A proposal for standardization in forensic equine DNA typing: allele nomenclature for 17 equine-specific STR loci

Structure and genetic variability of the Costa Rican Paso horse

The Costa Rican Paso Horse (CPC) is a breed developed in Costa Rica. The objectives were to estimate the genetic structure and evaluate the levels of genetic variability of the population. The genotypes of 14 microsatellites in 3654 records (2052 females and 1602 males) were analyzed. Expected (He) and observed (Ho) heterozygosity, polymorphic information content (CIP), fixation index (FIS), Shannon index, as well as Hardy-Weinberg disequilibrium (DHW) were evaluated. Kinship relationships (Rij) were estimated throughout the entire population. The effective population size (Ne) was calculated, alternating allele frequencies less than 0.05, 0.02 and 0.01. The Bayesian clustering study was carried out to infer how many lines are appropriate from the analysis of genotypes using multiple loci. The number of alleles per locus ranged from 7 to 17, with an average value of 9.6; nine loci presented DHW (P < 0.05); two loci presented negative FIS values, the same as Ho > He; the average of CIP, Ho and He was 0.254, 0.756 and 0.785, respectively. At the 12 loci where He > Ho, the differences ranged from 0.002 to 0.341 (0.036 on average). For Ne, the estimates were 201.9, 230.1, and 241.5. In the Rij, 54.86% of the estimates were in the interval of 0.01 to 77.7%. The number of lines that define the population corresponds to three, with an approximate composition of 33.1%, 32.4% and 34.5%, respectively. The CPC, as a subdivided population with DHW and a reduction in heterozygotes may be associated with possible Wahlund effects. Keywords: Wahlund effect, equines, genetic markers, synthetic breed, Hardy Weinberg.

Replacement of microsatellite markers by imputed medium-density SNP arrays for parentage control in German warmblood horses

In horses, parentage control is currently performed based on an internationally standardized panel of 17 microsatellite (MS) markers comprising 12 mandatory and five optional markers. Unlike MS, single nucleotide polymorphism (SNP) profiles support a wider portfolio of genomic applications, including parentage control. A transition to SNP-based parentage control is favorable, but requires additional efforts for ensuring generation-overlapping availability of marker genotypes of the same type. To avoid double genotyping of either parents or offspring for changing to SNP technology and enable efficient transition, we tested whether MS genotypes used for parentage control could be reliably imputed from a medium-density SNP panel in German warmblood horses. Imputation accuracy was tested in a tenfold cross-validation with two approaches: within breed (option A) and across breeds (option B). Average imputation accuracies of 97.98% (A) and 96.17% (B) were achieved, respectively. Due to interbreed differences in genotyping rates, five MS markers of low genotyping rate (GTR; < 90%) could be imputed with higher accuracy within breed (98.18%) than across breeds (90.73%). MS markers with high GTR performed homogeneously well in option B (98.44%) and showed slightly lower accuracy in option A (97.90%). Among these markers, AHT5 proved to be problematic for imputation regardless of the approach, revealing accuracies of 86.40% (A) and 88.70% (B). Better results for MS markers with high GTR and savings in computational processing justified the choice of option B for routine implementation. To date, more than 9500 horses have undergone the new parentage control based on imputed MS genotypes.

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.

Genetic Variability Trend of Lusitano Horse Breed Reared in Italy

The Lusitano Horse (LH) originates from Portugal, but is reared worldwide. Since 1994, the University of Milan has routinely tested the LHs bred in Italy for parentage control. This study aims to assess the genetic variability of the LH reared in Italy using 16 microsatellites markers. Moreover, the genetic variability changes over the years in the total population (n.384) and in unrelated horses (n.47) were evaluated. Horses were grouped according to their date of birth (1975–1990, 1991–2000, 2001–2010, 2010–2019). Standard genetic diversity parameters, including observed (Ho) and expected (He) heterozygosity, Hardy-Weinberg equilibrium (HWE; P-Val), allelic richness, and inbreeding coefficient (Fis) were estimated. In the whole period, the total population showed Ho as high as 0.69, low Fis (0.057), and imbalance for HWE. When considering the unrelated horses, Ho was seen to increase over time (from 0.594 in 1975–1990 to 0.68 in 2010–2019) and frequencies were in HWE, again having low and decreasing values of Fis (from 0.208 in 1975–1990 to 0.019 in 2010–2019). Bottleneck analysis excluded a recent population decline. Principal Coordinate Analysis at the individual level defined two clusters, the major cluster including all the most recent horses. An increasing number of dams (156% more from 2001–2010 to 2011–2019) supports the good variability recorded in the population so far. However, the high number of foals (77.2%) sired by only four stallions in recent years suggests caution in the choice of the sires for the future.

