Anna Bieber

Estimation of genetic parameters for novel functional traits in Brown Swiss cattle

The aim of this study was to estimate genetic parameters and accuracies of breeding values for a set of functional, behavior, and conformation traits in Brown Swiss cattle. These traits were milking speed, udder depth, position of labia, rank order in herd, general temperament, aggressiveness, milking temperament, and days to first heat. Data of 1,799 phenotyped Brown Swiss cows from 40 Swiss dairy herds were analyzed taking the complete pedigree into account. Estimated heritabilities were within the ranges reported in literature, with results at the high end of the reported values for some traits (e.g., milking speed: 0.42±0.06, udder depth: 0.42±0.06), whereas other traits were of low heritability and heritability estimates were of low accuracy (e.g., milking temperament: 0.04±0.04, days to first heat: 0.02±0.04). For most behavior traits, we found relatively high heritabilities (general temperament: 0.38±0.07, aggressiveness: 0.12±0.08, and rank order in herd: 0.16±0.06). Position of labia, arguably an indicator trait for pathological urovagina, was genetically analyzed in this study for the first time, and a moderate heritability (0.28±0.06) was estimated.

Accuracy of direct genomic values for functional traits in Brown Swiss cattle.

In this study, direct genomic values for the functional traits general temperament, milking temperament, aggressiveness, rank order in herd, milking speed, udder depth, position of labia, and days to first heat in Brown Swiss dairy cattle were estimated based on ~777,000 (777 K) single nucleotide polymorphism (SNP) information from 1,126 animals. Accuracy of direct genomic values was assessed by a 5-fold cross-validation with 10 replicates. Correlations between deregressed proofs and direct genomic values were 0.63 for general temperament, 0.73 for milking temperament, 0.69 for aggressiveness, 0.65 for rank order in herd, 0.69 for milking speed, 0.71 for udder depth, 0.66 for position of labia, and 0.74 for days to first heat. Using the information of ~54,000 (54K) SNP led to only marginal deviations in the observed accuracy. Trying to predict the 20% youngest bulls led to correlations of 0.55, 0.77, 0.73, 0.55, 0.64, 0.59, 0.67, and 0.77, respectively, for the traits listed above. Using a novel method to estimate the accuracy of a direct genomic value (defined as correlation between direct genomic value and true breeding value and accounting for the correlation between direct genomic values and conventional breeding values) revealed accuracies of 0.37, 0.20, 0.19, 0.27, 0.48, 0.45, 0.36, and 0.12, respectively, for the traits listed above. These values are much smaller but probably also more realistic than accuracies based on correlations, given the heritabilities and samples sizes in this study. Annotation of the largest estimated SNP effects revealed 2 candidate genes affecting the traits general temperament and days to first heat.

Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals

Stature is affected by many polymorphisms of small effect in humans1. In contrast, variation in dogs, even within breeds, has been suggested to be largely due to variants in a small number of genes2,3. Here we use data from cattle to compare the genetic architecture of stature to those in humans and dogs. We conducted a meta-analysis for stature using 58,265 cattle from 17 populations with 25.4 million imputed whole-genome sequence variants. Results showed that the genetic architecture of stature in cattle is similar to that in humans, as the lead variants in 163 significantly associated genomic regions (P < 5 × 10−8) explained at most 13.8% of the phenotypic variance. Most of these variants were noncoding, including variants that were also expression quantitative trait loci (eQTLs) and in ChIP–seq peaks. There was significant overlap in loci for stature with humans and dogs, suggesting that a set of common genes regulates body size in mammals.Meta-analysis of data from 58,265 cattle shows that the genetic architecture underlying stature is similar to that in humans, where many genomic regions individually explain only a small amount of phenotypic variance.

