Nina Moravčíková

Genomic characterization of Pinzgau cattle: genetic conservation and breeding perspectives

A genome-wide scan of Slovak Pinzgau cattle was prepared for the first time in order to estimate their genetic diversity at a more detailed level compared to previously published studies. The aim of this study was to describe the genetic diversity based on the runs of homozygosity (ROHs), linkage disequilibrium (LD) and effective population size (NeLD) using genome-wide data. Moreover, Bayesian clustering algorithms and multivariate methods were used to detect the population structure, potential admixture level and relationship between Austrian and Slovak Pinzgau cattle with respect to a large meta-population consisting of 15 European cattle breeds. The proportion of ROH segments ranged from 0.43 to 1.91% in Slovak Pinzgau, depending on the minimum size of an ROH. The genomic inbreeding coefficients were higher than the pedigree ones possibly due to the limited number of available generations in pedigree data. The observed NeLD was close to the limit value characterizing the endangerment status, based both on genomic and pedigree data. Population structure within analyzed breeds based on the Wright’s FST index, Nei’s genetic distances, and unsupervised as well as supervised analysis has been established. Overall, these analyses clearly distinguished populations based on their origin. A detailed analysis of the introgression of each breed into the Pinzgau breeds prepared using a Bayesian approach showed that the contribution of Holstein cattle in Austrian as well as Slovak Pinzgau was larger than contribution of beef breeds. A possible reason is the recent usage of Holstein sires to increase milk production. There are considerable differences between well-defined regions that clearly distinguish Austrian and Slovak Pinzgau, despite their close common history. Generally, the breeding program of Austrian Pinzgau is more focused on meat production than Slovak Pinzgau, which was clearly reflected in the obtained autozygosity islands. Considering the genetic establishment of Slovak Pinzgau population the genetic potential of the breed is insufficiently used. On a long term, more global breeding program including very close populations will be more efficient providing higher genetic progress and diversity. Established methodology how to distinguish genealogically close populations on high-throughput molecular information based of Slovak and Austrian Pinzgau can be proposed as general for analysis of differences in all highly related breeds.

GENETIC MARKERS AS ONE OF TOOLS FOR PRODUCTION OF TENDERNESS MEAT IN CATTLE

Meat tenderness is one of the major characteristic quality of beef not only for consumers but for breeders of beef cattle too. Selection of cattle focussed on an increment of meat tenderness is complicated because this trait has large variability not only between different breeds but between individuals of equal breed too. Similarly a measurement of meat tenderness is expensive because it make after slaughter of animal and ageing of meat post mortem. Therefore it was developed a several methods, by the help of which is possible increase tenderness of meat. However still exist variance in values of meat tenderness which are caused by distinctness genetic base of animal. By using molecular genetic methods was described the most significant candidate genes (CAPN1, CAST) coding formation of the calpains-calpastatin proteolytic system, which exercise an influence on tenderness. The single nucleotide polymorphisms (SNPs) in these genes were using to design commercially genetic marker panels GeneSTAR Tenderness and Igenity Tender-GENE. By help this commercially test is possible to make genotyping and selection of animals for production of tenderness beef meat in meat industry. doi:10.5219/102

Genetic diversity of local cattle

The Slovak Pinzgau breed faces the bottleneck effect and the loss of diversity due to unequal use of founders and a significant population decline. Further population size reduction can lead to serious problems. Information obtained here and in other studies from high-throughput genotyping of 179 individuals was used to characterise genetic diversity and differentiation of Slovak Pinzgau, Austrian Pinzgau, Cika and Piedmontese cattle by Bayesian clustering algorithm. A gene flow network for the clusters estimated from admixture results was produced. The low estimate of genetic differentiation (FST) in Pinzgau cattle populations indicated that differentiation among these populations is low, particularly owing to a common historical origin and high gene flow. Changes in the log marginal likelihood indicated Austrian Pinzgau as the most similar breed to Slovak Pinzgau. All populations except the Piedmontese one displayed two ways of gene flow among populations, indicating that Piedmontese cattle was involved in producing of the analysed breeds while these breeds were not involved in creation of Piedmontese. Genetic evaluation represents an important tool in breeding and cattle selection. It is more strategically important than ever to preserve as much of the livestock diversity as possible, to ensure a prompt and proper response to the needs of future generations. Information provided by the fine-scale genetic characterization of this study clearly shows that there is a difference in genetic composition of Slovak and Austrian populations, as well as the Cika and Piedmontese cattle. Despite its population size, the Slovak Pinzgau cattle have a potential to serve as a basic gene reserve of this breed, with European and world-wide importance.

