Genetic diversity and phylogenetic relationship of Angus herds in Hungary and analyses of their production traits.

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.

Association of myostatin gene polymorphism with echocardiographic and muscular ultrasonographic measurements in Hungarian thoroughbreds horses.

The g.66493737C/T polymorphism of the myostatin gene (MSTN) majorly influences muscle fiber composition and best race distance of Thoroughbreds. Thus, a better understanding of this process may lead to superior genetic exploitation for maximizing Thoroughbred athletic potential. Our objective is to investigate whether myostatin genotypes are associated with muscular development and cardiac variables of Thoroughbreds. Echocardiography and muscular ultrasonography were performed on three groups having C/C, C/T, and T/T genotypes, respectively. Each group consisted of 22 animals. Homogeneity of variance between the groups was checked by Levene's test. Multivariate analysis of variance was applied to determine differences in measured variables vs. MSTN genotypes. Fascicle length of anconeus and thickness of triceps brachii muscles showed significant differences between C/C and T/T genotypes (pFascicle-length-of-anconeus = 0.004, pthickness-of-triceps-brachii < 0.001). According to the primary outcome, there are associations between myostatin genotypes and cardiac variables. Aortic diameter at the sinus of Valsalva (end-diastole and end-systole) and aortic diameter at the valve (end-systole) indicated significant differences between C/C and T/T genotypes (paortic-diameter-at-the-sinus-of-Valsalva-end-diastole = 0.015, paortic-diameter-at-the-sinus-of-Valsalva-end-systole = 0.011, paortic-diameter-at-the-valve-end-systole = 0.014). Pearson correlation effect sizes were rFascicle-length-of-anconeus = 0.460, rthickness-of-triceps-brachii = 0.590, raortic-diameter-at-the-sinus-of-Valsalva-end-diastole = 0.423, raortic-diameter-at-the-sinus-of-Valsalva-end-systole = 0.450, and raortic-diameter-at-the-valve-end-systole = 0.462. C/C genotypes gave 22.1, 12.2, 6.3, 6.0, and 6.7% higher values compared to T/T genotypes, respectively. Differences regarding aortic diameter between genotype groups support the hypothesis that C/C animals have consequently increased cardiac output and aerobic capacity.

A comprehensive analysis of the genetic diversity and environmental adaptability in worldwide Merino and Merino-derived sheep breeds.

BACKGROUND: To enhance and extend the knowledge about the global historical and phylogenetic relationships between Merino and Merino-derived breeds, 19 populations were genotyped with the OvineSNP50 BeadChip specifically for this study, while an additional 23 populations from the publicly available genotypes were retrieved. Three complementary statistical tests, Rsb (extended haplotype homozygosity between-populations), XP-EHH (cross-population extended haplotype homozygosity), and runs of homozygosity (ROH) islands were applied to identify genomic variants with potential impact on the adaptability of Merino genetic type in two contrasting climate zones. RESULTS: The results indicate that a large part of the Merino's genetic relatedness and admixture patterns are explained by their genetic background and/or geographic origin, followed by local admixture. Multi-dimensional scaling, Neighbor-Net, Admixture, and TREEMIX analyses consistently provided evidence of the role of Australian, Rambouillet and German strains in the extensive gene introgression into the other Merino and Merino-derived breeds. The close relationship between Iberian Merinos and other South-western European breeds is consistent with the Iberian origin of the Merino genetic type, with traces from previous contributions of other Mediterranean stocks. Using Rsb and XP-EHH approaches, signatures of selection were detected spanning four genomic regions located on Ovis aries chromosomes (OAR) 1, 6 and 16, whereas two genomic regions on OAR6, that partially overlapped with the previous ones, were highlighted by ROH islands. Overall, the three approaches identified 106 candidate genes putatively under selection. Among them, genes related to immune response were identified via the gene interaction network. In addition, several candidate genes were found, such as LEKR1, LCORL, GHR, RBPJ, BMPR1B, PPARGC1A, and PRKAA1, related to morphological, growth and reproductive traits, adaptive thermogenesis, and hypoxia responses. CONCLUSIONS: To the best of our knowledge, this is the first comprehensive dataset that includes most of the Merino and Merino-derived sheep breeds raised in different regions of the world. The results provide an in-depth picture of the genetic makeup of the current Merino and Merino-derived breeds, highlighting the possible selection pressures associated with the combined effect of anthropic and environmental factors. The study underlines the importance of Merino genetic types as invaluable resources of possible adaptive diversity in the context of the occurring climate changes.

Position of Hungarian Merino among other Merinos, within-breed genetic similarity network and markers associated with daily weight gain.

