International Society For Animal Genetics Research Articles

Evaluation of the effectiveness of single nucleotide polymorphisms compared to microsatellite markers for parentage verification in Moroccan horses.

The International Society for Animal Genetics (ISAG) currently advocates for a transition towards single nucleotide polymorphism (SNP) markers as a potential alternative for equine parentage verification. To ascertain the efficacy of this transition, it is imperative to evaluate the performance of parentage testing using SNPs in juxtaposition with short tandem repeats (STRs). As per ISAG's recommendation, we used an equine genotyping-by-sequencing panel with 144 SNPs for this purpose. Equine parentage is currently realized using 16 microsatellites (STRs) excluding the LEX3 marker. In this study, 1074 horses were genotyped using the 144 SNPs panel, including 432 foals, 414 mares, and 228 stallions, from five different breeds: 293 Arabians, 167 Barbs, 189 Thoroughbreds, 73 Anglo-Arabians, and 352 Arabian-Barbs. As a result, two SNPs markers were eliminated from the panel system due to inconsistent amplification across all examined individuals leaving 142 SNPs markers for analysis. A comparative analysis between SNPs and STRs markers revealed that the mean expected heterozygosity was 0.457 for SNPs and 0.76 for STRs, while the mean observed heterozygosity stood at 0.472 for SNPs and 0.72 for STRs. Furthermore, the probability of identity was calculated to be 5.722 × 10-57 for SNPs and 1.25 × 10-15 for STRs markers. In alignment with the Hardy-Weinberg equilibrium in polyploids test, 110 out of the total SNPs were consistent with the Hardy-Weinberg equilibrium in polyploids test (p > 0.05). Employing both SNPs and STRs markers, the mean polymorphic information content was discerned to be 0.351 for SNPs and 0.72 for STRs. The cumulative exclusion probabilities for SNP markers exceeded 99.99%, indicating that the 142 SNPs panel might be adequate for parentage testing. In contrast, when utilizing STRs markers, the combined average exclusion probabilities for one and both parents were determined to be 99.8% and 99.9%, respectively. Our comprehensive study underscores the potential of SNPs in equine parentage verification, especially when compared to STRs in terms of exclusion probabilities. As a corollary, the application of SNPs for parentage verification and identification can significantly contribute to the conservation initiative for the five Moroccan horse breeds. Nonetheless, further research is required to address and replace the deficient SNPs within the panel.

Transmission ratio distortion detection by neutral genetic markers in the Pura Raza Española horse breed

Transmission Ratio Distortion (TRD) is a genetic phenomenon widely demonstrated in several livestock species, but barely in equine species. The TRD occurs when certain genotypes are over- or under-represented in the offspring of a particular mating and can be caused by a variety of factors during gamete formation or during embryonic development. For this study, 126 394 trios consisting of a stallion, mare, and offspring were genotyped using a panel of 17 neutral microsatellite markers recommended by the International Society for Animal Genetics for paternity tests and individual identification. The number of alleles available for each marker ranges from 13 to 18, been 268 the total number of alleles investigated. The TRDscan v.2.0 software was used with the biallelic procedure to identify regions with distorted segregation ratios. After completing the analysis, a total of 12 alleles (out of 11 microsatellites) were identified with decisive evidence for genotypic TRD; 3 and 9 with additive and heterosis patterns, respectively. In addition, 19 alleles (out of 10 microsatellites) were identified displaying allelic TRD. Among them, 14 and 5 were parent-unspecific and stallion-mare-specific TRD. Out of the TRD regions, 24 genes were identified and annotated, predominantly associated with cholesterol metabolism and homeostasis. These genes are often linked to non-specific symptoms like impaired fertility, stunted growth, and compromised overall health. The results suggest a significant impact on the inheritance of certain genetic traits in horses. Further analysis and validation are needed to better understand the TRD impact before the potential implementation in the horse breeding programme strategies.

Evaluation of parentage testing using single nucleotide polymorphism markers for draft horses in Japan.

