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. In the second objective, we hence investigated the effect of inclusion or exclusion of outliers from datasets on genetic diversity and population structure parameters. Results Distinct genetic origin of the Drežnica 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 Drežnica 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 Drežnica, Austrian and Italian goats analyzed here, still exhibit relatively high levels of genetic variability, homogeneous genetic structure and strong geographical partitioning. Conclusions Genetic diversity analyses revealed that the Slovenian Drežnica 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.

Background: Male infertility is a disorder of the reproductive system with a highly complex genetic landscape. In most cases, the reason for male infertility remains unknown; however, the importance of genetic abnormalities in the diagnosis of subfertility/infertility is becoming increasingly recognized. Several syndromes include impaired male fertility in the clinical picture, although a comprehensive analysis of genetic causes of the syndromology perspective of male reproduction is not yet available. Objectives:(1) To develop a catalog of syndromes and corresponding genes associated with impaired male fertility and (2) to visualize an up-to-date genome-phenome network of syndromic male subfertility. Materials and methods:Published literature was retrieved from the Online Mendelian Inheritance in Man, Orphanet, Human Phenotype Ontology and PubMed databases using keywords "male infertility," "syndrome," "gene," and "case report"; time period from 1980 to September, 2021. Retrieved data were organized as a catalog and complemented with identification numbers of syndromes (MIM ID) and genes (Gene ID).The genome-phenome network and the phenome network were visualized using Cytoscape and Gephi software platforms. Protein-protein interaction analysis was performed using STRING tool.Results: Retrieved syndromes were presented as (1) a catalog containing 63 syndromes and 93 associated genes, (2) a genome-phenome network including CHD7 and WT1 genes and Noonan and Kartagener syndromes, and (3) a phenome network including 63 syndromes, and 25 categories of clinical features. Discussion:The developed catalog will contribute to the advances and translational impact toward understanding the factors of syndromic male infertility. Visualized networks provide simple, flexible tools for clinicians and researchers to quickly generate hypotheses and gain a deeper understanding of underlying mechanisms affecting male reproduction.

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BackgroundLocal breeds retained unique genetic variability important for adaptive potential especially in light of challenges related to climate change. One objective was to perform, for the first time, a genome-wide diversity characterization using Illumina GoatSNP50 BeadChip of autochthonous Drežnica goat breed from Slovenia, 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.ResultsDistinct genetic origin of the Drežnica goat was demonstrated 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 Drežnica 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 Drežnica, Austrian and Italian goats analyzed here, still exhibit relatively high levels of genetic variability, homogeneous genetic structure and strong geographical partitioning.ConclusionsGenetic diversity analyses revealed that the Slovenian Drežnica 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 the breeding and management programs and therefore important for preserving genetic variability and uniqueness of local rare breeds.

Raziskave mikro RNA pri govedu, prašičih, ovcah in kokoših Mikro RNA (miRNA) so kratke nekodirajoče RNA, ki imajo pomembno funkcijo pri uravnavanju izražanja genov. Polimorfizmi v prekurzorjih miRNA, v tarčnih genih ali znotraj komponent, ki sodelujejo pri mehanizmu utišanja genov, pomembno prispevajo k fenotipski raznovrstnosti pri živalih. Zaradi te vloge so miRNA postale predmet naraščajočega zanimanja za raziskave v povezavi s proizvodnimi lastnostmi v živinoreji. V članku smo predstavili primere povezav med miRNA in fenotipom pri štirih vrstah rejnih živali: govedu, prašičih, ovcah in kokoših. Večina raziskav o delovanju miRNA je usmerjenih predvsem v mišično in maščobno tkivo, spolne žleze, razvoj zarodka in imunski odziv organizma. Delovanje miRNA vpliva tudi na produktivnost živali in posledično na ekonomsko uspešnost prireje. S tem, ko razumemo delovanje miRNA v različnih bioloških procesih, jih lahko uporabljamo za razvijanje novih strategij za izboljšanje produktivnosti rejnih živali. Ključne besede: živinoreja / genetika / mikro RNA Micro RNA research in cattle, pig, sheep, and chicken MicroRNAs (miRNAs) are small non-coding RNAs that play key roles in regulating gene expression. Polymorphisms in miRNA precursors, target genes or within components of silencing machinery contribute significantly to the phenotypic diversity in animals. Due to this role miRNAs became the subject of increased research interest in association with production traits in livestock. In this article we presented examples of associations between miRNA genes and phenotypes of four livestock species: cattle, pig, sheep, and chicken. Most miRNA research studies are focused on their functioning in muscle, adipose tissues, gonads, fetal development and immune system. MicroRNA functions also impact animal productivity and consequently economic success of farming. With understanding miRNA functions in various biological pathways it is possible to develop new strategies for improving the productivity of livestock.