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This study focused on the genomic differences between the Czechoslovakian wolfdog (CWD) and its ancestors, the Grey wolf (GW) and German Shepherd dog. The Saarloos wolfdog and Belgian Shepherd dog were also included to study the level of GW genetics retained in the genome of domesticated breeds. The dataset consisted of 131 animals and 143,593 single nucleotide polymorphisms (SNPs). The effects of demographic history on the overall genome structure were determined by screening the distribution of the homozygous segments. The genetic variance distributed within and between groups was quantified by genetic distances, the FST index, and discriminant analysis of principal components. Fine-scale population stratification due to specific morphological and behavioural traits was assessed by principal component and factorial analyses. In the CWD, a demographic history effect was manifested mainly in a high genome-wide proportion of short homozygous segments corresponding to a historical load of inbreeding derived from founders. The observed proportion of long homozygous segments indicated that the inbreeding events shaped the CWD genome relatively recently compared to other groups. Even if there was a significant increase in genetic similarity among wolf-like breeds, they were genetically separated from each other. Moreover, this study showed that the CWD genome carries private alleles that are not found in either wolves or other dog breeds analysed in this study.
Nina Moravčíková; Radovan Kasarda; Radoslav Židek; Luboš Vostrý; Hana Vostrá-Vydrová; Jakub Vašek; Daniela Čílová. Czechoslovakian Wolfdog Genomic Divergence from Its Ancestors Canis lupus, German Shepherd Dog, and Different Sheepdogs of European Origin. Genes 2021, 12, 832 .
AMA StyleNina Moravčíková, Radovan Kasarda, Radoslav Židek, Luboš Vostrý, Hana Vostrá-Vydrová, Jakub Vašek, Daniela Čílová. Czechoslovakian Wolfdog Genomic Divergence from Its Ancestors Canis lupus, German Shepherd Dog, and Different Sheepdogs of European Origin. Genes. 2021; 12 (6):832.
Chicago/Turabian StyleNina Moravčíková; Radovan Kasarda; Radoslav Židek; Luboš Vostrý; Hana Vostrá-Vydrová; Jakub Vašek; Daniela Čílová. 2021. "Czechoslovakian Wolfdog Genomic Divergence from Its Ancestors Canis lupus, German Shepherd Dog, and Different Sheepdogs of European Origin." Genes 12, no. 6: 832.
This study aimed to assess the level of biodiversity in selected local cattle populations as important food resources in Slovakia. The biodiversity level was derived from the genome-wide data collected for dairy (Jersey), dual-purpose (Slovak Pinzgau, Slovak Spotted), and beef breeds (Charolais, Limousine). The commonly used indices, genomic inbreeding (FROH, FGRM, FHOM, FUNI) and effective population size (NeLD), were used to quantify the impact of relatives mating on the genome of analysed populations. Even if the low NeLD estimates signalise significant loss of genetic variability within populations, the genomic inbreeding under 1% (except Jersey) showed that the intensity of diversity loss is not so rapid and can be managed by the re-arrangement of long-term breeding strategies. The analysis of genetic differentiation degree across populations assumed that the specialisation of breeds during their grading-up led to the specific nucleotide changes, especially in genes responsible for preferred phenotypic traits. The breed-specific differences observed mainly in the genome of Charolais (carcass traits) and Jersey (milk production traits) populations resulted from the polymorphisms in CAPN1 (μ-calpain) and CSN1S2 (casein alpha s2) genes, respectively. Obtained results confirmed that the specific haplotypes are strongly associated with the genetic nature of breed depending on production type.
Radovan Kasarda; Luboš Vostrý; Hana Vostrá-Vydrová; Kristína Candráková; Nina Moravčíková. Food Resources Biodiversity: The Case of Local Cattle in Slovakia. Sustainability 2021, 13, 1296 .
AMA StyleRadovan Kasarda, Luboš Vostrý, Hana Vostrá-Vydrová, Kristína Candráková, Nina Moravčíková. Food Resources Biodiversity: The Case of Local Cattle in Slovakia. Sustainability. 2021; 13 (3):1296.
Chicago/Turabian StyleRadovan Kasarda; Luboš Vostrý; Hana Vostrá-Vydrová; Kristína Candráková; Nina Moravčíková. 2021. "Food Resources Biodiversity: The Case of Local Cattle in Slovakia." Sustainability 13, no. 3: 1296.
