Developmental validation of DogFiler, a novel multiplex for canine DNA profiling in forensic casework

Development and validation of a novel 30-plex STR assay for canine individual identification and parentage testing

Domestic dogs are helpers in outdoor human work and companions for families; thus, individual canine identification and parentage testing are crucial in certain fields, including forensics and breeding programs. In this study, a six-dye fluorescent labeling multiplex amplification system containing 29 canine short tandem repeats (STRs) and the sex-determining marker DAmel was developed. The system was called the Tronfo Canine 30-plex STR Kit and was further validated according to the Scientific Working Group on DNA Analysis Methods and the Organization of Scientific Area Committees for Wildlife Forensics guidelines, including tests for PCR conditions, precision, species specificity, sensitivity, stability, repeatability and reproducibility, a population study, and a study of 16 paternity test cases. The results indicated that the novel canine STR assay was accurate, specific, reproducible, stable, and robust. Complete profiles were obtained with 31.25 pg of canine DNA. Additionally, 500 unrelated canine individuals were investigated using this novel system, and the combined power of discrimination and exclusion values were 0.999999999999999999 and 0.999996451039850, respectively. These results suggest that the Tronfo Canine 30-plex STR Kit is highly polymorphic, informative, and suitable for individual canine identification and parentage testing.

Patterns of Wolf Dispersal Respond to Harvest Density across an Island Complex

Wolves are highly mobile predators and can disperse across a variety of habitats and over long distances. However, less is known about dispersal capabilities across water and among islands. The biogeography of island systems fosters spatially structured local populations, and their degree of connectivity may influence the dynamics and long-term viability of the regional population. We sought to quantify wolf dispersal rate, distance, and dispersal sex bias throughout Prince of Wales Island, a 6670 km2 island in southeast Alaska, and the surrounding islands that constitute the wildlife management unit (9025 km2). We also investigated patterns of dispersal in relation to hunting and trapping intensity and wolf population density. We used DNA data collected during 2012-2021 long-term monitoring efforts and genotyped 811 wolves, 144 of which (18%) were dispersers. Annual dispersal rates were 9-23% and had a weakly positive relationship with wolf density. Wolves dispersed 41.9 km on average (SD = 23.7 km), and males and females did not disperse at different rates. Of the dispersing wolves, 107 died, and the majority (n = 81) died before they were able to settle. The leading manner of death was trapping (97% of mortalities), and wolves tended to disperse from areas with low harvest density to areas where harvest density was relatively higher. Dispersal occurred both to and from small islands and the larger Prince of Wales Island, indicating bidirectional as opposed to asymmetrical movement, and the genetic overlap of wolf groups demonstrates connectivity throughout this naturally patchy system. Island ecosystems have different predator-prey dynamics and recolonization processes than large, intact systems due to their isolation and restricted sizes; thus, a better understanding of the degree of population connectivity including dispersal patterns among islands in the Prince of Wales archipelago could help inform the management and research strategies of these wolves.

Poaching Forensics: Animal Victims in the Courtroom

Poaching and the international trade in wildlife are escalating problems driven by poverty and greed and coordinated by increasingly sophisticated criminal networks. Biodiversity loss, caused by habitat change, is exacerbated by poaching, and species globally are facing extinction. Forensic evidence underpins human and animal criminal investigations and is critical in criminal prosecution and conviction. The application of forensic tools, particularly forensic genetics, to animal case work continues to advance, providing the systems to confront the challenges of wildlife investigations. This article discusses some of these tools, their development, and implementations, as well as recent advances. Examples of cases are provided in which forensic evidence played a key role in obtaining convictions, thus laying the foundation for the future application of techniques to disrupt the criminal networks and safeguard biodiversity through species protection.

Variation in adult and pup wolf diets at natal den sites is influenced by forest composition and configuration

Although wolves are wide-ranging generalist carnivores throughout their life cycle, during the pup-rearing season wolf activity is focused on natal den sites where pup survival depends upon pack members provisioning food. Because prey availability is influenced by habitat quality within the home range, we investigated the relative importance of prey species for adults and pups and further examined the relationship between habitat characteristics, wolf diet, and litter size on Prince of Wales Island (POW) in Southeast Alaska. During 2012-2020, we detected 13 active den sites within the home ranges of nine wolf packs. We estimated minimum pup counts using motion-detecting cameras and individual genotypes from noninvasive samples (hair: n = 322; scat: n = 227) and quantified wolf diet composition using fecal DNA metabarcoding (n = 538). We assessed habitat composition, configuration, and connectivity within denning and annual home ranges estimated using wolf GPS-collar data. Contrary to expectations, wolves had a more constricted diet during denning season (April 15-July 31), and within this season pups had a narrower dietary niche (species richness [S] = 4) focused more on deer (relative frequency of occurrence [O/I] = 0.924) than adults (S = 15; deer O/I = 0.591). Litter size had a positive relationship with the relative frequency of deer in a wolf pack's diet. Wolf consumption of deer was positively associated with the proportion of young-growth forest (≤25 years old) within denning and annual home ranges. High levels of vegetation patch interspersion, and the density of closed logging roads were also important predictors, suggesting these habitat qualities were influential for increasing the availability of deer to wolves. Our results contrast with previous research indicating wolf pup diets included more alternate prey (i.e., beaver) than adults and emphasize the importance of deer to wolf viability on POW, especially during denning season.

