•There was a similar distribution of single nucleotide polymorphisms per autosome.•Two panels of markers obtained with the two variants of random forest were the same.•The overall correct ...classification rate on the test set was relatively high.•The use of random forest for polymorphism identification was, in general, effective.
The determination of breed composition or the population of origin has several practical applications, including the authentication of brand mono-breed products that have recently been developed in several livestock species, including cattle. Therefore, the aim of the present study was to verify the applicability of a random forest (RF) approach to distinguish between different dairy and beef cattle breeds based on a reduced panel of single nucleotide polymorphisms (SNPs). A total of 1,370 animals from 17 cattle breeds were genotyped with a 50 K SNP microarray. After SNP pruning, 5,296 SNPs were retained for further analysis. Six methods were used for determining panels of the most informative SNPs: Wright's fixation index (FST), principal component analysis (PCA), random forest (RF) based on the Gini index (GI; two variants) and RF based on the mean decrease in accuracy (MDA; two variants). There was a similar distribution of selected SNPs per BTA, especially for the FST and PCA methods. Two panels of 96 SNPs obtained with two variants of RF-GI and RF-MDA contained the same SNPs but with a different ranking. The percentage of correct classification on the test set (10% of cases randomly selected from the whole dataset) was 100% for the Angus, Hereford, Holstein, Brown Swiss, and Jersey breeds. For the Simmental, Piedmontese, Romagnola, Shorthorn, Norwegian Red, Charolais, Cika, Tyrol Grey, Limousin, Austrian Pinzgau, Slovak Pinzgau, and Slovak Spotted breeds, it was 75.00 – 87.50%, 0.00 – 66.67%, 66.67 – 100.00%, 80.00 – 100.00%, 0.00 – 50.00%, 75.00 – 100.00%, 0.00 – 66.67%, 90.91 - 100.00%, 91.67%, 81.82 - 100.00%, 93.33 - 100.00%, 55.56 - 100.00%, respectively. The overall correct classification rate (for all breeds together) was 87.14%, 94.29%, 90.00% and 88.57% for RF-GI, RF-MDA, FST and PCA, respectively. Consequently, the most accurate method for distinguishing between cattle breeds was RF based on the MDA, although the differences amongst models were not large.
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Local breeds retained unique genetic variability important for adaptive potential especially in light of challenges related to climate change. Our first objective was to perform, for the first time, ...a genome-wide diversity characterization using Illumina GoatSNP50 BeadChip of autochthonous Dreznica goat breed from Slovenia, and five and one local breeds from neighboring Austria and Italy, respectively. For optimal conservation and breeding programs of endangered local breeds, it is important to detect past admixture events and strive for preservation of purebred representatives of each breed with low or without admixture. In the second objective, we hence investigated the effect of inclusion or exclusion of outliers from datasets on genetic diversity and population structure parameters. Distinct genetic origin of the Dreznica goat was demonstrated as having closest nodes to Austrian and Italian breeds. A phylogenetic study of these breeds with other goat breeds having SNP data available in the DRYAD repository positioned them in the alpine, European and global context. Swiss breeds clustered with cosmopolitan alpine breeds and were closer to French and Spanish breeds. On the other hand, the Dreznica goat, Austrian and Italian breeds were closer to Turkish breeds. Datasets where outliers were excluded affected estimates of genetic diversity parameters within the breed and increased the pairwise genetic distances between most of the breeds. Alpine breeds, including Dreznica, Austrian and Italian goats analyzed here, still exhibit relatively high levels of genetic variability, homogeneous genetic structure and strong geographical partitioning. Genetic diversity analyses revealed that the Slovenian Dreznica goat has a distinct genetic identity and is closely related to the neighboring Austrian and Italian alpine breeds. These results expand our knowledge on phylogeny of goat breeds from easternmost part of the European Alps. The here employed outlier test and datasets optimization approaches provided an objective and statistically powerful tool for removal of admixed outliers. Importance of this test in selecting the representatives of each breed is warranted to obtain more objective diversity parameters and phylogenetic analysis. Such parameters are often the basis of breeding and management programs and are therefore important for preserving genetic variability and uniqueness of local rare breeds.
