Mojca Simčič

On the origin of the Slovenian Cika cattle.

In 2002, it was discovered that several Cika cattle in the mountain areas of Slovenia had escaped the official policy of cross-breeding. Here, we report a genetic characterization to assess their status as autochthonous breed. We compared genotypes for 14 microsatellite markers in 150 Cika cattle individuals with data from 16 Central European cattle breeds. We show that Cika cattle are genetically as diverse as other Eastern Alpine breeds, are more diverse than Austrian Simmental but less than the Balkan Busha cattle. STRUCTURE analysis showed Pinzgauer admixture in several individuals but also indicated a unique genetic identity for Cika. This analysis also allowed a selection of the most genetically pure Cika individuals as assessed by the panel of microsatellites. These original Cika cattle form an Eastern Alpine breed cluster together with Pinzgauer and Pustertaler cattle. Cika cattle should be considered as an authentic and valuable genetic resource, which offers clear opportunities for sustainable agriculture and landscape conservation in marginal and mountain areas.

Recovery of Native Genetic Background in Admixed Populations Using Haplotypes, Phenotypes, and Pedigree Information – Using Cika Cattle as a Case Breed

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.

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.

Effects of two finishing diets on growth performance, carcass characteristics and feeding behaviour of Slovenian Cika and Simmental young bulls

This study aimed at comparing the effects of a traditional finishing roughage-based diet and a higher energy diet, on growth, carcass characteristics, and feeding behaviour of Slovenian Cika and Simmental bulls (20 per breed). The experimental diets were: extensive (EXT) based on grass silage, and semi-intensive (S-INT) in which a part of the roughage was replaced with maize silage and sunflower meal. Each diet was fed ad libitum to 10 Cika (547 days old) and 10 Simmental (442 days old) bulls housed in group pens of five animals each. Growth performance was similar in both breeds, but Cika reached commercial finishing 1 month earlier than Simmental (139 vs 167 days; P = 0.016). Bulls fed S-INT had higher final weight (645.3 vs 590.1 kg; P = 0.05), average daily growth (1.05 vs 0.83 kg; P = 0.026), and feed intake (11.7 vs 10.6 kg dry matter (DM)/day; P < 0.001) than EXT bulls. Regardless of breed and diet, bulls ate 77–80% of the daily DM in the first 8 h after feed delivery. Bulls fed EXT showed longer standing (406.4 vs 355.8 min; P < 0.001) and eating (217.2 vs 155.3 min; P < 0.001) and shorter ruminating (77.5 vs 92.9 min; P < 0.001) times than S-INT bulls during the first 8 h of feed delivery. Cika bulls had lower full reticulo-rumen weights relative to slaughter weights (8.7 vs 10.7%; P = 0.002) than Simmental. The positive findings obtained with Cika cattle should encourage farmers to finish their young Cika male stocks for beef production, thus contributing to the maintenance of this animal genetic resource, and also to increase the energy density of the grass-based finishing diets by feeding supplements.

Growth and carcass traits of young bulls sired by Charolais and Limousin

Abstract A brown cattle is dual purpose cattle in Slovenia mainly used for milk production. This study included 90 crossbred young bulls of two genotypes, 70 Brown x Limousin (BRxLIM) and 20 Brown x Charolais (BRxCHA). The aim of this study was to determine some growth and carcass characteristics of crossbred young bulls. Data were analysed by GLM procedure considering sire breed and year nested within sire breed as fixed effects and slaughter age as linear regression. Sire breed statistically significantly affected slaughter weight, hot carcass weight, net daily gain, dressing percentage and index of conformation. All three included effects statistically significantly affected only slaughter weight, hot carcass weight and net daily gain.

Conservation of a domestic metapopulation structured into related and partly admixed strains

Preservation of genetic diversity is one of the most pressing challenges in the planetary boundaries concept. Within this context, we focused on genetic diversity in a native, unselected and highly admixed domesticated metapopulation. A set of 1,828 individuals from 60 different cattle breeds was analysed using a medium density SNP chip. Among these breeds, 14 Buša strains formed a metapopulation represented by 350 individuals, while the remaining 46 breeds represented the global cattle population. Genetic analyses showed that the scarcely selected and less differentiated Buša metapopulation contributed a substantial proportion (52.6%) of the neutral allelic diversity to this global taurine population. Consequently, there is an urgent need for synchronized maintenance of this highly fragmented domestic metapopulation, which is distributed over several countries without sophisticated infrastructure and highly endangered by continuous replacement crossing as part of the global genetic homogenization process. This study collected and evaluated samples, data and genomewide information and developed genome‐assisted cross‐border conservation concepts. To detect and maintain genetic integrity of the metapopulation strains, we designed and applied a composite test that combines six metrics based on additive genetic relationships, a nearest neighbour graph and the distribution of semiprivate alleles. Each metric provides distinct information components about past admixture events and offers an objective and powerful tool for the detection of admixed outliers. The here developed conservation methods and presented experiences could easily be adapted to comparable conservation programmes of domesticated or other metapopulations bred and kept in captivity or under some other sort of human control.

Carcass and meat quality of young Cika and Simmental bulls finished under similar conditions

Twenty indigenous Cika and 20 young Simmental bulls (slaughtered at 560–718 days) were finished on two diets (extensive vs semi-intensive). When fed similar rations, Cika bulls at a ‘suitable’ finished level, had a significantly higher dressing percentage (+2.5%), more total fat (+13.7%), a lower percentage of tendons (–22.7%) and bones (–7.7%), a higher lean meat to bones ratio (+8.1%) and a greater percentage of intramuscular fat (+45.9%) than the Simmental bulls. Their meat also had a significantly lower pH (–4.0%), higher redness (+13.74%), yellowness (+15.0%) and drip loss (after 2 days, +28.3%) and a more intense flavour (+6.1%). Cika fat contained higher proportions of saturated fatty acids (+6.86%) and less polyunsaturated fatty acids (–30.8%) than Simmental fat. However, it appears that the main difference between these two breeds were the slower growth rate of the Cika and their lower weight but greater age when a finished state was reached relative to the Simmental.

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.

Estimation of genetic parameters for body weight in Charolais calves in Slovenia

Abstract The aim of the present study was to estimate genetic parameters for growth traits of Charolais calves in Slovenia. Analysed traits included birth weight (BW), weight at the beginning (WB) and at the end of grazing season (WE), as well as yearling weight (WY). Data were collected on 340 Charolais calves. The total number of records, including pedigree data (parents and grandparents) was 401 animals. (Co)variance components were estimated by REML method for the animal model that included fixed effects of sex, parity and year of birth in the models for all traits. Age of calves at the beginning of grazing season was included as linear regression in models for all traits except for birth weight. The age of calves at the end of grazing season, and age at approximately one year were included as linear regression in the models for corresponding weights. Random effects included direct and maternal additive genetic effects. Direct heritabilities (ha2) were decreased from 0.74 at birth to 0.19 at yearling weight. Inversely, maternal heritabilities (hm2) were increased from 0.04 at birth to 0.12 at all other included weights. Direct-maternal genetic correlation (ram) was negative for all weights except for yearling weight (0.10).