Genome-Wide Association Study for Milk Somatic Cell Score in Holstein Friesian Cows in Slovenia.

Mastitis is a serious challenge for the dairy industry, leading to economic losses and affecting milk quality. The aim of this study is to identify genetic factors associated with mastitis resistance by conducting a genome-wide association study (GWAS) for the somatic cell score (SCS). Phenotypic records of 350 Holstein Friesian cows were obtained from the Slovenian Cattle Recording Scheme Database and consisted of around 1500 lactation data from 2012 to 2023 collected on a single farm in Slovenia.

Selection Signatures Reveal Candidate Genes for the Cornish Rex Breed-Specific Phenotype.

Many coat color, behavioral and morphological traits are specific and fixed across cat breeds, with several variants influencing these traits being common among different breeds. In the domestic cat, rexoid mutations have been documented in several breeds. In the Cornish Rex, four bp deletion in the gene has been found to cause a frame shift and a premature stop codon.

A Single-Cell Transcriptome of Bovine Milk Somatic Cells.

The production of milk by dairy cows far exceeds the nutritional needs of the calf and is vital for the economical use of dairy cattle. High milk yield is a unique production trait that can be effectively enhanced through traditional selection methods. The process of lactation in cows serves as an excellent model for studying the biological aspects of lactation with the aim of exploring the mechanistic base of this complex trait at the cellular level.

Identification of potentially pathogenic variants for autism spectrum disorders using gene-burden analysis.

Gene- burden analyses have lately become a very successful way for the identification of genes carrying risk variants underlying the analysed disease. This approach is also suitable for complex disorders like autism spectrum disorder (ASD). The gene-burden analysis using Testing Rare Variants with Public Data (TRAPD) software was conducted on whole exome sequencing data of Slovenian patients with ASD to determine potentially novel disease risk variants in known ASD-associated genes as well as in others.

How Can We Advance Integrative Biology Research in Animal Science in 21st Century? Experience at University of Ljubljana from 2002 to 2022.

In this perspective analysis, we strive to answer the following question: how can we advance integrative biology research in the 21st century with lessons from animal science? At the University of Ljubljana, Biotechnical Faculty, Department of Animal Science, we share here our three lessons learned in the two decades from 2002 to 2022 that we believe could inform integrative biology, systems science, and animal science scholarship in other countries and geographies. Cultivating multiomics knowledge through a conceptual lens of integrative biology is crucial for life sciences research that can stand the test of diverse biological, clinical, and ecological contexts. Moreover, in an era of the current COVID-19 pandemic, animal nutrition and animal science, and the study of their interactions with human health (and vice versa) through integrative biology approaches hold enormous prospects and significance for systems medicine and ecosystem health.

IMPACT OF STATIC PROGRESSIVE STRETCH ON RANGE OF MOTION AFTER TOTAL KNEE REPLACEMENT IN PATIENTS WITH HAEMOPHILIA.

Background: Haemophilic arthropathy is often associated with a loss of range of motion. Total knee arthroplasty is an effective treatment option for patients with end-stage haemophilic arthropathy of the knee. However, even after arthroplasty, the range of motion sometimes remains insufficient.

Impaired Neurodevelopmental Genes in Slovenian Autistic Children Elucidate the Comorbidity of Autism With Other Developmental Disorders.

Autism spectrum disorders (ASD) represent a phenotypically heterogeneous group of patients that strongly intertwine with other neurodevelopmental disorders (NDDs), with genetics playing a significant role in their etiology. Whole exome sequencing (WES) has become predominant in molecular diagnostics for ASD by considerably increasing the diagnostic yield. However, the proportion of undiagnosed patients still remains high due to complex clinical presentation, reduced penetrance, and lack of segregation analysis or clinical information.

The Consequences of Mitochondrial T10432C Mutation in Cika Cattle: A "Potential" Model for Leber's Hereditary Optic Neuropathy.

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).

Large-scale mitogenome sequencing reveals consecutive expansions of domestic taurine cattle and supports sporadic aurochs introgression.

The contribution of domestic cattle in human societies is enormous, making cattle, along with other essential benefits, the economically most important domestic animal in the world today. To expand existing knowledge on cattle domestication and mitogenome diversity, we performed a comprehensive complete mitogenome analysis of the species (802 sequences, 114 breeds). A large sample was collected in South-east Europe, an important agricultural gateway to Europe during Neolithization and a region rich in cattle biodiversity.

Genetic diversity and population structure of six autochthonous pig breeds from Croatia, Serbia, and Slovenia.

Background: The importance of local breeds as genetic reservoirs of valuable genetic variation is well established. Pig breeding in Central and South-Eastern Europe has a long tradition that led to the formation of several local pig breeds. In the present study, genetic diversity parameters were analysed in six autochthonous pig breeds from Slovenia, Croatia and Serbia (Banija spotted, Black Slavonian, Turopolje pig, Swallow-bellied Mangalitsa, Moravka and Krskopolje pig).

Genetic variants of the hypoxia-inducible factor 3 alpha subunit (Hif3a) gene in the Fat and Lean mouse selection lines.

Background: Adipose tissue hypoxia and members of the hypoxia-inducible factor alpha (HIFA) are involved in development of obesity. However, the mechanism and functions of HIF3A, one of three HIFA paralogs, in fat deposition have not been sufficiently studied.

Methods And Results: In the present study, we investigated whether Hif3a sequence variants are associated with divergent fat deposition in mouse selection lines for fatness and leanness.

Post-genotyping optimization of dataset formation could affect genetic diversity parameters: an example of analyses with alpine goat breeds.

Background: 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 Drežnica 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.