Monitoring for the genetic structure of Mezen breed of horses in terms of DNA microsatellites

Mezenskaya horse (Mezenka) is Russia’s aboriginal breed. It is a domestic selection in the northern territories of Arkhangelsk region. The breed is perfectly adapted to the conditions of the Far North, and has a number of valuable economic and biological qualities. At present, it has a limited gene pool and is bred only in the Mezensky district, where one gene pool-breeding farm is operating and so is a number of basic farms, where selection and breeding activities take place with the breed. Due to a small population of Mezen horses, the challenge of preserving its intra-breed diversity is very urgent. To determine the degree of genetic variability in the Mezen population, the alleles-fond was monitored. A comparative analysis of the genetic structure of the breed was done on DNA microsatellites at time-intervals of 10 years (2000, 2010 and 2020). Crista samples of 198 horses were studied in specialized laboratories. It was established that the breed has wide genetic diversity in 17 loci of nuclear DNA. The population’s alleles-fond includes from 128, 139, and 133 alleles respectively (with an average value of 7.53, 8.18, and 7.82 alleles per locus). The most common alleles are AHT4O, AHT5N, ASB2K, ASB23S, CA425N, HMS1J, HMS1M, HMS2H, HMS3M, HMS7L, HTG4M, HTG6O, HTG7K, HTG7O and LEX3M. Mezen horses revealed 6 rare, lowfrequency (0.004–0.056) alleles not found in the horse populations of domestic selection. The average value of the polymorphic level (Ae) in the breed over the years is 4.16, 4.21 and 4.06, respectively. The highest polymorphism is found in locus ASB17 (6.49–6.90–6.76); the lowest, in locus HTG6 (1.71–1.66–1.67) and HMS7 (1.77–1.95–1.77). A slight deficit of heterozygous genotypes (Fis = 0.003) was observed in Mezen horses in 2010. In 2000 and 2020, the observed heterozygosity (Ho) exceeds the expected value (He), which indicates the absence of intra-population inbreeding (Fis = –0.014 and –0.011, respectively). The results obtained testify to the effectiveness of breeding activities carried out to preserve, improve and maintain genetic diversity in the population.

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.

Development of a 19-plex short tandem repeat typing system for individual identification and parentage testing of horses (Equus caballus)

Individual identification of horses for pedigree verification and registration is important for the sustainable development of the horse industry. Horse individual identification and parentage tests commonly use the 17 short tandem repeats (STRs) recommended by the International Society for Animal Genetics (ISAG) and the locus LEX33. While many multiplex STR typing systems have been established for the horse, a sex determining marker is usually absent, and none of them can simultaneously detect all 17 ISAG recommended loci and the locus LEX33. Here, we present a 19-plex STR typing system that contains the 17 ISAG recommend loci, the locus LEX33 and amelogenin as sex determining loci. The results of our sensitivity, species specificity, stutter analysis and population data analysis, indicate that this system is a specific, sensitive, and robust tool for the identification of individuals, parentage testing and genetic research in the horse.

Assessment of genetic diversity using microsatellite markers to compare donkeys (Equus asinus) with horses (Equus caballus)

Objective

The study aimed to evaluate the diversity of donkey populations by comparing with the diversity of Thoroughbred and Jeju Halla horses; identified breeding backgrounds can contribute to management and conservation of donkeys in South Korea.

Methods

A total of 100 horse (50 Thoroughbreds and 50 Jeju Halla horses) and 79 donkeys samples were genotyped with 15 microsatellite markers (AHT4, AHT5, ASB2, ASB17, ASB23, CA425, HMS1, HMS2, HMS3, HMS6, HMS7, HTG4, HTG10, LEX3, and VHL20), to identify genetic diversity and relationships among horses and donkeys.