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The aim of this study was to estimate genetic parameters of 26 individual and four composite type traits in first parity Cika cows. An analysis of variance was performed with the generalized linear ...model procedure of the SAS/STAT statistical package, where the fixed effects of year of recording, cow's age at recording and days after calving as a linear regression were included in the model. The variance components for the direct additive genetic effect and the herd effect in all type traits were estimated using the REML method in the VCE-6 software package. The estimated heritabilities ranged from 0.42 to 0.67 for the measured body frame traits, from 0.36 to 0.80 for the scored autochthonous traits, from 0.11 to 0.61 for the scored body frame traits, and from 0.20 to 0.47 for the scored udder traits. The estimated heritabilities for the composite traits called "autochthonous characteristics", "muscularity", "body frame" and "udder" were 0.55, 0.19, 0.19, and 0.26, respectively. The estimated genetic correlations among the measured body frame traits were positive and high, while the majority of them among the scored body frame traits were low to moderate. The estimated proportions of variance explained by the herd effect for the composite traits "autochthonous characteristics," "muscularity," "body frame" and "udder" were 0.09, 0.28, 0.14, and 0.10, respectively. The estimated heritabilities for the type traits of first parity Cika cows were similar to those reported for other breeds where breeding values have been routinely predicted for a long time. All estimated genetic parameters are already used for breeding value prediction in the Cika cattle population.
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.
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There is a growing concern about the loss of animal genetic resources. The aim of this study was to analyze the genetic diversity and potential peculiarity of the endangered Kosovar sheep breed ...Balusha. For this purpose, a dataset consisting of medium-density SNP chip genotypes (39,879 SNPs) from 45 Balusha sheep was generated and compared with SNP chip genotypes from 29 individuals of a second Kosovar breed, Bardhoka. Publicly available SNP genotypes from 39 individuals of the relatively closely located sheep breeds Istrian Pramenka and Ruda were additionally included in the analyses. Analysis of heterozygosity, allelic richness and effective population size was used to assess the genetic diversity. Inbreeding was evaluated using two different methods (
,
). The standardized
(
) and cross-population extended haplotype homozygosity (XPEHH) methods were used to detect signatures of selection. We observed the lowest heterozygosity (
= 0.351) and effective population size (Ne
= 25, Ne
= 228) for the Balusha breed. The mean allelic richness levels (1.780-1.876) across all analyzed breeds were similar and also comparable with those in worldwide breeds.
estimates (0.023-0.077) were highest for the Balusha population, although evidence of decreased inbreeding was observed in
results for the Balusha breed. Two Gene Ontology (GO) TERMs were strongly enriched for Balusha, and involved genes belonging to the melanogenesis and T cell receptor signaling pathways, respectively. This could result from selection for the special coat color pattern of Balusha (black head) and resistance to certain infectious diseases. The analyzed diversity parameters highlight the urgency to preserve the local Kosovar Balusha sheep as it is clearly distinguished from other sheep of Southeastern Europe, has the lowest diversity level and may harbor valuable genetic variants, e.g., for resistance to infectious diseases.
While mitogenome mutations leading to pathological manifestations are rare, more than 200 such mutations have been described in humans. In contrast, pathogenic mitogenome mutations are rare in ...domestic animals and have not been described at all in cattle. In the small local Slovenian cattle breed Cika, we identified (next-generation sequencing) two cows with the T10432C mitogenome mutation in the ND4L gene, which corresponds to the human T10663C mutation known to cause Leber's hereditary optic neuropathy (LHON). Pedigree analysis revealed that the cows in which the mutation was identified belong to two different maternal lineages with 217 individual cows born between 1997 and 2020. The identified mutation and its maternal inheritance were confirmed by Sanger sequencing across multiple generations, whereas no single analysis revealed evidence of heteroplasmy. A closer clinical examination of one cow with the T10432C mutation revealed exophthalmos, whereas histopathological examination revealed retinal ablations, subretinal oedema, and haemorrhage. The results of these analyses confirm the presence of mitochondrial mutation T10432C with homoplasmic maternal inheritance as well as clinical and histopathological signs similar to LHON in humans. Live animals with the mutation could be used as a suitable animal model that can improve our understanding of the pathogenesis of LHON and other mitochondriopathies.
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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 (F
) 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.
