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

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Quantitative trait loci for fertility traits in Finnish Ayrshire cattle

v2008okBEL/EG

Quantitative trait loci for fertility traits in Finnish Ayrshire cattle

A whole genome scan was carried out to detect quantitative trait loci (QTL) for fertility traits in Finnish Ayrshire cattle. The mapping population consisted of 12 bulls and 493 sons. Estimated breeding values for days open, fertility treatments, maternal calf mortality and paternal non-return rate were used as phenotypic data. In a granddaughter design, 171 markers were typed on all 29 bovine autosomes. Associations between markers and traits were analysed by multiple marker regression. Multi-trait analyses were carried out with a variance component based approach for the chromosomes and trait combinations, which were observed significant in the regression method. Twenty-two chromosome-wise significant QTL were detected. Several of the detected QTL areas were overlapping with milk production QTL previously identified in the same population. Multi-trait QTL analyses were carried out to test if these effects were due to a pleiotropic QTL affecting fertility and milk yield traits or to linked QTL causing the effects. This distinction could only be made with confidence on BTA1 where a QTL affecting milk yield is linked to a pleiotropic QTL affecting days open and fertility treatments

The effect of dietary rumen-protected trans-10,cis-12 conjugated linoleic acid or a milk fat-depressing diet on energy metabolism, inflammation, and oxidative stress of dairy cows in early lactation

The objective of this study was to determine the effects of milk fat depression induced by supplementing conjugated linoleic acid (CLA; trans-10,cis-12 and cis-9,trans-11 CLA) or feeding a higher starch and oil-containing diet (HSO) on metabolic changes in dairy cows after calving. The main hypothesis was that the 2 strategies to decrease milk fat yield could have different effects on performance, energy balance (EB), and inflammatory status in early lactation. Thirty-three Nordic Red dairy cows were used in a randomized block design from 1 to 112 d of lactation and fed one of the following treatments: control (CON), CLA-supplemented diet, or HSO diet. Dry matter intake and milk yield were measured daily whereas milk composition was measured weekly throughout the experiment. Nutrient digestibility, EB, and plasma hormones and metabolites were measured at 3, 7, 11, and 15 wk of lactation in respiration chambers. The HSO diet led to lower intakes of dry matter, neutral detergent fiber, and gross energy compared with CON and CLA diets. The CLA diet and especially the HSO diet resulted in lower energy-corrected milk yield during the first 7 wk of lactation than those fed CON. The EB was numerically higher for HSO and CLA diets compared with CON at wk 3 and 7. Plasma glucose concentration was higher by the CLA diet at wk 3 and by the HSO diet from wk 3 to 15 compared with CON. Plasma nonesterified fatty acids were higher at wk 3 in the CON group (indicating more lipid mobilization) but decreased thereafter to similar levels with the other groups. The HSO-fed cows had higher plasma ceruloplasmin, paraoxonase, and total bilirubin concentrations in the entire experiment and showed the highest levels of reactive oxygen metabolites. These results suggest an increased inflammatory and oxidative stress state in the HSO cows and probably different regulation of the innate immune system. This study provides evidence that milk fat depression induced by feeding HSO (as well as CLA) decreased milk fat secretion and improved EB compared with CON in early lactation. The increase in plasma glucose and paraoxonase levels with the HSO diet may imply a better ability of the liver to cope with the metabolic demand after parturition. However, the negative effect of HSO on feed intake, and the indication of increased inflammatory and oxidative stress warrant further studies before the HSO feeding strategy could be supported as an alternative to improve EB in early lactation

