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In the present study, two missense variants within ATGL (rs331307082) and MYOM1 (rs326001585) genes were tested for their potential usage as genetic markers related to pig production traits. The genotyping was performed on 519 pigs representing 990 synthetic sire line. The association analysis indicated that ATGL gene affected the panel of fattening parameters (test daily gain, age at slaughter), meatiness traits (meat percentage in the carcasses; the weight of loin, ham and primary cuts, and loin eye area), and meat quality characteristics (water exudation). In turn, MYOM1 polymorphism was related to loin weight, the weight of primary cuts and weight of loin backfat. Pigs with AA genotype were characterized by significantly higher loin and primary cut weights compared to opposite homozygotes GG (PMYOM1 polymorphism did not affect pork quality traits. The results allowed us to propose the new genetic markers which may be used in pig selection to obtain appropriate meatiness and fatness level in carcasses without decreasing meat quality.

The aim of the study was to determine the degree of relatedness between individuals in the Polish Hunting Dog population and to assess the genetic variability of the population based on pedigree analysis and molecular DNA testing. Pedigree data on Polish Hunting Dogs provided by the Polish Kennel Club was used. In total, data on 2783 individuals were obtained. DNA was obtained from cheek swabs taken from 177 dogs of the tested breed. A panel of 21 markers (Short Tandem Repeat - STR) was used. On the basis of genotypes in microsatellite loci, assessment of the Hardy-Weinberg genetic equilibrium was also carried out in the analyzed dog population using the χ2 test. The pedigree data contributed to identification of 26 founders. The Founder Genome Equivalent was 4.17, Founder Genomes Surviving was 17.03 and effective population size (Mean Ne) was estimated at 28.51. The gene diversity was 0.8802, the population mean kinship was 0.1198, and the mean inbreeding was 0.1151. Studies of STR markers revealed polymorphic information content – PIC = 0.56, and the estimated values of expected heterozygosity were generally close to the observed heterozygosity values and on average amounted to 0.6050 and 0.6142, respectively. The calculated average inbreeding coefficient (FIS) value was negative −0.012, which suggests a low level of inbreeding in the examined breed as well as avoidance of related animals in mates.

Application of next generation sequencing for large scale genotyping in livestock is limited by high costs and challenging data analysis process. However, available restriction enzyme-based enrichment techniques like e.g. genotyping-by-sequencing (GBS) are promising tools allowing reduction of financial outlies by a high sample multiplexing and narrowing down the sequenced genome areas to the randomly distributed read tags. In this study, we tested the performance of standard, PstI endonuclease-adapted GBS protocol for population genetics in cattle, horse and sheep with application of different, including low-depth sequencing setups. It was found that the detected SNPs display desirable polymorphism parameters and are evenly scattered across the whole genome including gene coding regions. It was also shown that the SNPs can be successfully applied in population genetics, revealing the genetic differentiation of the studied breeds. The GBS approach represents a cost-effective alternative to existing genotyping methods which may find adoption in various research applications.