Article Details: Received: 2020-05-21 | Accepted: 2020-06-02 | Available online: 2020-06-30https://doi.org/10.15414/afz.2020.23.02.102-108The submission aims to present results of the five-year research project, oriented on the evaluation of genetic diversity of selected populations of economically important animal species in Slovakia, their sustainable adaptation and production potential in the context of preservation of genetic resources and food safety. Under the supervision of Department of Animal Genetics and Breeding Biology, Faculty of Agrobiology and Food Resources of the Slovak University of Agriculture in Nitra run between 2015- 2019 project called Molecular-genetic diversity and production potential of animal genetic resources in Slovakia (APVV-14-0054). Considering the difficulty and complexity of studied issues was research realized in close collaboration with the University of Natural Resources and Life Sciences Vienna (BOKU) and Zagreb University. Erosion of genetic diversity represents the main threat for food safety of mankind. Individuals of economically important animal species groups accumulate risks and threats of loss of sustainable adaptation as a reaction to the environment due to intense selective breeding. It is therefore important and needed to focus on permanent monitoring and evaluation of diversity of economically important breeds based on the diverse parameter and suitable methods.Keywords: Genetic diversity, economically important breeds, Animal genetic resources, SlovakiaReferencesKADLEČÍK, O., HAZUCHOVÁ, E., MORAVČÍKOVÁ, N. and KUKUČKOVÁ, V. (2017b). Genetic diversity in Slovak spotted breed. AGROFOR, 2(3), 124–131.KADLEČÍK, O., HAZUCHOVÁ, E., PAVLÍK, I. and KASARDA, R. (2016). Genetická diverzita slovenského strakatého a holštajnského dobytka (1. vyd). Nitra: Slovenská poľnohospodárska univerzita.KADLEČÍK, O., MORAVČÍKOVÁ, N. and KASARDA, R. (2017a). Biodiverzita populácií zvierat. Nitra: Slovenská poľnohospodárska univerzita.KASARDA, R., KADLEČÍK, O. and MORAVČÍKOVÁ, N. (2019b). Genetická diverzita slovenského pinzgauského plemena (1. vyd). Nitra: Slovenská poľnohospodárska univerzita.KASARDA, R., KADLEČÍK, O., TRAKOVICKÁ, A. and MORAVČÍKOVÁ, N. (2019c). Genomic and pedigree-based inbreeding in Slovak Spotted cattle. AGROFOR, 4(1), 102–110.KASARDA, R., MORAVČÍKOVÁ, N. and KADLEČÍK, O. (2016d). Spatial structure of the Lipizzan horse gene pool based on microsatellite variations analysis. AGROFOR, 1(2), 125–132.KASARDA, R., MORAVČÍKOVÁ, N. and KADLEČÍK, O. (2018d). Genetic structure of warmblood horses on molecular-genetic level. Agriculture and Forestry, 64(1), 7–13.KASARDA, R., MORAVČÍKOVÁ, N. and POKORÁDI, J. (2016a). Manažment farmového chovu a biodiverzita jeleňa lesného na Slovensku. Nitra: Slovenská poľnohospodárska univerzita.KASARDA, R., MORAVČÍKOVÁ, N. and VLČEK, M. (2018b). Genetic parameters of claw traits and milk yield in Slovak Holstein cattle. V Genetic days 2018 (s. 24). České Budějovice: University of South Bohemia.KASARDA, R., MORAVČÍKOVÁ, N., CANDRÁK, J., MÉSZÁROS, G., VLČEK, M., KUKUČKOVÁ, V. and KADLEČÍK, O. (2017b). Genome-wide mixed model association study in population of Slovak Pinzgau cattle. Agriculturae conspectus scientificus, 82(3), 267–271.KASARDA, R., MORAVČÍKOVÁ, N., HALO, M., HORNÝ, M., LEHOCKÁ, K., OLŠANSKÁ, B., BUJKO, J. and CANDRÁK, J. (2019e). Trend vývoja genomického inbrídingu v populácii plemena lipican. V Aktuálne smerovanie v chove koní (1. s. 32– 36). Nitra: Slovenská poľnohospodárska univerzita.KASARDA, R., MORAVČÍKOVÁ, N., KADLEČÍK, O., TRAKOVICKÁ, A. and CANDRÁK, J. (2018a). The impact of artificial selection on runs of homozygosity in Slovak Spotted and Pinzgau cattle. Slovak journal of animal science, 51(3), 91–103.KASARDA, R., MORAVČÍKOVÁ, N., KADLEČÍK, O., TRAKOVICKÁ, A., HALO, M. and CANDRÁK, J. (2019a). Level of inbreeding in Norik of muran horse: Pedigree vs. Genomic data. Acta Universitatis Agriculturae et Silviculturae Mendelianae Brunensis, 67(6), 1457–1463.KASARDA, R., MORAVČÍKOVÁ, N., KADLEČÍK, O., TRAKOVICKÁ, A., ŽITNÝ, J., TERPAJ, V.P., MINDEKOVÁ, S. and NEUPANE MLYNEKOVÁ, L. (2019d). Common origin of local cattle breeds in western region of Carpathians. Danubian Animal Genetic Resource, 4, 37–42.KASARDA, R., MORAVČÍKOVÁ, N., KUKUČKOVÁ, V., KADLEČÍK, O., TRAKOVICKÁ, A. and MÉSZÁROS, G. (2016c). Evidence of selective sweeps through haplotype structure of Pinzgau cattle. Acta agriculturae Slovenica, 107(5), 160–164.KASARDA, R., MORAVČÍKOVÁ, N., KUKUČKOVÁ, V., TRAKOVICKÁ, A. and KADLEČÍK, O. (2016b). Progress in methodology of genetic diversity monitoring in pinzgau cattle. Slovak journal of animal science, 49(4), 176.KASARDA, R., MORAVČÍKOVÁ, N., KUKUČKOVÁ, V., TRAKOVICKÁ, A. and KADLEČÍK, O. (2017a). Characterization of Slovak dual-purpose cattle breed diversity based on genomic data. Slovak journal of animal science, 50(4), 165.KASARDA, R., MORAVČÍKOVÁ,...
Radovan Kasarda; Ľubica Jamborová; Nina Moravčíková. Genetic diversity and production potential of animal food resources: Review article. Acta fytotechnica et zootechnica 2020, 23, 1 .
