Anamarija Smetko's research while affiliated with University of Natural Resources and Life Sciences Vienna and other places

The aim of the study was to analyze genetic trend for litter size in Black Slavonian pig. Study included 12,118 records for litter size, expressed as number of piglets born alive from 1995 to 2014 for 3661 sow of Black Slavonian breed. Repeatability model was used to estimate genetic parameters and breeding values for litter size. Genetic trend for litter size u was variable and no expressed changes in analysed period were observed. This was caused by the lack of systematic selection and insufficient quality of data which should be improved. Genetic improved in analysed population might be obtained by application of modern selection methods.

Livestock conservation practice is changing rapidly in light of policy developments, climate change and diversifying market demands. The last decade has seen a step change in technology and analytical approaches available to define, manage and conserve Farm Animal Genomic Resources (FAnGR). However, these rapid changes pose challenges for FAnGR conservation in terms of technological continuity, analytical capacity and integrative methodologies needed to fully exploit new, multidimensional data. The final conference of the ESF Genomic Resources program aimed to address these interdisciplinary problems in an attempt to contribute to the agenda for research and policy development directions during the coming decade. By 2020, according to the Convention on Biodiversity's Aichi Target 13, signatories should ensure that “…the genetic diversity of …farmed and domesticated animals and of wild relatives …is maintained, and strategies have been developed and implemented for minimizing genetic erosion and safeguarding their genetic diversity.” However, the real extent of genetic erosion is very difficult to measure using current data. Therefore, this challenging target demands better coverage, understanding and utilization of genomic and environmental data, the development of optimized ways to integrate these data with social and other sciences and policy analysis to enable more flexible, evidence-based models to underpin FAnGR conservation. At the conference, we attempted to identify the most important problems for effective livestock genomic resource conservation during the next decade. Twenty priority questions were identified that could be broadly categorized into challenges related to methodology, analytical approaches, data management and conservation. It should be acknowledged here that while the focus of our meeting was predominantly around genetics, genomics and animal science, many of the practical challenges facing conservation of genomic resources are societal in origin and are predicated on the value (e.g., socio-economic and cultural) of these resources to farmers, rural communities and society as a whole. The overall conclusion is that despite the fact that the livestock sector has been relatively well-organized in the application of genetic methodologies to date, there is still a large gap between the current state-of-the-art in the use of tools to characterize genomic resources and its application to many non-commercial and local breeds, hampering the consistent utilization of genetic and genomic data as indicators of genetic erosion and diversity. The livestock genomic sector therefore needs to make a concerted effort in the coming decade to enable to the democratization of the powerful tools that are now at its disposal, and to ensure that they are applied in the context of breed conservation as well as development.

As Black Slavonian pig was forgotten and replaced by commercial hybrid pigs, after mid 1950s population declined drastically. Today’s population was founded from 46 sows and 6 boars in 1996 while currently consist of 1064 sows and 163 boars. Aim of this study was to evaluate the genetic structure and genetic variability in autochthonous Black Slavonian pig breed using pedigree. The quality of the pedigree information was evaluated by percentage of known ancestors, which was about 35.16%. Increase in pedigree completeness over the years is evident. Number of inbred Black Slavonian animals was 1695. Average inbreeding was 3.2%, with evident growth observed by year. Effective number of founders was 50.8 for males and 51.1 for females. Effective number of ancestors was, 35.8 for male and 34.8 for female animals, respectively. The proportion of the genes contributed to the reference population of males and females by the most important ancestor was 7.1% and 9.1%. The first 15 ancestors for males and 12 for females explained around 50% variability in the gene pool. Average effective population size via number of parents for the last 10 years of Black Slavonian pig is 189.2. In order to perform proper selection decisions, additional work should be done to increase the quality of pedigree data affecting the reliability of estimated parameters and genetic structure of the population.

Genome-wide association studies (GWAS) based on thousands of single nucleotide polymorphisms (SNPs) allows exploring genes associated with economically important traits. The objective of this study was to perform GWAS in small population of genotyped bulls of Slovenian Brown Swiss (BSW) breed to identify SNP markers associated with dairy traits: milk yield (MY), fat yield (FY), and protein yield (PY). The daughter yield deviations of 182 progeny tested bulls were used as phenotypes. For each bull, genotypes were scored for 34,450 SNPs across the whole genome. Single SNP analysis was performed to detect significant associations among SNPs and dairy traits across the genome. Two models were considered: 1) linear regression model considering one marker at a time, and 2) linear regression model with admixture components for accounting population stratification. The Bonferroni correction resulted in 52 significant SNPs using model 1). Correction for population stratification based on selected criteria was shown to have great impact on the analysis and then no significant associations among SNPs and dairy traits have been detected. Therefore, the results were sensitive to population stratification and together with the small data set did not give much power to accurately estimate associations. Further improvements should be made on the enlargement of number of genotyped bulls in order to detect association signals and the identification of genes associated with dairy traits in Slovenian BSW breed.