Development of a 17-Plex of Penta- and Tetra-Nucleotide Microsatellites for DNA Profiling and Paternity Testing in Horses

Tetranucleotide and pentanucleotide short tandem repeat (hereafter termed tetraSTR and pentaSTR) polymorphisms have properties that make them desirable for DNA profiling and paternity testing. However, certain species, such as the horse, have far fewer tetraSTRs than other species and for this reason dinucleotide STRs (diSTRs) have become the standard for DNA profiling in horses, despite being less desirable for technical reasons. During our testing of a series of candidate genes as potentially underlying a heritable condition characterized by megaesophagus in the Friesian horse breed, we found that good tetraSTRs do exist in horses but, as expected, at a much lower frequency than in other species, e.g., dogs and humans. Using a series of efficient methods developed in our laboratory for the production of multiplexed tetraSTRs in other species, we identified a set of tetra- and pentaSTRs that we developed into a 17-plex panel for the horse, plus a sex-identifying marker near the amelogenin gene. These markers were tested in 128 horses representing 16 breeds as well as crossbred horses, and we found that these markers have useful genetic variability. Average observed heterozygosities (Ho) ranged from 0.53 to 0.89 for the individual markers (0.66 average Ho for all markers), and 0.62-0.82 for expected heterozygosity (He) within breeds (0.72 average He for all markers). The probability of identity (PI) within breeds for which 10 or more samples were available was at least 1.1 x 10⁻¹¹, and the PI among siblings (PIsib) was 1.5 x 10⁻⁵. Stutter was ≤ 11% (average stutter for all markers combined was 6.9%) compared to the more than 30% typically seen with diSTRs. We predict that it will be possible to develop accurate allelic ladders for this multiplex panel that will make cross-laboratory comparisons easier and will also improve DNA profiling accuracy. Although we were only able to exclude candidate genes for Friesian horse megaesophagus with no unexcluded genes that are possibly causative at this point in time, the study helped us to refine the methods used to develop better tetraSTR multiplexed panels for species such as the horse that have a low frequency of tetraSTRs.

Development of novel microsatellite markers to analyze the genetic structure of dog populations in Taiwan

Objective

Alongside the rise of animal-protection awareness in Taiwan, the public has been paying more attention to dog genetic deficiencies due to inbreeding in the pet market. The goal of this study was to isolate novel microsatellite markers for monitoring the genetic structure of domestic dog populations in Taiwan.

Methods

A total of 113 DNA samples from three dog breeds - beagles (BEs), bichons (BIs), and schnauzers (SCs) - were used in subsequent polymorphic tests applying the 14 novel microsatellite markers that were isolated in this study.

Results

The results showed that the high level of genetic diversity observed in these novel microsatellite markers provided strong discriminatory power. The estimated probability of identity (P(ID)) and the probability of identity among sibs (P(ID)sib) for the 14 novel microsatellite markers were 1.7×10-12 and 1.6×10-5, respectively. Furthermore, the power of exclusion (PE) for the 14 novel microsatellite markers was 99.98%. The neighbor-joining (NJ) trees constructed among the three breeds indicated that the 14 sets of novel microsatellite markers were sufficient to correctly cluster the BEs, BIs, and SCs. The principal coordinate analysis (PCoA) plot showed that the dogs could be accurately separated by these 14 loci baled on different breeds; moreover, the Beagles from different sources were also distinguished. The first, the second, and the third principal coordinates could be used to explain 44.15, 26.35 and 19.97% of the genetic variation.

Conclusion

The results of this study could enable powerful monitoring of the genetic structure of domestic dog populations in Taiwan.

Standardization of a SNP panel for parentage verification and identification in the domestic cat (Felis silvestris catus)

The domestic cat (Felis silvestris catus) is a valued companion animal throughout the world. Over 60 different cat breeds are accepted for competition by the cat fancy registries in different countries. Genetic markers, including short tandem repeats and SNPs, are available to evaluate and manage levels of inbreeding and genetic diversity, population and breed structure relationships, and individual identification for forensic and registration purposes. The International Society of Animal Genetics (ISAG) hosts the Applied Genetics in Companion Animals Workshop, which supports the standardization of genetic marker panels and genotyping for the identification of cats via comparison testing. SNP panels have been in development for many species, including the domestic cat. An ISAG approved core panel of SNPs for use in cat identification and parentage analyses is presented. SNPs (n = 121) were evaluated by different university-based and commercial laboratories using 20 DNA samples as part of the ISAG comparison testing procedures. Different SNP genotyping technologies were examined, including DNA arrays, genotyping-by-sequencing and mass spectroscopy, to select a robust and efficient panel of 101 SNPs as the ISAG core panel for cats. The SNPs are distributed across all chromosomes including two on the X chromosome and an XY pseudo-autosomal sexing marker (zinc-finger XY; ZFXY). A population study demonstrated that the markers have an average polymorphic information content of 0.354 and a power of exclusion greater than 0.9999. The SNP panel should keep testing affordable while also allowing for the development of additional panels to monitor health, phenotypic traits, hybrid cats and highly inbred cats.

Towards Forensic DNA Phenotyping for Predicting Visible Traits in Dogs

The popularity of dogs as human companions explains why these pets regularly come into focus in forensic cases such as bite attacks or accidents. Canine evidence, e.g., dog hairs, can also act as a link between the victim and suspect in a crime case due to the close contact between dogs and their owners. In line with human DNA identification, dog individualization from crime scene evidence is mainly based on the analysis of short tandem repeat (STR) markers. However, when the DNA profile does not match a reference, additional information regarding the appearance of the dog may provide substantial intelligence value. Key features of the dog's appearance, such as the body size and coat colour are well-recognizable and easy to describe even to non-dog experts, including most investigating officers and eyewitnesses. Therefore, it is reasonable to complement eyewitnesses' testimonies with externally visible traits predicted from associated canine DNA samples. Here, the feasibility and suitability of canine DNA phenotyping is explored from scratch in the form of a proof of concept study. To predict the overall appearance of an unknown dog from its DNA as accurately as possible, the following six traits were chosen: (1) coat colour, (2) coat pattern, (3) coat structure, (4) body size, (5) ear shape, and (6) tail length. A total of 21 genetic markers known for high predicting values for these traits were selected from previously published datasets, comprising 15 SNPs and six INDELS. Three of them belonged to SINE insertions. The experiments were designed in three phases. In the first two stages, the performance of the markers was tested on DNA samples from dogs with well-documented physical characteristics from different breeds. The final blind test, including dogs with initially withheld appearance information, showed that the majority of the selected markers allowed to develop composite sketches, providing a realistic impression of the tested dogs. We regard this study as the first attempt to evaluate the possibilities and limitations of forensic canine DNA phenotyping.