AMA StyleRadovan Kasarda, Ľubica Jamborová, Nina Moravčíková. Genetic diversity and production potential of animal food resources: Review article. Acta fytotechnica et zootechnica. 2020; 23 (2):1.
Chicago/Turabian StyleRadovan Kasarda; Ľubica Jamborová; Nina Moravčíková. 2020. "Genetic diversity and production potential of animal food resources: Review article." Acta fytotechnica et zootechnica 23, no. 2: 1.
Radovan Kasarda; Nina Moravčíková; Ondrej Kadlečík; Anna Trakovická; Marko Halo; Juraj Candrák. Level of Inbreeding in Norik of Muran Horse: Pedigree vs. Genomic Data. Acta Universitatis Agriculturae et Silviculturae Mendelianae Brunensis 2019, 67, 1457 -1463.
AMA StyleRadovan Kasarda, Nina Moravčíková, Ondrej Kadlečík, Anna Trakovická, Marko Halo, Juraj Candrák. Level of Inbreeding in Norik of Muran Horse: Pedigree vs. Genomic Data. Acta Universitatis Agriculturae et Silviculturae Mendelianae Brunensis. 2019; 67 (6):1457-1463.
Chicago/Turabian StyleRadovan Kasarda; Nina Moravčíková; Ondrej Kadlečík; Anna Trakovická; Marko Halo; Juraj Candrák. 2019. "Level of Inbreeding in Norik of Muran Horse: Pedigree vs. Genomic Data." Acta Universitatis Agriculturae et Silviculturae Mendelianae Brunensis 67, no. 6: 1457-1463.
Nina Moravčíková; Radovan Kasarda; Ondrej Kadlečík; Anna Trakovická; Marko Halo; Juraj Candrák. Runs of Homozygosity as Footprints of Selection in the Norik of Muran Horse Genome. Acta Universitatis Agriculturae et Silviculturae Mendelianae Brunensis 2019, 67, 1165 -1170.
AMA StyleNina Moravčíková, Radovan Kasarda, Ondrej Kadlečík, Anna Trakovická, Marko Halo, Juraj Candrák. Runs of Homozygosity as Footprints of Selection in the Norik of Muran Horse Genome. Acta Universitatis Agriculturae et Silviculturae Mendelianae Brunensis. 2019; 67 (5):1165-1170.
Chicago/Turabian StyleNina Moravčíková; Radovan Kasarda; Ondrej Kadlečík; Anna Trakovická; Marko Halo; Juraj Candrák. 2019. "Runs of Homozygosity as Footprints of Selection in the Norik of Muran Horse Genome." Acta Universitatis Agriculturae et Silviculturae Mendelianae Brunensis 67, no. 5: 1165-1170.
Anna Trakovická; Klára Vavrišínová; Michal Gábor; Martina Miluchová; Radovan Kasarda; Nina Moravčíková. The impact of diacylglycerol O-acyltransferase 1 gene polymorphism on carcass traits in cattle. Journal of Central European Agriculture 2019, 20, 12 -18.
AMA StyleAnna Trakovická, Klára Vavrišínová, Michal Gábor, Martina Miluchová, Radovan Kasarda, Nina Moravčíková. The impact of diacylglycerol O-acyltransferase 1 gene polymorphism on carcass traits in cattle. Journal of Central European Agriculture. 2019; 20 (1):12-18.
Chicago/Turabian StyleAnna Trakovická; Klára Vavrišínová; Michal Gábor; Martina Miluchová; Radovan Kasarda; Nina Moravčíková. 2019. "The impact of diacylglycerol O-acyltransferase 1 gene polymorphism on carcass traits in cattle." Journal of Central European Agriculture 20, no. 1: 12-18.
Nina Moravcikova; Ondrej Kadlecik; Anna Trakovicka; Radovan Kasarda. AUTOZYGOSITY ISLAND RESULTING FROM ARTIFICIAL SELECTION IN SLOVAK SPOTTED CATTLE. The Journal "Agriculture and Forestry" 2018, 64, 1 .
AMA StyleNina Moravcikova, Ondrej Kadlecik, Anna Trakovicka, Radovan Kasarda. AUTOZYGOSITY ISLAND RESULTING FROM ARTIFICIAL SELECTION IN SLOVAK SPOTTED CATTLE. The Journal "Agriculture and Forestry". 2018; 64 (4):1.
Chicago/Turabian StyleNina Moravcikova; Ondrej Kadlecik; Anna Trakovicka; Radovan Kasarda. 2018. "AUTOZYGOSITY ISLAND RESULTING FROM ARTIFICIAL SELECTION IN SLOVAK SPOTTED CATTLE." The Journal "Agriculture and Forestry" 64, no. 4: 1.
The aim of presented study was to assess the most suitable way how to distinguishdifferent breeds based on molecular markers. One of the most difficult aspects ofquality assurance schemes is their reliability. The verification of fraud needs greatefforts in control strategies. The use of DNA markers has been shown to be auseful tool for individual identification. It is necessary to use modern statisticalmethod based on data mining and supervised learning. Supervised patternrecognition techniques use the information about the class membership of thesamples to a certain group (class or category) in order to classify new unknownsamples 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 andidentification on individual level. A result of provided study shows the possibilityto classify unknown samples according to genetic data. Model is also useful forclassification on many logical levels as brand, region and many others. If we takein the account only Slovak and Austrian Pinzgau cattle, based on SNP chip data, itis not possible to separate them using Bayesian approach. Once we considered withthe admixture of breeds involved in the historical development as well asinbreeding, selection signatures and migration, we were able to separate evengenetically similar breeds. It is possible distinguish between closely relatedpopulations based on different markers. We just need to select the appropriate typeof analysis.