Results

The observed number of alleles per locus ranged from 1 (ASB17, HMS1) to 14 (AHT5), with a mean value of 4.87, 8.00, and 5.87 in Thoroughbreds, Jeju Halla horses, and donkeys, respectively. Of the 15 markers, AHT4, AHT5, ASB23, CA425, HMS2, HMS3, HTG4, HTG10, and LEX3 loci had relatively high polymorphism information content (PIC) values (PIC>0.5) in these three populations. Mean levels of genetic variation were H_E = 0.6721 and H_O = 0.6600 in Thoroughbreds, H_E = 0.7898 and H_O = 0.7100 in Jeju Halla horses, and H_E = 0.5635 and H_O = 0.4861 in donkeys. Of the 15 loci in donkeys, three loci had negative inbreeding coefficients (FIS), with a moderate mean FIS (0.138). The FIS estimate for the HTG4 marker was highest (0.531) and HMS6 marker was lowest (−0.001). The total probability of exclusion value of 15 microsatellite loci was 0.9996 in donkeys.

Conclusion

Genetic cluster analysis showed that the genetic relationship among 79 donkeys was generally consistent with pedigree records. Among the three breeds, donkeys and Thoroughbred horses formed clearly different groups, but the group of Jeju Halla horses overlapped with that of Thoroughbred horses, suggesting that the loci would be suitable for donkey parentage testing. Therefore, the results of this study are a valid tool for genetic study and conservation of donkeys.

Dynamics of the Inbreeding Coefficient and Homozygosity in Thoroughbred Horses in Russia

The Thoroughbred (TB) horse has hugely impacted the development of horse breeding around the world. This breed has unique genetic qualities due to having had a closed studbook for approximately 300 years. In Russia, TBs have been bred since the second half of the 18th century. Here, we analyzed the genetic diversity and the inbreeding level in TB horses (n = 9680) for the period from 1990 to 2018 using polymorphisms of 17 microsatellite loci. We found that the genetic structure of the TB breed in Russia is represented by 100 alleles of panel STR (short tandem repeat) loci and has been stable for the past three decades. The conducted monitoring revealed a slight increase in the Wright's inbreeding coefficient in all age and sex groups of TB horses (stallions, broodmares, and foals) from 0.68% to 0.90%, which was followed by a decrease in the degree of heterozygosity, Ho, from 68.5% to 67.6%. The Spearman's rank correlation coefficient between the level of inbreeding and the degree of homozygosity was estimated (r = 0.022; p > 0.05). The obtained data on the DNA genotypes of horses of different breeds provide a unique base for the evaluation of genetic variability and the control of genetic variability of horses in selection programs.

Genetic Testing in the Horse

Genetic testing in horses began in the 1960s, when parentage testing using blood group markers became the standard. In the 1990s, parentage testing shifted from evaluating blood groups to DNA testing. The development of genetics and genomics in both human and veterinarian medicine, along with continued technological advances in the last 2 decades, has helped unravel the causal variants for many horse traits. Genetic testing is also now possible for a variety of phenotypic and disease traits and is used to assist in breeding and clinical management decisions. This article describes the genetic tests that are currently available for horses.

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.

Assessment of line differentiation in the Thoroughbred horse breed using DNA microsatellite loci

The Thoroughbred (TB) horse is the best racehorse breed used in the racing industry. This breed has had a closed studbook for about 300 years. In Russia TB horses have been bred since the second half of the XVIII century. The modern Russian Stud Book register of TB horses is partially presented by stallions and broodmares imported from different countries. The genealogical structure of the breed is represented by 17 lines, among which the Northern Dancer line dominates (30.9 %). The study of features of different lines of TB was carried out on 17 loci of DNA microsatellites (VHL20, HTG4, AHT4, HMS7, HTG6, AHT5, HMS6, ASB23, ASB2, HTG10, HTG7, HMS3, HMS2, ASB17, LEX3, HMS1 and CA425) to assess genetic differentiation of the genealogical structure. The results of the DNA typing of 8091 Thoroughbred horses across microsatellite loci show that the gene pool of the domestic population is represented by 100 alleles typical of the breed. A comparative analysis of the genotypes of horses representing different lines indicates that they differ in the number of alleles (85–99), allele frequencies, the level of polymorphism Ae (2.93–3.48) and the degree of the observed heterozygosity Ho (0.653–0.739). The genetic distances between the lines varied in a wide range from 0.014 (Nasrullah – Northern Dancer) to 0.125 (Massine – Teddy). The correspondence to HWE was maintained in most lines, which is confirmed by the negative values of Fis. Cluster analysis demonstrated the correspondence of the obtained dendrogram of Nei’s genetic distances to its genealogical scheme of lines. Genetic differentiation of lines by index Fst varied in a range 0.005–0.073 at the mean value Fst = 0.024. The data indicate genetic differentiation of lines of TB at the STR markers and confirm the effectiveness of the system of linear breeding for the maintenance of interbreed biodiversity.