Summary: The aim of this study is to reveal the genetic variability and population structure of maternal lines of the Polish Konik—a native Polish horse breed of the primitive type included in the Polish conservation programme. The analysis was carried out on the basis of 17 microsatellite markers routinely used for parentage testing. The structural analysis indicated the likelihood of three genetic clusters (using the Structure and Structure Harvester software). F-statistics indicated a low level of inbreeding. All mean population coefficients were close to those obtained for representatives of male founder lines. The population seemed to be stable. However, due to a previous bottleneck event, breeding strategies should focus on avoiding inbreeding depression, preventing the decrease of genetic variability, and sustaining the active female lines. The aim of the conservation programme is to maintain the population size of endangered livestock breeds of less economic importance at a level that ensures the survival of the breed, the preservation of genetic diversity, and the preservation of as many pedigree lines as possible. The Polish Konik, a native Polish primitive-type horse breed and is one of the breeds included in such a programme in Poland. Presently, there are only 16 (of the 35 maternal lines known in 1962), some of which are endangered. We examined the genetic variability and structure of the Polish Konik maternal lines (176 individuals) on the basis of the pedigree data and 17 microsatellite markers (STRs) from parentage testing. The overall mean number of alleles was 7.647 (±0.411), the effective number of alleles was 3.935 (±0.271), the mean number of alleles for which the frequency was equal to or lower than 5% was 4.471 (±0.286), and the mean information index was 1.506 (±0.087). The structure of the population and admixture patterns were calculated with the Structure and Structure Harvester software. The structural analysis indicated three likely genetic clusters, as the most optimal K value was estimated as 3, with ∆K of 15.4188. The F-statistics results indicated a low level of inbreeding (average inbreeding coefficient FIT was 0.0188, coefficient of differentiation FST was 0.0304, and mean inbreeding index value FIS was −0.0119). Variability monitoring should be carried out in order to avoid inbreeding depression, while breeding strategies should be designed to prevent the decrease of genetic variability in the Polish horse breed and to sustain the active female lines.

In all sport disciplines, excellent coordination of movements is crucial for achieving mastery. The ability to learn new motor skills quickly and effectively is dependent on efficient myelination which varies between individuals. It has been suggested that these differences may play a role in athletic performance. The process of myelination is under transcriptional control by Myelin Regulatory Factor (MYRF) as well as other transcription factors (SOX10 and OLIG2). We analyze a panel of 28 single nucleotide polymorphisms (SNPs) located within the frequencies of common variants of MYRF, SOX10 and OLIG2 genes in professional athletes compared to non-athletes. No significant differences were detected after correction for multiple testing by false discovery rate (FDR) for any of the models tested. However, some deviations from the expected distribution was found for seven SNPs (rs174528, rs139884, rs149435516 and rs2238001, rs7943728, rs61747222, and rs198459). The MYRF alleles rs7943728 and rs61747222 showed a correlation with the level of sport achievement among the athletes. Even though the athletes did not differ from the non-athlete controls in the distribution of most SNPs analyzed, some interesting differences of several variants were noted. Presented results indicate that genetic variants of MYRF and SOX10 could be genetic factors weakly predisposing for successful athletic performance.

In the recent years, particular attention was given to the research aimed at optimizing the use of tumour epigenetic markers. One of the best known epigenetic changes associated with the process of carcinogenesis is aberrant DNA methylation. The aim of the present research was to evaluate the methylation profile of genes potentially important in the diagnosis and/or prognosis of equine sarcoids, the most commonly detected skin tumours in Equidae. The methylation status of potential promoter sequences of nine genes: APC, CCND2, CDKN2B, DCC, RARβ, RASSF1, RASSF5, THBS1 and TRPM1, was determined using bisulfite sequencing polymerase chain reaction (BSP-CR). The results of this study did not reveal any changes in the level of DNA methylation in the analysed group of candidate genes between the tumour and healthy tissues. Despite numerous reports describing the aberrant methylation of the promoters of the analysed genes in human cancers, the data obtained did not confirm the existence of such relationships in the examined tumour tissues, which excludes the possibility of using these genes for the diagnosis of the equine sarcoid.

Mitochondrial DNA (mtDNA) is a molecular tool that is very effective in genetic research, including phylogenetic analysis. The non-coding region is the most variable fragment of mtDNA, showing variability in length and nucleobase composition and containing three domains: two hypervariable peripheral regions and the conserved domain (D-loop) in the middle. The Anseriformes are amongst the best studied avian groups, including approximately 150 species and containing geese, swans, ducks (Anatidae), the Magpie goose (Anseranatidae) and screamers (Anhimidae). The most numerous family is the Anatidae, appearing in close relationships within the phylogenetic branches of the species. There are differences between the non-coding region of the Anatidae in comparison to other avian control regions. In the article presented below the control region sequences and the phylogeny of the Anatidae were reviewed.