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.

Balancing at the Borderline of a Breed: A Case Study of the Hungarian Short-Haired Vizsla Dog Breed, Definition of the Breed Profile Using Simple SNP-Based Methods.

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.

Parentage testing and looking for single nucleotide markers associated with antler quality in deer (Cervus elaphus).

To provide a cost-efficient parentage testing kit for red deer (Cervus elaphus), a 63 SNP set has been developed from a high-density Illumina BovineHD BeadChip containing 777 962 SNPs after filtering of genotypes of 50 stags. The successful genotyping rate was 38.6 % on the chip. The ratio of polymorphic loci among effectively genotyped loci was 6.5 %. The selected 63 SNPs have been applied to 960 animals to perform parentage control. Thirty SNPs out of the 63 had worked on the OpenArray platform. Their combined value of the probability of identity and exclusion probability was 4.9 × 10 - 11 and 0.99803, respectively. A search for loci linked with antler quality was also performed on the genotypes of the above-mentioned stags. Association studies revealed 14 SNPs associated with antler quality, where low-quality antlers with short and thin main beam antlers had values from 1 to 2, while high-quality antlers with long and strong main beams had values between 4 and 5. The chance for a stag to be correctly identified as having high-value antlers is expected to be over 88 %.

Role of genes related to performance and reproduction of Thoroughbreds in training and breeding - A review.

Thoroughbreds have been selected for speed and stamina since the 1700s. This selection resulted in structural and functional system-wide adaptations that enhanced physiological characteristics for outstanding speed of 61-71 kph (38-44 mph) between 1,000 and 3,200 m (5 furlongs - 2 miles). At present, horseracing is still an economically important industrial sector, therefore intensive research is underway to explore genes that allow the utilisation of genetic abilities and are significant in breeding and training. This study aims to provide an overview of genetic research and its applicability related to Thoroughbreds.

Identification of markers associated with estimated breeding value and horn colour in Hungarian Grey cattle.

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.

Evaluation of porcine semen quality by portable and desktop CASA systems - Short communication.

When using artificial insemination in porcine reproduction, one of the most important requirements is the suitable quality of semen regarding its total motility (TM) and progressive motility (PM). Computer-assisted sperm analysis (CASA) is an appropriate method to analyse the quality of semen. Recently a portable instrument has been developed to help specialists in their everyday field work. In our study, semen quality was measured simultaneously by the portable device (Ongo) and a laboratory CASA system (Microptic) to compare TM and PM values obtained by these appliances at a concentration of 50 × 106 spermatozoa/mL. Agreement between measurements was evaluated with a Bland-Altman plot. Strong correlation was found between the investigated instruments for all the three parameters, i.e. sperm concentration, TM and PM. However, a few measurements fell outside the defined range of acceptance.

Effect of single-nucleotide polymorphisms on specific reproduction parameters in Hungarian Large White sows.

The aim of this study was to reveal the effect of single-nucleotide polymorphisms (SNPs) on the total number of piglets born (TNB), the litter weight born alive (LWA), the number of piglets born dead (NBD), the average litter weight on the 21st day (M21D) and the interval between litters (IBL). Genotypes were determined on a high-density Illumina Porcine SNP 60K BeadChip. Data screening and data identification were performed by a multi-locus mixed-model. Statistical analyses were carried out to find associations between individual genotypes of 290 Hungarian Large White sows and the investigated reproduction parameters. According to the analysis outcome, three SNPs were identified to be associated with TNB. These loci are located on chromosomes 1, 6 and 13 (-log10P = 6.0, 7.86 and 6.22, the frequencies of their minor alleles, MAF, were 0.298, 0.299 and 0.364, respectively). Two loci showed considerable association (-log10P = 10.35 and 10.46) with LWA on chromosomes 5 and X, the MAF were 0.425 and 0.446, respectively. Seven loci were found to be associated with NBD. These loci are located on chromosomes 5, 6, 13, 14, 15, 16 and 18 (-log10P = 10.95, 5.43, 8.29, 6.72, 6.81, 5.90, and 5.15, respectively). One locus showed association (-log10P = 5.62) with M21D on chromosome 1 (the MAF was 0.461). Another locus was found to be associated with IBL on chromosome 8 (-log10P = 7.56; the MAF was 0.438). The above-mentioned loci provide a straightforward possibility to assist selection by molecular tools and, consequently, to improve the competitiveness of the Hungarian Large White (HLW) breed.

Assessment of genetic diversity and phylogenetic relationship of Limousin herds in Hungary using microsatellite markers.