The aim of the study was to research milk yield, composition and hygienic quality of routinely produced milk from Lipizzan mares. It was the first known case of adapting mares of this breed to the ...routine machine milking procedure. Three Lipizzan mares included in the routine machine milking produced commercial quantities of mare’s milk. Milk from Lipizzan horse breed was for the first time obtained and analysed in such quantity. The mares were milked consecutively three times per day during five days in a week, and during weekends, they were joined with their foals. The average values were as follows: daily milk yield (MY) was 8.24 kg, fat content (FC) was 4.027 g/kg, protein content (PC) was 15.064 g/kg, lactose content (LC) was 63.218 g/kg, somatic cell count (SCC) was 6.556 x 10³/ml, total bacteria count (TBC) was 114.689 x 10³/ml, and average freezing point (FP) was -0.505 °C. Consecutive milking significantly influenced PC, LC, SCC, and TBC. FC tended to increase with days in milk, whereas PC, SCC, and TBC decreased during the lactation stage. Significant differences between mares were found in PC, LC, SSC and TBC. Interaction between consecutive milking and mare was significant only for FC. The study confirmed that warmblooded horse breed can be used for commercial milk production along with coldblooded breeds. Routine machine milk production with use of Lipizzan mares could add an economic value to the indigenous breed and serve as an additional reason for its preservation.Key words: milk composition; milk yield; days in milk; consecutive milking; hygienic quality KOLIČINA, SESTAVA IN HIGIENSKA KAKOVOST MLEKA PRIDOBLJENEGA Z RUTINSKO STROJNO MOLŽO LIPICANSKIH KOBILPovzetek: Pridobili in raziskali smo komercialno količino namolženega mleka kobil lipicanske pasme. Rutinska mehanska molža treh kobil je potekala na raziskovalni ustavnovi, registrirani za prirejo kobiljega mleka. Rezultati so pokazali, da je bila povprečna dnevna količina mleka (KM) 8,24 kg, mleko pa je v povprečju vsebovalo 4,027 g maščobe/kg, 15,064 g beljakovin/kg in 63,218 g laktoze/kg. Povprečno število somatskih celic v mleku je bilo 6,556 x 10³/ml, povprečno skupno število mikroorganizmov 114,689 x 10³/ml, povprečna zmrziščna točka (ZT) mleka pa -0,505 °C. Rezultati analize variance so pokazali, da se količina beljakovin in laktoze ter število somatskih celic in skupno število mikroorganizmov statistično značilno razlikujejo glede na zaporedno molžo ter med posameznimi kobilami ter da se količina beljakovin, število somatskih celic in skupno število mikroorganizmov v mleku zmanjšuje z napredovanjem laktacije, medtem ko se vsebnost maščob povečuje. Interakcija med zaporedno molžo in kobilo je statistično značilno vplivala le na vsebnost maščob. Gre za prvo raziskavo mleka kobil lipicanske pasme, kar omogoča nadaljno primerjavo med pasmami. Uporaba kobil te slovenske avtohtone pasme konj za komercialno rutinsko prirejo mleka bi predstavljala njeno dodatno gospodarsko vrednost in s tem razlog za ohranitev.Ključne besede: sestava mleka; količina mleka; stadij laktacije; zaporedna molža; higienska kakovost mleka
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The aim of this study was to estimate the effect of feeding system on the growth rate and carcass quality of crossbred Improved Jezersko-Solčava x Texel (JSRT) lambs and to evaluate the effect of sex ...on these traits. The trial was conducted in nature according to the traditional rearing systems. The trial included 44 crossbred lambs, which were born and reared until the slaughter in three different flocks. In the age of 10 days suckled lambs were offered with ad libitum corresponding diets according to the feeding system. All lambs were slaughtered in seven consecutive days by the same procedure. The effect of feeding system significantly affected daily gain from birth to slaughter, EUROP carcass conformation and shoulder width. Likewise, the effect of sex significantly affected daily gain from birth to slaughter and internal fatness of carcasses. According to carcass cuts the feeding system significantly affected only the proportion of neck and leg. Considering meat quality traits, feeding system had a significant effect on the pH 45 and CIE a* values. In this study, we could speculate that more than the feeding system the growth and the carcass traits as well as meat traits were affected by the amount of the supplement.
Goat’s daily diet is usually based on grazing, hay and/or feed supplements. Feed supplements are crucial in the diet of high productive goats to achieve their genetic potential and breeders must ...choose balanced feeding regime to produce large quantities of milk without affecting the technological quality of milk. In the present study, we evaluated the influence of two commercially available feed supplements on goat milk coagulation properties and rheological properties of yoghurts. Goats of the Slovenian Alpine breed (61) were fed with two feed supplements during the 3-year experiment. Feed supplement 1 (FS1) had higher proportions of barley and alfalfa, while feed supplement 2 (FS2) had added premix of minerals and vitamins and had higher proportions of wheat and sunflower meal. Con¬sequently, FS1 had more crude fibres, which is the most probable reason for approximately 15 % higher firmness, consistency and cohesiveness (P<0.05) of yoghurts in FS1 group, compared to the FS2 group. Moreover, the rennet coagulation time (r) was shorter (P<0.05) in the FS1 group, compared to the FS2 group. Curd firmness 30 min after enzyme addition (a30) was also higher in FS1 group although the results were not statistically significant. Taking together, our results indicate that goats fed with FS1 produced milk with better technological properties compared to those fed with FS2, despite the fact that there were no significant differences in chemical composition of milk from each group. We showed that careful selection of feed supplement’s constituents could improve technological properties of goat milk. However, further studies are needed to evaluate the mechanisms of the observed differences.
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