We evaluated the utility of single nucleotide polymorphism (SNP) markers for parentage testing in Breton (BR) and Percheron (PR) horses in Japan using the proposed International Society for Animal Genetics (P-ISAG) 147 SNP panel and 414 autosomal SNPs. Genomic DNA was extracted from 98 horses of two breeds, BR (n = 47) and PR (n = 51), and sequenced using next-generation sequencing. The average minor allele frequencies for the P-ISAG panel for BR and PR were 0.306 and 0.301, respectively. The combined probabilities of exclusion (PEs) given two parents and one offspring: exclude a relationship (PE01) and given one parent and one offspring: exclude their relationship (PE02) were over 0.9999 for both breeds. Using the P-ISAG panel, no exclusion or doubtful cases were identified in 35 valid parent-offspring pairs, suggesting that the P-ISAG panel is helpful for parentage verification in both breeds. In contrast, as 0.18% of falsely accepted parentages were observed in the parentage discovery cases, additional markers such as the combination of the P-ISAG panel and 414 autosomal SNPs (561-SNP set) presented here should be used to identify valid parent-offspring pairs of horses with unknown parentage relationships.

Analysis of genetic diversity and structure of Mongolian horse using microsatellite markers

Mongolian horses are one of the oldest horse breeds, and are very important livestock in Mongolia as they are used in various fields such as transportation, food (milk, meat), and horse racing. In addition, research and preservation on pure Mongolian breeds are being promoted under the implementation of the new Genetics of Livestock Resources' act in Mongolia. However, despite the implementation of this act, genetic research on Mongolian horses using microsatellites (MS) has not progressed enough. Therefore, this study was conducted to analyze the genetic polymorphism of five breeds (Gobi shankh, Tes, Gal shar, Darkhad, and Undurshil) using 14 MS markers recommended by International Society for Animal Genetics (ISAG). The mean number of alleles (MNA) was 8.29, expected heterozygosity frequency (HExp) was 0.767, observed heterozygosity frequency (HObs) was 0.752, and polymorphism information content (PIC) was 0.729. The Nei's genetic distance analysis showed that the genetic distance between Gobi shankh and Darkhad horses was the farthest, and the other three breeds, Tes, Gal shar, and Undurshil were found to be close to each other. Similarly, the principal coordinate analysis (PCoA) and factorial correspondence analysis (FCA) showed that the Gobi shankh and Darkhad horses were genetically distinct from other breeds. On the other hand, it appears that Tes, Gal shar, and Undurshil horses, which are genetically similar, most likely interbred with each other. Therefore, it is expected that these results will help the conservation of genetic resources in Mongolia and the establishment of policies related to Mongolian horses.

Genetic structure of reconstituted native Carpathian goat breed based on information from microsatellite markers

Abstract The aim of the study was to evaluate the genetic structure of the reconstituted native Carpathian goat breed based on information from microsatellite markers. The study analysed of 14 microsatellite markers recommended by the International Society for Animal Genetics (ISAG) for goats individual identification and parentage testing. Blood samples were taken from 249 Carpathian goats from 14 farms. All microsatellite markers deployed in this analysis showed sufficient polymorphism to assess genetic variation in Carpathian goats and the ISAG-recommended panel for goat individual identification and parentage testing is a highly useful one. The present study showed the status of the genetic structure of the reconstituted population of Carpathian goats. Carpathian goats maintained in Poland were characterized by relatively high genetic diversity (the average of alleles per locus was 9.143), high values of heterozygosity and a low level of inbreeding coefficient. The obtained parameters indicate the correctness of the breeding activities carried out within the framework of the programme for the protection of genetic resources and give guidelines for taking further steps related to the breeding of this valuable native breed.