Veronika Kukučková; Radovan Kasarda; Július Žitný; Nina Moravčíková. GENETIC MARKERS AND BIOSTATISTICAL METHODS AS APPROPRIATE TOOLS TO PRESERVE GENETIC RESOURCES. AGROFOR 2018, 3, 1 .
AMA StyleVeronika Kukučková, Radovan Kasarda, Július Žitný, Nina Moravčíková. GENETIC MARKERS AND BIOSTATISTICAL METHODS AS APPROPRIATE TOOLS TO PRESERVE GENETIC RESOURCES. AGROFOR. 2018; 3 (2):1.
Chicago/Turabian StyleVeronika Kukučková; Radovan Kasarda; Július Žitný; Nina Moravčíková. 2018. "GENETIC MARKERS AND BIOSTATISTICAL METHODS AS APPROPRIATE TOOLS TO PRESERVE GENETIC RESOURCES." AGROFOR 3, no. 2: 1.
Veronika Kukučková; Nina Moravčíková; Ino Curik; Mojca Simčič; Gábor Mészáros; Radovan Kasarda. Genetic diversity of local cattle. Acta Biochimica Polonica 2018, 65, 421 -424.
AMA StyleVeronika Kukučková, Nina Moravčíková, Ino Curik, Mojca Simčič, Gábor Mészáros, Radovan Kasarda. Genetic diversity of local cattle. Acta Biochimica Polonica. 2018; 65 (3):421-424.
Chicago/Turabian StyleVeronika Kukučková; Nina Moravčíková; Ino Curik; Mojca Simčič; Gábor Mészáros; Radovan Kasarda. 2018. "Genetic diversity of local cattle." Acta Biochimica Polonica 65, no. 3: 421-424.
The aim of present study was to identify the polymorphisms in genes encodingcalpastatin (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 DNAfor genotyping was obtained from in total 56 blood samples of Pinzgau bulls. Afterextraction, the concentration of DNA was controlled by the spectrophotometrymeasurement. The genotyping of each individual was carried out by using PCRRFLPmethods. The average value of observed (0.37±0.05) and expectedheterozygosity (0.39±0.06) clearly indicated the prevalence of homozygousindividuals. Observed Wright's fixation indexes showed positive values across allloci (0.03±0.06), which confirmed slight deficiency of heterozygote animalscompared to the Hardy-Weinberg equilibrium expectations. The Hardy-Weinbergequilibrium was found in population, which signalizes only slight impact of factorssuch as selection, migration or inbreeding. The effectiveness of loci allele impact inpopulations has been described also by effective allele numbers (1.68±0.13) thatexpressed the decrease of allele activity in population. The loss of heterozygosityin analysed population was found across all of genetic markers. Each of theevaluated indicators clearly points to the need of genetic diversity monitoring.Moreover, the analyses of single nucleotide polymorphisms in genes significantlyinvolved in control of economically important production traits are still very usablemethods for identification of genetic markers that can be used in marker assistedselection of cattle.
Anna Trakovická; Nina Moravčíková; Rudolf Nádaský; Radovan Kasarda. POLYMORPHISMS IN CANDIDATE GENES FOR BEEF QUALITY IN PINZGAU CATTLE. AGROFOR 2018, 3, 1 .
AMA StyleAnna Trakovická, Nina Moravčíková, Rudolf Nádaský, Radovan Kasarda. POLYMORPHISMS IN CANDIDATE GENES FOR BEEF QUALITY IN PINZGAU CATTLE. AGROFOR. 2018; 3 (1):1.
Chicago/Turabian StyleAnna Trakovická; Nina Moravčíková; Rudolf Nádaský; Radovan Kasarda. 2018. "POLYMORPHISMS IN CANDIDATE GENES FOR BEEF QUALITY IN PINZGAU CATTLE." AGROFOR 3, no. 1: 1.
The objective of the study was to evaluate inbreeding and genetic diversity inSlovak Spotted cattle. Reference population contained genealogic information on36949 animals (129 sires and 36820 cows) that were used in the analyses. Pedigreecompleteness indexes in the first three generations were on the level of 100 %, inthe 5th generation it was 60 %. Since 1970, inbreeding trend was positive withsignificant increasing in 1990. Average relationship was 0.8 %, inbreeding rate0.36 % 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 geneticdiversity 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 inbreedinglevel 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 offounder unequal contributions. F statistic showed fines superiority ofheterozygosity by sire lines subpopulations, in the whole sire group (FIS = - 0.12)and their minimal differentiation (FST = 0,098). Obtained results showed thatinbreedization process started in this population. Monitoring and better geneticmanagement are important from the point of its further sustainable development.
Ondrej Kadlečík; Eva Hazuchová; Nina Moravčíková; Veronika Kukučková; Radovan Kasarda. GENETIC DIVERSITY IN SLOVAK SPOTTED BREED. AGROFOR 2018, 2, 1 .
AMA StyleOndrej Kadlečík, Eva Hazuchová, Nina Moravčíková, Veronika Kukučková, Radovan Kasarda. GENETIC DIVERSITY IN SLOVAK SPOTTED BREED. AGROFOR. 2018; 2 (3):1.