Standardization of a SNP panel for parentage verification and identification in the domestic cat (Felis silvestris catus).

The domestic cat (Felis silvestris catus) is a valued companion animal throughout the world. Over 60 different cat breeds are accepted for competition by the cat fancy registries in different countries. Genetic markers, including short tandem repeats and SNPs, are available to evaluate and manage levels of inbreeding and genetic diversity, population and breed structure relationships, and individual identification for forensic and registration purposes.

Topics and trends in Mountain Livestock Farming research: a text mining approach.

Pasture-based and small-scale livestock farming systems are the main source of livelihood in the mountain primary sector, ensuring socioeconomic sustainability and biodiversity in rural communities throughout Europe and beyond. Mountain livestock farming (MLF) has attracted substantial research efforts from a wide variety of scientific communities worldwide. In this study, the use of text mining and topic modelling analysis drew a detailed picture of the main research topics dealing with MLF and their trends over the last four decades.

Genomic Characterization of the Istrian Shorthaired Hound.

Istrian shorthaired hound is an old indigenous Croatian dog breed with historical traces of its origin, which date back to the 14th century. Due to its intelligence and great hunting abilities, it is considered an excellent hunting dog. Despite its ancient origin, there is no data on genetic diversity, population structure, and degree of inbreeding that could be used for advanced management and conservation of this breed.

Correction to: Genome-wide SNP data unveils the globalization of domesticated pigs.

An amendment to this paper has been published and can be accessed via the original article.

Population structure and genetic history of Tibetan Terriers.

Background: Tibetan Terrier is a popular medium-sized companion dog breed. According to the history of the breed, the western population of Tibetan Terriers includes two lineages, Lamleh and Luneville. These two lineages derive from a small number of founder animals from the native Tibetan Terrier population, which were brought to Europe in the 1920s.

Differentiation of some Pramenka sheep breeds based on morphometric characteristics.

For the purpose of the morphometric characterization and differentiation of local sheep breeds that belong to the group of breeds called Pramenka or Zackel, two Slovenian (Bela Krajina and Istrian Pramenka) and four Montenegrin sheep breeds (Bardoka, Sjenička, Pivska Pramenka, and Zeta Žuja) were studied. The variation of morphometric measures and nine morphometric indices were analysed. Principal component analysis (PCA) was applied in order to provide an easier description of body size and shape.

polymorphism (rs650082970) is associated with somatic cell count in goat milk.

Pathogens invading the mammary gland are recognized through a range of pattern recognition receptors (PRRs), residing on the plasma membrane of mammary epithelial cells. Toll-like receptor 2 () signalling is responsible for recognition of Gram-positive bacteria, which are the most common mastitis-causing pathogens in goats. Somatic cell counts (SCC) in milk are routinely determined in goat dairy flocks and serve as an indicator of milk quality, which is highly correlated to intramammary infections.

Molecular Mechanisms of Syndromic Cryptorchidism: Data Synthesis of 50 Studies and Visualization of Gene-Disease Network.

Cryptorchidism is one of the most frequent congenital birth defects in male children and is present in 2-4% of full-term male births. It has several possible health effects including reduced fertility, increased risk for testicular neoplasia, testicular torsion, and psychological consequences. Cryptorchidism is often diagnosed as comorbid; copresent with other diseases.

Genetic diversity of autochthonous pig breeds analyzed by microsatellite markers and mitochondrial DNA D-loop sequence polymorphism.

The evaluation of the genetic structure of autochthonous pig breeds is very important for conservation of local pig breeds and preservation of diversity. In this study, 18 microsatellite loci were used to detect genetic relationship between autochthonous pig breeds [Black Slavonian (BS), Turopolje pig (TP), and Croatian wild boar] and to determine phylogenetic relationship among Croatian autochthonous pig breeds and certain Asian and European pigs using the mitochondrial DNA (mtDNA) D-loop sequence polymorphism. Relatively high degree of genetic variation was found between the observed populations.

Genome-wide SNP data unveils the globalization of domesticated pigs.

Background: Pigs were domesticated independently in Eastern and Western Eurasia early during the agricultural revolution, and have since been transported and traded across the globe. Here, we present a worldwide survey on 60K genome-wide single nucleotide polymorphism (SNP) data for 2093 pigs, including 1839 domestic pigs representing 122 local and commercial breeds, 215 wild boars, and 39 out-group suids, from Asia, Europe, America, Oceania and Africa. The aim of this study was to infer global patterns in pig domestication and diversity related to demography, migration, and selection.

Expression of estrogen receptor 1 and progesterone receptor in primary goat mammary epithelial cells.

The exact role and sensitivity of cells to estrogen and progesterone mediated through the steroid receptors during lactation is not known. Expression of estrogen receptor 1 (ESR1) and progesterone receptor (PGR) was quantified in mammary tissue-derived primary goat mammary epithelial cells (pgMECs) to determine the influence of donor tissue physiology (lactating and juvenile) and cell culture growth conditions (basal and lactogenic) on ESR1 and PGR expression in the derived cells. Relative messenger RNA (mRNA) levels for both receptors were the highest in cell lines derived from mammary tissue of juvenile goats.

Cellular reprogramming in farm animals: an overview of iPSC generation in the mammalian farm animal species.

Establishment of embryonic stem cell (ESC) lines has been successful in mouse and human, but not in farm animals. Development of direct reprogramming technology offers an alternative approach for generation of pluripotent stem cells, applicable also in farm animals. Induced pluripotent stem cells (iPSCs) represent practically limitless, ethically acceptable, individuum-specific source of pluripotent cells that can be generated from different types of somatic cells.