Genetic diversity and population structure of Mongolian regional horses with 14 microsatellite markers

ObjectiveThis study aimed to identify the genetic diversity and population structure of Mongolian horse populations according to the province of residence (Khentii, KTP; Uvs, USP; Omnogovi and Dundgovi, GOP; Khovsgol, KGP) using 14 microsatellite (MS) markers.MethodsA total of 269 whole blood samples were obtained from the four populations (KTP, USP, GOP, KGP) geographically distinct provinces. Multiplex polymerase chain reaction (PCR) was conducted using 14 MS markers (AHT4, ASB2, ASB17, ASB23, CA425, HMS1, HMS2, HMS3, HMS6, HMS7, HTG4, HTG6, HTG7, and VHL20), as recommended by the International Society for Animal Genetics. Capillary electrophoresis was conducted using the amplified PCR products, alleles were determined. Alleles were used for statistical analysis of genetic variability, Nei’s DA genetic distance, principal coordinate analysis (PCoA), factorial corresponding analysis (FCA), and population structure.ResultsOn average, the number of alleles, expected heterozygosity (HExp), observed heterozygosity (HObs), and polymorphic information content among all populations were 11.43, 0.772, 0.757, and 0.737, respectively. In the PCoA and FCA, GOP, and KGP were genetically distinct from other populations, and the KTP and USP showed a close relationship. The two clusters identified using Nei’s DA genetic distance analysis and population structure highlighted the presence of structurally clear genetic separation.ConclusionOverall, the results of this study suggest that genetic diversity between KTP and USP was low, and that between GOP and KGP was high. It is thought that these results will help in the effective preservation and improvement of Mongolian horses through genetic diversity analysis and phylogenetic relationships.

Formation of the genetic structure of cattle populations by single locus DNA fragments depending on their productivity direction and origin

Aim. Our work was aimed at investigating the specificities in the formation of the genetic structure of populations depending on the productivity direction of cattle, bred in Ukraine, using single locus DNA fragments, and studying the impact of the parental form on genetic polymorphism of modern intensive specialized breeds as a factor. Methods. The following methods were used in the work: veterinary methods (peripheral blood sampling); molecular-genetic meth- ods (the isolation and genotyping of DNA samples of dairy (83 animals), meat (192 animals) and aboriginal (43 ani- mals) cattle, bred in Ukraine, were performed by 10 microsatellite loci from the list, recommended by the International Society for Animal Genetics (ISAG); the complex of statistics methods was used for mathematic-statistical analysis, using modern software. Results. The analysis by 10 microsatellite loci demonstrated the specificities of genetic dif- ferentiation and the similarities between the investigated cattle populations, bred in Ukraine. Our results provide new information about the impact of artificial selection factors on single locus DNA fragments under the specialization of cattle breeds. The impact of the factor of ancestral form on the genetic structure was determined and confirmed by the same polymorphism spectra of the investigated DNA fragments in the maternal and derivative breeds. Another con- firmation was found in the differences, observed in animals of different productivity directions, which are a probable result of the breed-forming process, demonstrated by the results of the mathematic calculations of the data obtained. It was shown that microsatellite DNA loci are highly informative markers of genetic processes, occurring in domestic cattle populations. Conclusions. The specificities in the formation of the genetic structure of populations depending on the productivity direction of animals were determined. The impact of the parental form on genetic polymorphism of modern intensive specialized breeds was noted. It was found that among 10 microsatellite loci, used by us, there were loci in each group of animals, regarding which the hypothesis about their neutrality was reliably rejected accord- ing to the results of Ewens-Watterson test: for dairy cattle (INRA023, ETH3, ETH225, BM1824, BM2113, ETH10 and SPS115), for meat cattle (TGLA122 and ETH225), and for aboriginal cattle (TGLA126, INRA023 and TGLA227). We determined a high level of genetic diversity, remarkable for each investigated cattle population, bred in Ukraine, and general tendencies of differentiation in the selected populations depending on the targeted breeding work, on the level of polymorphism of microsatellite DNA loci (Friedman’s test: P < 0.01), and a similar genetic picture for a number of loci of investigated DNA fragments, which may be related to the history of creating these breeds.