Chicago/Turabian StyleOndrej Kadlečík; Eva Hazuchová; Nina Moravčíková; Veronika Kukučková; Radovan Kasarda. 2018. "GENETIC DIVERSITY IN SLOVAK SPOTTED BREED." AGROFOR 2, no. 3: 1.
Radovan Kasarda; Nina Moravčíková; Ondrej Kadlečík. GENETIC STRUCTURE OF WARMBLOOD HORSES ON MOLECULAR-GENETIC LEVEL. The Journal "Agriculture and Forestry" 2018, 64, 1 .
AMA StyleRadovan Kasarda, Nina Moravčíková, Ondrej Kadlečík. GENETIC STRUCTURE OF WARMBLOOD HORSES ON MOLECULAR-GENETIC LEVEL. The Journal "Agriculture and Forestry". 2018; 64 (1):1.
Chicago/Turabian StyleRadovan Kasarda; Nina Moravčíková; Ondrej Kadlečík. 2018. "GENETIC STRUCTURE OF WARMBLOOD HORSES ON MOLECULAR-GENETIC LEVEL." The Journal "Agriculture and Forestry" 64, no. 1: 1.
The aim of this study was to analyse the genomic regions that have been target of natural selection with respect to identifying the loci responsible mainly for fitness traits across six alpine cattle breeds. The genome-wide scan for selection signatures was performed using genotyping data from totally 465 animals. After applying data quality control, overall 35 873 single nucleotide polymorphisms were useable for the subsequent analysis. The detection of genomic regions affected by natural selection was carried out using the approach of principal component analysis. The analysis was based on the assumption that markers extremely related to the population structure are also candidates for local adaptation potential of the population. Based on the expected false discovery rate equal to 10% up to 1138 loci were identified as outliers. The strongest signals of selection were found in genomic regions on BTA 1, 2, 3, 6, 9, 11, 13, and 22. Most genes located in the identified regions have been previously associated with immunity system as well as body growth and muscle formation that mainly reflect the pressure of both natural and artificial selection in respect to adaptation of analysed breeds to the local environmental conditions. The results also signalized that those regions represent a correlated selection response in way to maintain the fitness of analysed breeds.
N. Moravčíková; M. Simčič; G. Mészáros; J. Sölkner; V. Kukučková; M. Vlcek; A. Trakovická; O. Kadlečík; R. Kasarda. Genomic response to natural selection within alpine cattle breeds. Czech Journal of Animal Science 2018, 63, 136 -143.
AMA StyleN. Moravčíková, M. Simčič, G. Mészáros, J. Sölkner, V. Kukučková, M. Vlcek, A. Trakovická, O. Kadlečík, R. Kasarda. Genomic response to natural selection within alpine cattle breeds. Czech Journal of Animal Science. 2018; 63 (No. 4):136-143.
Chicago/Turabian StyleN. Moravčíková; M. Simčič; G. Mészáros; J. Sölkner; V. Kukučková; M. Vlcek; A. Trakovická; O. Kadlečík; R. Kasarda. 2018. "Genomic response to natural selection within alpine cattle breeds." Czech Journal of Animal Science 63, no. No. 4: 136-143.
In this study, we aimed to estimate and compare genetic diversity of two native draught horse breeds and check the possible influence of Noriker breed population on these native breeds. Genetic analyses of relationships and admixture were performed in two native endangered draught horse populations (Silesian Noriker and Czech-Moravian Belgian horses) and one open breed (Noriker). Totally 104 alleles from 13 microsatellite loci were detected in 1298 horses. The average number of alleles per locus was the highest in the Czech-Moravian Belgian horse (7.62) and the lowest in the Silesian Noriker (7.31), the differences were non-significant, whereas the observed and expected heterozygosities per breed ranged from 0.680 (Czech-Moravian Belgian) to 0.719 (Noriker) and from 0.678 (Silesian Noriker) to 0.714 (Noriker). The estimates of Wright’s FST between each pair of breeds indicated a low level of genetic segregation. At the individual level across the analyzed population, formation of two clusters was observed with respect to historical breed development. Moreover, the membership probability outputs showed that the frequencies of alleles varied across the two main regions represented by the Czech-Moravian Belgian and other analyzed breeds. Our results indicated high genetic variability, low inbreeding, and low genetic differentiation, especially between Silesian Noriker and Noriker, which is caused by the high level of admixture. This high level of admixture was in accordance with geographical location, history, and breeding practices of the analyzed breeds. The Silesian Noriker and Noriker breeds seem to be the most genetically related and the decision to consider them as the same population is thus highly supported. The study provides data and information utilizable in the management of conservation programs planned to reduce inbreeding and to minimize loss of genetic variability.
H. Vostra-Vydrova; L. Vostrý; B. Hofmanová; N. Moravčíková; Z. Vesela; I. Vrtkova; A. Novotná; R. Kasarda. Genetic diversity and admixture in three native draught horse breeds assessed using microsatellite markers. Czech Journal of Animal Science 2018, 63, 85 -93.
AMA StyleH. Vostra-Vydrova, L. Vostrý, B. Hofmanová, N. Moravčíková, Z. Vesela, I. Vrtkova, A. Novotná, R. Kasarda. Genetic diversity and admixture in three native draught horse breeds assessed using microsatellite markers. Czech Journal of Animal Science. 2018; 63 (No. 3):85-93.