Impact of US Brown Swiss genetics on milk quality from low-input herds in Switzerland: interactions with grazing intake and pasture type

This study investigated the effect of, and interactions between, contrasting crossbreed genetics (US Brown Swiss [BS] × Improved Braunvieh [BV] × Original Braunvieh [OB]) and feeding regimes (especially grazing intake and pasture type) on milk fatty acid (FA) profiles. Concentrations of total polyunsaturated FAs, total omega-3 FAs and trans palmitoleic, vaccenic, α-linolenic, eicosapentaenoic and docosapentaenoic acids were higher in cows with a low proportion of BS genetics. Highest concentrations of the nutritionally desirable FAs, trans palmitoleic, vaccenic and eicosapentaenoic acids were found for cows with a low proportion of BS genetics (0-24% and/or 25-49%) on high grazing intake (75-100% of dry matter intake) diets. Multivariate analysis indicated that the proportion of OB genetics is a positive driver for nutritionally desirable monounsaturated and polyunsaturated FAs while BS genetics proportion was positive driver for total and undesirable individual saturated FAs. Significant genetics × feeding regime interactions were also detected for a range of FAs.

Estimation of genetic parameters for individual udder quarter milk content traits in Brown Swiss cattle

The aim of this study was to estimate genetic parameters and accuracies of breeding values for milk content traits of individual udder quarters in Brown Swiss cattle. Data of 1,799 phenotyped cows from 40 Swiss dairy herds were analyzed, taking the complete pedigree into account. Fat, protein, lactose, and urea contents, somatic cell score (SCS), and information about hyperkeratosis were available for each udder quarter. The milk of rear udder quarters was found to have significantly higher lactose content and significantly lower fat content than milk of the front udder quarters. The same trend found for fat content was observed for protein content, whereas no differences between the udder quarters were observed for urea content, SCS, or hyperkeratosis. Heritabilities for each udder quarter were in the following ranges: fat content 0.09±0.06 to 0.14±0.06, protein content 0.20±0.09 to 0.33±0.07, lactose content 0.04±0.03 to 0.16±0.07, urea content 0.13±0.07 to 0.22±0.08, SCS 0.18±0.06 to 0.32±0.07, and hyperkeratosis 0.12±0.04 to 0.26±0.05. In our study, hyperkeratosis, protein content, and SCS showed higher heritabilities in the front udder quarters, fat content had higher heritabilities in the rear udder quarters, and no systematic pattern in heritability was observed for lactose content or urea content. Additive genetic correlations between all udder quarters were >0.90 for protein and urea contents, whereas they were remarkably low (<0.60) for SCS. For fat and lactose contents, the genetic correlations between the 2 front or between the 2 rear quarters, respectively, were notably higher than correlations between 1 front and 1 rear quarter, suggesting that the front and the rear udders could be considered as partly genetically different organs. The variability within the udder as such was found to be of low heritability (<0.10) in general, but repeatability was moderate to high for some traits (lactose content: 0.33±0.05, protein content: 0.53±0.05). Some of these findings can be explained by differences in the physiological background of the traits.

Characteristics of organic dairy major farm types in seven European countries

This study aimed to identify organic dairy major farm types (MFTs) in seven European countries, describe these MFTs in an open research database and assess central characteristics of the MFTs. This was conducted in a three-step procedure including (1) Identification of organic MFTs in seven European countries: Austria, Switzerland, Germany, Denmark, Lithuania, Poland and Sweden, based on existing data from dairy databases and consultations with experts within the respective fields of knowledge; (2) Collection of data on farm characteristics, management procedures, production level and herd health from at least 10 farms per MFT and country and (3) Creating an open research database on MFT characteristics, description of essential characteristics of MFTs and assessment of similarities and differences between farms within and across MFTs. The results indicate variations in herd characteristics such as production level, herd size, farm size, housing system, milking system and cow health status between organic dairy farms in these seven European countries. It also indicates variations in management strategies such as feeding, animal health management and recruitment strategies across the organic dairy sector in Europe. These variations seem to be associated with differences between regions and countries in the conditions for organic dairy production, such as topography, land availability and regulations.