Correlations between microsatellite DNA heterozygosity and reproductive traits in Large White sows

The main aim of this paper was to determine whether heterozygosity (assessed using microsatellite genotypes) was correlated with the reproductive traits in sows. The study was conducted on two herds of sows of the Large White sows breed at the Limited Liability Company “Tavriys’ki svyni” (Kherson region, Ukraine) and the Agricultural Private Enterprise “Techmet-Yug” (Mykolayiv region, Ukraine). During the study, we used eleven microsatellite loci recommended by International Society for Animal Genetics (ISAG) – S0101, S0155, S0228, S0355, S0386, Sw24, Sw72, Sw240, Sw857, Sw936 and Sw951. The litter records included information on the total number of piglets born (TNB), number of piglets born alive (NBA), number of stillborn piglets (NSB), frequency of stillborn piglets (FSB), litter size at weaning (NW) in the first five parities. Individual heterozygosity estimates (for each microsatellite loci separately) and microsatellite multilocus heterozygosity (for all used loci) estimates (MLH) were used in our analysis. ANOVA was used to determine the relationship of the dependent effects (reproductive traits) to single locus heterozygosity using two classes: 0 (for homozygous individuals) and 1 (for heterozygous individuals). In addition, the following indicators were calculated for each genotype: the squared distances (d2) between alleles within an individual for each microsatellite loci and mean squared distances (mean d2) between alleles within an individual for 11 microsatellite loci. Spearman’s rank correlation coefficients were used to measure the association between d2 (for each microsatellite loci) and reproductive traits in sows. ANOVA on reproductive traits of sows belonging to different MLH and mean d2 classes was also undertaken. For sows from the Agricultural Private Enterprise “‘Techmet-Yug” were observed negative associations between heterozygosity and reproductive traits. We conclude that care should be taken when crossing between different breeders (English and Hungarian selection) to avoid outbreeding depression.

تخمین ساختار تنوع، تنگنای ژنتیکی سه جمعیت گوسفند بومی کشور عراق با استفاده از نشانگرهای میکروساتلایت

The aim of the present study was to estimate the molecular characteristics, structure, genetic diversity and genetic bottlenecks in the three sheep populations native to Iraq (Awassi, Naaimi, and Arabi). For this purpose, 12 microsatellite loci with chromosomal distribution distributions (1, 2, 5, 9 and 14) were used according to the recommendations of FAO and the International Society for Animal Genetics (ISAG). Sixty samples of whole animal blood (both sex) were randomly collected from the relevant populations in Karbala, Najaf and Babel provinces. The genomic DNA extraction, quality and quantity, preparation of PCR, electrophoresis photography was done accordingly based on standard available methods. After observation of raw genotype per investigated loci, allele binning was done for minimizing genotyping errors. More than 9 types of molecular statistical indices (allele frequencies, observed and effective number of alleles, observed and expected heterozygosity, PIC, Wright coefficient, Shannon index, F-statistical indices, genetic distance and the bottleneck) Checked out. The results were presented in two parts: evaluation of microsatellite loci utility and evaluation of genetic diversity within and between the population. The results of the first part showed that the highest polymorphism was observed in OarFCB226 and TGLA13 markers and the rest had the lowest polymorphism. The results of the second part showed that the Awaasi and Arabi breed have the highest and lowest diversity, respectively. The highest genetic distance was between Arabi and Naaimi breeds and the smallest was between Naaimi and Awassi breeds. Furthermore, bottleneck L-Shape curve showed that the studied populations are in a genetic predicament.

Microsatellite-Based Genetic Structure and Hybrid Detection in Alpacas Bred in Poland