Subgroup detection in genotype data using invariant coordinate selection

Background: The current gold standard in dimension reduction methods for high-throughput genotype data is the Principle Component Analysis (PCA). The presence of PCA is so dominant, that other methods usually cannot be found in the analyst's toolbox and hence are only rarely applied.Results: We present a modern dimension reduction method called 'Invariant Coordinate Selection' (ICS) and its application to high-throughput genotype data. The more commonly known Independent Component Analysis (ICA) is in this framework just a special case of ICS. We use ICS on both, a simulated and a real dataset to demonstrate first some deficiencies of PCA and how ICS is capable to recover the correct subgroups within the simulated data. Second, we apply the ICS method on a chicken dataset and also detect there two subgroups. These subgroups are then further investigated with respect to their genotype to provide further evidence of the biological relevance of the detected subgroup division. Further, we compare the performance of ICS also to five other popular dimension reduction methods.Conclusion: The ICS method was able to detect subgroups in data where the PCA fails to detect anything. Hence, we promote the application of ICS to high-throughput genotype data in addition to the established PCA. Especially in statistical programming environments like e.g. R, its application does not add any computational burden to the analysis pipeline

The effect of dietary forage to concentrate ratio and forage type on milk phospholipids and fatty acid composition of polar lipids

The effects of grass silage and red clover silage on milk fatty acid (FA) composition are extensively studied, but little is known of their impacts on minor lipid constituents of milk fat globule membrane. We investigated the effects of forage:concentrate (FC) ratio in grass silage-based diets and forage type (grass silage vs. red clover silage) on selected molecular species of milk phospholipids (PL) and the FA composition of PL. Ten multiparous Nordic Red cows were offered following dietary treatments: grass silage-based diets containing 70:30 (HG) or 30:70 (LG) FC ratio or a red clover silage-based diet (RC) comprising 50:50 FC ratio on a dry matter basis. The most abundant molecular species within the phosphatidylcholines was 16:0–18:1 phosphatidylcholine that was increased by 18% in HG compared with LG milk. Dietary treatments did not affect the relative proportion of 18:1–18:1+18:0–18:2 phosphatidylethanolamine that was the most prevalent species (ca. 44–45%) in that class. We identified the d18:1–22:0 sphingomyelin as the most abundant sphingomyelin species that tended to increase in HG milk compared with LG. The FC ratio did not affect the relative proportions of saturated FA nor monounsaturated FA in PL, but the proportion of cis-9 18:1 was elevated in HG vs. LG milk, whereas the proportion of 18:2n-6 was 50% higher in LG vs. HG milk. The RC diet increased monounsaturated FA and 18:3n-3 levels in PL compared with grass silage-based diets and decreased the relative proportion of saturated FA. However, the RC diet did not affect the relative proportion of polyunsaturated FA in PL, although red clover silage typically increases the proportion of polyunsaturated FA in milk fat. This study provides valuable knowledge of the minor lipid components in milk on species level in relation to common feeding strategies in high-forage systems

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

Cognition and resective surgery for diffuse infiltrative glioma: an overview

Compared to classical oncological outcome measures such as time to progression and survival, the importance of cognitive functioning in patients with diffuse infiltrative brain tumors has only recently been recognized. Apart from the relatively low incidence and the invariably fatal outcome of gliomas, the general assumption that cognitive assessment is time-consuming and burdensome contributes to this notion. Our understanding of the effects of brain surgery on cognition, for instance, is largely based on studies in surgical patients with refractory epilepsy, with only a limited number of studies in surgical patients with gliomas. The impact of other factors affecting cognition in glioma patients such as direct tumor effects, radiotherapy and chemotherapy, and medical treatment, including anti-epileptic drugs and steroids, have been studied more extensively. The purpose of this paper is to provide an overview of cognition in patients with diffuse infiltrative gliomas and the impact of resective surgery as well as other tumor and treatment-related factors

A heritable subset of the core rumen microbiome dictates dairy cow productivity and emissions

A 1000-cow study across four European countries was undertaken to understand to what extent ruminant microbiomes can be controlled by the host animal and to identify characteristics of the host rumen microbiome axis that determine productivity and methane emissions. A core rumen microbiome, phylogenetically linked and with a preserved hierarchical structure, was identified. A 39-member subset of the core formed hubs in co-occurrence networks linking microbiome structure to host genetics and phenotype (methane emissions, rumen and blood metabolites, and milk production efficiency). These phenotypes can be predicted from the core microbiome using machine learning algorithms. The heritable core microbes, therefore, present primary targets for rumen manipulation toward sustainable and environmentally friendly agriculture