Animal Forensic Genetics

Animal forensic genetics, where the focus is on non-human species, is broadly divided in two: domestic species and wildlife. When traces of a domestic species are relevant to a forensic investigation the question of species identification is less important, as the material comes from either a dog or a cat for instance, but more relevant may be the identification of the actual pet. Identification of a specific animal draws on similar methods to those used in human identification by using microsatellite markers. The use of cat short tandem repeats to link a cat hair to a particular cat paved the way for similar identification of dogs. Wildlife forensic science is becoming accepted as a recognised discipline. There is growing acceptance that the illegal trade in wildlife is having devasting effects on the numbers of iconic species. Loci on the mitochondrial genome are used to identify the most likely species present. Sequencing the whole locus may not be needed if specific bases can be targeted. There can be benefits of increased sensitivity using mitochondrial loci for species testing, but occasionally there is an issue if hybrids are present. The use of massively parallel DNA sequencing has a role in the identification of the ingredients of traditional medicines where studies found protected species to be present, and a potential role in future species assignments. Non-human animal forensic testing can play a key role in investigations provided that it is performed to the same standards as all other DNA profiling processes.

Microsatellite DNA Analysis of Genetic Diversity and Parentage Testing in the Popular Dog Breeds in Poland

There is growing concern that extreme breed standardization contributes to a reduction of the effective population size and high levels of inbreeding, resulting in the loss of genetic diversity in many breeds. This study examined genetic diversity among eight popular dog breeds in Poland and evaluated the effectiveness of a 21-microsatellite (STR) panel recommended by the International Society for Animal Genetics (ISAG) for parent verification. The following breeds were characterized: German Shepherd, Maltese, Irish Wolfhound, Yorkshire Terrier, Biewer Yorkshire Terrier, Golden Retriever, Labrador Retriever, and French Bulldog. STRUCTURE analysis showed breed distinctiveness among all the dog breeds under study. Reynold’s distance ranged between θ_w = 0.634 and θ_w = 0.260. The studied breeds showed a medium level of genetic differentiation; the mean number of alleles per locus ranged from 3.4 to 6.6, and the effective number of alleles from 2.1 to 3.5. The mean degree of heterozygosity varied from 49% to 69% and from 47% to 68% for H_O and H_E, respectively. The population inbreeding coefficient (FIS) indicated an absence of inbreeding in the studied breeds. The average polymorphism information content (PIC) values for most of the breeds were higher than 0.5. The cumulative power of discrimination (PD) for all the markers in all breeds reached high values (close to 1.0), while the probability of identity (P_ID) was low, ranging between 10⁻¹¹ and 10⁻¹⁹. The cumulative exclusion probability when the genotypes of one (PE₁) and both parents (PE₂) are known and showed that the parentage can be confirmed with a probability of 94.92% to 99.95% and 99.78% to 99.9999%, respectively.

Optimisation and application of a forensic microsatellite panel to combat Greater-one horned rhinoceros (Rhinoceros unicornis) poaching in India

The Greater one-horned (GoH) rhinoceros is one of the most charismatic endemic megaherbivores of the Indian subcontinent. Threatened by poaching, habitat loss and disease, the species is found only in small areas of its historical distribution. Increasing demands for rhino horns in chinese traditional medicine has put the existing population under continuing threat, and large profits and low conviction rates make poaching difficult to contain. DNA forensics such as the RhoDIS-Africa program has helped in combating illegal rhino horn trade, but the approach is yet to be optimised for Indian GoH rhinoceros. Here we followed the International Society for Forensic Genetics (ISFG) guidelines to establish a 14 dinucleotide microsatellite panel for Indian GoH rhinoceros DNA profiling. Selected from a large initial pool (n = 34), the microsatellite markers showed high polymorphism, stable peak characteristics, consistent allele calls and produced precise, reproducible genotypes from different types of rhino samples. The panel also showed low genotyping error and produced high statistical power during individual identification (P_IDsibs value of 1.2*10^-4). As part of the official RhoDIS-India program, we used this panel to match poached rhino carcass with seized contraband as scientific evidence in court procedure. This program now moves to generate detailed allele-frequency maps of all GoH rhinoceros populations in India and Nepal for development of a genetic database and identification of poaching hotspots and trade routes across the subcontinent and beyond.

Comparison of Behavior and Genetic Structure in Populations of Family and Kenneled Beagles

In dogs, the social and spatial restriction associated with living in a kennel environment could lead to chronic stress and the development of abnormal behaviors (“kennel-dog syndrome”). However, little is known about how kenneled dogs differ from their conspecifics living as pets in human families. In the current study, using a test battery exposing the dogs to novel stimuli, we compared the behavior of three groups of beagles: (1) kenneled dogs living in a restricted environment with limited human contact (N = 78), (2) family dogs living in human families as pets (N = 37), and (3) adopted dogs born in the kenneled population but raised in human families (N = 13). We found one factor comprising most of the test behaviors, labeled as Responsiveness. Family dogs and adopted dogs scored higher in Responsiveness than kenneled dogs. However, 23% of the kenneled dogs were comparable to family and adopted dogs based on a cluster analysis, indicating a similar (positive) reaction to novel stimuli, while 77% of the kenneled dogs were unresponsive (mostly immobile) in at least part of the test. To assess if the behavioral difference between the family and kenneled dogs could be due to genetic divergence of these two populations and/or to lower genetic diversity of the kenneled dogs, we analyzed their genetic structure using 11 microsatellite markers. We found no significant difference between the populations in their genetic diversity (i.e., heterozygosity, level of inbreeding), nor any evidence that the family and kenneled populations originated from different genetic pools. Thus, the behavior difference between the groups more likely reflects a G × E interaction, that is, the influence of specific genetic variants manifesting under specific environmental conditions (kennel life). Nevertheless, some kenneled individuals were (genetically) more resistant to social and environmental deprivation. Selecting for such animals could strongly improve the welfare of kenneled dog populations. Moreover, exploring the genetic background of their higher resilience could also help to better understand the genetics behind stress- and fear-related behaviors.