Simple SummaryAlpacas (Vicugna pacos) are South American members of the tribe Lamini of the Camelidae family. They are bred for their fiber, which is considered a luxury material. Interest in alpaca breeding is increasing in Poland, but the local alpaca population is relatively young and heterogeneous. The poor quality of alpaca fiber results from uncontrolled crossing with llamas (Lama glama). Hybridization between the two species is a well-known phenomenon among alpaca breeders worldwide and is the cause of poor fiber quality, which leads to economic losses. Microsatellite markers can distinguish alpacas from llamas and indicate the level of admixture. However, it is difficult to determine in which generation the admixture took place. The high genetic diversity of alpacas bred in Poland has emerged as a consequence of their mixed origins. In this context, the microsatellite markers recommended by the International Society for Animal Genetics have been shown to be highly useful for individual identification and parentage testing of alpacas.This study aimed to characterize the population structure and genetic diversity of alpacas maintained in Poland using 17 microsatellite markers recommended by the International Society for Animal Genetics. The classification of llamas, alpacas, and hybrids of both based on phenotype is often difficult due to long-term admixture. Our results showed that microsatellite markers can distinguish alpacas from llamas and provide information about the level of admixture of one species in another. Alpacas admixed with llamas constituted 8.8% of the tested individuals, with the first-generation hybrid displaying only 7.4% of llama admixture. The results showed that Poland hosts a high alpaca genetic diversity as a consequence of their mixed origin. More than 200 different alleles were identified and the average observed heterozygosity and expected heterozygosity values were 0.745 and 0.768, respectively, the average coefficient of inbreeding was 0.034, and the average polymorphism information content value was 0.741. The probability of exclusion for one parent was estimated at 0.99995 and for two parents at 0.99999.

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.

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 θw = 0.634 and θw = 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 HO and HE, 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 (PID) 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.

Genetic diversity of the free-living population of Przewalski's horses in the Chernobyl Exclusion Zone

The present study is aimed at evaluating the genetic diversity, genetic status and the extent of hybridization with the domestic horse for the Przhevalski’s horse (Equus ferus przewalskii Poliakov 1881) population free-ranging in the territory of the Chernobyl Exclusion Zone (CEZ) in Belarus and Ukraine. The sample size included 12 individuals (10 sampled in the Belarusian part of the CEZ and 2 from the Ukrainian part of the CEZ). Ten microsatellites recommended by the International Society for Animal Genetics (ISAG) for horse genetic status and pedigree determination were used as markers in this study. The fragment analysis data obtained utilising this microsatellite panel determined that two individuals from Belarus possess no allelic variants typical for Przhevalski’s horse. Most of the other individuals presented diagnostically valuable allelic variants. Demographic history analysis for the population did not indicate any drastic population shrinkage events in the population’s recent history. The studied population is characterised by heterogeneous population structure with signs of inbreeding (0.21 %), intermediate level of genetic diversity (He = 0.63) and allelic richness (5.15), possesses 16 unique alleles among 2 microsatellite loci and valuable alleles for loci HMS3 and HMS7 (46.4 and 67.9 % specific alleles for Przhevalski’s horse, respectively). Genetic structure evaluation for the population was performed via Bayesian population structure analysis and factorial correspondence analysis (FCA), which indicated the presence of intrapopulation genetic subdivision. Taking into account the obtained indicators of genetic diversity, we may conclude on the relatively favourable status of Przewalski’s horse in the exclusion zone with good potential for the long-term existence of the species population in the wild. In order to minimise inbreeding effects and the risk of a decline in genetic diversity in the population of Przewalski’s horse of the exclusion zone, as well as to increase the value of this free-living group to preserve the gene pool of the species as a whole, it is necessary to provide detailed genetic monitoring of the livestock’s state, as well as develop a regional population management plan, including measures aimed to minimise the possibility of further hybridisation of wild horses with domestic ones.

An inter-laboratory study of DNA-based identity, parentage and species testing in animal forensic genetics

The probative value of animal forensic genetic evidence relies on laboratory accuracy and reliability. Inter-laboratory comparisons allow laboratories to evaluate their performance on specific tests and analyses and to continue to monitor their output. The International Society for Animal Genetics (ISAG) administered animal forensic comparison tests (AFCTs) in 2016 and 2018 to assess the limitations and capabilities of laboratories offering forensic identification, parentage and species determination services. The AFCTs revealed that analyses of low DNA template concentrations (≤300 pg/µL) constitute a significant challenge that has prevented many laboratories from reporting correct identification and parentage results. Moreover, a lack of familiarity with species testing protocols, interpretation guidelines and representative databases prevented over a quarter of the participating laboratories from submitting correct species determination results. Several laboratories showed improvement in their genotyping accuracy over time. However, the use of forensically validated standards, such as a standard forensic short tandem repeat (STR) kit, preferably with an allelic ladder, and stricter guidelines for STR typing, may have prevented some common issues from occurring, such as genotyping inaccuracies, missing data, elevated stutter products and loading errors. The AFCTs underscore the importance of conducting routine forensic comparison tests to allow laboratories to compare results from each other. Laboratories should keep improving their scientific and technical capabilities and continuously evaluate their personnel’s proficiency in critical techniques such as low copy number (LCN) analysis and species testing. Although this is the first time that the ISAG has conducted comparison tests for forensic testing, findings from these AFCTs may serve as the foundation for continuous improvements of the overall quality of animal forensic genetic testing.

