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Chromosomal abnormalities are a common cause of infertility in horses. However, they are difficult to detect using automated methods. Here, we propose a simple methodology based on single nucleotide polymorphism (SNP)-array data that allows us to detect the main chromosomal abnormalities in horses in a single procedure. As proof of concept, we were able to detect chromosomal abnormalities in 33 out of 268 individuals, including monosomies, chimerisms, and male and female sex-reversions, by analyzing the raw signal intensity produced by an SNP array-based genotyping platform. We also demonstrated that the procedure is not affected by the SNP density of the array employed or by the inbreeding level of the individuals. Finally, the methodology proposed in this study could be performed in an open bioinformatic environment, thus permitting its integration as a flexible screening tool in diagnostic laboratories and genomic breeding programs., (© 2021 Stichting International Foundation for Animal Genetics.)

Poland is the largest European producer of goose, while goose breeding has become an essential and still increasing branch of the poultry industry. The most frequently bred goose is the White Kołuda ® breed, constituting 95% of the country's population, whereas geese of regional varieties are bred in smaller, conservation flocks. However, a goose's genetic diversity is inaccurately explored, mainly because the advantages of the most commonly used tools are strongly limited in non-model organisms. One of the most accurate used markers for population genetics is single nucleotide polymorphisms (SNP). A highly efficient strategy for genome-wide SNP detection is genotyping-by-sequencing (GBS), which has been already widely applied in many organisms. This study attempts to use GBS in 12 conservative goose breeds and the White Kołuda ® breed maintained in Poland. The GBS method allowed for the detection of 3833 common raw SNPs. Nevertheless, after filtering for read depth and alleles characters, we obtained the final markers panel used for a differentiation analysis that comprised 791 SNPs. These variants were located within 11 different genes, and one of the most diversified variants was associated with the EDAR gene, which is especially interesting as it participates in the plumage development, which plays a crucial role in goose breeding.

Application of next generation sequencing for large scale genotyping in livestock is limited by high costs and challenging data analysis process. However, available restriction enzyme-based enrichment techniques like e.g. genotyping-by-sequencing (GBS) are promising tools allowing reduction of financial outlies by a high sample multiplexing and narrowing down the sequenced genome areas to the randomly distributed read tags. In this study, we tested the performance of standard, PstI endonuclease-adapted GBS protocol for population genetics in cattle, horse and sheep with application of different, including low-depth sequencing setups. It was found that the detected SNPs display desirable polymorphism parameters and are evenly scattered across the whole genome including gene coding regions. It was also shown that the SNPs can be successfully applied in population genetics, revealing the genetic differentiation of the studied breeds. The GBS approach represents a cost-effective alternative to existing genotyping methods which may find adoption in various research applications., (Copyright © 2018 Elsevier Inc. All rights reserved.)

Characterisation of copy number variation (CNV) and loss of heterozygosity (LOH) has pro- vided evidence for the relationship of this type of genetic variation with the occurrence of a broad spectrum of diseases, including cancer lesions. The role of CNVs and germinal or somatic LOHs in canine mammary tumours is still unknown. Therefore, the aim of this study was to identify CNVs and LOHs in canine mammary tumours. Forty-eight samples obtained from normal (n=24) and tumour (n=24) tissues of dogs were analysed. In the study, we used CanineHD BeadChip assay (Illumina) and OncoSNP software to identify copy number alternations in genomes of dif- ferent dog breeds and in different mammary cancer types occurring in this species. The analyses revealed that, in the case of CNV, the amplification-type variants were longer and more frequent than deletions. Based on the analysis of the frequency of different types of aberrations in the in- dividual parts of the genome, regions that are particularly susceptible to structural aberrations were indicated. The fraction of genes identified within these regions was associated with major processes of neoplastic transformation. Association analysis of such traits as tumour grading as well as the size and age of dogs demonstrated that structural aberrations were more frequent in dogs diagnosed with tumour malignancy grade II and III, in dogs with a larger body size, and in large dogs aged 7-8. The promising results of these pioneering investigations prompt continuation thereof to analyse other types of cancer., (Copyright© by the Polish Academy of Sciences.)

