Genome-wide association analysis of milk yield traits in Nordic Red Cattle using imputed whole genome sequence variants

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Genomewide transcriptome profiling of milk derived primary bovine mammary epithelial cells after pathogen challenge

A method was developed to collect and cultivate primary bovine mammary epithelial cells (pbMECs) from milk samples of healthy lactating cows. Cell cultures from ten Nordic Red cows were used in a pathogen challenge study with two common pathogens, Escherichia coli and Staphylococcus aureus. Transcriptomewide changes in gene expression were monitored at four time points after challenge. We present here preliminary results from two cows, showing that pathogen specific differences in gene expression can be detected in the pbMECs, reflecting differences in the immune responses triggered by each pathogen

APOE Genotypes, Lipid Profiles, and Associated Clinical Markers in a Finnish Population with Cardiovascular Disease Risk Factors

Introduction: The APOE ε4 allele predisposes to high cholesterol and increases the risk for lifestyle-related diseases such as Alzheimer’s disease and cardiovascular diseases (CVDs). The aim of this study was to analyse interrelationships of APOE genotypes with lipid metabolism and lifestyle factors in middle-aged Finns among whom the CVD risk factors are common. Methods: Participants (n = 211) were analysed for APOE ε genotypes, physiological parameters, and health- and diet-related plasma markers. Lifestyle choices were determined by a questionnaire. Results: APOE genotypes ε3/ε4 and ε4/ε4 (ε4 group) represented 34.1% of the participants. Genotype ε3/ε3 (ε3 group) frequency was 54.5%. Carriers of ε2 (ε2 group; ε2/ε2, ε2/ε3 and ε2/ε4) represented 11.4%; 1.9% were of the genotype ε2/ε4. LDL and total cholesterol levels were lower (p < 0.05) in the ε2 carriers than in the ε3 or ε4 groups, while the ε3 and ε4 groups did not differ. Proportions of plasma saturated fatty acids (SFAs) were higher (p < 0.01), and omega-6 fatty acids lower (p = 0.01) in the ε2 carriers compared with the ε4 group. The ε2 carriers had a higher (p < 0.05) percentage of 22:4n-6 and 22:5n-6 and a lower (p < 0.05) percentage of 24:5n-3 and 24:6n-3 than individuals without the ε2 allele. Conclusions: The plasma fatty-acid profiles in the ε2 group were characterized by higher SFA and lower omega-6 fatty-acid proportions. Their lower cholesterol values indicated a lower risk for CVD compared with the ε4 group. A novel finding was that the ε2 carriers had different proportions of 22:4n-6, 22:5n-6, 24:5n-3, and 24:6n-3 than individuals without the ε2 allele. The significance of the differences in fatty-acid composition remains to be studied.Peer reviewe

Copy number variation in cattle breeds

Detecting all classes of genetic variation in livestock species, such as cattle, is a pre-requisite to studying their association to traits of interest. Copy Number Variations (CNVs) are classes of polymorphic DNA regions including deletions, duplications and insertions of DNA fragments of at least 0.5 kb to several Mb, that are copy number variable when compared to a reference genome. CNVs can be identified using various approaches, among those the SNP array data are low cost, dense coverage, and high throughput. The aim of this study was to obtain a consensus genome map of Copy Number Variable Regions (CNVRs) in the Brown Swiss (dataset of 192 bulls), Red Pied Valdostana (dataset of 143 bulls) and Finnish Ayrshire (dataset of 243 bulls) cattle breeds all genotyped on the Illumina Bovine HD BeadChip, and two SNP based CNV calling algorithms. Brown Swiss cattle originated in the Swiss Alps, kept as a triple purpose breed. Once imported in the US, it was mainly selected for increased milk production. The Valdostana Red Pied cattle is the most common autochthonous dual purpose breed in the region Valle d\u2019Aosta in Italy (13,000 animals in 2013, almost all of them registered in the Herd Book). The Finnish Ayrshire is the most common cattle in Finland. CNVs were called with the PennCNV and SVS7 software and were summarized to CNVRs at the population level as overlapping CNV calls within breed. PennCNV identified 2,377, 1,723 and 1,689 for the Italian Brown Swiss, the Red Pied Valdostana and the Finnish Ayrshire, respectively. SVS7 detected 370, 235 and 2,063 for the three cattle breeds. These regions were annotated with Ensembl v78 Bos taurus gene set (UMD3.1) and genomic regions harboring QTL for production and functional traits. The comparison among CNVRs here identified provided common regions in the breeds. The results of this study are a comprehensive genomic analysis of cattle CNVs derived from SNP data, which will be a valuable genomic variation resource and will enrich the bovine CNV map in the cattle genome, providing new information for association studies with traits included in the selection programs