Гетерозиготність за мікросателітними ДНК-маркерами та жива маса телиць південної м’ясної породи

The purpose of this study was to determine whether heterozygosity (assessed using microsatellite genotypes) was correlated with the body weight of heifers from birth to 18 months. The study was conducted on the heifers’ herd of the Taurian intra-breed type Southern meat cattle breed at Askaniiske State Research Enterprise (Ukraine, Kherson Region). During the study, we used ten microsatellite loci recommended by International Society for Animal Genetics (ISAG) TGLA227, BM2113, TGLA53, ETH10, SPS115, TGLA122, INRA023, BM1818, ETH3 and BM1824. The heifer’s body weight was measured at birth, at weaning, and at the age 8, 12, 15 and 18 months. Individual heterozygosity estimates (for each microsatellite loci separately) and microsatellite multilocus heterozygosity (for all used loci) estimates (MLH) were used in the analysis. ANOVA was used to determine the relationship of the dependent effects (body weight at different ages) to single locus heterozygosity using two classes: 0 (for homozygous individuals) and 1 (for heterozygous individuals). In addition, the following indicators were calculated for each genotype: the squared distances (d2) between the length of both alleles within the individual genotype for each microsatellite loci, as well as the mean squared distance (multilocus d2) between the lengths of both alleles within the individual genotype for ten microsatellite loci. Spearman’s rank correlation coefficients were used to measure the association between d2 scores (for each microsatellite loci) and body weight at different ages. The influence of different grades of estimates of MLH and mean d2 classes was also assessed based on ANOVA. Heterozygosity at locus BM2113 was significantly (P < 0.01) associated with heifer’s body weight at the age of 15 months and heterozygosity at locus BM1818 was significantly (P < 0.05) associated with heifer’s body weight at the age of 8 months. Significant Spearman’s rank correlations (P < 0.01...0.05) were also observed between the body weight and d2 score for four microsatellite loci BM2113, SPS115, ETH3 and BM1824. Individual mean heterozygosity estimates for 10 microsatellite loci and mean d2 estimates were weakly associated with weight performance in Southern meat cattle breed heifers.

Алельний поліморфізм мікросателітних локусів ДНК яєчних курей

The analysis of allelic polymorphism of five industrial egg crosses of chickens by five microsatellite DNA loci (ADL0268, MCW216, LEI0094, ADL0278, and MCW248) was carried out. DNA loci were chosen according to the recommendations of the International Society for Animal Genetics (ISAG). Based on the results of mathematical-statistical processing and data analysis, the spectra and frequencies of allelic variability, the peculiarities of allele pools, were identified, and unique alleles were identified. In general, the species Gallus gallus is characterized by a specific character of allelic spectra for all investigated microsatellite DNA loci (P <0.001). The highest rates of allelic variability were recorded in brown crosses "Lohmann brown" and "Hisex brown" (Na (LimNa)=(9.2 (5-17) and 7.4 (6-11), respectively). The studied crosses were characterized by a shift in allelic spectra towards a decrease in the fragment length. “Lohmann white” stands out among the birds of other crosses by high consolidation for individual alleles for all studied microsatellites (from ADL278114 – 0.343 and ADL268108 – 0.485 to LEI094259 – 0.720, MCW0248213 – 0.785 and MCW0216137 – 0.920). Unique alleles with the highest frequency were found in brown cross chickens, and in the “Hy-Line W-98” bird, they were not found. The number of unique alleles identified varied from 1 ("Hisex white") to 11 ("Lohmann brown"). Locus LEI094 turned out to be the most polymorphic in terms of the number of unique alleles – 10 such allelic variants were identified for it. No unique alleles were identified at the ADL0268 locus. The obtained estimates criterion χ2 of K. Pearson indicate significant differences in the frequency distribution of alleles for all studied loci. When using the MICROSATELLITE ANALYSER software, it was found that the nature of the variability of the studied microsatellite DNA loci in five industrial crosses of the egg chickens, both in the number of identified alleles and in the nature of their distribution, corresponded to the stepwise mutation model (SMM).