Intrafollicular oocyte transfer in the horse: effect of autologous vs. allogeneic transfer and time of administration of ovulatory stimulus before transfer

PURPOSE

To assess meiotic and developmental competence after transfer of immature cumulus-oocyte complexes (COCs) to the preovulatory follicles of mares (intrafollicular oocyte transfer (IFOT)).

METHODS

In Experiment 1, mares received an ovulatory stimulus at IFOT. Thirty hours later, COCs were recovered from the follicle, and mature oocytes underwent ICSI and embryo culture. In Experiments 2 and 3, autologous vs. allogeneic COCs were used. The mares were inseminated and embryos were recovered. In Experiment 3, the ovulatory stimulus was administered 9 h (autologous) and 15 h (allogeneic) before IFOT. In Experiment 4, only allogeneic COCs were used; the ovulatory stimulus was administered 9 or 15 h before IFOT. Excess embryos (autologous) and parentage-verified embryos (allogeneic) were considered IFOT-derived.

RESULTS

In Experiment 1, 36/54 IFOT oocytes (67%) were recovered, of which 56% were mature, vs. 49% of in vitro matured oocytes (P > 0.1). After ICSI, blastocyst rates were 25% and 18%, respectively (P > 0.1). In Experiment 2, 0/6 autologous and 2/6 allogeneic IFOT yielded IFOT-derived embryos. In Experiment 3, 0/7 autologous and 2/5 allogeneic IFOT yielded IFOT-derived embryos. The proportion of mares yielding IFOT-derived embryos was lower after autologous vs. allogeneic IFOT (0/13 vs. 4/11; P < 0.05). In Experiment 4, 1/8 9-h and 1/7 15-h IFOT yielded IFOT-derived embryos.

CONCLUSIONS

Transferred oocytes mature within the follicle and can maintain developmental competence. Allogeneic IFOT was more efficient than was autologous IFOT. The time of ovulatory stimulation did not affect embryo yield. The IFOT procedure is still not repeatable enough to be recommended for clinical use.

Effect of intra-ovarian injection of mesenchymal stem cells in aged mares

PURPOSE

This study aims to determine if intra-ovarian injection of bone marrow-derived mesenchymal stem cells (MSCs) improves or restores ovarian function in aged females.

METHODS

Prospective randomized study of eight aged mares and six young mares receiving intra-ovarian injection of MSCs or vehicle. Main outcome measures were antral follicle count and serum anti-Müllerian hormone (AMH) (aged and young mares), and for aged mares, oocyte meiotic and developmental competence; gross and histological ovarian assessment; evaluation of presence of chimerism in recovered granulosa cells and in ovarian tissue samples; and gene expression in ovarian tissue as assessed by RNA sequencing.

RESULTS

Injection of MSCs was not associated with significant changes in follicle number, oocyte recovery rate on follicle aspiration, oocyte maturation rate, or blastocyst rate after ICSI in aged mares, or in changes in follicle number in young mares. There were no significant changes in peripheral AMH concentrations, indicating a lack of effect on growing follicles. MSC donor DNA was not recovered in granulosa cells or in ovarian tissue, indicating lack of persistence of injected MSC. RNA sequencing revealed significant differences in gene expression between MSC- and vehicle-injected ovaries.

CONCLUSIONS

Intra-ovarian injection of bone marrow-derived MSCs altered gene expression but did not improve ovarian function in aged mares.