The highly selective breeding of Arabian horses results in inbreeding depression and genetic disorders, thereby causing significant economic loss. The Polish population of Arabians has a great impact on many breeding programmes. The aim of the current study was to monitor genetic variants involved in the most common genetic disorders of this breed. A total of 808 elite Arabian horses were screened for cerebellar abiotrophy (CA), severe combined immunodeficiency (SCID) and lavender foal syndrome (LFS) genetic disorders by Sanger sequencing and allelic discrimination methods. The investigated population was clear of LFS. The unfavourable SCID allele was detected in three heterozygous horses (q = 0.00185). Regarding CA, the minor allele frequency was q = 0.04029. This is the first report of SCID carriers in Poland. This investigation demonstrates the value of genetic testing to support breeding decisions and to facilitate genetic disease monitoring.

Poland is the largest European producer of goose, while goose breeding has become an essential and still increasing branch of the poultry industry. The most frequently bred goose is the White Kołuda® breed, constituting 95% of the country’s population, whereas geese of regional varieties are bred in smaller, conservation flocks. However, a goose’s genetic diversity is inaccurately explored, mainly because the advantages of the most commonly used tools are strongly limited in non-model organisms. One of the most accurate used markers for population genetics is single nucleotide polymorphisms (SNP). A highly efficient strategy for genome-wide SNP detection is genotyping-by-sequencing (GBS), which has been already widely applied in many organisms. This study attempts to use GBS in 12 conservative goose breeds and the White Kołuda® breed maintained in Poland. The GBS method allowed for the detection of 3833 common raw SNPs. Nevertheless, after filtering for read depth and alleles characters, we obtained the final markers panel used for a differentiation analysis that comprised 791 SNPs. These variants were located within 11 different genes, and one of the most diversified variants was associated with the EDAR gene, which is especially interesting as it participates in the plumage development, which plays a crucial role in goose breeding.

OBJECTIVE: In this study, for the first time we report the genome-wide DNA methylation profile of skin tumour in horses and describe differentially methylated genomic regions (DMRs) with respect to healthy skin. MATERIALS & METHODS: The comparative analysis of DNA methylation patterns detected using Reduced Representation Bisulfite Sequencing (RRBS) technique, allowed identification of 136 regions showing differential methylation between sarcoid and normal skin tissue. RESULTS: Most of the identified DMRs were short fragments, less than 1 kb in size, located in the intergenic regions. Among identified DMRs there were also regions located within genes directly or indirectly related with oncogenesis. We additionally validated 9 CpG sites showing hypomethylation and 9 CpG sites that were hypermethylated in lesional sample, confirming the identified changes in the DNA methylation. CONCLUSION: Knowledge on the changes taking place in the process of DNA methylation may provide a basis for the development of new alternative diagnostic or therapeutic approaches to equine sarcoids.

The aim of this study was to evaluate the genetic variability of the White Kołuda&reg, goose and 12 conservative flocks: Kielecka, Podkarpacka, Garbonosa, Pomerian, Rypinska, Landes, Lubelska, Suwalska, Kartuska, Romanska, Slowacka, and Kubanska, maintained in Poland using microsatellite data. The genetic diversity of geese kept in Poland remains poorly analyzed at the molecular level. In total 392 samples were examined with the usage of 15 microsatellite markers. 119 alleles were identified and the number of alleles per locus ranged from 1 to 13. The highest number of alleles was observed in TTUCG5 (16) and the lowest in CAUD-G007 (2), while CKW47 was monomorphic. The lowest value of expected heterozygosity (He) was observed in Landes, while the highest in Romanska. Similarly, the observed heterozygosity (Ho) was the lowest in Landes but the highest in Kartuska. The polymorphism information content (PIC) indicates loci TTUCG5 as the most valuable microsatellite marker among those examined. The Structure software was used for the first time to identify goose populations, revealing high admixture between breeds and their close genetic propinquity. Moreover, the presented panel of microsatellite markers remained polymorphic and is useful for population studies of geese and assessment of genetic diversity.