Evaluation of the International Society forAnimal Genetics bovine single nucleotide polymorphism parentage panel in South African Bonsmara and Drakensberger cattle.

A panel of 200 single nucleotide polymorphisms (SNPs) have been recommended by the International Society for Animal Genetics (ISAG) for use in parentage verification of cattle. While the SNPs included on the ISAG panel are segregating in European Bos taurus and Bos indicus breeds, their applicability in South African (SA) Sanga cattle has never been evaluated. This study, therefore, assessed the usefulness of the ISAG panel in SA Bonsmara (BON) and Drakensberger (DRB) cattle. Genotypes of 185 ISAG SNPs from 64 BON and 97 DRB sire-offspring pairs were available, all of which were validated with 119,375 SNPs. Of the 185 ISAG SNPs, 14 and 18 in the BON and DRB, respectively (9 in common to both breeds), were either monomorphic, exhibited at least one discordance between validated sire-offspring pairs, or had poor call rate or clustering issue. The mean minor allele frequency of the 185 ISAG SNPs was 0.331 in the BON and 0.359 in the DRB. The combined probability of parentage exclusion (PE) was the same (99.46%) for both breeds, while the probability of identity varied from 1.61 × 10-48 (BON) to 1.11 × 10-54 (DRB). Fifteen (23.4%) and 32 (33%) of the already validated sire-offspring pairs for the BON and DRB, respectively, were determined by the ISAG panel to be false-negatives based on a threshold of having at least two discordant SNPs. In comparison to sire discovery using the 119,375 SNPs, sire discovery using only the ISAG panel identified correctly 44 (out of 64 identified using the 119,375 SNPs) unique sire-offspring BON pairs and 62 (out of 97 identified using the 119,375 SNPs) unique sire-offspring DRB when all sires were masked. Five BON and three DRB offspring had > 1 sire nominated. This study demonstrated that the use of the ISAG panel may result in incorrect exclusions and multiple candidate sires for a given animal. Selection of more informative SNPs is, therefore, necessary in the pursuit of a low-cost and effective SNP panel for indigenous cattle breeds in SA.

Genetic structure of different equine breeds by microsatellite DNA loci

Aim. Our work was aimed at the evaluation of genetic diversity of three domestic equine breeds which differ by the history of their formation and use. Methods. Genotyping of DNA samples of three breeds of horses, namely, Hucul (78 animals), Thoroughbred (51 animals) and Ukrainian Saddle Horse (152 animals), was conducted by 11 microsatellite loci, recommended by the International Stud Book Committee (ISBC) and the International Society for Animal Genetics (ISAG). The mathematical analysis involved parametric and non-parametric methods of statistics. Results. The results of polymorphism analysis of the gene funds for Hucul, Thoroughbred and Ukrainian Saddle horses by 11 microsatellite DNA loci were fi rst presented in Ukraine. It was demonstrated that the study of microsatellite DNA loci allows both determining the reliability of origin of pedigree animals and controlling population processes in different breeds and the polymorphy of the very breeds. Conclusions. The molecular and genetic analysis of equine breeds, differing by their provenance, demonstrated specifi cities of genetic structure of each breed, which correspond to the formation history of their gene funds. The populational-genetic analysis using different mathematical methods is recommended for the purposes of evaluating and forecasting microevolution processes, controlling gene fund formation both during the breeding work and within the system of preserving genetic biodiversity

Genetic Diversity and Population Structure of Polish Konik Horse Based on Individuals from All the Male Founder Lines and Microsatellite Markers.

