Veronika Kukučková

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 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.

GENOMIC DETERMINATION OF THE MOST IMPORTANT FATHER LINES OF SLOVAK PINZGAU COWS

The aim of this study was to assess genetic structure of Slovak Pinzgau population based on polymorphism at molecular markers using statistical methods. Female offspring of 12 most frequently used bulls in Slovak Pinzgau breeding programme were investigated. Pinzgau cattle were found to have a high level of diversity, supported by the number of alleles observed across loci (average 5.31, range 2-11) and by the high within-breed expected heterozygosity (average 0.66, range 0.64- 0.73). The state of genetic diversity is satisfying and standard for local populations. Detection of 12 possible subpopulation structures provided us with detailed information of the genetic structure. The Bayesian approach was applied, detecting three, as the most probable number of clusters. The similarity of each subpopulation using microsatellites was confirmed also by high-throughput molecular data. The observed inbreeding (FROH=2.3%) was higher than that expected based on pedigree data (FPED=0.4%) due to the limited number of available generations in pedigree data. One of the most important steps in development of efficient autochthonous breed protection programs is characterization of genetic variability and assessment of the population structure. The chosen set of microsatellites confirmed the suitability in determination of the subpopulations of Pinzgau cattle in Slovakia. The state of genetic diversity at more detailed level was successfully performed using bovineSNP50 BeadChip.