Horses are one of the longest-living species of farm animals. Advanced age is often associated with a decrease in body condition, dysfunction of immune system, and late-onset disorders. Due to this, the search for new solutions in the prevention and treatment of pathological conditions of the advanced age of horses is desirable. That is why the identification of aging-related changes in the horse genome is interesting in this respect. In the recent years, the research on aging includes studies of age-related epigenetic effects observed on the DNA methylation level. We applied reduced representation bisulfite sequencing (RRBS) to uncover a range of age DMR sites in genomes of blood leukocytes derived from juvenile and aged horses of native Hucul breed. Genes colocated with age-related differentially methylated regions (age DMRs) are the members of pathways involved in cellular signal transduction, immune response, neurogenesis, differentiation, development, and cancer progression. A positive correlation was found between methylation states and gene expression in particular loci from our data set. Some of described age DMR-linked genes were also reported elsewhere. Obtained results contribute to the knowledge about the molecular basis of aging of equine blood cells.

One of epigenetic features of mammalian genomes is methylation of DNA. This nucleotide modification might exert suppressive effect on gene transcription. We have described putative relevance of methylation of one of immune cells related gene (ITGAL) observed in the set of 11 equine tissues. Comparison between qualitative RT-PCR results and DNA bisulfite sequencing of investigated set of tissues pointed to potential correlations between tissue specific methylation and tissue specific transcription in ITGAL locus. These findings might be important for studies on genetic and epigenetic background of autoimmune disorders in the horse.

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 and epigenetic alterations in the equine sarcoid, a locally invasive skin tumour of equids, are still poorly characterized. Numerous studies have provided reliable evidence for the relationship between the development of cancer and the loss of function of a number of tumour suppressor genes. In the present study, we assessed methylation levels in the promoter region of SFN, S100A14 and POU2F3 genes in sarcoid samples to clarify whether DNA methylation may be associated with previously identified changes in the expression level of these genes during the course of tumour progression. Using bisulfite sequencing and clone sequencing, we detected that lesional samples had a significantly higher rate of DNA methylation in the analyzed S100A14A region than the corresponding normal skin tissue. A frequent methylation of the SFN and POU2F3 promoter sequences were observed in both the tumour samples and the control skin tissues. Further studies are needed to evaluate the role of aberrant methylation in sarcoid progression and to understand the mechanisms involved in reduced expression of SFN, S100A14 and POU2F3 genes in the lesional tissues.

DNA methylation patterns and their relation with genetic polymorphisms were determined in the equine OAS1 locus. Genetic variants of OAS1 were previously found to be associated with susceptibility to West Nile virus infections in horses. The subject of the study were white blood cells of 13 juvenile and 13 old horses from AA and HC breed and a set of solid tissues from a single adult horse. The aim was to determine the degree of variation of CpG methylation profiles with concern for tissue type, horse breed and age. Results of direct BSPCR and cloned BSPCR sequencing revealed that all of determined CpG islands (CGIs) were hypermethylated in exception to CGI covering OAS1 promoter and exon 1. One of intragenic CGIs displayed variability of methylation patterns across eight tissue types. The variability of particular sub-types of white blood cells between AA and HC horses were considered as the possible cause of interbreed differences of methylation levels. Comparison of sequence variability between converted and unconverted DNAs of both horse breeds showed polymorphisms of CpG sites to be the source of monoallelic methylation in exception to the polymorphic CpGs located in the OAS1 promoter. Two of them are new polymorphic variants in the OAS1 promoter region. Application of methylation data in conjunction with genetic variation detected at the OAS1 locus might be useful to deepen the knowledge about mechanisms underlying immunity to viral infections in the horse.