The genetic basis for the selection of dairy goats with enhanced resistance to gastrointestinal nematodes

Gastrointestinal nematodes (GIN) severely affect small ruminant production worldwide. Increasing problems of anthelmintic resistance have given strong impetus to the search for alternative strategies to control GIN. Selection of animals with an enhanced resistance to GIN has been shown to be successful in sheep. In goats, the corresponding information is comparatively poor. Therefore, the present study was designed to provide reliable data on heritabilities of and genetic correlations between phenotypic traits linked to GIN and milk yield in two major dairy goat breeds (Alpine and Saanen). In all, 20 herds totalling 1303 goats were enrolled in the study. All herds had (i) a history of gastrointestinal nematode infection, (ii) uniform GIN exposure on pasture and (iii) regular milk recordings. For all goats, individual recordings of faecal egg counts (FEC), FAMACHA© eye score, packed cell volume (PCV) and milk yield were performed twice a year with an anthelmintic treatment in between. The collected phenotypic data were multivariately modelled using animal as a random effect with its covariance structure inferred from the pedigree, enabling estimation of the heritabilities of the respective traits and the genetic correlation between them. The heritabilities of FEC, FAMACHA© and PCV were 0.07, 0.22 and 0.22, respectively. The genetic correlation between FEC and FAMACHA© was close to zero and −0.41 between FEC and PCV. The phenotypic correlation between FEC and milk yield was close to zero, whereas the genetic correlation was 0.49. Our data suggest low heritability of FEC in Saanen and Alpine goats and an unfavourable genetic correlation of FEC with milk yield.

Correction to: Characteristics of organic dairy major farm types in seven European countries

The original version of this article unfortunately contained an error in the author name.

Short communication: Genomic prediction using imputed whole-genome sequence variants in Brown Swiss Cattle

The accuracy of genomic prediction determines response to selection. It has been hypothesized that accuracy of genomic breeding values can be increased by a higher density of variants. We used imputed whole-genome sequence data and various single nucleotide polymorphism (SNP) selection criteria to estimate genomic breeding values in Brown Swiss cattle. The extreme scenarios were 50K SNP chip data and whole-genome sequence data with intermediate scenarios using linkage disequilibrium-pruned whole-genome sequence variants, only variants predicted to be missense, or the top 50K variants from genome-wide association studies. We estimated genomic breeding values for 3 traits (somatic cell score, nonreturn rate in heifers, and stature) and found differences in accuracy levels between traits. However, among different SNP sets, accuracy was very similar. In our analyses, sequence data led to a marginal increase in accuracy for 1 trait and was lower than 50K for the other traits. We concluded that the inclusion of imputed whole-genome sequence data does not lead to increased accuracy of genomic prediction with the methods.

Genome-wide association studies using copy number variants in Brown Swiss Dairy cattle.

Detecting Copy Number Variation (CNV) in cattle provides the opportunity to study their association with quantitative traits (Winchester et al., 2009; Zhang et al., 2009; Hou et al., 2011; Clop et al., 2012; de Almeida et al., 2016;). The aim of this study was to map CNVs in 1,410 Brown Swiss males and females using Illumina BovineHD Genotyping BeadChip data and to perform a genome-wide association analysis for production functional and health traits. After quality control, CNVs were called with the GoldenHelix SVS 8.3.1 and PennCNV software and were summarized to CNV regions (CNVRs) at a population level, using BEDTools. Additionally, common CNVRs between the two software were set as consensus. CNV-association studies were executed with the CNVRuler software using a linear regression model. Genes within significant associated CNVRs for each trait were annotated with a GO analysis using the DAVID Bioinformatics Resources 6.7. The quality control filtered out 294 samples. The GoldenHelix SVS 8.3.1 software identified 25,030 CNVs summarized to 398 CNVRs while PennCNV identified 62,341 CNVs summarized to 5,578 CNVRs. A total of 127 CNVRs were identified to be significantly associated with one or more of the evaluated traits. The result of this study is a comprehensive genomic analysis of the Brown Swiss breed, which enriches the bovine CNV map in its genome. Finally, the results of the association studies deliver new information for quantitative traits considered in selection programs of the Brown Swiss breed.