Simple SummaryWe investigated the genetic diversity of Polish Konik in sire lines. The Polish Konik horse is a Polish native horse breed of a primitive type and is one of the breeds managed via a conservation program. Due to the small number of breed founders (six male lines) and paternal lineages with unknown representation, the genetic diversity and structure of the population should be monitored regularly. This is the first characterization of the genetic diversity of Polish Konik paternal lines based on microsatellite markers (STRs). The fixation index (FST), which measures population differentiation, was low for all the studied markers and its mean value was 0.0305. Our analysis also revealed that there has been no inbreeding in the Polish Konik population for the studied group. This monitoring of genetic diversity could be helpful for the Polish Konik breeding and conservation programs and also for making informed decisions in the management of paternal lineages.The Polish Konik horse is a primitive native breed included in the genetic resource conservation program in Poland. After World War II, intensive breeding work began, aimed at rebuilding this breed. Now, the whole Polish Konik population is represented by six male founder lines (Wicek, Myszak, Glejt I, Goraj, Chochlik and Liliput). Individuals representing all six paternal lineages were selected based on their breeding documentation. We performed a fragment analysis with 17 microsatellite markers (STRs) recommended by the International Society for Animal Genetics (ISAG). The genetic diversity and structure within the paternal lineages and the whole of the studied group were investigated. The average allelic richness was 6.497 for the whole studied group. The fixation index (FST; measure of population differentiation) was low (about 3%), the mean inbreeding coefficient (FIT) was low and close to 0, and the mean inbreeding index value (FIS) was negative. The mean expected heterozygosity was established at 0.7046 and was lower than the observed heterozygosity. The power of discrimination and power of exclusion were 99.9999%. The cumulative parentage exclusion probability equaled 99.9269% when one parental genotype was known and 99.9996% with both parents’ genotypic information was available. About 3% of the genetic variation was caused by differences in the breed origin and about 97% was attributed to differences among individuals. Our analysis revealed that there has been no inbreeding in the Polish Konik breed for the studied population. The genetic diversity was high, and its parameters were similar to those calculated for native breeds from other countries reported in the literature. However, due to the small number of breed founders and paternal lineages with unknown representation, the population’s genetic diversity and structure should be monitored regularly.

Genetic polymorphism of buffalo Bubalus bubalis bubalis by cytogenetic and molecular markers

Aim. To estimate genetic polymorphism of buffaloes Bubalus bubalis bubalis by the characteristics of karyotype and microsatellite loci of DNA. Methods. The method of preparing chromosome preparations using blood lymphocytes of 30 animals and the analysis of 9 microsatellite loci of DNA, recommended by the International Society for Animal Genetics (ISAG) for cattle genotyping, were used in the investigation. Results. Based on the results of the analysis of GTG–stained preparations of metaphase chromosomes, it was determined that the karyotype of the investigated animals consisted of 25 pairs of chromosomes, which identifi ed them as river (murrah) buffaloes (Bubalus bubalis bubalis). The average frequency of detected quantitative and structural chromosome aberrations in the buffalo population under investigation was 13.58±3.18 % for males and 14.8±2.88 % for females. Active centers of nucleolus organizers were found on six pairs of chromosomes: 3p, 4p, 6q, 21q, 23q and 24q. In nine investigated microsatellite loci of DNA, 61 allele variants were identifi ed with the variation from four alleles (ILST 006) to 11 (TGLA) with the average number of alleles per locus being 6.77. The expected heterozygosity (He) exceeded the average value of the observed heterozygosity (Ho) which demonstrated the use of inbreeding in the breeding of the investigated group of animals. Conclusions. The application of quantitative and morphological characteristics of the karyotype and microsatellite DNA– markers (ILST005 (ILSTS005), ILST006 (D7S8), BM1818 (D23S21), BM2113 (D2S26), ETH10 (D5S3), ETH225 (D9S1), SPS115(D15), TGLA126 (D20S1), TGLA122 (D21S6) demonstrated their informative value and reasonability of their use for genetic monitoring of buffaloes in Ukraine with the purpose of developing selection programs of keeping and breeding this species.