Specificity of chess training promotes sedentary lifestyle and may reduce chess players participation in different physical activities. Limited physical activity leads to decrease of physical fitness and may augment the risk of overweight and obesity. It is suggested that these athletes will characterize more frequently lower physical fitness and weight/height proportions disorders. The aim of the study was evaluation of physical fitness and its relationship with age and body build of athletes.A sample of 73 individuals (35 girls--48% and 38 boys--52%) aged 8-19 years took part in this study. All competitors were members of national team and Polish representatives for the European and world chess championship. Chess players' physical fitness was measured by EUROFIT tests.With reference to the Polish population chess players characterized higher level of physical fitness. In six tests of EUROFIT chess players had better standardized results than controls. Sit ups (mean standardized result 0.842), shuttle run 10 x 5 m (0.577), standing broad jump (0.552) and flamingo balance (0.371) were very well performed by chess players. Only in one test, bent arm hang, sportsmen achieved worse results (-0.719). Permanent decrease of chess players' physical fitness with age was also observed.Although chess players' physical fitness was satisfied in comparison to age-matched control, it is recommended to include in their training more exercises developing strength. Because of changes in body build with age and decrease of physical fitness, chess players ought to participate in regular physical activity. Therefore chess organisers should provide the variety of active forms that can be chosen by competitors in their leisure time.

Proper nutrition plays significant role in children's development and health protection in adults, as well. Therefore such a study is extremely important particularly among youth population. It is well known that adequate nutrition also helps to achieve high sport results. The aim of the study was the nutritional habits evaluation of young chess players.A total of 75 chess players aged 8-19 years took part in the study. Among them there were 36 girls (48%) and 39 boys (52%). Subjects belonged to the Polish Chess Academy, medalists of the Polish, European and world youth championships and members of the Polish national team. Used questionnaire allowed to collect data about regular diet of young athletes.Recommended number of 4-5 meals per day was consumed only by 55% persons. Another observed disadvantageous nutritional habit among responders was missing first breakfasts (75%), especially during competitions. Less than half of subjects declared regular meals intake during the day (from 25 to 43%). Moreover, it was noticed, that 13,3% chess players ate vegetables and fruits only one time per day. Sweets were taken at least one time per day by 22 to 50% participants.Due to numerous nutritional mistakes in studied population it is compulsory to conduct nutritional education among athletes and among their parents and coaches as well.

Short tandem repeat (STR) loci, i.e. microsatellites are a class of genetic markers commonly used for population studies and parentage control. This study determined the usefulness of microsatellite markers recommended by International Society for Animal Genetics (ISAG) for identification and pedigree analysis in horses based on the example of Polish Hucul horse population (Equus caballus). The set of seventeen microsatellites loci was tested (AHT4, AHT5, ASB2, HMS2, HMS3, HMS6, HMS7, HTG10, HTG4, HTG6, HTG7, VHL20, ASB17, ASB23, CA425, HMS1, LEX3) for 216 individuals. All samples were genotyped and mean number of alleles per locus was estimated (7.00). Means of observed (Ho) and expected (He) heterozygosity were calculated 0.7288 and 0.7027, respectively. The observed heterozygosity was similar to the results of research on Hucul horse population in another area of Carpathians Mountains. The average polymorphism information content (PIC) for analyses of seventeen microsatellite markers indicates the usefulness of this set of markers for Hucul horse parentage testing.

Allelic and haplotypic variations at 27 SNP sites identified in four CpG islands of OAS1 were described in a group of Anglo-Arabian and Hucul horses. Variation in the type of less frequent alleles was the source of variability among breeds. A number of putative LD blocks were identified which could be used to study changes in the genetic structure between generations of both breeds concerning susceptibility to flaviviral infections. Some of the identified SNPs may have an impact on the transcriptional activity of OAS1 or could lead to amino acid substitution influencing proper function of OAS1 enzyme. In the light of recent studies, the described genetic variability of investigated CpG islands might be important in view of the effectiveness of viral incorporation into the host genome.