Dog-bite-related attacks: A new forensic approach

Dog attacks today represent a health hazard considering that prevention strategies have not always been successful. The identification of the dog that attacked the victim is necessary, considering the civil or criminal consequences for the animal's owner. An accurate scene analysis must be performed collecting a series of important information. Forensic investigations in dog attacks involve different methods, such as the evaluating of the canine Short Tandem Repeat (STR) typing in saliva traces on wounds or bite mark analysis, however, these techniques cannot always be applied. The effort to find new methods to identify the dog that attacked the victim represents a very interesting field for the forensic community. This study aims to propose an innovative approach, based on the identification of the victim's profile in the dog's mouth, using a buccal swab on the suspected aggressor dog, to find the victim's genetic profile. In addition, a further goal of this study is to determine the persistence time of hexogen DNA in the dog's mouth to define a timeframe for performing this particular technique. For this purpose, ten different dogs were used to aggressively bite a bovine sample (reference sample) to simulate the victim. For each dog two buccal swabs were taken at different time intervals: 30', 45', 60', 90', 120', 150', 180' and 240'. The typing of the swabs provided an interpretable profile after 45' while traces of bovine profile were found until 150' after the dog attack simulation. These results could be improved using the human identification kit, which is more sensitive. In the light of this experimental study, the forensic community should consider using this approach in real casework studies with the aim of collecting new data, validating this technique for forensic use.

A novel 13-plex STR typing system for individual identification and parentage testing of donkeys (Equus asinus)

BACKGROUND

Previous studies investigating donkey parentage and genetic diversity used horse-specific multiplex systems. However, several mis-allele and null-allele issues were found with some of the horse primers when used in donkeys. In 2017, the International Society for Animal Genetics (ISAG) recommended 13 dinucleotide short tandem repeats (STRs) (AHT4, ASB23, HMS2, HMS3, HMS6, HMS7, HMS18, HTG7, HTG10, TKY297, TKY312, TKY337 and TKY343) as a core panel that should be used to identify individuals and to test for parentage in donkeys. To date, no single multiplex STR typing system containing all 13 donkey STRs recommended by the ISAG has been reported.

OBJECTIVES

To establish a novel and donkey-specific multiplex STR typing system containing all 13 recommended STRs.

STUDY DESIGN

Assay development and validation in field population.

METHODS

Primers for seven of the STRs were redesigned and conditions for polymerase chain reaction (PCR) were optimised. We analysed the allele sequences, sensitivity, species-specificity and stutter ratios of this new system.

RESULTS

A 13-plex STR typing system for donkey was established. A full profile could be generated from a single PCR reaction using as little as 5 ng of DNA template with the 13 pairs of primers labelled with fluorescent dyes. An allele ladder, containing 101 alleles from the 13 STRs, was generated. No full genotype profile was generated with these primers if DNA from humans, or 11 other commonly encountered animals, was used. Genotypes could be generated for the horse and horse-donkey hybrids (mule and hinny). Stutter ratios and population genetic parameters were calculated based on samples from 150 donkeys. The combined probabilities of paternity exclusion for this system were 0.988907326 (CPEduo) and 0.999665018 (CPEtrio).

MAIN LIMITATIONS

This system cannot detect sex.

CONCLUSIONS

Our results indicate that our donkey-specific 13-plex STR typing system is sensitive, species-specific and robust for individual identification, paternity testing and population genetic analysis in donkeys, and has potential forensic applications.

Forensic characterization and statistical considerations of the CaDNAP 13-STR panel in 1,184 domestic dogs from Germany, Austria, and Switzerland

Crime scene samples originating from domestic dogs such as hair, blood, or saliva can be probative as possible transfer evidence in human crime and in dog attack cases. In the majority of such cases canine DNA identification using short tandem repeat (STR) analysis is the method of choice, which demands, among others, a systematic survey of allele frequency data in the relevant dog populations. A set of 13 highly polymorphic canine STR markers was used to analyze samples of 1,184 dogs (including 967 purebred dogs) from the so-called DACH countries (Germany, Austria, Switzerland). This CaDNAP 13-STR panel has previously been validated for canine identification in a forensic context. Here, we present robust estimates of allele frequencies, which are essential to assess the weight of the evidence by estimating the probability of a matching DNA profile within the dog population under question, e.g. in the form of a random match probability (RMP). The geographical provenance of the tested dogs showed a negligible influence on the observed genotype variation. Therefore, we combined the STR data from all three countries into a single dog population sample (DPS). In contrast, pronounced genetic differentiation between dog breeds was found by principal component analysis and sub-structure analysis with the STRUCTURE software. These findings entailed the need to account for the effects of DPS breed composition on allele frequency estimates. A possible strategy, which was favored here, relies on collecting a DPS that is guided by the breed composition of the relevant dog population. In total, dogs from 166 different breeds were included in our DPS, 64 of them including at least 5 individuals (n = 771 dogs). Sampling reflected the abundance of breeds in the DACH countries with the following being the most common ones: German Shepherds (population frequency: 14.3%), Dachshunds (5.9%), Labrador Retrievers (3.9%), and Golden Retrievers (3.2%). The pedigree listing of the purebred dogs in our DPS ranked German Shepherds (DPS frequency 8.5%) first, followed by Labrador Retrievers (3.9%), Golden Retrievers (3%), and Dachshunds (2.5%). RMP values based on overall allele frequencies and accounting for substructure using F_ST between breeds ranged between 10-13 and 10-14 and represent a conservative approach of RMP assessment.