GENETIC DIVERSITY IN SLOVAK SPOTTED BREED

The objective of the study was to evaluate inbreeding and genetic diversity in Slovak Spotted cattle. Reference population contained genealogic information on 36949 animals (129 sires and 36820 cows) that were used in the analyses. Pedigree completeness indexes in the first three generations were on the level of 100 %, in the 5 generation it was 60 %. Since 1970, inbreeding trend was positive with significant increasing in 1990. Average relationship was 0.8 %, inbreeding rate 0.36 % and ΔF = 0.094 %. In the reference population 43 % animals was inbred, 68 % of sires and 33 % cows, with also 67 % purebred cows, as well. Total genetic diversity loss in the reference population and population of cows was the same, closely under 1%, in purebred cows 1.19 % and sires even due to higher inbreeding level 1.78 %. Genetic diversity loss was more influenced by the genetic drift 0.80% in the reference population, 1.47% in sire group, than by effective number of founder unequal contributions. F statistic showed fines superiority of heterozygosity by sire lines subpopulations, in the whole sire group (FIS = 0.12) and their minimal differentiation (FST = 0,098). Obtained results showed that inbreedization process started in this population. Monitoring and better genetic management are important from the point of its further sustainable development.

GENETIC MARKERS AND BIOSTATISTICAL METHODS AS APPROPRIATE TOOLS TO PRESERVE GENETIC RESOURCES

The aim of presented study was to assess the most suitable way how to distinguish different breeds based on molecular markers. One of the most difficult aspects of quality assurance schemes is their reliability. The verification of fraud needs great efforts in control strategies. The use of DNA markers has been shown to be a useful tool for individual identification. It is necessary to use modern statistical method based on data mining and supervised learning. Supervised pattern recognition techniques use the information about the class membership of the samples to a certain group (class or category) in order to classify new unknown samples in one of the known classes on the basis of its pattern of measurements. Large scale of supervised learning oriented method was used for traceability and identification on individual level. A result of provided study shows the possibility to classify unknown samples according to genetic data. Model is also useful for classification on many logical levels as brand, region and many others. If we take in the account only Slovak and Austrian Pinzgau cattle, based on SNP chip data, it is not possible to separate them using Bayesian approach. Once we considered with the admixture of breeds involved in the historical development as well as inbreeding, selection signatures and migration, we were able to separate even genetically similar breeds. It is possible distinguish between closely related populations based on different markers. We just need to select the appropriate type of analysis.

POLYMORPHISMS IN CANDIDATE GENES FOR BEEF QUALITY IN PINZGAU CATTLE

The aim of present study was to identify the polymorphisms in genes encoding calpastatin (CASTUoG), calpain (CAPN1, CAPN2), diacylglycerol Oacyltransferase (DGAT1), thyroglobulin (TG5), and Stearoyl-CoA Desaturase (SCD) in order to analyse genetic structure of Pinzgau cattle. The genomic DNA for genotyping was obtained from in total 56 blood samples of Pinzgau bulls. After extraction, the concentration of DNA was controlled by the spectrophotometry measurement. The genotyping of each individual was carried out by using PCRRFLP methods. The average value of observed (0.37±0.05) and expected heterozygosity (0.39±0.06) clearly indicated the prevalence of homozygous individuals. Observed Wrights fixation indexes showed positive values across all loci (0.03±0.06), which confirmed slight deficiency of heterozygote animals compared to the Hardy-Weinberg equilibrium expectations. The Hardy-Weinberg equilibrium was found in population, which signalizes only slight impact of factors such as selection, migration or inbreeding. The effectiveness of loci allele impact in populations has been described also by effective allele numbers (1.68±0.13) that expressed the decrease of allele activity in population. The loss of heterozygosity in analysed population was found across all of genetic markers. Each of the evaluated indicators clearly points to the need of genetic diversity monitoring. Moreover, the analyses of single nucleotide polymorphisms in genes significantly involved in control of economically important production traits are still very usable methods for identification of genetic markers that can be used in marker assisted selection of cattle.

Effect of selected polymorphisms of genes lep, MTHFR and FTO to BMI level and gender-specificity

The aim of this study is to investigate the effect of selected polymorphisms LEP (G2548A), MTHFR (C677T) and FTO ( rs1121980 ) on body mass index in humans. In the study participated 79 people from Slovakia with some genetic relatedness. Genomic DNA was isolated from the buccal swabs using a commercial kit Qiagen DNA Mini Kit (Qiagen). The detection of SNP polymorphisms in human genes LEP, MTHFR and FTO was performed using molecular genetics methods such as PCR-RFLP and ARMS. The most common genotypes in all 3 polymorphism were found in heterozygous form (for LEP AG = 0.5190, for MTHFR CT = 0.519, for FTO CT =0.4051). The LEP gene had increased frequency of G allele (0.5506), the MTHFR gene T allele (0.6646) and FTO gene T allele (0.50635). The least frequent genotype in LEP was AA (0.1899), in MTHFR was TT (0.0759), in FTO it was CC (0.2911). According to the results we can assume that the genotypes AA (LEP G2548A), CC (FTO rs1121980 ) and TT (MTHFR C677T) in case of women have a protective effect on the prevalence of obesity, based on BMI, compared to the other genotypes and this polymorphism is gender-specific. Added anthropometric measurements, blood test and extension of the group in the future evaluation could increase the statistical relevance in relation to obesity and gender-specificity.