Genetic diversity and population structure of Polish Arabian horses assessed through breeding and microsatellite data

Polish Arabian horses are one of the most important populations of this breed in the world. Their post-war history can be divided into two periods, with the dominant role of state studs until 1989, and the increasing significance of private breeding in the next years. The goal of the study was to evaluate genetic diversity and structure of the population under a new breeding policy. The analyses of breeding and microsatellite data from 1996 to 2012 provide a coherent picture of the population with constant flow of horses only in one direction from state to private studs. An increase in the number of broodmares was observed, from 396 mares in 1996 to 1021 mares in 2012. The proportion of foreign sires used in Polish studs also increased, from 7.1% to 37.0%. An increasing number of alleles and progressive differentiation in mares were observed. STRUCTURE analysis indicated that the Polish horses were clearly separated from foreign horses used in Polish breeding, although only one of the 75 alleles found can be considered as typically Polish. The high heterozygosity is an important feature of the Polish population; however, the decrease of heterozygosity in state broodmares was noted. This issue needs to be studied further.

Forensic genetics and genomics: Much more than just a human affair

While traditional forensic genetics has been oriented towards using human DNA in criminal investigation and civil court cases, it currently presents a much wider application range, including not only legal situations sensu stricto but also and, increasingly often, to preemptively avoid judicial processes. Despite some difficulties, current forensic genetics is progressively incorporating the analysis of nonhuman genetic material to a greater extent. The analysis of this material-including other animal species, plants, or microorganisms-is now broadly used, providing ancillary evidence in criminalistics in cases such as animal attacks, trafficking of species, bioterrorism and biocrimes, and identification of fraudulent food composition, among many others. Here, we explore how nonhuman forensic genetics is being revolutionized by the increasing variety of genetic markers, the establishment of faster, less error-burdened and cheaper sequencing technologies, and the emergence and improvement of models, methods, and bioinformatics facilities.

Diversity and effective population size of four horse breeds from microsatellite DNA markers in South-Central Mexico

Abstract. The South-Central region of Mexico has experienced a sizeable introduction of purebred horses for recreational aims. A study was designed to assess effective population sizes and genetic diversity and to verify the genetic integrity of four horse breeds. Using a 12-microsatellite panel, Quarter Horse, Azteca, Thoroughbred and Creole (CRL) horses were sampled and analysed for diversity and genetic structure. Genetic diversity parameters showed high numbers of heterozygous horses but small effective population sizes in all breeds. Population structure results suggested some degree of admixture of CRL with the other reference breeds. The highly informative microsatellite panel allowed the verification of diversity in introduced horse populations and the confirmation of small effective population sizes, which suggests a risk for future breed integrity.

Genetic diversity of Halla horses using microsatellite markers

BACKGROUND

Currently about 26,000 horses are breeding in Korea and 57.2% (14,776 horses) of them are breeding in Jeju island. According to the statistics published in 2010, the horses breeding in Jeju island are subdivided into Jeju horse (6.1%), Thoroughbred (18.8%) and Halla horse (75.1%). Halla horses are defined as a crossbreed between Jeju and Thoroughbred horses and are used for horse racing, horse riding and horse meat production. However, little research has been conducted on Halla horses because of the perception of crossbreed and people's weighted interest toward Jeju horses.

METHOD

Using 17 Microsatellite (MS) Markers recommended by International Society for Animal Genetics (ISAG), genomic DNAs were extracted from the hair roots of 3,880 Halla horses breeding in Korea and genetic diversity was identified by genotyping after PCR was performed.

RESULTS AND CONCLUSION

In average, 10.41 alleles (from 6 alleles in HTG7 to 17 alleles in ASB17) were identified after the analysis using 17 MS Markers. The mean value of Hobs was 0.749 with a range from 0.612(HMS1) to 0.857(ASB2). Also, it was found that Hexp and PIC values were lowest in HMS1 (0.607 and 0.548, respectively), and highest in LEX3(0.859 and 0.843, respectively), and the mean value of Hexp was 0.760 and that of PIC was 0.728. 17 MS markers used in this studies were considered as appropriate markers for the polymorphism analysis of Halla horses. The frequency for the appearance of identical individuals was 5.90 × 10-20 when assumed as random mating population and when assumed as half-sib and full-sib population, frequencies were 4.08 × 10-15 and 3.56 × 10-8, respectively. Based on these results, the 17 MS markers can be used adequately for the Individual Identification and Parentage Verification of Halla horses. Remarkably, allele M and Q of ASB23 marker, G of HMS2 marker, H and L of HTG6 marker, L of HTG7 marker, E of LEX3 marker were the specific alleles unique to Halla horses.