OBJECTIVE: This study was conducted to investigate basic information on genetic structure and characteristics of Limousin population in Hungary. Obtained results will be taken into consideration when adopting the new breeding strategy by the Association of Hungarian Limousin and Blonde d'Aquitaine Breeders (AHLBB). METHODS: Genetic diversity and phylogenetic relationship of 3,443 Limousin cattle from 16 different herds were investigated by performing genotyping using 18 microsatellite markers. Amplified DNA was genotyped using an automated genetic analyzer. RESULTS: Mean of effective alleles (ne) of the populations was 3.77. Population C had the lowest number of effective alleles (3.01) and the lowest inbreeding coefficient (FIS) value (-0.15). Principal component analysis of estimated genetic distance (FST) values (p<0.000) revealed two herds (C and E) distinct from the majority of other Limousin herds. The pairwise FST values of population C compared to the others (0.066 to 0.120) fell into the range of moderate genetic distance: 0.050 to 0.150, while population E displayed also moderate genetic distance (FST values in range 0.052 to 0.064) but only to six populations (G, H, J, L, N, and P). FST(C-E) was 0.148, all other pairs -excluding C and E herds- displayed low genetic distance (FST<0.049). Population D, F, I, J, K, L, N, O, and P carried private alleles, which alleles belonged to 1.1% of the individuals. Most probable number of clusters (K) were 2 and 7 determined by Structure and BAPS software. CONCLUSION: This study showed useful genetic diversity and phylogenetic relationship data that can be utilized for the development of a new breeding strategy by AHLBB. The results presented could also contribute to the proper selection of animals for further whole genome scan studies of Limousins.

Effect of single-nucleotide polymorphisms on the breeding value of fertility and breeding value of beef in Hungarian Simmental cattle.

The objective of this study was to estimate the effect of single-nucleotide polymorphisms (SNPs) on the breeding value of fertility (BVF) and the breeding value of beef (BVB) in Hungarian Simmental cattle. Genotypes were determined on a high-density Illumina Bovine DNA Chip. Data screening and data identification were performed by multi-locus mixed-model. Statistical analyses were carried out to find associations between individual genotypes and the investigated quality values. Three loci showed considerable association with BVF (-log10 P = 9.5, 9.9 and 14.5, respectively) on chromosomes 9, 28 and 29, respectively. The frequencies of their minor alleles (MAF) were 0.375, 0.355 and 0.354, respectively. Two loci showed association with BVB (-log10 P = 25.3 and 22.7) on chromosomes 2 and 11, respectively (their MAF were 0.438 and 0.229). The abovementioned loci provide a straightforward possibility to assist selection by molecular tools.

Effect of single nucleotide polymorphisms on intramuscular fat content in Hungarian Simmental cattle.

OBJECTIVE: To estimate effect of single nucleotide polymorphisms on the intramuscular fat content (IMF) of Hungarian Simmental bulls. METHODS: Genotypes were determined on high-density Illumina Bovine DNA Chip. After slaughtering of animals, chemical percentage of intramuscular fat was determined from longissimus dorsi muscle. A multi-locus mixed-model was applied for statistical analyses. RESULTS: Analyses revealed four loci (rs43284251, rs109210955, rs41630030, and rs41642251) to be highly associated (-log10P>12) with IMF located on chromosome 1, 6, 13, and 17, respectively. The frequency of their minor alleles was 0.426, 0.221, 0.162, and 0.106. CONCLUSION: The loci above can be useful in selection programs and gives the possibility to assist selection by molecular tools.

Males and females contribute unequally to offspring genetic diversity in the polygynandrous mating system of wild boar.

The maintenance of genetic diversity across generations depends on both the number of reproducing males and females. Variance in reproductive success, multiple paternity and litter size can all affect the relative contributions of male and female parents to genetic variation of progeny. The mating system of the wild boar (Sus scrofa) has been described as polygynous, although evidence of multiple paternity in litters has been found. Using 14 microsatellite markers, we evaluated the contribution of males and females to genetic variation in the next generation in independent wild boar populations from the Iberian Peninsula and Hungary. Genetic contributions of males and females were obtained by distinguishing the paternal and maternal genetic component inherited by the progeny. We found that the paternally inherited genetic component of progeny was more diverse than the maternally inherited component. Simulations showed that this finding might be due to a sampling bias. However, after controlling for the bias by fitting both the genetic diversity in the adult population and the number of reproductive individuals in the models, paternally inherited genotypes remained more diverse than those inherited maternally. Our results suggest new insights into how promiscuous mating systems can help maintain genetic variation.

How immunogenetically different are domestic pigs from wild boars: a perspective from single-nucleotide polymorphisms of 19 immunity-related candidate genes.

