Interactions between TNF-α, LTF and mLYZ Gene Variants in Determining Somatic Cell Count in Jersey Cows

The aim of the research was to establish if there are any statistically significant associations between the polymorphisms of the selected genes (TNF-α, LTF, mLYZ) and natural log-transformed SCC (LnSCC) and search for possible interactions between the genetic variants of the selected genes in determining various SCC values in milk. The study included 171 Jersey cows. Two alternative approaches were compared: the standard simple model accounting for the additive effect of a single locus only, and the full model including both additive and dominance effects of TNF-α, LTF and mLYZ as well as the interactions between them. The results obtained with the full model are different from those obtained with the standard model including only the additive effects of individual genes. The results presented above prove the existence of complex functional interactions between lactoferrin, lysozyme and tumor necrosis factor and suggest that the alleles of the genes that encode them might interact with each other too

Association of <i>TLR4</i> and <i>CARD15/NOD2</i> polymorphisms with SCC in Holstein–Friesian cattle

<i>Mastitis</i> is one of the most important dairy cattle diseases which results in economic losses in dairy production. <i>Mastitis</i> cases can be classified as subclinical or clinical. All forms of <i>mastitis</i> lead to changes in milk composition and induce an increase in somatic cell count (SCC). SCC is a very important and basic indicator of udder health. An increase in SCC is usually caused by the immune response to the invasion of pathogens contributing to <i>mastitis</i>. The aim of this study was to investigate associations between the polymorphisms of selected genes (<i>TLR4</i> and <i>CARD15/NOD2</i>) whose products are involved in the identification of pathogen-associated molecular patterns (PAMPs) during the innate immune response to infection, and immunity to <i>mastitis</i> expressed as SCC. The genes under study were also examined for epistatic effects as well as effects of interactions with parity and stages of lactation. In all the studied classes, allele G of <i>TLR4</i> had a favourable additive effect with negative values, contributing to a lower lnSCC. Allele A of <i>CARD15/NOD2</i> had a desirable additive effect which varied with time and the changing internal environment during lactation. With regard to the dominance effect, allele A of <i>CARD15/NOD2</i> was found to be significantly associated with a higher SCC in milk in the first lactation and in the third stage of each single lactation. Moreover, statistically significant epistatic effects were found, in particular additive–additive and dominance–additive interactions were favourably associated with SCC which was lower than expected in the case of no epistasis

Polymorphism of IGF-1 gene in Holstein-Fresian cows

Celem niniejszych badań była charakterystyka genetyczna stada krów na podstawie polimorfizmu w regionie promotorowym genu IGF-1 oraz ustalenie ewentualnych zależności pomiędzy wykrytym polimorfizmem a cechami użytkowości mlecznej. Badaniem objęto 185 krów rasy polska holsztyńsko-fryzyjska odmiany czarno-białej. Polimorfizm genu IGF-1 oznaczano metodą ACRS-PCR. W analizowanym stadzie stwierdzono następujące częstości alleli: T – 0,43, C – 0,57. Porównując obserwowane i oczekiwane częstości genotypów odnotowano, iż badana populacja nie znajdowała się w stanie równowagi genetycznej. Heterozygotyczność analizowanego stada wyniosła 0,64. Analizując cechy użytkowości mlecznej w zależności od poszczególnych genotypów stwierdzono, iż genotyp CC w większości przypadków powiązany był z wyższymi wartościami ocenianych cech, jednak różnice te nie zostały potwierdzone statystycznie.The aim of this study was to estimate genetic characteristics of cows herd based on polymorphism in the promoter region of IGF-1 gene as well as determine possible relationships between detected polymorphism and milk performance traits. Investigations were carried out on 185 cows of Polish Holstein-Fresian breed, variety black-and-white. Polymorphism of IGF-1 gene was determined by use ACRS-PCR method. The comparison between the number of observed genotypes and the theoretical number of genotypes showed loss of genetic equilibrium in investigated population. Heterozygosity of analyzed herd was 0.64. Analyzing milk performance traits in relation to individual genotypes it was affirmed that genotype CC in most cases was associated with higher values of examined traits, however these differences were not confirmed statistically

