Genetic parameters for dry matter intake, energy balance, residual energy intake, and liability to diseases in German Holstein and Fleckvieh dairy cows.

Selection for feed efficiency (FE) is a hot topic in dairy cow breeding. Dry matter intake (DMI) and residual energy intake (REI) are mostly discussed as new selection traits. Selection for lower DMI or REI seems to increase FE if other traits, such as milk yield or health, are not affected negatively. However, genetic relationships with other traits have not been adequately investigated because of the difficulties in recording sufficient feed intake data for genetic evaluations. The aim of this study was to examine the genetic relationships between FE-related traits and liability to diseases throughout lactation. First, heritabilities for all traits are presented. Subsequently, genetic correlations between DMI, energy-corrected milk yield, energy balance (EB), and REI on the one hand and 3 disease categories (mastitis, claw and leg diseases, and all diseases) on the other throughout lactation in German Holstein (GH) dairy cows are illustrated. Production and health data from the projects optiKuh and eMissionCow were used. Data consisted of weekly observations recorded over a 325-wk period in 2,387 GH and over a 300-wk period in 632 Fleckvieh (FV) primiparous and multiparous dairy cows from 13 dairy research farms in Germany. Variance and covariance components were estimated univariately or bivariately with linear random regression models for production data and threshold random regression models for health data. Heritabilities for DMI, EB, and REI were on average 0.17 and 0.15, 0.14 and 0.15, as well as 0.11 and 0.14 in GH and FV, respectively. Heritabilities on the underlying scale for mastitis, claw and leg diseases, and all diseases were on average 0.17 and 0.16, 0.18 and 0.12, as well as 0.15 and 0.11 in GH and FV, respectively. In GH, almost all genetic correlations were negative, especially in early lactation. Within the first 50 d in milk, genetic correlations between DMI and REI on the one hand and disease categories on the other ranged from -0.25 to -0.14 for mastitis, from -0.31 to -0.13 for claw and leg diseases, and from -0.58 to -0.30 for all diseases. Consequently, selection for lower DMI or REI could lead to a higher liability to diseases, especially in early lactation. A possibility to mitigate these undesirable side effects could be lactation stage-specific selection for FE. For FV, further studies with more data are needed to assess genetic relationships.

Evaluation of the electrolyte status in hyperprolific sows on the farrowing process under different housing conditions.

In order to expand previous knowledge about the farrowing process of hyperprolific sows, the effect of calcium, magnesium and phosphor concentration in the blood and the importance of husbandry were examined. The study was performed in a small educational agriculture institution in Germany comprising 61 sows of a hyperprolific hybrid line (BHZP db.Viktoria). The sows were either kept in farrowing crates (n = 36) or pens (n = 25). Blood samples were taken every 30 min during the farrowing process, using a central venous catheter (Cavafix Certo®, 16G, 32 cm, B. Braun SE, Melsungen, Germany) placed in an ear vein. Samples for ionized calcium concentration (Caion) were analyzed directly using epoc® BGEM test cards (Alere GmbH, Cologne, Germany). Samples for total calcium (Catot), magnesium (Mg) and phosphor concentration (Pi) were deep-frozen (minus 80 °C, Innova® U202, Eppendorf SE, Hamburg, Germany) for photometric analysis at a later date. With an average farrowing duration of 267.6 ± 108.1 min (min. 71, max. 602 min), an average of 17.2 ± 4.2 piglets were born. Eutocic farrowing duration was 193.1 ± 75.2a minutes. Dystocic farrowing duration was 324.9 ± 94.1b minutes (a:b p < 0.0001). Farrowing duration did not differ between housing conditions (277.1 ± 117.4 min in crates, 275.0 ± 99.0 min in pens, p > 0.05). Dystocic farrowings were characterized by the occurrence of (at least) one time lapse of more than 60 min without piglet expulsion. In general, 35 of 61 sows suffered from dystocic parturition and received obstetrical intervention. 20 of 36 (55.6%) crate housed sows and 15 of 25 (60%) sows in pens experienced dystocic parturition (p > 0.05). Catot measured at the beginning of the expulsion stage had a prognostic value for the rest of the farrowing process. Above a threshold value of 2.385 mmol/l, eutocic parturition could be expected, while sows with a lower Catot value generally suffered from dystocic farrowings. Also, sows with eutocia had significantly higher Catot values during parturition than sows with dystocia (p = 0.001). The beginning of the lactation period was characterized by a rise in Caion (1.17 ± 0.04 to 1.21 ± 0.06 mmol/l; p < 0.0001). Mg was significantly higher before than during farrowing (p = 0.0003). During parturition, Mg decreased gradually from 0.86 ± 0.1 to 0.84 ± 0.1 mmol/l. Afterwards, Mg values showed an 18.45% increase. Sows without farrowing complications showed significantly higher Mg than those suffering from dystocia (p = 0.024). The same significant trend was observed for Pi (p = 0.002). The deficiencies in Catot/ion, Mg and Pi led to insufficient contractions and thus to farrowing problems. Parturition in the pen showed a general positive effect on the well-being of the sows and a stabilizing influence on the metabolic conditions compared to parturition in the crate. Sows in pens had higher Catot (p = 0.055) and Mg (p = 0.0004). In conclusion, the results provide clear evidence that a large proportion of hyperprolific sows suffer from previously unknown deficiencies electrolyte homeostasis around and during parturition, which is reflected by the large number of dystocic farrowings and the deficiencies in electrolyte concentrations during dystocia.

