István Anton

The aim of this study was to identify SNPs in the cattle genome associated with estimated breeding values of feet (EBV_feet) in Holstein-Friesian (HF) cows in Hungary. Foot health is of major importance in dairy cattle industry whereas claw disorders are leading to lameness and thus result in low fertility rates and productivity. Genotyping was performed using the EuroG_MDv4 microarray platform. The final database comprised 2963 animals and 59,151 SNPs. EBV_feet values have been divided into high and low groups. All calculations regarding the genetic differentiation (genome-wide and locus-specific) between high- and low-value groups for EBV_feet, linear regression, and haplotype association tests have been performed with the SNP and Variation Suite software. Thirty-nine SNPs associated with EBV_feet were determined on BTAs 3, 7, 8, 15, 21, and X. The maximum values of the identified SNPs were 0.22 for F_{st_marker}, 23.1 for the −log10(p) of the linear regression, and 26.3 for the −log10(p) of the haplotype association tests on BTA 3. The closest genes to SNPs associated with estimated breeding values for feet (EBV_feet) are mainly associated with tissue structure, immune response, metabolism, growth, development, transport and signaling. Our results could add additional information to the genetic programs focusing on the improvement of foot health in HF cattle.

Hair whorl patterns are usually used as a predictor of equine laterality, temperament and reactions to various environmental stimuli. Thus, temperament and motor laterality may be deducted in order to ease the daily work, training, handling and transportation of Thoroughbreds. We aimed to identify the number, position and orientation of hair whorl patterns to find the association between environment stimuli and the laterality, affability, trainability and anxiety of 81 individuals. We analyzed hair whorls with SPSS (Statistical Package for the Social Sciences) accompanied by a laterality paddock test and temperament questionnaire. All of our examined Thoroughbreds showed at least one circular whorl on their head. Mostly, the whorls were located on the top of the head. Compared to previous studies, the presence of linear whorls on the body was also high. We found that the counterclockwise head and clockwise whorls were associated with left and right front leg preference (p < 0.001).

Our genome-wide association study identified single-nucleotide polymorphisms (SNPs) associated with estimated breeding values (EBVs) for udder traits and longevity in Holstein-Friesian cows. While no SNP was individually associated with multiple EBVs, the functional profiles of the associated genes revealed overlapping biological processes across traits, including cell signaling, transcription regulation, immune response, metabolism, and cellular maintenance. Notably, nearby SNPs BTB-01738708 and ARS-BFGL-NGS-111478 were associated with EBV_longevity and EBV_udder and located near numerous genes, including GPR85, BMT2, IFRD1, and DOCK4, suggesting a potential for shared genetic influence on these traits. Our findings provide insights into the complex genetic architecture of these economically important traits and highlight the need for further research, including fine-mapping and functional genomics, to elucidate the specific variants and their effects.

The primary objective of any conservation breeding program is to preserve the genetic diversity of populations. This objective is a persistent challenge, especially in small populations which are prone to loss of heterozygosity. In this study, we proposed a novel parent-selection strategy aimed at the long-term maintenance of high levels of genetic diversity. Our approach is based on estimating the Probability of Offspring Heterozygosity (POH)—the likelihood that a mating will produce heterozygous offspring—using SNP genotype data. This strategy was evaluated through computer simulations, where parental pairs with the highest POH values were preferentially selected to produce the next generation. Simulations explored the effects of varying the number of breeding pairs, and the number of unlinked SNP markers. Selection based on POH resulted in observed heterozygosity (H_OBS) consistently exceeding expected heterozygosity (H_EXP), a trend that was sustained for up to 1000 generations. While further evaluation is needed within more complex population genetic frameworks—accounting for linkage disequilibrium, recombination, optimal contribution, and phenotypic selection—our findings highlight the potential of POH as a valuable tool for enhancing genetic diversity in conservation breeding programs.