The coexistence of wild boars and domestic pigs across Eurasia makes it feasible to conduct comparative genetic or genomic analyses for addressing how genetically different a domestic species is from its wild ancestor. To test whether there are differences in patterns of genetic variability between wild and domestic pigs at immunity-related genes and to detect outlier loci putatively under selection that may underlie differences in immune responses, here we analyzed 54 single-nucleotide polymorphisms (SNPs) of 19 immunity-related candidate genes on 11 autosomes in three pairs of wild boar and domestic pig populations from China, Iberian Peninsula, and Hungary. Our results showed no statistically significant differences in allele frequency and heterozygosity across SNPs between three pairs of wild and domestic populations. This observation was more likely due to the widespread and long-lasting gene flow between wild boars and domestic pigs across Eurasia. In addition, we detected eight coding SNPs from six genes as outliers being under selection consistently by three outlier tests (BayeScan2.1, FDIST2, and Arlequin3.5). Among four non-synonymous outlier SNPs, one from TLR4 gene was identified as being subject to positive (diversifying) selection and three each from CD36, IFNW1, and IL1B genes were suggested as under balancing selection. All of these four non-synonymous variants were predicted as being benign by PolyPhen-2. Our results were supported by other independent lines of evidence for positive selection or balancing selection acting on these four immune genes (CD36, IFNW1, IL1B, and TLR4). Our study showed an example applying a candidate gene approach to identify functionally important mutations (i.e., outlier loci) in wild and domestic pigs for subsequent functional experiments.

Microsatellite markers for identification and parentage analysis in the European wild boar (Sus scrofa).

BACKGROUND: The wild boar (Sus scrofa) is among the most widespread mammal species throughout the old world. Presently, studies concerning microsatellites in domestic pigs and wild boars have been carried out in order to investigate domestication, social behavior and general diversity patterns among either populations or breeds. The purpose of the current study is to develop a robust set of microsatellites markers for parentage analyses and individual identification. FINDINGS: A set of 14 previously reported microsatellites markers have been optimized and tested in three populations from Hungary, Portugal and Spain, in a total of 167 samples. The results indicate high probabilities of exclusion (0.99999), low probability of identity (2.0E(-13) - 2.5E(-9)) and a parentage assignment of 100%. CONCLUSIONS: Our results demonstrate that this set of markers is a useful and efficient tool for the individual identification and parentage assignment in wild boars.

Breeding for scrapie resistance in the Hungarian sheep population.

The first results of the Hungarian sheep prion protein (PrP) genotyping programme are discussed in this paper. To obtain initial genotype frequency data 10 commercial (Hungarian Merino, German Mutton Merino, Merino Landschaf, German Blackheaded, Suffolk, Texel, Ile de France, Charollais, Lacaune, British Milksheep) and 4 indigenous (Gyimes Racka, Hortobágy Racka, Tsigaja, Cikta) breeds were sampled in 2003 and 2004, and the PrP genotypes were determined by microsequencing analysis with capillary electrophoresis. In all commercial breeds, a higher number of sheep were genotyped in 2005 (3648) and in 2006 (3834) within the breeding programme to increase scrapie resistance, and the estimated frequency data were compared to the initial figures to evaluate the efficiency of selection. The new developments arising from the identification of the so-called 'atypical' scrapie cases are also discussed.

Effect of DGAT1 and TG gene polymorphisms on intramuscular fat and on milk production traits in different cattle breeds in Hungary.

The objective of this study was to estimate the effect of the thyroglobulin (TG) locus on beef quality traits in some beef cattle breeds and to investigate the effect of the DGAT1 locus on milk production traits in the Hungarian Holstein Friesian population. TG and DGAT1 genotypes were determined by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay. At the TG locus TT bulls showed the highest fat percentage values in the longissimus dorsi muscle (m. longissimus dorsi); the difference between CC and TT genotypes was significant. DGAT1 GC/GC cows had the highest milk, fat and protein yield values. Due to the relatively small number of GC/GC cows the difference proved to be significant only between AA/AA and AA/GC genotypes.

Detection of single-nucleotide polymorphisms coding for three ovine prion protein variants by primer extension assay and capillary electrophoresis.

An alternative method is described for the determination of ovine prion protein allelic variants at codon 136, 154, and 171. The four mutations responsible for amino acid changes are typed simultaneously. The technique utilizes dideoxy chain termination reaction using fluorescently labeled dideoxy nucleotides. The single-base extended primers are resolved on a capillary electrophoresis instrument. Data obtained by our approach are presented according to genotype distribution in some breeds as a part of the validation procedure.