Genetic heterogeneity and diversity of North American golden retrievers using a low density STR marker panel

Thirty-three autosomal short tandem repeat (STR) markers were used to evaluate genetic heterogeneity and diversity in 525 golden retrievers (GRs). This breed was selected because of its popularity and artificial selection for conformation vs. performance phenotypes. Seven additional STRs were used to evaluate the highly polymorphic dog leukocyte antigen (DLA) class I and class II regions. From 3 to 13 alleles were found at each of the 33 loci (mean 7) and the average effective alleles (Ne) was 3.34. The observed heterozygosity was 0.65 and the expected heterozygosity was 0.68. The resulting fixation index was 0.035 indicating that the population was randomly breeding. We found that modern GRs retain 46% of genomic diversity present in all canids and 21/175 (12%) and 20/90 (22%) of the known DLA class I and class II haplotypes, respectively. Selection for performance or conformation led to a narrowing of genomic and DLA diversity with conformation having a greater effect than performance. A comparison was made between coefficient of inbreeding (COI) determined from 10 or 12 generation pedigrees and DNA based internal relatedness values. A weak but significant correlation was observed between IR score and 10 or 12 generation COI (r = 0.38, p<0.0001 and r = 0.40, p<0.0001, respectively). IR values were higher in conformation than performance lines but only significant at p = 0.17. This was supported by 10 and 12 generation COI values that were significantly (p<0.0001) higher in conformation than performance lines. We demonstrate herein that a low density of STR markers can be utilized to study the genetic makeup of GRs.

Polymorphism analyses of 19 STRs in Labrador Retriever population from China and its heterozygosity comparisons with other retriever breeds

Pure breed dogs of Western origin are increasingly more popular in China as is a need to differentiate breeds and individual dogs for personal and forensic reasons. Research on genetic diversities of the canine population in China is rarely conducted. In this study, genetic distributions and forensic efficiencies of 19 canine STR loci in Labrador Retriever population from China were evaluated by using one available commercial canine kit in China. This panel was used to genetically define 214 Labrador Retrievers in China, as an example of one of the most important Western breeds and to compare them with Labrador Retrievers from America based on three overlapping STR loci. Moreover, genetic relationship analyses between Labrador Retriever population and two reference populations in America were performed. All 19 STR loci were polymorphic and conformed to Hardy-Weinberg equilibrium in the studied population. The STR panel was able to discern individual dogs with a high degree of accuracy. Breed-wide genetic heterozygosity comparisons based on present and published allele frequencies revealed that the studied population had the lower genetic heterozygosity than canine populations in America. Principal component analysis among Labrador Retriever population and other reference populations showed that the studied Labrador Retrievers were genetically close to the retriever breeds in America. Population genetic structure analyses among these canine breeds further revealed genetic differentiations between the studied Labrador Retriever population and other compared breeds. In conclusion, these STR loci had relatively high forensic values in Labrador Retriever population in China, which could be employed for individual identification and kinship testing.

OzPythonPlex: An optimised forensic STR multiplex assay set for the Australasian carpet python (Morelia spilota)

Reptile species, and in particular snakes, are protected by national and international agreements yet are commonly handled illegally. To aid in the enforcement of such legislation, we report on the development of three 11-plex assays from the genome of the carpet python to type 24 loci of tetra-nucleotide and penta-nucleotide repeat motifs (pure, compound and complex included). The loci range in size between 70 and 550 bp. Seventeen of the loci are newly characterised with the inclusion of seven previously developed loci to facilitate cross-comparison with previous carpet python genotyping studies. Assays were optimised in accordance with human forensic profiling kits using one nanogram template DNA. Three loci are included in all three of the multiplex reactions as quality assurance markers, to ensure sample identity and genotyping accuracy is maintained across the three profiling assays. Allelic ladders have been developed for the three assays to ensure consistent and precise allele designation. A DNA reference database of allele frequencies is presented based on 249 samples collected from throughout the species native range. A small number of validation tests are conducted to demonstrate the utility of these multiplex assays. We suggest further appropriate validation tests that should be conducted prior to the application of the multiplex assays in criminal investigations involving carpet pythons.

An autosomal recessive mutation in SCL24A4 causing enamel hypoplasia in Samoyed and its relationship to breed-wide genetic diversity

Background

Pure breeding of dogs has led to over 700 heritable disorders, of which almost 300 are Mendelian in nature. Seventy percent of the characterized mutations have an autosomal recessive mode of inheritance, indicative of positive selection during bouts of inbreeding primarily for new desired conformational traits. Samoyed suffer from several common complex genetic disorders, but up to this time only two X-linked and one autosomal dominant disorder have been identified. Previous studies based on pedigrees and SNP arrays have concluded that Samoyed breeders have done a good job in maintaining genetic diversity and avoiding excessive inbreeding. This may explain why autosomal recessive disorders have not occurred to the extent observed in many other breeds. However, an enamel hypoplasia analogous to a form of autosomal recessive amelogenesis imperfecta (ARAI) in humans has been recently characterized in Samoyed, although the causative mutation appears to have existed for three or more decades. The rise of such a mutation indicates that bouts of inbreeding for desired conformational traits are still occurring despite an old and well-defined breed standard. Therefore, the present study has two objectives: 1) measure genetic diversity in the breed using DNA and short tandem repeats (STR), and 2) identify the exact mutation responsible for enamel hypoplasia in the breed, possible explanations for its recent spread, and the effect of eliminating the mutation on existing genetic diversity.

