP154

KP155

KP156 Scharpendos***

KP157 Scharpendos***

KP158 Scharpendos***

Belgian Tervueren

West Highland White

Terrier

KP163 West Highland White

Terrier

KP164 Whippet

KP165 Whippet

KP166 Xoloitzquintli*

KP159

KP160

KP161

KP162

100% Maltese

100% Neapolitan Mastiff

100% Newfoundland

25% Kritikos Lagonikos, 12,5% English Setter,

62,5% Mixed-breed Groups (Mountain dogs, Middle East and

African, Sporting, Asian, Herding)

12,5% Kuvasz, 12,5% Schipperke, 12,5% White Swiss

Shepherd, 62,5% Mixed-breed Goups (companion, herding)

Sample failed

100% Great Pyrenees

Sample failed

100% Samoyed

12,5% English Cocker Spaniel, 12,5% Irish Water Spaniel,

75% Mixed-breed Groups (herding, Middle East and African,

sporting, terrier)

25% Dutch Shepherd Dog, 12,5% Puli, 62,5% Mixed-breed Groups

(terrier, sporting, herding)

12,5% English Cocker Spaniel, 12,5% Parson Russel Terrier, 75%

Mixed-breed Groups (sporting, herding)

100% Belgian Sheepdog

50% Belgian Sheepdog, 50% Belgian Tervuren

75% Belgian Sheepdog, 25% Belgian Tervuren

100% West Highland White Terrier

100% Whippet

25% Chihuahua, 12,5% Boykin Spaniel, 12,5% Manchester Terrier

(Toy), 50% Mixed-breed Groups (companion, terrier, hound)

25% Chihuahua, 25% Yorkshire Terrier, 12,5% Manchester Terrier

(Toy), 37,5% Mixed-breed Groups (herding, sporting, companion,

Middle East and African)

37,5% Chow Chow, 25% Samoyed, 12,5% Keeshond, 25%

Mixed-breed (Middle East and African, guard, sporting)

62,5% Chow Chow, 12,5% Keeshond, 12,5% Korean Jindo, 12,5%

Samoyed

KP167 Xoloitzquintli*

KP168 Eurasier***

KP169 Eurasier***

KP170 Eurasier***

KP171 Mixed

KP172 Mixed puppy from police

KP173 Mixed puppy from police

KP174 Mixed puppy from police

KP175 Mixed puppy from police

KP176 Mixed puppy from police

KP177 Mixed puppy from police

KP178 Mixed puppy from police

KP179

KP180

KP181

KP182

KP183

KP184

Mixed puppy from police

Dandie Dinmont Terrier

Siberian Husky

KP185 Mixed

KP186 Mixed

KP187

KP188

KP189

KP190

KP191

KP192

KP193

KP194

Saluki

Airedal Terrier

Coton de Tulear

Saluki

50% Chow Chow, 25% Samoyed, 12,5% Keeshond, 12,5% Mixed-

breed Groups (Middle East and African, companion, sporting,

guard)

37,5% Labrador Retriever, 25% German Shepherd, 12,5% Golden

Retriever, 12,5% Rottweiler, 12,5% Samoyed

25% American Staffordshire Terrier, 25% American Bulldog,

12,5% Boxer, 12,5% Cane Corso, 12,5% Golden Retriever, 12,5%

Labrador Retriever

25% American Staffordshire Terrier, 25% Cane Corso, 12,5%

Boxer, 12,5% American Bulldog, 12,5% Bullmastiff, 12,5%

Labrador Retriever

37,5% American Staffordshire Terrier, 25% Cane Corso, 12,5%

Boxer, 12,5% American Bulldog, 12,5% Labrador Retriever

37,5% American Staffordshire Terrier, 25% Cane Corso, 12,5%

American Bulldog, 12,5% Bullmastiff, 12,5% Labrador Retriever

25% American Staffordshire Terrier, 25% American Bulldog, 25%

Cane Corso, 12,5% Labrador Retriever, 12,5% Mixed-breed Groups

(sporting, guard, terrier)

37,5% American Staffordshire Terrier, 25% American Bulldog,

12,5%Labrador Retriever,25% Mixed-breed Groups (guard,herding)

25% American Staffordshire Terrier, 12,5% Boxer, 12,5%

American Bulldog, 12,5% Golden Retriever, 12,5% Labrador

Retriever, 25% Mixed-breed Groups (guard, herding, sporting)