Genomic variation across cervid species in respect to the estimation of red deer diversity

Abstract The aim of this study was to assess the genetic variations and relationships across evolutionary related cervid species in order to estimate the genetic diversity of the Red deer population that inhabits the forest area in the south-western part of Slovakia. The study was based on the application of cross-species SNP genotyping. The genomic data were obtained from a total of 86 individuals representing six genera (Axis, Dama, Cervus, Alces, Rangifer, and Odocoileus) using Illumina BovineSNP50 BeadChip. From 38.85% of successfully genotyped loci up to 1,532 SNPs showed polymorphism and were informative for subsequent analyses of the diversity and interspecific genetic relationships. Generally, a good level of observed heterozygosity was found across all species. The value of FIS (0.23±0.13) signalised the increase of a homozygous proportion within them. The application of molecular variance analysis to the hierarchical population structure showed that most of the variation was conserved within separate species (96%). The performed diversity analysis of Slovak Red deer population and comparative analysis of their phylogenic relationships among subspecies from genus Cervus did not identify a remarkable loss of genetic variability. Also, were not identified any degree of admixture that could be due to the historical background of deer farming in Slovakia or reintroduction and hybridisation by other species from genus Cervus (C. canadensis, and C. nippon) which are the major risk of loss of autochthonous Red deer populations in many areas of Central Europe. The analysis of individual’s ancestry showed consistent results with patterns of evaluated group differentiations which means low migration rates among all species.

Inheritance of coat colour in Slovak Pinzgau cattle

The objective of the work was analysis of chestnut coat colour inheritance of Slovak Pinzgau cattle in accordance to age and farming system. In 304 cows of breeding groups P0,P1,P2 and R3 born between 2000 to 2010 from four breeding herds (4 agricultural cooperatives and JSC: PD Smrecany – farm Veterna Poruba, PD Spisske Bystre – farm Kvetnica, Agria Liptovský Ondrej JSC – farm Liptovska Porubka, PD LCV Cimhova) was measured intensity of coat colour. For objective measurement of coat colour the handheld Minolta Chromameter CM-2600d was applied using the CIE L*a*b* colour space. The instrument recorded the values L*, a* and b*. The L* value shows the lightness of the colour, a* value indicates the red/green, while the b* value indicates the yellow/blue chromaticity of the colour. The values C* (Chroma/saturation) and h (hue) were derived from the values a* and b*. Average lightness in observed animals was 22.60; average of the red chroma was 8.84 resp. 13.32 for the yellow chroma. Saturation of coat colour was 16.19 resp. 0.97 for hue.

Extent of genome-wide linkage disequilibrium in Pinzgau cattle

The aim of this study was to describe the extent of linkage disequilibrium (LD) based on genotyping data in Pinzgau cattle population. DNA samples were obtained from 19 bulls of active Pinzgau cattle population in Slovakia. Genotyping was carried out in commercial lab using an Illumina BovineSNP50 BeadChip. The genotyping array contained 54,609 single nucleotide polymorphisms (SNPs). After quality control SNPs localized on sex chromosomes were excluded. A total of 42,248 (79.97%) SNPs were found to be polymorphic. The distribution of SNPs over entire genomes of all chromosomes was not uniform. The minor allele frequencies across autosomal loci ranged from 0.266 (BTA4) to 0.280 (BTA23) with average value 0.273±0.133. Only adjacent SNPs with distance less than 5 Mb and LD (r2) values from 0.01 to 0.99 were used in the characterization of LD extent. After filtering, the genome coordinates of 31,063 SNP markers covered all regions of autosomes on the length 2519232 kb. The spacing across genome between adjacent SNPs was in average 46.89±47.48 kb and within autosomes ranged from 43.65 kb (BTA25) to 52.59 kb (BTA5). The distribution of SNPs on different chromosomes ranged from 633 (79.13%) on BTA29 to 1123 (83.62%) on BTA14. The average LD between adjacent markers within autosomes reached values from 0.189 to 0.234 for chromosomes BTA 29 and 21, respectively. Division of r2-values over all 29 autosomes were performed according to their physical intermarker distances and averaged within the groups for analysis of distance effect on LD. The results of our study indicated the rapid decay of LD with increasing distance between markers. Further investigation will be oriented on evaluation of effective population size based on LD data. This could allow improvement of our knowledge about genetic diversity and its use for breed preservation of original phenotype supported by the current selection schemes and breeding programmes.