Results

The recent discovery of an autosomal recessive amelogenesis imperfecta (ARAI) in Samoyed provides an opportunity to study the mutation as well as genetic factors that favored its occurrence and subsequent spread. The first step in the study was to use 33 short tandem repeat (STR) loci on 25/38 autosomes and seven STRs across the dog leukocyte antigen (DLA) class I and II regions on CFA12 to determine the DNA-based genetic profile of 182 individuals from North America, Europe and Australia. Samoyed from the three continents constituted a single breed with only slight genetic differences. Breed-wide genetic diversity was low, most likely from a small founder population and subsequent artificial genetic bottlenecks. Two alleles at each autosome locus occurred in 70–95% of the dogs and 54% of alleles were homozygous. The number of DLA class I and II haplotypes was also low and three class I and two class II haplotypes occurred in 80–90% of individuals. Therefore, most Samoyed belong to two lines, with most dogs possessing a minority of existing genetic diversity and a minority of dogs containing a majority of diversity. Although contemporary Samoyed lack genetic diversity, the bulk of parents are as unrelated as possible with smaller subpopulations either more inbred or outbred than the total population. A familial disorder manifested by hypocalcification of enamel has been recently identified. A genome wide association study (GWAS) on seven affected and five unrelated healthy dogs pointed to a region of extended homozygosity on Canis familiaris autosome 8 (CFA8). The region contained a gene in the solute carrier 24 family (SCL24A4) that encodes a protein involved in potassium dependent sodium/calcium exchange and transport. Mutations in this gene were recently found to cause a similar type of enamel hypoplasia in people. Sequencing of this candidate gene revealed a 21 bp duplication in exon 17. A test for the duplication was in concordance with the disease phenotype. The exact incidence of affected dogs is unknown, but 12% of the 168 healthy dogs tested were heterozygous for the mutation. This population was biased toward close relatives, so a liberal estimate of the incidence of affected dogs in the breed would be around 3.6/1000. Theoretical calculations based on the comparison of the whole population with a population devoid of carriers indicated that eliminating the trait would not affect existing genetic diversity at this time.

Conclusions

The contemporary Samoyed, like many other breeds, has retained only a small portion of the genetic diversity that exists among all dogs. This limited genetic diversity along with positive genetic selection for desirable traits has led to at least three simple non-recessive genetic disorders and a low incidence of complex genetic traits such as autoimmune disease and hip dysplasia. Unlike many other pure breeds, the Samoyed has been spared the spate of deleterious autosomal recessive traits that have plagued many other pure breeds. However, ARAI due to a mutation in the SCL24A4 gene has apparently existed in the breed for several decades but is being increasingly diagnosed. The increase in diseased dogs is most likely due to a period of intensified positive selection for some desired conformational trait. A genetic test has been developed for identifying the mutation carriers which will enable the breeders to eliminate enamel hypoplasia in Samoyed by selective breeding and it appears that this mutation can be eliminated now without loss of genetic diversity.

Population genetic study of 10 short tandem repeat loci from 600 domestic dogs in Korea

Dogs have long shared close relationships with many humans. Due to the large number of dogs in human populations, they are often involved in crimes. Occasionally, canine biological evidence such as saliva, bloodstains and hairs can be found at crime scenes. Accordingly, canine DNA can be used as forensic evidence. The use of short tandem repeat (STR) loci from biological evidence is valuable for forensic investigations. In Korea, canine STR profiling-related crimes are being successfully analyzed, leading to diverse crimes such as animal cruelty, dog-attacks, murder, robbery, and missing and abandoned dogs being solved. However, the probability of random DNA profile matches cannot be analyzed because of a lack of canine STR data. Therefore, in this study, 10 STR loci were analyzed in 600 dogs in Korea (344 dogs belonging to 30 different purebreds and 256 crossbred dogs) to estimate canine forensic genetic parameters. Among purebred dogs, a separate statistical analysis was conducted for five major subgroups, 97 Maltese, 47 Poodles, 31 Shih Tzus, 32 Yorkshire Terriers, and 25 Pomeranians. Allele frequencies, expected (Hexp) and observed heterozygosity (Hobs), fixation index (F), probability of identity (P(ID)), probability of sibling identity (P(ID)sib) and probability of exclusion (PE) were then calculated. The Hexp values ranged from 0.901 (PEZ12) to 0.634 (FHC2079), while the P(ID)sib values were between 0.481 (FHC2079) and 0.304 (PEZ12) and the P(ID)sib was about 3.35 × 10(-)⁵ for the combination of all 10 loci. The results presented herein will strengthen the value of canine DNA to solving dog-related crimes.

SkydancerPlex: A novel STR multiplex validated for forensic use in the hen harrier (Circus cyaneus)

The hen harrier (Circus cyaneus) is a bird of prey which is heavily persecuted in the UK because it preys on the game bird red grouse (Lagopus lagopus scoticus). To help investigations into illegal killings of hen harrier, a STR multiplex kit containing eight short tandem repeat (STR) markers and a chromohelicase DNA binding protein 1 (CHD 1) sexing marker was developed. The multiplex kit was tested for species specificity, sensitivity, robustness, precision, accuracy and stability. Full profiles were obtained with as little as 0.25 ng of template DNA. Concurrent development of an allelic ladder to ensure reliable and accurate allele designation across laboratories makes the SkydancerPlex the first forensic DNA profiling system in a species of wildlife to be fully validated according to SWGDAM and ISFG recommendations. An average profile frequency of 3.67 × 10(-8), a PID estimate of 5.3 × 10(-9) and a PID-SIB estimate of 9.7 × 10(-4) make the SkydancerPlex an extremely powerful kit for individualisation.

A search for genetic diversity among Italian Greyhounds from Continental Europe and the USA and the effect of inbreeding on susceptibility to autoimmune disease

Background

Previous studies documented the problem of inbreeding among Italian Greyhounds (IG) from the USA and its possible role in a multiple autoimmune disease syndrome. The present study is an extension of these earlier experiments and had two objectives: 1) to identify pockets of additional genetic diversity that might still exist among IG from the USA and Continental Europe, and 2) to determine how loss of genetic diversity within the genome and in the dog leukocyte antigen (DLA) complex relates to the problem of autoimmune disease in IG from the USA. Genetic testing was conducted using 33 short tandem repeat (STR) loci across 25 chromosomes and 7 STR loci that associated with specific dog leukocyte antigen (DLA) class I and II haplotypes. Standard genetic assessment tests based on allele frequencies and internal relatedness (IR) were used as measures of breed-wide and individual heterozygosity.