25% American Staffordshire Terrier, 25% American Bulldog, 25%

Cane Corso, 12,5% Golden Retriever, 12,5% Labrador Retriever

100% Dandie Dinmont Terrier

100% Siberian Husky

25% Dachshund (Miniature Wirehaired), 25% Shih Tzu, 12,5%

Dachshund (Wirehaired), 12,5% Parson Russel Terrier, 12,5%

Pekingese, 12,5% Tibetan Spaniel

37,5% Dachshund (Wirehaired), 25% Shih Tzu,

25% Tibetan Spaniel, 12,5% Lhaso Apso

100% Saluki

100% Airedal Terrier

100% Coton de Tuelar

100% Saluki

KP195 Broholmer***

KP196 Broholmer***

KP197 Broholmer***

KP198 Havanese

25% Newfoundlander, 12,5% Boxer, 12,5% German Wirehaired

Pointer, 12,5% Mastiff, 37,5% Mixed-breed Groups (sporting,

herding, companion, mountain dogs)

25% Boxer, 25% Newfoundlander, 12,5% German Shorthaired

Pointer, 12,5% German Wirehaired Pointer, 12,5% White Swiss

Shepherd, 12,5% Mixed-breed Groups (terrier, herding, mountain

dogs, sporting)

37,5% Newfoundlander, 62,5% Mixed-breed Groups (herding,

sporting,guard)

100% Havanese

Samples from the Swedish Amstaffs sent to Wisdom Health to be analyzed by Wisdom Panel 4.0:

Andy

Asko

Boss

Bruno

Ciara

Daisy

Doris

Ella

Franko

Harry

Inka

Kenny

Loke

Maya

Nea

Oscar

Zafira

Santos

Shanti

Stella

Breed

American Staffordshire Terrier

Results from Wisdom Panel

100% American Staffordshire Terrier

Appendix 2

Protocol from Section of Animal Genetics, Bioinformatics and breeding, Department of Veterinary

and Animal Sciences at University of Copenhagen for DNA extraction with Promega Kit.

Oprensning af DNA fra Swab eller Gyno brush (PROMEGA KIT)

Noter: Anvend filterspidser når der tages fra kittet. Skyl saks samt pincet med ethanol mellem hver

prøve.

1. Tænd for ryste-varmeblok på 55 °C

Overfør swab’en til et 2,0 mL rør (klip forsigtigt skaftet af swab’en

over, så røret kan lukkes)

Brug rene og klorbehandlede picetter og sakse, husk at gøre dem rene til næste gang.

Tilsæt 900 μL Cell lysis solution og inkuber i 20 min. Vortex prøverne 2-3

gange undervejs.

Tag forsigtigt swab’en op og overfør til nyt rent 2,0

mL rør

(NB! Den skal tilbage igen)

Spin v. max speed i 5 min, fjern supernantanten og kom swab’en og evt. rester af væsken

tilbage.

Tilsæt 600 μL nuclei lysis solution, 15 μL EDTA og 20 μL Proteinase K. (Tilsæt proteinase

K i stinkskabet)

7. Inkubér 3 timer ved 55°c v. 700 rpm.

Spind kort ned i mini spind og tilsæt 3 μL RNase, vortex. Inkuber v. 37°c i 15 min (Hvis der

er kommet blodprøver af forældredyrene, kan de startes her og køres parallelt)

Tag swab’en op og smid væk.

NB! Kør den op af siden så al væsken kommen ned i røret.

10.

(Stinkskab!!!) Tilsæt 200 μL Protein Precipitation solution, vortex 20 sek., stå på is i 5 min.

11. Spin v. max speed i 10 min

12. Overfør supernantanten til nyt 2,0 mL rør.

13.

Fæld med 650 μL isopropanol. Vend og ryst prøven godt (Stinkskab!!!)

14. Spin 10 min. v. max speed.

15. Fjern supernantanten til affaldsbøtte C2

16.

Vask m. 500 μL 70% EtOH, spin 5 min ved max.

17. Fjern supernantanten og lufttørre i 5 min.

18.

Genopløs i 16 μl 1xTE buffer.

19. Vortex godt, spin ned og lad stå O.N. v.16 °c på rystebordet mål derefter OD.

Appendix 3

Wisdom Panel report from a purebred dog.

Appendix 4

Wisdom Panel report from a mixed-breed dog.