Polish Red cattle is one of the few indigenous breeds of European red cattle which is characterized by several desired features, such as high disease resistance, good health, longevity, good fertility, and high nutritional value of milk. Currently, Polish Red cattle population is a subject of two independent breeding programs: (i) improvement program and (ii) genetic resources conservation program. The aim of the improvement program is the genetic progress in terms of milk production and body conformation traits, while the conservation program mainly focuses on protection of the genetic resources of Polish Red cattle and preservation of the existing, original gene pool. By the analysis of F ST genetic distances across genome-wide SNP panel, we detected diversifying selection signatures among these two subpopulations and indicated (among others) the significance of DGAT1 and FGF2 genes for milk production traits in these cattle. We also found that among genes being presumably under selection in terms of milk production, there are genes responsible, for example, for mammary gland development (e.g., SOSTDC1, PYGO2, MED1, and CCND1) and immune system response (e.g., IL10RA, IL12B, and IL21). The most important finding of this study is that the most pronounced genetic differences between the analyzed populations were associated with β-defensin genes (e.g., DEFB1, DEFB4A, DEFB5, DEFB7, DEFB10, DEFB13, EBD, BNBD-6, and LAP) located within so-called bovine cluster D on BTA27. The β-defensins are expressed mainly in the mammary gland and are antimicrobial peptides against the Gram-negative and Gram-positive bacteria, viruses, and other unicellular parasites. This suggests that antimicrobial resistance of mammary gland is of high importance during selection towards increased milk production and that genes responsible for this process are selected together with increasing levels of productivity.

Genetic improvement of animals based on artificial selection is leading to changes in the frequency of genes related to desirable production traits. The changes are reflected by the neutral, intergenic single nucleotide polymorphims (SNPs) being in long-range linkage disequilibrium with functional polymorphisms. Genome-wide SNP analysis tools designed for cattle, allow for scanning divergences in allelic frequencies between distinct breeds and thus for identification of genomic regions which were divergently selected in breeds' histories. In this study, by using Bovine SNP50 assay, we attempted to identify genomic regions showing the highest differences in allele frequencies between two distinct cattle breeds - preserved, unselected Polish Red breed and highly selected Holstein cattle. Our study revealed 19 genomic regions encompassing 55 protein-coding genes and numerous quantitative trait loci which potentially may underlie some of the phenotypic traits distinguishing the breeds., (© 2014 Japanese Society of Animal Science.)

Animal genomics is currently undergoing dynamic development, which is driven by the flourishing of high-throughput genome analysis methods. Recently, a large number of animals has been genotyped with the use of whole-genome genotyping assays in the course of genomic selection programmes. The results of such genotyping can also be used for studies on different aspects of livestock genome functioning and diversity. In this article, we review the recent literature concentrating on various aspects of animal genomics, including studies on linkage disequilibrium, runs of homozygosity, selection signatures, copy number variation and genetic differentiation of animal populations. Our work is aimed at providing insight into certain achievements of animal genomics and to arouse interest in basic research on the complexity and structure of the genomes of livestock.

The breed assignment in cattle is one of the issues of molecular genetics which needs further testing and development. Although several statistical approaches have been developed to enable such application, the obtained results strongly depend on specific populations differentiation and power of markers discrimination or their informativeness. Currently, all breeding animals are being tested for parentage with the use of panel of 12 microsatellite markers, which in near future probably will be replaced by about 100 single nucleotide polymorphisms (SNPs). Despite the fact that SNPs are mainly bi-allelic, the multilocus genotypes can reach the level of polymorphism of a panel of microsatellite markers. In this study we attempted to determine the breed of origin of 741 cattle by using 120 SNPs dedicated for parentage testing and included in the BovineSNP50 BeadChip genotyping assay (Illumina). The applied Bayesian and frequency-based methods allowed such differentiation, however, the reliability of the results was not completely satisfying, suggesting that the studied markers are not the best tool for breed assignment.

According to increasing interest in the use of high density SNP (single nucleotide polymorphism) genotyping assays for genome-wide genetic studies in farm animals, there is a need to assess the usefulness of currently available genomic tools for application in different breeds. The performance of the assays may differ between the breeds because of discrepancies in allele frequencies of the polymorphisms or differences in linkage disequilibrium patterns. In this study we attempted to test the performance of the Bovine SNP50 v2 genotyping assay (Illumina) for population genetic and other applications in the Polish Red cattle breed. We found that 37,977 of the 53,438 autosomal markers included in the assay give high quality genomic information and can be used for different applications concerning this breed. The remaining markers were denoted as "of limited use" or redundant because of their weak performance, deviation from Hardy-Weinberg equilibrium, low minor allele frequency, high linkage disequilibrium with other neighboring markers or location on sex chromosomes.