Chicago/Turabian StyleH. Vostra-Vydrova; L. Vostrý; B. Hofmanová; N. Moravčíková; Z. Vesela; I. Vrtkova; A. Novotná; R. Kasarda. 2018. "Genetic diversity and admixture in three native draught horse breeds assessed using microsatellite markers." Czech Journal of Animal Science 63, no. No. 3: 85-93.
Radovan Kasarda; Michal Vlček; Juraj Candrák; Nina Moravčíková. Estimation of heritability for claw traits in Holstein cattle using Bayesian and REML approaches. Journal of Central European Agriculture 2018, 19, 784 -790.
AMA StyleRadovan Kasarda, Michal Vlček, Juraj Candrák, Nina Moravčíková. Estimation of heritability for claw traits in Holstein cattle using Bayesian and REML approaches. Journal of Central European Agriculture. 2018; 19 (4):784-790.
Chicago/Turabian StyleRadovan Kasarda; Michal Vlček; Juraj Candrák; Nina Moravčíková. 2018. "Estimation of heritability for claw traits in Holstein cattle using Bayesian and REML approaches." Journal of Central European Agriculture 19, no. 4: 784-790.
Received: 2016-05-24 | Accepted: 2016-08-02 | Available online: 2017-06-20http://dx.doi.org/10.15414/afz.2017.20.01.28–30The aim of this study was to calculate the inbreeding coefficients of the most used sires in population of Slovak Pinzgau and summarize milk production of theirs daughters as main criterion in present in selection of sires besides pedigree based level of inbreeding of future progeny. The runs of homozygosity (ROH) greater than 4 Mb cover on average 1.9 % of genome, ROH ˃ 8 Mb cover 1.3 % and ROH ˃ 16 Mb cover 0.4. Obtained results were compared to genealogical pedigree analysis; the observed inbreeding was higher than that expected based on pedigree data (0.16 %), despite the fact that ROH > 16 Mb representing recent inbreeding approximately three generations ago. The average milk performance of evaluated Slovak Pinzgau cows has been 5259 kg of milk, 3.6 % of protein and 3.85 % of fat. These results are important for the management of the Pinzgau population in Slovakia due to more precise values of inbreeding obtained as well as knowledge about the ancient inbreeding which was not possible to estimate from the pedigree data.Keywords: inbreeding, milk performance, runs of homozygosity, Slovak Pinzgau cattleReferencesALBRECHTSEN A., NIELSEN F.C. and NIELSEN R. (2010) Ascertainment biases in SNP chips affect measures of population divergence. Molecular Biology and Evolution, vol. 27, pp. 2534-2547. doi: http://dx.doi.org/10.1093/molbev/msq148BJELLAND, D.W. et al. (2013) Evaluation of inbreeding depression in Holstein cattle using whole-genome SNP markers and alternative measures of genomic inbreeding. Journal of Dairy Science, vol. 96, pp. 4697-4706. doi:http://dx.doi.org/10.3168/jds.2012-6435CHARLESWORTH, D. and WILLIS, J. (2009) The genetics of inbreeding depression. Nature Reviews Genetics, vol. 10, pp. 783-796. doi:http://dx.doi.org/10.1038/nrg2664FERENČAKOVIĆ, M. et al. (2011) Runs of Homozygosity Reveal Genomewide Autozygosity in the Austrian Fleckvieh Cattle. Agriculturae Conspectus Scientificus, vol. 76, no. 4, pp. 325-328.GURGUL, A., et al. (2016) The use of runs of homozygosity for estimation of recent inbreeding in Holstein cattle. Journal of Applied Genetics, vol. 57, pp. 1-4. doi:http://dx.doi.org/10.1007/s13353-016-0337-6GUTIÉRREZ, J.P. et al. (2008) Individual increase in inbreeding allows estimating realised effective sizes from pedigrees. Genetics Selection Evolution, vol. 40, pp. 359-378. doi:http://dx.doi.org/10.1186/1297-9686-40-4-359MARRAS, G. et al. (2015) Analysis of runs of homozygosity and their relationship with inbreeding in five cattle breeds farmed in Italy. Animal Genetics, vol. 46, no. 2, pp. 110-121. doi:http://dx.doi.org/10.1111/age.12259PAVLÍK, I. et al. (2014) Joint genealogical analysis as a tool for diversity evaluation in Pinzgau cattle populations. Archive Tierzucht, vol. 57, no. 14, pp. 1-12. doi:http://dx.doi.org/10.7482/0003-9438-57-014PURCELL, S. et al. (2007) PLINK: a toolset for whole-genome association and population-based linkage analysis. The American Journal of Human Genetics, vol. 81, pp. 559-575. doi:http://dx.doi.org/10.1086/519795SAS Institute Inc: SAS/STAT Software. (2011) Cary NC: SAS Institute Inc: Version 9.3.THE BREEDING SERVICES OF THE SLOVAK REPUBLIC. (2014) Results of dairy herd milk recording in Slovak Republic for control year 2013-2014. [Online]. Available at http://pssr.sk/org/publ/2014/hd/rocenka/ml_13_14/rocenka/Mliekova_rocenka_2014.pdf. [Accessed: 1st March 2017].