Appendix 5

Complete list of alleles found by microsatellite genotyping in the Swedish and American Amstaff

samples.

Samples marked with red were not included in the analysis.

Sample Name Marker

Andy

AHT121

Asko

Boss

Bruno

Ciara

Daisy

Doris

Ella

Franko

Harry

Inka

KP85

KP86

KP87

KP88

KP89

KP90

Kenny

Loke

Maya

Nea

Oscar

Santos

Shanti

Stella

Vand

Zafira

AHT121

Allele 1 Allele 2

100

104

102

108

104

100

104

Sample Name Marker

Andy

INRA21

Asko

Boss

Bruno

Ciara

Daisy

Doris

Ella

Franko

Harry

Inka

KP85

KP86

KP87

KP88

KP89

KP90

Kenny

Loke

Maya

Nea

Oscar

Santos

Shanti

Stella

Vand

Zafira

INRA21

Allele 1

101

Allele 2

113

101

Sample Name Marker

Andy

Asko

Boss

Bruno

Ciara

Daisy

Doris

Ella

Franko

Harry

Inka

KP85

KP86

KP87

KP88

KP89

KP90

Kenny

Loke

Maya

Nea

Oscar

Santos

Shanti

Stella

Vand

Zafira

AHT137

Allele 1 Allele 2

137

147

137

147

137

143

131

151

147

137

149

147

145

137

147

149

147

137

145

147

Sample Name Marker

Andy

Asko

Boss

Bruno

Ciara

Daisy

Doris

Ella

Franko

Harry

Inka

KP85

KP86

KP87

KP88

KP89

KP90

Kenny

Loke

Maya

Nea

Oscar

Santos

Shanti

Stella

Vand

Zafira

INU005

Allele 1

132

124

110

126

124

110

118

110

124

110

124

110

124

126

124

Allele 2

124

132

130

132

126

124

132

124

132

126

132

Sample Name Marker

Andy

Asko

Boss

Bruno

Ciara

Daisy

Doris

Ella

Franko

Harry

Inka

KP85

KP86

KP87

KP88

KP89

KP90

Kenny

Loke

Maya

Nea

Oscar

Santos

Shanti

Stella

Vand

Zafira

AHTh171

Allele 1

231

225

219

215

219

233

225

221

229

231

225

219

229

225

231

225

221

233

221

225

Allele 2

233

229

233

Sample Name Marker

Andy

Asko

Boss

Bruno

Ciara

Daisy

Doris

INU030

Allele 1

150

124

150

144

150

144

150

Allele 2

229

233

235

225

Ella

Franko

Harry

Inka

KP85

KP86

KP87

KP88

KP89

150

152

239

229

233

229

225

233

KP90

Kenny

Loke

Maya

Nea

Oscar

Santos

Shanti

Stella

Vand

Zafira

150

Sample Name Marker

Andy

Asko

Boss

Bruno

Ciara

Daisy

Doris

Ella

Franko

Harry

Inka

KP85

KP86

KP87

KP88

KP89

KP90

Kenny

Loke

Maya

Nea

Oscar

Santos

Shanti

Stella

Vand

Zafira

AHTh260

Allele 1

238

246

238

246

240

238

240

246

238

250

246

240

238

246

238

240

Allele 2

240

246

240

Sample Name Marker

Andy

Asko

Boss

Bruno

Ciara

Daisy

Doris

Ella

INU055

Allele 1

210

218

210

218

210

218

210

218

210

214

210

214

218

210

218

214

Allele 2

218

214

246

248

246

252

250

246

Franko

Harry

Inka

KP85

KP86

KP87

KP88

KP89

KP90

214

212

218

220

246

250

246

Kenny

Loke

Maya

Nea

Oscar

Santos

Shanti

Stella

Vand

Zafira

Sample Name Marker

Andy

Asko

Boss

Bruno

Ciara

Daisy

Doris

Ella

Franko

Harry

Inka

KP85

KP86

KP87

KP88

KP89

KP90

Kenny

Loke

Maya

Nea

Oscar

Santos

Shanti

Stella

Vand

Zafira

AHTk211

Allele 1

Allele 2

Sample Name Marker

Andy

Asko

Boss

Bruno

REN162C04

Allele 1

202

200

202

200

202

200

202

206

202

Allele 2

206

208

206

Ciara

Daisy

Doris

Ella