Scans for signatures of selection in Russian cattle breed genomes reveal new candidate genes for environmental adaptation and acclimation

Domestication and selective breeding has resulted in over 1000 extant cattle breeds. Many of these breeds do not excel in important traits but are adapted to local environments. These adaptations are a valuable source of genetic material for efforts to improve commercial breeds. As a step toward this goal we identified candidate regions to be under selection in genomes of nine Russian native cattle breeds adapted to survive in harsh climates. After comparing our data to other breeds of European and Asian origins we found known and novel candidate genes that could potentially be related to domestication, economically important traits and environmental adaptations in cattle. The Russian cattle breed genomes contained regions under putative selection with genes that may be related to adaptations to harsh environments (e.g., AQP5, RAD50, and RETREG1). We found genomic signatures of selective sweeps near key genes related to economically important traits, such as the milk production (e.g., DGAT1, ABCG2), growth (e.g., XKR4), and reproduction (e.g., CSF2). Our data point to candidate genes which should be included in future studies attempting to identify genes to improve the extant breeds and facilitate generation of commercial breeds that fit better into the environments of Russia and other countries with similar climates

Accuracy of genomic prediction of dry matter intake in Dutch Holsteins using sequence variants from meta-analyses

We evaluated the accuracy of biology informed genomic prediction for dry matter intake in 2,162 Dutch Holstein cows. Sequence variants were selected from meta-analyses including GWAS summary statistics for QTL and metabolomic QTL in several dairy and crossbred beef populations. Selected variants were prioritized in GBLUP models in a five-fold cross-validation. The accuracies were compared to genomic prediction based on routine 50k genotype data. The average accuracy for the 50k scenario was 0.683. Adding selected sequence variants in the GBLUP model did not improve the accuracies for dry matter intake. Next steps will include testing Bayesian variable selection methods to prioritize variants in genomic prediction for dry matter intake

An intervention study of individual, apoE genotype-based dietary and physical-activity advice: impact on health behavior

Issue release date: March 2015201

Genetic diversity and genomic signatures of selection among cattle breeds from Siberia, eastern and northern Europe

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Molecular anatomy of the cytoplasmic domain of bovine growth hormone receptor, a quantitative trait locus

Quantitative trait loci (QTL) studies have indicated growth hormone receptor (GHR) as a candidate gene affecting cattle milk yield and composition. In order to characterize genetic variation at GHR in cattle, we studied European and East African breeds with different histories of selection, and Bos grunniens, Ovis aries, Sus scrofa, Bison bison and Rangifer tarandus as references. We sequenced most of the cytoplasmic domain (900 bp of exon 10), 89 bp of exon 8, including the putative causative mutation for the QTL effect, and 390 bp of intron 8 for comparison. In the cytoplasmic domain, seven synonymous and seven non-synonymous single nucleotide polymorphisms (SNP) were identified in cattle. Three non-synonymous SNPs were found in sheep and one synonymous SNP in yak, while other studied species were monomorphic. Three major haplotypes were observed, one unique to African breeds, one unique to European breeds and one shared. Bison and yak haplotypes are derivatives of the European haplotype lineage. Most of the exon 10 non-synonymous cattle SNPs appear at phylogenetically highly conserved sites. The polymorphisms in exon 10 cluster around a ruminant-specific tyrosine residue, suggesting that this site may act as an additional signalling domain of GHR in ruminants. Alternative explanations for the persistent polymorphism include balancing selection, hitch-hiking, pleiotropic or sexually antagonistic fitness effects or relaxed functional constraints