Results

The results of these tests demonstrated that IG from the USA and Continental Europe belonged to a single breed but were genetically distinguishable by genomic allele frequencies, DLA class I and II haplotypes, and principal coordinate analysis (PCoA). In the second part of the study, 85 IG from the USA that had suffered various autoimmune disorders (case) and 104 healthy dogs (control) of comparable age were studied for genetic associations with disease. Case dogs were found to be significantly more homozygous in the DLA regions than control dogs. Principal coordinate analysis did not differentiate case from control populations. No specific STR-associated DLA-class I or II haplotype was associated with increased autoimmune disease risks. Reasons for the loss of genetic diversity and increased homozygosity among IG from the USA were studied using registration data and deep pedigrees. The breed in the USA started from a small number of founders from Europe and has remained relatively isolated and small in numbers, limiting breeding choices especially in the period before modern transportation and artificial insemination. An additional cause of lost diversity and increased homozygosity has been the influence of famous sires and their show-winning progeny. The most influential of these sires was Ch. Dasa’s King of the Mountain (King) born in 1978. Virtually all contemporary IG from the USA have King at least once in 10 generation pedigrees and 18 % of the genome of contemporary IG from the USA is shared with King.

Conclusions

It was concluded that artificial genetic bottlenecks have concentrated numerous genetic polymorphisms responsible for autoimmune disease and that these risk factors did not originate in a specific individual or bloodline of the breed. Rather, they were of ancestral origin in both purebred and random bred dogs and inherited by descent. Italian Greyhound breeders in the USA have several options to improve breed health: 1) breed against homozygosity within the genome and in the DLA region, 2) avoid breeding dogs that have suffered an autoimmune disorder, 3) increase diversity by incorporating the genetic differences that exist in IG from Continental Europe, or 4) outcross to other small sighthound breeds. The latter two approaches must be undertaken with care to avoid introduction of new deleterious traits and to maximize retention and dissemination of new genetic diversity.

The effect of genetic bottlenecks and inbreeding on the incidence of two major autoimmune diseases in standard poodles, sebaceous adenitis and Addison's disease

BACKGROUND

Sebaceous adenitis (SA) and Addison's disease (AD) increased rapidly in incidence among Standard Poodles after the mid-twentieth century. Previous attempts to identify specific genetic causes using genome wide association studies and interrogation of the dog leukocyte antigen (DLA) region have been non-productive. However, such studies led us to hypothesize that positive selection for desired phenotypic traits that arose in the mid-twentieth century led to intense inbreeding and the inadvertent amplification of AD and SA associated traits.

RESULTS

This hypothesis was tested with genetic studies of 761 Standard, Miniature, and Miniature/Standard Poodle crosses from the USA, Canada and Europe, coupled with extensive pedigree analysis of thousands more dogs. Genome-wide diversity across the world-wide population was measured using a panel of 33 short tandem repeat (STR) loci. Allele frequency data were also used to determine the internal relatedness of individual dogs within the population as a whole. Assays based on linkage between STR genomic loci and DLA genes were used to identify class I and II haplotypes and disease associations. Genetic diversity statistics based on genomic STR markers indicated that Standard Poodles from North America and Europe were closely related and reasonably diverse across the breed. However, genetic diversity statistics, internal relatedness, principal coordinate analysis, and DLA haplotype frequencies showed a marked imbalance with 30 % of the diversity in 70 % of the dogs. Standard Poodles with SA and AD were strongly linked to this inbred population, with dogs suffering with SA being the most inbred. No single strong association was found between STR defined DLA class I or II haplotypes and SA or AD in the breed as a whole, although certain haplotypes present in a minority of the population appeared to confer moderate degrees of risk or protection against either or both diseases. Dogs possessing minor DLA class I haplotypes were half as likely to develop SA or AD as dogs with common haplotypes. Miniature/Standard Poodle crosses being used for outcrossing were more genetically diverse than Standard Poodles and genetically distinguishable across the genome and in the DLA class I and II region.

CONCLUSIONS

Ancestral genetic polymorphisms responsible for SA and AD entered Standard Poodles through separate lineages, AD earlier and SA later, and were increasingly fixed by a period of close linebreeding that was related to popular bloodlines from the mid-twentieth century. This event has become known as the midcentury bottleneck or MCB. Sustained positive selection resulted in a marked imbalance in genetic diversity across the genome and in the DLA class I and II region. Both SA and AD were concentrated among the most inbred dogs, with genetic outliers being relatively disease free. No specific genetic markers other than those reflecting the degree of inbreeding were consistently associated with either disease. Standard Poodles as a whole remain genetically diverse, but steps should be taken to rebalance diversity using genetic outliers and if necessary, outcrosses to phenotypically similar but genetically distinct breeds.

Less is More--Optimization of DNA Extraction from Canine Feces

Although most DNA crime laboratories may not encounter fecal samples often, they are a familiar sample type in non-human forensic laboratories due to their prevalence in the environment. Fecal matter can be challenging due to low numbers of nucleated cells and the presence of inhibitors that impede amplification success. Sampling location (internal vs. external), sampling quantity (10-200 mg), and various extraction protocols (silica matrix, bead beating, and clean-up column) were evaluated to maximize DNA yield. The greatest yield of intact DNA was obtained using a modified silica matrix extraction protocol (VGL-Fecal) on 30-50 mg of fecal matter collected from the external surface of a stool that had been dried for 24 h. This optimized sampling and extraction protocol was applied to a pilot study where DNA yield and genotyping success were evaluated. By optimizing our collection, sampling, and extraction procedures, a reliable method for maximizing the yield of canine fecal DNA was developed.