The genetic background of clinical mastitis in Holstein-Friesian cattle

Mastitis is an inflammatory disease of the mammary gland, which has a significant economic impact and is an animal welfare concern. This work examined the association between single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) with the incidence of clinical mastitis (CM). Using information from 16 half-sib pairs of Holstein-Friesian cows (32 animals in total) we searched for genomic regions that differed between a healthy (no incidence of CM) and a mastitis-prone (multiple incidences of CM) half-sib. Three cows with average sequence depth of coverage below 10 were excluded, which left 13 half-sib pairs available for comparisons. In total, 191 CNV regions were identified, which were deleted in a mastitis-prone cow, but present in its healthy half-sib and overlapped in at least nine half-sib pairs. These regions overlapped with exons of 46 genes, among which APP (BTA1), FOXL2 (BTA1), SSFA2 (BTA2), OTUD3 (BTA2), ADORA2A (BTA17), TXNRD2 (BTA17) and NDUFS6 (BTA20) have been reported to influence CM. Moreover, two duplicated CNV regions present in nine healthy individuals and absent in their mastitis-affected half-sibs overlapped with exons of a cholinergic receptor nicotinic \u3b1 10 subunit on BTA15 and a novel gene (ENSBTAG00000008519) on BTA27. One CNV region deleted in nine mastitis-affected sibs overlapped with two neighbouring long non-coding RNA sequences located on BTA12. Single nucleotide polymorphisms with differential genotypes between a healthy and a mastitis-affected sib included 17 polymorphisms with alternate alleles in eight affected and healthy half-sib families. Three of these SNPs were located introns of genes: MET (BTA04), RNF122 (BTA27) and WRN (BTA27). In summary, structural polymorphisms in form of CNVs, putatively play a role in susceptibility to CM. Specifically, sequence deletions have a greater effect on reducing resistance against mastitis, than sequence duplications have on increasing resistance against the disease

Analysis of copy number variations in Holstein-Friesian cow genomes based on whole-genome sequence data

Thirty-two whole genome DNA sequences of cows were analyzed to evaluate inter-individual variability in the distribution and length of copy number variations (CNV) and to functionally annotate CNV breakpoints. The total number of deletions per individual varied between 9,731 and 15,051, whereas the number of duplications was between 1,694 and 5,187. Most of the deletions (81%) and duplications (86%) were unique to a single cow. No relation between the pattern of variant sharing and a family relationship or disease status was found. The animal-averaged length of deletions was from 5,234 to 9,145 bp and the average length of duplications was between 7,254 and 8,843 bp. Highly significant inter-individual variation in length and number of CNV was detected for both deletions and duplications. The majority of deletion and duplication breakpoints were located in intergenic regions and introns, whereas fewer were identified in noncoding transcripts and splice regions. Only 1.35 and 0.79% of the deletion and duplication breakpoints were observed within coding regions. A gene with the highest number of deletion breakpoints codes for protein kinase cGMP-dependent type I, whereas the T-cell receptor \u3b1 constant gene had the most duplication breakpoints. The functional annotation of genes with the largest incidence of deletion/duplication breakpoints identified 87/112 Kyoto Encyclopedia of Genes and Genomes pathways, but none of the pathways were significantly enriched or depleted with breakpoints. The analysis of Gene Ontology (GO) terms revealed that a cluster with the highest enrichment score among genes with many deletion breakpoints was represented by GO terms related to ion transport, whereas the GO term cluster mostly enriched among the genes with many duplication breakpoints was related to binding of macromolecules. Furthermore, when considering the number of deletion breakpoints per gene functional category, no significant differences were observed between the "housekeeping" and "strong selection" categories, but genes representing the "low selection pressure" group showed a significantly higher number of breakpoints

The assessment of inter-individual variation of whole-genome DNA sequence in 32 cows

Despite the growing number of sequenced bovine genomes, the knowledge of the population-wide variation of sequences remains limited. In many studies, statistical methodology was not applied in order to relate findings in the sequenced samples to a population-wide level. Our goal was to assess the population-wide variation in DNA sequence based on whole-genome sequences of 32 Holstein-Friesian cows. The number of SNPs significantly varied across individuals. The number of identified SNPs increased with coverage, following a logarithmic curve. A total of 15,272,427 SNPs were identified, 99.16\ua0% of them being bi-allelic. Missense SNPs were classified into three categories based on their genomic location: housekeeping genes, genes undergoing strong selection, and genes neutral to selection. The number of missense SNPs was significantly higher within genes neutral to selection than in the other two categories. The number of variants located within 3'UTR and 5'UTR regions was also significantly different across gene families. Moreover, the number of insertions and deletions differed significantly among cows varying between 261,712 and 330,103 insertions and from 271,398 to 343,649 deletions. Results not only demonstrate inter-individual variation in the number of SNPs and indels but also show that the number of missense SNPs differs across genes representing different functional backgrounds