Similarity in sex and reproductive state, but not relatedness, influence the strength of association in the social network of feral horses in the Blauwe Kamer Nature Reserve

Relatedness is likely to affect the decisions of animals regarding their affiliations with conspecifics. Social network analysis provides tools to describe the social structure of animals. Here, we investigate the social network of a population of 27 unmanaged Konik horses in the Blauwe Kamer Nature Reserve, in the Netherlands. We test three hypotheses: (1) that related individuals will have stronger associations; (2) that individuals with low values of average relatedness to their neighbors in the network will have more links and (3) homophily, the tendency of individuals to associate with similar others, will lead to stronger associations among individuals of similar sex, reproductive state, age and rank in the social network. We videotaped 22 horses (excluding foals) and their interactions. Relatedness was calculated from the pedigree, which was based on parentage, determined by DNA analysis. The social network was based on spatial proximity data. There was no significant influence of relatedness on strength of associations in the network or an influence of age- or rank-homophily. We argue that the lack of a relatedness effect is not likely to have been caused by an inability to detect kinship. Strength of associations in the social network was significantly affected by the tendency of the horses to associate with individuals of the same sex and the same reproductive state. This social network pattern is not common in mammals, and the study of unexplained variation in choice and strength of associations may have important implications for other equids increasingly confined to reserves worldwide.

Genetic diversity in Hucul and Polish primitive horse breeds

Abstract. Pedigree and molecular data were used to evaluate genetic diversity in the Polish populations of the Polish primitive horse (also known as Polish Konik) and Hucul breeds over the time period of 30 years (1980–2011). Based on genotypes in 12 microsatellite loci (for 3865 Polish primitive horses and 1627 Huculs), as well as on pedigree data derived from over 7000 individuals (both breeds), several indices describing structure of the analysed populations were estimated. For both analysed breeds, we observed an increasing trend of inbreeding since 1980 which seems to be much more stable (oscillating around 10 % in the Polish primitive horse and 5 % in Hucul) since the beginning of 2000s when they were included in conservation programs in Poland. We observed that generally, indices related to genetic diversity are higher in the Hucul breed. Our study indicated that genetic diversity in the Polish primitive horse and Hucul breeds in Poland is still relatively high and conservation programs should be continued to keep it on the "safe" level in the future.

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.

Identification of sample donor by 24-plex short tandem repeat in a post-race equine plasma containing dexamethasone

BACKGROUND

Animal sport such as horseracing is tainted with drug abuse as are human sports. Treatment of racehorses on race day with therapeutic medications in most cases is banned, and thus, it is essential to monitor the illicit use of drugs in the racing horse to maintain integrity of racing, ensure fair competition and protect the health, safety and welfare of the horse, jockeys and drivers. In the event of a dispute over the identity of the sample donor, if the regulator can provide evidence that the DNA genotype profile of the post-race sample matched that of the alleged donor, then the potential drug violation case might be easily resolved without legal challenges.

CASE DESCRIPTION

We present a case study of a racehorse sample that tested positive for dexamethasone in a post-race plasma sample in Pennsylvania (PA) but the result was challenged by the trainer of the horse. Dexamethasone is a synthetic glucocorticoid widely used in the management of musculoskeletal problems in horses but its presence in the horse during competition is banned by the PA Racing Commissions. The presence of dexamethasone in the post-competition plasma sample was confirmed using liquid chromatography-tandem mass spectrometry. However, this finding was challenged by the trainer of the horse alleging that the post-race sample was not collected from his/her horse and thus petitioned the Commission to be absolved of any wrong-doing. To resolve the dispute, a DNA test was ordered by the PA Racing Commission to identify the correct donor of the dexamethasone positive sample. For this purpose, a 24-plex short tandem repeat analysis to detect 21 equine markers and three human markers was employed. The results indicated that all the samples tested had identical DNA profiles and thus, it was concluded that the samples were collected from the same horse and that the probability of drawing a false conclusion was approximately zero (1.5 × 10(-15)).

CONCLUSIONS

The plasma sample confirmed for the presence of dexamethasone was collected from the alleged horse.

