Blood cell chimerism is a common phenomenon occurring in cattle coming from double or multiple parturitions and can be observed as two DNA profiles present in blood of each of twin born animals. In the era of genomics, a large number of animals is being genotyped with high throughput genotyping methods, which are giving limited insight into the performance of single markers and rather only statistical description of the results is available for a common user. This hampers the detailed analysis of the results obtained and direct identification of the causes of poorer performance of some samples. In this study we describe the influence of analysis of DNA obtained from blood samples of cattle with genetic chimerism on basic parameters of Infinium technology-based Illumina’s genotyping arrays. The results obtained may help to identify such samples, especially when no precise information about the animals’ origin is available
The conservation of farm animal genetic resources and their protection against genetic erosion requires knowledge of biodiversity status. Genetic variation in populations can be estimated using both traditional pedigree-based methods and molecular techniques. SNP microarrays are a new generation of molecular genetic tools, which have found application in analysis of biodiversity in populations of domestic and wild sheep, in studies of resistance to intestinal parasites and foot rot, and in searching for markers associated with meat and milk yield, or colour inheritance traits. The aim of the study is the review of recent literature on the biodiversity and the use of molecular markers for population genetics in different breeds and populations of sheep.
One of epigenetic features of mammalian genomes is methylation of DNA. This nucleotide modification might exert suppressive effect on gene transcription. We have described putative relevance of methylation of one of immune cells related gene (ITGAL) observed in the set of 11 equine tissues. Comparison between qualitative RT-PCR results and DNA bisulfite sequencing of investigated set of tissues pointed to potential correlations between tissue specific methylation and tissue specific transcription in ITGAL locus. These findings might be important for studies on genetic and epigenetic background of autoimmune disorders in the horse.
In this study, we have attempted to analyse the impact of dietary fats on the liver transcriptome in pigs. Four nutritional groups were created. The animals’ diets differed among groups in terms of the presence of corn dried distillers’ grains with solubles (DDGS) (group I - no DDGS, groups II, III, IV - 20% DDGS) as well as the type of fat (rapeseed oil - groups I and II, beef tallow - group III, coconut oil - group IV) used. Using the RNA-Seq method we identified 39 differentially expressed genes (DEGs) as a result of Cuffdiff analysis of the differences among all groups. Analysis of these genes with Panther Gene Classification System revealed that among identified DEGs, genes responsible for lipid and fatty acids metabolism are overrepresented as well as the genes engaged in oxidoreductase and catalytic activity. The article presents for the first time the RNAseq analysis of the liver transcriptome in pigs fed with different sources of fats. The results may be useful for the elaboration of new therapies for cardiovascular diseases in humans as well as for the preparation of new nutrition strategies in animals.
Sarcoid is the most common skin cancer in horses. The etiology of the tumor is associated with BPV infection (BPV-1, -2, -13), which is an inducer of malignant transformation. The comparative genomic hybridization (CGH) technique identifying the unbalanced chromosome aberrations was used to analyze the genome of equine sarcoid cells and to diagnose the chromosome rearrangements involving large deletions or amplification. The results were based on the analysis of 100 metaphases and their karyograms as well as the diagram showing the average ratio of the intensity of the green to red fluorescence, using MetaSystems software (Isis). Based on a comparison of the fluorescence intensity ratios we found duplication in the subtelomeric regions of chromosome pairs 1, 4, 7, 8 and 23. Duplicated region of chromosome pair 1 also included the coding region of the rDNA. In the chromosome 23 next to the duplication occurring in the centromeric region of q arm (23q11) we also found the presence of deletions involving 23q18-23q19 region. For the chromosome pairs 25 to 31 and the X chromosome the software failed to generate CGH diagram, but on the individual karyograms we were able to observe fluorescence signals characteristic of duplication (red), in rDNA regions of chromosome pairs 28 and 31. The study showed that duplications of DNA present in the sarcoid cells are found mainly in the telomeric and rDNA regions. The presence of the duplication of telomeric regions is associated with increased activity of the telomerase enzyme, which is a hallmark of cancer cells, affecting the immortality of these cells. Accordingly, duplications of rDNA coding regions increase activity of nucleolar organizer region which is a tumor marker.
The aim of the study was to analyse the genetic basis of piebald coat colour in Hucul horses and to verify their coat colour in breeding records. Tests were performed with DNA purified from the whole blood samples of 242 Hucul horses with different coat colour patterns. DNA was analysed to identify an inversion in ECA3 (PCR). The results confirmed that the inversion on ECA3 is a direct factor determining piebald (tobiano) colour in the analysed Hucul horses. No inversion was observed in any of the solid coloured horses, but it was present in all the piebald ones. It was also identified in 18% (11 of 61) of the horses from the group of horses qualified in the passport as solid coloured with white markings. In fact, these horses had the tobiano gene that is phenotypically identifiable as crypto-tobiano, which may give the false impression of having white markings and lead to error when describing a horse. This is an important issue, in particular with regard to the breed standard, which eliminates Hucul horses with white markings from breeding.
In the recent years, particular attention was given to the research aimed at optimizing the use of tumour epigenetic markers. One of the best known epigenetic changes associated with the process of carcinogenesis is aberrant DNA methylation. The aim of the present research was to evaluate the methylation profile of genes potentially important in the diagnosis and/or prognosis of equine sarcoids, the most commonly detected skin tumours in Equidae. The methylation status of potential promoter sequences of nine genes: APC, CCND2, CDKN2B, DCC, RARβ, RASSF1, RASSF5, THBS1 and TRPM1, was determined using bisulfite sequencing polymerase chain reaction (BSP-CR). The results of this study did not reveal any changes in the level of DNA methylation in the analysed group of candidate genes between the tumour and healthy tissues. Despite numerous reports describing the aberrant methylation of the promoters of the analysed genes in human cancers, the data obtained did not confirm the existence of such relationships in the examined tumour tissues, which excludes the possibility of using these genes for the diagnosis of the equine sarcoid.
The aim of this study was to identify mutations in the D-loop region of mtDNA in head, neck, and limb tumours in dogs, and determination of their relationship with the process of neoplastic transformation. Blood and tumour tissue samples from 19 dogs with diagnosed sporadic malignant tumours were analysed. DNA extraction, amplification, and sequencing of the mtDNA D-loop, and bioinformatic analyses were performed. Five mutations and 19 polymorphisms were observed in 68.42% of all tumours. Polymorphic variants were noted in 42.86% of the head and neck tumours and in 58.33% of the limb tumours. Mutations were observed in 21.05% of dogs. The mutations were found in 28.57% of the head and neck tumours and in 16.66% of the limb tumours. The mutations were identified in 50% of the studied epithelial cancers. In the mesenchymal tumours, no mutations in the D-loop region were observed. Mitochondrial haplotype A17 was found in over 40% cases of limb tumours. No association between the age, breed, sex, type of tumour, and detected polymorphic variants were observed. Different mutational changes in the D-loop sequences of mtDNA identified in the blood and tumour tissues may indicate a relationship between the type of tumour and individual changes in the D-loop nucleotide sequences of mtDNA.