Franko

Harry

Inka

KP85

KP86

KP87

KP88

KP89

KP90

Kenny

Loke

Maya

Nea

Oscar

Santos

Shanti

Stella

Vand

Zafira

208

206

202

206

208

206

208

206

208

Sample Name Marker

Asko

Boss

Bruno

Ciara

Daisy

Doris

Ella

Franko

Harry

Inka

KP85

KP86

KP87

KP88

KP89

KP90

Kenny

Loke

Maya

Nea

Oscar

Santos

Shanti

Stella

Vand

Zafira

AHTk253

Allele 1

286

288

292

286

292

286

288

292

288

286

Allele 2

288

Sample Name Marker

Asko

Boss

Bruno

REN169D01

Allele 1

212

210

212

210

212

214

210

212

218

212

210

216

Allele 2

216

218

212

216

212

216

212

216

212

216

218

216

218

216

218

216

292

Ciara

Daisy

Doris

Ella

292

Franko

Harry

Inka

KP85

292

KP86

KP87

KP88

KP89

292

KP90

Kenny

Loke

Maya

Nea

Oscar

Santos

288

292

Shanti

Stella

Vand

Zafira

Sample Name Marker

Andy

Asko

Boss

Bruno

Ciara

Daisy

Doris

Ella

Franko

Harry

Inka

KP85

KP86

KP87

KP88

KP89

KP90

Kenny

Loke

Maya

Nea

Oscar

Santos

Shanti

Stella

Vand

Zafira

Amelogenin

Allele 1

Allele 2

Sample Name Marker

Andy

Asko

Boss

Bruno

Ciara

Daisy

Doris

Ella

REN169O18

REN169O1

REN169O18

REN169O81

Allele 1

156

168

170

166

162

156

166

162

170

156

164

168

156

168

170

168

156

168

162

168

170

Allele 2

168

170

168

170

168

170

Franko

Harry

Inka

KP85

KP86

KP87

KP88

KP89

KP90

Kenny

Loke

Maya

Nea

Oscar

Santos

Shanti

Stella

Vand

Zafira

Sample Name Marker

Andy

Asko

Boss

Bruno

Ciara

Daisy

Doris

Ella

Franko

Harry

Inka

KP85

KP86

KP87

KP88

KP89

KP90

Kenny

Loke

Maya

Nea

Oscar

Santos

Shanti

Stella

Vand

Zafira

CXX279

Allele 1

124

118

124

118

124

118

120

118

116

124

118

124

118

Allele 2

126

Sample Name Marker

Andy

Asko

Boss

Bruno

Ciara

Daisy

REN247M23

Allele 1

268

271

268

272

268

270

268

272

Allele 2

270

272

270

272

126

Doris

Ella

Franko

Harry

124

130

120

118

124

Inka

KP85

KP86

KP87

KP88

KP89

KP90

Kenny

Loke

Maya

Nea

REN247M23

270

268

270

272

270

272

266

272

126

130

Ocar

Santos

Shanti

Stella

Vand

Zafira

272

Sample Name Marker

Andy

Asko

Boss

Bruno

Ciara

Daisy

Doris

Ella

Franko

Harry

Inka

KP85

KP86

KP87

KP88

KP89

KP90

Kenny

Loke

Maya

Nea

Oscar

Santos

Shanti

Stella

Vand

Zafira

FH2054

Allele 1

160

152

160

152

160

152

156

152

160

152

156

160

152

160

156

152

156

Allele 2

164

160

164

160

164

160

176

160

Sample Name Marker

Andy

Asko

Boss

Bruno

Ciara

Daisy

Doris

Ella

Franko

Harry

Inka

KP85

KP86

KP87

KP88

KP89

KP90

REN54P11

Allele 1

236

222

226

234

228

236

Allele 2

236

160

164

160

156

160

164

Kenny

Loke

Maya

Nea

Oscar

Santos

Shanti

Stella

Vand

Zafira

160

164

Sample Name Marker

Andy

Asko

Boss

Bruno

Ciara

Daisy

Doris

Ella

Franko

Harry

Inka

KP85

KP86

KP87

KP88

KP89

KP90

Kenny

Loke

Maya

Nea

Oscar

Santos

Shanti

Stella

Vand

Zafira

FH2848

Allele 1

238

240

238

240

238

240

238

240

238

228

238

240

238

240

238

240

Allele 2

240

242

240

244

240

244

240