Radovan Kasarda; Veronika Kukučková; Nina Moravčíková. The most important sires in Pinzgau population. Acta fytotechnica et zootechnica 2017, 20, 1 .
AMA StyleRadovan Kasarda, Veronika Kukučková, Nina Moravčíková. The most important sires in Pinzgau population. Acta fytotechnica et zootechnica. 2017; 20 (2):1.
Chicago/Turabian StyleRadovan Kasarda; Veronika Kukučková; Nina Moravčíková. 2017. "The most important sires in Pinzgau population." Acta fytotechnica et zootechnica 20, no. 2: 1.
Received: 2016-05-24 | Accepted: 2016-07-28 | Available online: 2017-06-20http://dx.doi.org/10.15414/afz.2017.20.01.23–27The aim of this study was to determine the population structure and to perform genome-wide scan of footprints of natural selection in cattle using principal component analysis. The applied statistics to identify the SNPs associated with selection pressure focused mainly on the extreme values of FST index. In our study the alternative individual-based approach adopted in the PCAdapt R package has been used. This approach is based on the assumption that markers extremely related to the population structure are also candidates for local adaptation of the population. The genotype data of 350 animals originating from four historically or geographically connected populations (Austrian Pinzgau, Slovak Pinzgau, Brown Swiss, Tyrol Grey) have been used to test this approach in cattle. As expected based on breed's origin the principal component analysis showed the division of animals in to the 3 separate clusters and the eigenvalues suggested to use of K=3 as optimal number. The analysis of genomic regions harbouring signals revealed the candidate genes previously associated with muscle formation and immunity system. Detecting signals of adaptation that were also the targets of historical selection will allow in the future a better understanding of cattle origin.Keywords: local adaptation, selection, cattle, SNP50 BeadChip, PCAdapt, population subdivisionReferencesAKEY, J. M. et al. (2002) Interrogating a high-density SNP map for signatures of natural selection. Genome Research, vol. 12, pp. 1805-1814. doi:http://dx.doi.org/10.1101/gr.631202ALLENDORF, F. W., HOHENLOHE, P. A. and LUIKART, G. (2010) Genomics and the future of conservation genetics. Nature Reviews Genetics, vol. 11, no. 10, pp. 697-709. doi:http://dx.doi.org/10.1038/nrg2844BIERNE, N., ROZE, D. and WELCH, J. J. (2013) Pervasive selection or is it . . .? Why are FST outliers sometimes so frequent?. Molecular Ecology, vol. 22, pp. 2061-2064. doi:http://dx.doi.org/10.1111/mec.12241DRUET, T. et al. (2013). Identification of large selective sweeps associated with major genes in cattle. Animal Genetics, vol. 44, pp. 758-762. doi:http://dx.doi.org/10.1111/age.12073DUFORET-FREBOURG, N. et al. (2015) Detecting genomic signatures of natural selection with principal component analysis: application to the 1000 genomes data. Molecular biology and evolution, vol. 33, pp. 1082-1093. doi:http://dx.doi.org/10.1093/molbev/msv334DUFORET-FREBOURG, N., BAZIN, E. and BLUM, M. G. B. (2014) Genome scans for detecting footprints of local adaptation using a bayesian factor model. Molecular biology and evolution, vol. 31, pp. 2483-2495. doi:http://dx.doi.org/10.1093/molbev/msu182FERENČAKOVIĆ, M., SOLKNER, J. and CURIK, I. (2013) Estimating autozygosity from high-throughput information: effects of SNP density and genotyping errors. Genetic Selection Evolution, vol. 45, no. 1, pp. 42. doi:http://dx.doi.org/10.1186/1297-9686-45-42Flori, L. et al. (2009) The genome response to artificial selection: a case study in dairy cattle. PLoS One, vol. 4, e6595. doi:http://dx.doi.org/10.1371/journal.pone.0006595GIUSTI, J. et al. (2013) Expression of genes related to quality of Longissimus dorsi muscle meat in Nellore (Bos indicus) and Canchim (5/8 Bos taurus × 3/8 Bos indicus) cattle. Meat Science, vol. 94, no. 2, pp. 247-252. doi:http://dx.doi.org/10.1016/j.meatsci.2013.02.006GOWANE, G. R. et al. (2014) The Expression of IL6 and 21 in Crossbred Calves Upregulated by Inactivated Trivalent FMD Vaccine. Animal Biotechnology, vol. 25, no. 2, pp. 108-118. doi:http://dx.doi.org/10.1080/10495398.2013.834826GUTIÉRREZ-GIL, B., ARRANZ, J. J. and WIENER, P. (2015) An interpretive review of selective sweep studies in Bos taurus cattle populations: identification of unique and shared selection signals across breeds. Frontiers genetics, vol. 6, pp. 167. doi:http://dx.doi.org/10.3389/fgene.2015.00167LUU, K., BAZIN, E. and BLUM, M. G. B. (2016) pcadapt: An R package for performing genome scans for selection based on principal component analysis. bioRxiv. doi:http://dx.doi.org/10.1101/056135MANCINI, G. et al. (2014) Signatures of selection in five Italian cattle breeds detected by a 54K SNP panel. Molecular Biology Reports, vol. 41, pp. 957-965. doi:http://dx.doi.org/10.1007/s11033-013-2940-5MARTINS, H. et al. (2016) Identifying outlier loci in admixed and in continuous populations using ancestral population differentiation statistics. bioRxiv, p. 054585. doi:http://dx.doi.org/10.1101/054585MCCLURE, M. C. et al. (2012) Genome-wide association analysis for quantitative trait loci influencing Warner–Bratzler shear force in five taurine cattle breeds. Animal Genetics, vol. 43, no. 6, pp. 662-673. doi:http://dx.doi.org/10.1111/j.1365-2052.2012.02323.xNIELSEN, R. (2005) Molecular signatures of natural selection. Annual Review of Genetics, vol. 39, pp. 197-218. doi:http://dx.doi.org/10.1146/annurev.genet.39.073003.112420NOVEMBRE, J. et al. (2008) Genes mirror geography within Europe. Nature, vol. 456, pp. 98-101. doi:http://dx.doi.org/10.1038/nature07566OLEKSYK, T. K., SMITH, M. W. and O'BRIEN, S. J. (2010) Genome-wide scan for footprints of natural selection. Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 365, pp. 185-205. doi:http://dx.doi.org/10.1098/rstb.2009.0219QANBARI, S. et al. (2011) Application of site and haplotype-frequency based approaches for detecting selection signatures in cattle. BMC Genomics, vol. 12, pp. 318. doi:http://dx.doi.org/10.1186/1471-2164-12-318STELLA, A. et al. (2010) Identification of selection signatures in cattle breeds selected for dairy production. Genetics, vol. 185, pp. 1451-1461. doi:http://dx.doi.org/10.1534/genetics.110.116111STOREY, J. D. (2002) A direct approach to false discovery rates. Journal of the Royal Statistical Society, Series B, vol. 64, pp. 479-498....