Current and future directions of DNA in wildlife forensic science

Wildlife forensic science may not have attained the profile of human identification, yet the scale of criminal activity related to wildlife is extensive by any measure. Service delivery in the arena of wildlife forensic science is often ad hoc, unco-ordinated and unregulated, yet many of those currently dedicated to wildlife conservation and the protection of endangered species are striving to ensure that the highest standards are met. The genetic markers and software used to evaluate data in wildlife forensic science are more varied than those in human forensic identification and are rarely standardised between species. The time and resources required to characterise and validate each genetic maker is considerable and in some cases prohibitive. Further, issues are regularly encountered in the construction of allelic databases and allelic ladders; essential in human identification studies, but also applicable to wildlife criminal investigations. Accreditation and certification are essential in human identification and are currently being strived for in the forensic wildlife community. Examples are provided as to how best practice can be demonstrated in all areas of wildlife crime analysis and ensure that this field of forensic science gains and maintains the respect it deserves. This review is aimed at those conducting human identification to illustrate how research concepts in wildlife forensic science can be used in the criminal justice system, as well as describing the real importance of this type of forensic analysis.

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.

Comparison of the effectiveness of microsatellites and SNP panels for genetic identification, traceability and assessment of parentage in an inbred Angus herd

During the last decade, microsatellites (short tandem repeats or STRs) have been successfully used for animal genetic identification, traceability and paternity, although in recent year single nucleotide polymorphisms (SNPs) have been increasingly used for this purpose. An efficient SNP identification system requires a marker set with enough power to identify individuals and their parents. Genetic diagnostics generally include the analysis of related animals. In this work, the degree of information provided by SNPs for a consanguineous herd of cattle was compared with that provided by STRs. Thirty-six closely related Angus cattle were genotyped for 18 STRs and 116 SNPs. Cumulative SNPs exclusion power values (Q) for paternity and sample matching probability (MP) yielded values greater than 0.9998 and 4.32E(-42), respectively. Generally 2-3 SNPs per STR were needed to obtain an equivalent Q value. The MP showed that 24 SNPs were equivalent to the ISAG (International Society for Animal Genetics) minimal recommended set of 12 STRs (MP ∼ 10(-11)). These results provide valuable genetic data that support the consensus SNP panel for bovine genetic identification developed by the Parentage Recording Working Group of ICAR (International Committee for Animal Recording).

Development of the first standardised panel of two new microsatellite multiplex PCRs for gilthead seabream (Sparus aurata L.)

The high number of multiplex PCRs developed for gilthead seabream (Sparus aurata L.) from many different microsatellite markers does not allow comparison among populations. This highlights the need for developing a reproducible panel of markers, which can be used with safety and reliability by all users. In this study, the first standardised panel of two new microsatellite multiplex PCRs was developed for this species. Primers of 138 specific microsatellites from the genetic linkage map were redesigned and evaluated according to their genetic variability, allele size range and genotyping reliability. A protocol to identify and classify genotyping errors or potential errors was proposed to assess the reliability of each marker. Two new multiplex PCRs from the best assessed markers were designed with 11 markers in each, named SMsa1 and SMsa2 (SuperMultiplex Sparus aurata). Three broodstocks (59, 47 and 98 breeders) from different Spanish companies, and a sample of 80 offspring from each one, were analysed to validate the usefulness of these multiplexes in the parental assignation. It was possible to assign each offspring to a single parent pair (100% success) using the exclusion method with SMsa1 and/or SMsa2. In each genotyped a reference sample (Ref-sa) was used, and its DNA is available on request similar to the kits of bin set to genotype by genemapper (v.3.7) software (kit-SMsa1 and kit-SMsa2). This will be a robust and effective tool for pedigree analysis or characterisation of populations and will be proposed as an international panel for this species.

Towards standardization of canine STRs: a proposed nomenclature for six markers from the ISAG comparison-test panel

Eight short tandem repeat markers included in the International Society for Animal Genetics panel of 24 loci investigated in canine comparison tests were analysed in a sample of pure-breed dogs, with the purpose of defining an allele nomenclature based on the number of repeats. A regression analysis of the raw data produced by the sequencer, coupled with the direct sequencing of selected alleles, allowed us to propose a system of nomenclature for six of the eight loci (four di-nucleotidic: AHT121, AHTh137, REN169018 and REN64E19, and two tetra-nucleotidic: FH2001 and FH2328). The remaining two loci (INU055 and FH2848) showed a pattern of fragments that did not resolve in a simple allele series. This work may be useful to establish a basis for comparing data across different laboratories for a set of validated canine markers, which can be used in population genetics, forensics and other analyses.