Abstract The aim of this study was to obtain unbiased estimates of the diversity parameters, the population history, and the degree of admixture in Cika cattle which represents the local admixed breeds at risk of extinction undergoing challenging conservation programs. Genetic analyses were performed on the genome-wide Single Nucleotide Polymorphism (SNP) Illumina Bovine SNP50 array data of 76 Cika animals and 531 animals from 14 reference populations. To obtain unbiased estimates we used short haplotypes spanning four markers instead of single SNPs to avoid an ascertainment bias of the BovineSNP50 array. Genome-wide haplotypes combined with partial pedigree and type trait classification show the potential to improve identification of purebred animals with a low degree of admixture. Phylogenetic analyses demonstrated unique genetic identity of Cika animals. Genetic distance matrix presented by rooted Neighbour-Net suggested long and broad phylogenetic connection between Cika and Pinzgauer. Unsupervised clustering performed by the admixture analysis and two-dimensional presentation of the genetic distances between individuals also suggest Cika is a distinct breed despite being similar in appearance to Pinzgauer. Animals identified as the most purebred could be used as a nucleus for a recovery of the native genetic background in the current admixed population. The results show that local well-adapted strains, which have never been intensively managed and differentiated into specific breeds, exhibit large haplotype diversity. They suggest a conservation and recovery approach that does not rely exclusively on the search for the original native genetic background but rather on the identification and removal of common introgressed haplotypes would be more powerful. Successful implementation of such an approach should be based on combining phenotype, pedigree, and genome-wide haplotype data of the breed of interest and a spectrum of reference breeds which potentially have had direct or indirect historical contribution to the genetic makeup of the breed of interest.

The aim of this study was to obtain unbiased estimates of the diversity parameters, the population history, and the degree of admixture in Cika cattle which represents the local admixed breeds at risk of extinction undergoing challenging conservation programs. Genetic analyses were performed on the genome-wide Single Nucleotide Polymorphism (SNP) Illumina Bovine SNP50 array data of 76 Cika animals and 531 animals from 14 reference populations. To obtain unbiased estimates we used short haplotypes spanning four markers instead of single SNPs to avoid an ascertainment bias of the BovineSNP50 array. Genome-wide haplotypes combined with partial pedigree and type trait classification show the potential to improve identification of purebred animals with a low degree of admixture. Phylogenetic analyses demonstrated unique genetic identity of Cika animals. Genetic distance matrix presented by rooted Neighbour-Net suggested long and broad phylogenetic connection between Cika and Pinzgauer. Unsupervised clustering performed by the admixture analysis and two-dimensional presentation of the genetic distances between individuals also suggest Cika is a distinct breed despite being similar in appearance to Pinzgauer. Animals identified as the most purebred could be used as a nucleus for a recovery of the native genetic background in the current admixed population. The results show that local well-adapted strains, which have never been intensively managed and differentiated into specific breeds, exhibit large haplotype diversity. They suggest a conservation and recovery approach that does not rely exclusively on the search for the original native genetic background but rather on the identification and removal of common introgressed haplotypes would be more powerful. Successful implementation of such an approach should be based on combining phenotype, pedigree, and genome-wide haplotype data of the breed of interest and a spectrum of reference breeds which potentially have had direct or indirect historical contribution to the genetic makeup of the breed of interest.

Trypanosomosis is a serious cause of reduction in productivity of cattle in tsetse-fly infested areas. Baoule and other local Taurine cattle breeds in Burkina Faso are trypanotolerant. Zebuine cattle, which are also kept there are susceptible to trypanosomosis but bigger in body size. Farmers have continuously been intercrossing Baoule and Zebu animals to increase production and disease tolerance. The aim of this study was to compare levels of zebuine and taurine admixture in genomic regions potentially involved in trypanotolerance with background admixture of composites to identify differences in allelic frequencies of tolerant and non-tolerant animals. The study was conducted on 214 animals (90 Baoule, 90 Zebu, and 34 composites), genotyped with 25 microsatellites across the genome and with 155 SNPs in 23 candidate regions. Degrees of admixture of composites were analyzed for microsatellite and SNP data separately. Average Baoule admixture based on microsatellites across the genomes of the Baoule- Zebu composites was 0.31, which was smaller than the average Baoule admixture in the trypanosomosis candidate regions of 0.37 (P = 0.15). Fixation index FST measured in the overall genome based on microsatellites or with SNPs from candidate regions indicates strong differentiation between breeds. Nine out of 23 regions had FST ≥ 0.20 calculated from haplotypes or individual SNPs. The levels of admixture were significantly different from background admixture, as revealed by microsatellite data, for six out of the nine regions. Five out of the six regions showed an excess of Baoule ancestry. Information about best levels of breed composition would be useful for future breeding ctivities, aiming at trypanotolerant animals with higher productive capacity.

Očuvanje genetskih resursa predstavlja odgovornost svakog naroda, stoga su mnoge zemlje prepoznale potrebu unaprijeđenja praćenja, očuvanja i dokumetniranja životinjskih genetskih resursa. Animalna proizvodnja je od vitalnog značaja za čovječanstvo i očuvanje genetske raznolikosti u populacijama životinja čime im se osigurava budućnost. Nužno je da svaka zemlja razvije najbolju pojedinačnu strategiju ili politiku očuvanja farmskih životinjskih genetskih resursa prije dizajniranja nacionalnog krioprezervacijskog programa. Osnivanje i integracija banke gena u uzgojne programe i programe očuvanja izvornih i zaštićenih pasmina od značaja je za održivost ukupnih genetskih resursa u Hrvatskoj. Ključne riječi: banka gena, izvorne pasmine, genetska varijabilnost, Hrvatska

The aim of this study was to estimate genetic parameters for number of piglets born alive on family farms in Croatia. Data from 30 breeding organizations were analysed. Repeatability model was used to estimate genetic parameters for litter size. Estimated heritability for number of piglets born alive on family farms was je 0,06. The largest proportion of phenotypic variance was explained by common litter environment effect. Estimates for permanent environmental effect were negligible. The results of the analysis imply that additional efforts should be done in order to obtain precise measuring and recording data.