This study aimed to find SNPs that have an effect on the estimated breeding values (EBVs) of milk (MY), fat (FY), and protein yield (PY) of Holstein Friesian cows in Hungary. Holstein Friesian cows (n = 2963) were genotyped on a Eurogenomics (EuroG_MDv4) chip. The EBVs for MY, FY, and PY were obtained from the Association of Hungarian Holstein Breeders (AHHB). The loci associated with the EBVs were identified via three approaches: the calculation of genetic distance of the SNPs (F_{st_marker}), linear regression, and haplotype association tests. Nine SNPs were significantly associated with MY, FY, and PY located on BTA 2, 5, 28, and X. Among the nine SNPs identified, BTB-00219372 on BTA 5 had a positive β coefficient for MY and a negative β coefficient for FY and PY. In addition, BovineHD3000027615 on BTA X had a positive β coefficient for both MY and PY, as well as a negative β coefficient for FY. The identified SNPs were located near several genes that remain unstudied in cattle, which are potential targets for closer scrutiny in relation to milk properties. The markers associated with two or three EBVs could be used in selection with high efficiency to accelerate genetic development and help AHHB experts achieve their breeding. Most marker effects point in the same direction on EBVs; however, we found that BTB-00219372 and BovineHD3000027615 could be used with caution to increase one EBV while decreasing the other EBV or EBVs.

Objective: This study aims to investigate the genetic structure and characteristics of the Angus cattle population in Hungary. The survey was performed with the assistance of the Hungarian Hereford, Angus, Galloway Association (HHAGA).Methods: Genetic parameters of 1,369 animals from 16 Angus herds were analyzed using the genotyping results of 12 microsatellite markers with the aid of PowerMarker, Genalex, GDA-NT2021, and STRUCTURE software. Genotyping of DNA was performed using an automated genetic analyzer. Based on pairwise identity by state values of animals, the Python networkx 2.3 library was used for network analysis of the breed and to identify the central animals.Results: The observed numbers of alleles on the 12 loci under investigation ranged from 11 to 18. The average effective number of alleles was 3.201. The overall expected heterozygosity was 0.659 and the observed heterozygosity was 0.710. Four groups were detected among the 16 Angus herds. The breeders’ information validated the grouping results and facilitated the comparison of birth weight, age at first calving, number of calves born and productive lifespan data between the four groups, revealing significant differences. We identified the central animals/herd of the Angus population in Hungary. The match of our group descriptions with the phenotypic data provided by the breeders further underscores the value of cooperation between breeders and researchers.Conclusion: The observation that significant differences in the measured traits occurred among the identified groups paves the way to further enhancement of breeding efficiency. Our findings have the potential to aid the development of new breeding strategies and help breeders keep the Angus populations in Hungary under genetic supervision. Based on our results the efficient use of an upcoming genomic selection can, in some cases, significantly improve birth weight, age at first calving, number of calves born and the productive lifespan of animals.

Objective: In this study, we aimed to position the Hungarian Merino among other Merino-derived sheep breeds, explore the characteristics of our sampled animals' genetic similarity network within the breed, and highlight single nucleotide polymorphisms (SNPs) associated with daily weight-gain.Methods: Hungarian Merino (n = 138) was genotyped on Ovine SNP50 Bead Chip (Illumina, San Diego, CA, USA) and positioned among 30 Merino and Merino-derived breeds (n = 555). Population characteristics were obtained via PLINK, SVS, Admixture, and Treemix software, within-breed network was analysed with python networkx 2.3 library. Daily weight gain of Hungarian Merino was standardised to 60 days and was collected from the database of the Association of Hungarian Sheep and Goat Breeders. For the identification of loci associated with daily weight gain, a multi-locus mixed-model was used.Results: Supporting the breed's written history, the closest breeds to Hungarian Merino were Estremadura and Rambouillet (pairwise FST values are 0.035 and 0.036, respectively). Among Hungarian Merino, a highly centralised connectedness has been revealed by network analysis of pairwise values of identity-by-state, where the animal in the central node had a betweenness centrality value equal to 0.936. Probing of daily weight gain against the SNP data of Hungarian Merinos revealed five associated loci. Two of them, OAR8_17854216.1 and s42441.1 on chromosome 8 and 9 (–log10P>22, false discovery rate<5.5e-20) and one locus on chromosome 20, s28948.1 (–log10P = 13.46, false discovery rate = 4.1e-11), were close to the markers reported in other breeds concerning daily weight gain, six-month weight, and post-weaning gain.Conclusion: The position of Hungarian Merino among other Merino breeds has been determined. We have described the similarity network of the individuals to be applied in breeding practices and highlighted several markers useful for elevating the daily weight gain of Hungarian Merino.