Evaluation of microsatellite markers for populations studies and forensic identification of African lions (Panthera leo)

The South African lion (Panthera leo) population is highly fragmented. One-third of its wild lions occur in small (<1000 km(2)) reserves. These lions were reintroduced from other areas of the species' historical range. Management practices on these reserves have not prioritized genetic provenance or heterozygosity. These trends potentially constrain the conservation value of these lions. To ensure the best management and long-term survival of these subpopulations as a viable collective population, the provenance and current genetic diversity must be described. Concurrently, poaching of lions to supply a growing market for lion bones in Asia may become a serious conservation challenge in the future. Having a standardized, validated method for matching confiscated lion parts with carcasses will be a key tool in investigating these crimes. We evaluated 28 microsatellites in the African lion using samples from 18 small reserves and 1 captive facility in South Africa, two conservancies in Zimbabwe, and Kruger National and Kgalagadi Transfrontier Parks to determine the loci most suited for population management and forensic genetic applications. Twelve microsatellite loci with a match probability of 1.1×10(-5) between siblings were identified for forensics. A further 10 could be added for population genetics studies.

Effectiveness of single-nucleotide polymorphisms to investigate cattle rustling

Short tandem repeats (STR)s have been the eligible markers for forensic animal genetics, despite single-nucleotide polymorphisms (SNP)s became acceptable. The technology, the type, and amount of markers could limit the investigation in degraded forensic samples. The performance of a 32-SNP panel genotyped through OpenArrays(TM) (real-time PCR based) was evaluated to resolve cattle-specific forensic cases. DNA from different biological sources was used, including samples from an alleged instance of cattle rustling. SNPs and STRs performance and repeatability were compared. SNP call rate was variable among sample type (average = 80.18%), while forensic samples showed the lowest value (70.94%). The repeatability obtained (98.7%) supports the used technology. SNPs had better call rates than STRs in 12 of 20 casework samples, while forensic index values were similar for both panels. In conclusion, the 32-SNPs used are as informative as the standard bovine STR battery and hence are suitable to resolve cattle rustling investigations.

Use of non-human DNA analysis in forensic science: a mini review

Analysis of non-human DNA in forensic science, first reported about two decades ago, is now commonplace. Results have been used as evidence in court in a variety of cases ranging from abduction and murder to patent infringement and dog attack. DNA from diverse species, including commonly encountered pets such as dogs and cats, to plants, viruses and bacteria has been used and the sheer potential offered by such analyses has been proven. In this review, using case examples throughout, we detail the considerable literature in this field.

Validation of two canine STR multiplex-assays following the ISFG recommendations for non-human DNA analysis

To gain general acceptance forensic DNA testing in animals needs to improve standardization of analysis methods and data interpretation. Recently, the International Society of Forensic Genetics (ISFG) took particular care of this topic by publishing recommendations for forensic non-human DNA analysis following the successful example of human DNA analysis in order to provide a basis for harmonization of the still existing inter-laboratory variability. By following these recommendations we demonstrate the performance of two short tandem repeat (STR) multiplexes for forensic identity testing of canine biological material. Thirteen STRs and two sex-specific markers were selected and validated according to the ISFG guidelines. Population genetic parameters were calculated based on 295 dog samples collected in Austria (124) and Germany (171). A repeat-based nomenclature of the mainly tetrameric STRs and corresponding allelic ladders are presented. All 146 different alleles included in the ladders were sequenced for correct allele calling. Additionally, a canine cell line (DH82-D3167) was evaluated as standard reference material.

Extraction of nuclear DNA from rhinoceros horn and characterization of DNA profiling systems for white (Ceratotherium simum) and black (Diceros bicornis) rhinoceros

Rhinoceros horn is now worth more, per unit weight, than gold, diamonds, or cocaine. Rhinoceros horn has been used in traditional Asian medicine as a presumed cure for a wide range of ailments. Rhinoceros poaching in South Africa has, on average, more than doubled each year over the past 5 years with the rapid economic growth in east and southeast Asia being assumed to be the primary factor driving the increased demand for horn. Here we report on the characterization of methods for genomic DNA extraction from rhinoceros horn and on DNA profiling systems for white (Ceratotherium simum) and black (Diceros bicornis) rhinoceros. The DNA profiling system described includes 22 short tandem repeat (STR), or microsatellite, markers and a gender marker (ZF1), which have been used previously in various studies on rhinoceros. Using a θ value of 0.1, a conservative estimate of random match probability in 5 white rhinoceros ranged from 1:7.3x10(6) to 1:3.0x10(8). Given that the total population of white rhinoceros is approximately 20,000 such random match probabilities indicate that the genotyping system described provides data which can be used for evidentiary purposes. Furthermore, the methods are appropriate for use in investigations involving trace amounts of rhinoceros horn and the matching of profiles obtained from seized rhinoceros horn with material collected from live animals or poached carcasses.

Genetic characterization, at the mitochondrial and nuclear DNA levels, of five Canary Island dog breeds

Many studies presenting genetic analysis of dog breeds have been conducted without the inclusion of island dog breeds, although isolation can be one of the main factors in their origin. Here we report the genetic analysis at the nuclear and mitochondrial DNA levels of five Canary Island dog breeds (Canarian Warren Hound, Canary Island Mastiff, Garafiano Shepherd, La Palma Rat-Hunter and El Hierro Wolfhound) to fill this gap and, at the same time, genetically characterize these breeds. We identified 168 alleles in autosomal microsatellites and 16 mitochondrial haplotypes. Observed and expected heterozygosities ranged from 0.556 to 0.783 and from 0.737 to 0.943 respectively. Furthermore, three haplotypes were newly described and exclusive to a particular breed (A17+ in the Canary Island Mastiff; A33+ in the Canarian Warren Hound; Bi in the La Palma Rat-Hunter). The outcome of our analyses also revealed different breed histories consistent with historical documents and hypothetical origin designations. Although mtDNA haplotypes showed poor breed discriminating power, autosomal markers allowed a clear clustering of each single population. We expect that our results, together with further analyses, will help to make the population histories of island dog breeds clearer.