Nina Moravčíková; Veronika Kukučková; Gábor Mészáros; Johann Sölkner; Ondrej Kadlečík; Radovan Kasarda. Assessing footprints of natural selection through PCA analysis in cattle. Acta fytotechnica et zootechnica 2017, 20, 1 .
AMA StyleNina Moravčíková, Veronika Kukučková, Gábor Mészáros, Johann Sölkner, Ondrej Kadlečík, Radovan Kasarda. Assessing footprints of natural selection through PCA analysis in cattle. Acta fytotechnica et zootechnica. 2017; 20 (2):1.
Chicago/Turabian StyleNina Moravčíková; Veronika Kukučková; Gábor Mészáros; Johann Sölkner; Ondrej Kadlečík; Radovan Kasarda. 2017. "Assessing footprints of natural selection through PCA analysis in cattle." Acta fytotechnica et zootechnica 20, no. 2: 1.
Nina Moravcikova; Radovan Kasarda; Ondrej Kadlecik. THE DEGREE OF GENETIC ADMIXTURE WITHIN SPECIES FROM GENUS CERVUS. The Journal "Agriculture and Forestry" 2017, 63, 1 .
AMA StyleNina Moravcikova, Radovan Kasarda, Ondrej Kadlecik. THE DEGREE OF GENETIC ADMIXTURE WITHIN SPECIES FROM GENUS CERVUS. The Journal "Agriculture and Forestry". 2017; 63 (1):1.
Chicago/Turabian StyleNina Moravcikova; Radovan Kasarda; Ondrej Kadlecik. 2017. "THE DEGREE OF GENETIC ADMIXTURE WITHIN SPECIES FROM GENUS CERVUS." The Journal "Agriculture and Forestry" 63, no. 1: 1.
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.
Radovan Kasarda; Nina Moravčíková; Anna Trakovická; Zuzana Krupová; Kadlečík Ondrej. Genomic variation across cervid species in respect to the estimation of red deer diversity. Acta Veterinaria 2017, 67, 43 -56.
AMA StyleRadovan Kasarda, Nina Moravčíková, Anna Trakovická, Zuzana Krupová, Kadlečík Ondrej. Genomic variation across cervid species in respect to the estimation of red deer diversity. Acta Veterinaria. 2017; 67 (1):43-56.
Chicago/Turabian StyleRadovan Kasarda; Nina Moravčíková; Anna Trakovická; Zuzana Krupová; Kadlečík Ondrej. 2017. "Genomic variation across cervid species in respect to the estimation of red deer diversity." Acta Veterinaria 67, no. 1: 43-56.
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.
Veronika Kukučková; Nina Moravčíková; Maja Ferenčaković; Mojca Simčič; Gábor Mészáros; Johann Sölkner; Anna Trakovická; Ondrej Kadlečík; Ino Curik; Radovan Kasarda. Genomic characterization of Pinzgau cattle: genetic conservation and breeding perspectives. Conservation Genetics 2017, 18, 893 -910.
AMA StyleVeronika Kukučková, Nina Moravčíková, Maja Ferenčaković, Mojca Simčič, Gábor Mészáros, Johann Sölkner, Anna Trakovická, Ondrej Kadlečík, Ino Curik, Radovan Kasarda. Genomic characterization of Pinzgau cattle: genetic conservation and breeding perspectives. Conservation Genetics. 2017; 18 (4):893-910.
Chicago/Turabian StyleVeronika Kukučková; Nina Moravčíková; Maja Ferenčaković; Mojca Simčič; Gábor Mészáros; Johann Sölkner; Anna Trakovická; Ondrej Kadlečík; Ino Curik; Radovan Kasarda. 2017. "Genomic characterization of Pinzgau cattle: genetic conservation and breeding perspectives." Conservation Genetics 18, no. 4: 893-910.