The aim of this study was to determine the breed boundary of the Hungarian Short-haired Vizsla (HSV) dog breed. Seventy registered purebred HSV dogs were genotyped on approximately 145,000 SNPs. Principal Component Analysis (PCA) and Admixture analysis certified that they belong to the same population. The outer point of the breed demarcation was a single Hungarian Wire-haired Vizsla (HWV) individual, which was the closest animal genetically to the HSV population in the PCA analysis. Three programs were used for the breed assignment calculations, including the widely used GeneClass2.0 software and two additional approaches developed here: the ‘PCA-distance’ and ‘IBS-central’ methods. Both new methods calculate a single number that represents how closely a dog fits into the actual reference population. The former approach calculates this number based on the PCA distances from the median of HSV animals. The latter calculates it from identity by state (IBS) data, measuring the distance from a central animal that is the best representative of the breed. Having no mixed-breed dogs with known HSV genome proportion, admixture animals were simulated by using data of HSV and HWV individuals to calibrate the inclusion/exclusion probabilities for the assignment. The numbers generated from these relatively simple calculations can be used by breeders and clubs to keep their populations under genetic supervision.

Studies of wild boar, Sus scrofa Linnaeus 1758, in urban and suburban areas of Budapest, Hungary, have indicated that these populations do not have continuous contact. Based on the assumption that the city has a discrete population, we hypothesized that the urban wild boar would differ genetically from those in suburban areas. Analysis of single-nucleotide polymorphism (SNP) data using the GeneSeek Genomic Profiler (GGP) Porcine 50 K system (Neogen, Scotland, UK) differentiated three populations: Buda (B) from the Western bank of the Danube; Buda Surrounding (BS); and Valkó (V) from the Eastern bank of the Danube. The coefficient of genetic differentiation (F_ST) for the B and BS populations was low. The inbreeding coefficients of the populations BS and V were close to zero, while population B had a high positive value reflecting the influence of founders and the inbreeding of the continuous urban population. The genome regions that were most differentiated between the B and BS populations were analyzed based on the F_ST values of the SNP markers using a mixed linear multi-locus model and BayeScan software. The most differentiated marker, WU_10.2_18_56278226, was found on chromosome 18. The surrounding region contained several candidate genes that could play important roles in adaptations related to human-induced stress. Two of these, encoding the adenylate cyclase 1 (ADCY1) and inhibin beta A chain precursor (INHBA) genes, were sequenced. While IHBA gene did not display variation, the allele distribution of the ADCY1 gene in the B population was significantly different from that of the BS population supporting the parapatric differentiation of wild boar.

Objective: This study was conducted to estimate effect of single nucleotide polymorphisms (SNP) on the estimated breeding value of Hungarian Grey (HG) bulls and to find markers associated with horn colour.Methods: Genotypes 136 HG animals were determined on Geneseek high-density Bovine SNP 150K BeadChip. A multi-locus mixed-model was applied for statistical analyses.Results: Six SNPs were identified to be associated (–log10P>10) with green and white horn. These loci are located on chromosome 1, 3, 9, 18, and 25. Seven loci (on chromosome 1, 3, 6, 9, 10, 28) showed considerable association (–log10P>10) with the estimated breeding value.Conclusion: Analysis provides markers for further research of horn colour and supplies markers to achieve more effective selection work regarding estimated breeding value of HG.