Gametic phase disequilibrium between the syntenic multiallelic HTG4 and HMS3 markers widely used for parentage testing in Thoroughbred horses

Validation of parentage and horse breed registries through DNA typing relies on estimates of random match probabilities with DNA profiles generated from multiple polymorphic loci. Of the twenty-seven microsatellite loci recommended by the International Society for Animal Genetics for parentage testing in Thoroughbred horses, eleven are located on five chromosomes. An important aspect in determining combined exclusion probabilities is the ascertainment of the genetic linkage status of syntenic markers, which may affect reliable use of the product rule in estimating random match probabilities. In principle, linked markers can be in gametic phase disequilibrium (GD). We aimed at determining the extent, by frequency and strength, of GD between the HTG4 and HMS3 multiallelic loci, syntenic on chromosome 9. We typed the qualified offspring (n (1) = 27; n (2) = 14) of two Quarter Bred stallions (registered by the Brazilian Association of Quarter Horse Breeders) and 121 unrelated horses from the same breed. In the 41 informative meioses analyzed, the frequency of recombination between the HTG4 and HMS3 loci was 0.27. Consistent with genetic map distances, this recombination rate does not fit to the theoretical distribution for independently segregated markers. We estimated sign-based D' coefficients as a measure of GD, and showed that the HTG4 and HMS3 loci are in significant, yet partial and weak, disequilibrium, with two allele pairs involved (HTG4 M/HMS3 P, D'(+) = 0.6274; and HTG4 K/HMS3 P, D'(-) = -0.6096). These results warn against the inadequate inclusion of genetically linked markers in the calculation of combined power of discrimination for Thoroughbred parentage validation.

Microsatellite based ovine parentage testing to identify the source responsible for the killing of an endangered species

In this study, we present an animal forensic genetics case in which we applied ovine microsatellite based parentage testing to the resolution of an act against protected wildlife. The aim was to identify the origin of the animal responsible for the death of an Egyptian vulture (Neophron percnopterus) that had been poisoned through consumption of a Latxa Blond Face breed lamb. Thus, we carried out a 22 microsatellite based parentage test in order to identify the parents of the lamb in the flock which grazes in the same place where the vulture's remains were found. Multiple parentage analysis revealed two possible parents, one ewe and one ram, with a combined paternity/maternity index (PI) higher than 9.09E9 and a likelihood (W) value of 99.9999%, assuming 50% probability a priori. This result confirmed the flock of origin of the poisoned lamb and shows that the microsatellite panel described herein is a potentially useful tool for the resolution of animal forensic cases.

Genotyping in the Brazilian Criollo Horse Stud Book: resources and perspectives

The goal of this research was to evaluate the ability of the genotyping information available in the Brazilian Criollo Horse Stud Book to describe the genetic variability of the breed and the exclusion probability determined in comparative tests. Altogether, two softwares were used in the analyses of the available genotypes: Cervus 3.0.3 and Genepop 4.0. Eight microsatellite markers totaled 109 alleles, with an average of 13.6 +/- 0.6 alleles per locus. Large differences between expected and observed heterozygosity were ubiquitous (0.821 +/- 0.07 and 0.470 +/- 0.17, respectively). Although the estimated null allele frequency caused initial concern (0.284 +/- 0.199), it is likely that it was a reflection of the inbreeding coefficients found (0.432 +/- 0.184). All loci showed significant deviation from Hardy-Weinberg equilibrium, with heterozygote deficit (P < 0.0001) and genotypic linkage disequilibrium with at least one marker. The high polymorphic information content (0.798 +/- 0.088) could not warrant exclusion power for three loci (HMS7, HMS6 and HTG4) above 50% (0.491 +/- 0.158). However, combined exclusion probability reached 99.61%, a level close to ideal. The results demonstrate the excellent performance of the markers assessed in describing the genetic status of the breed and suggest the considerable ability to establish parentage.