Residual energy intake, energy balance, and liability to diseases: Genetic parameters and relationships in German Holstein dairy cows.

Residual energy intake (REI) is an often-suggested trait for direct selection of dairy cows for feed efficiency. Cows with lower REI seem to be more efficient but are also in a more severe negative energy balance (EB), especially in early lactation. A negative EB leads to a higher liability to diseases. Due to this fact, this study aims to investigate the genetic relationship between REI and liability to diseases. Health and production data were recorded from 1,370 German Holstein dairy cows from 8 research farms over a period of 2 yr. We calculated 2 phenotypes for REI that considered the following energy sinks: milk energy content, metabolic body weight, body weight change, body condition score, and body condition score change. Genetic parameters were estimated with threshold or linear random regression models from days in milk (DIM) 1 to 305. Heritabilities for REI, EB, and all diseases ranged from 0.12 to 0.39, 0.15 to 0.31, and 0.09 to 0.20, respectively. Genetic correlations between selected DIM for REI and EB were higher for adjacent DIM than for more distant DIM. Pearson correlation coefficients between estimated breeding values (EBV) for REI and EB varied between 0.47 and 0.81; they were highest in mid lactation. Correlations between EBV for all diseases and REI as well as EB were negative, with lowest values in early lactation. Within the first 50 DIM, proportions of diseased days for cows with lowest EBV for REI were almost twice as high as for cows with highest EBV for REI. In conclusion, selecting dairy cows for lower REI should be treated with caution because of an unfavorable relationship with liability to diseases, especially in early lactation.

Derivation of economic values for German dairy breeds by means of a bio-economic model-with special emphasis on functional traits.

To assess the economic importance of breeding traits, economic values (EV) were derived for 3 German dairy cattle breeds: German Holstein (HOL), Angler (ANG), and Red and White Dual-Purpose (RDN). For that purpose, the stochastic bio-economic model SimHerd (SimHerd A/S, Viborg, Denmark) was used, which simulates the expected monetary gain in dairy herds. The EV was calculated as the alteration in average net return of the herd responding to a marginal change in the trait of interest. When deriving EV using SimHerd, economic consequences resulting from changes in the age structure of a dairy herd (i.e., structural herd effects) are considered. However, this requires the simulation of relationships between traits in the bio-economic model. To avoid double counting, the EV of a trait was corrected for effects from alterations in correlated traits using multiple regression analysis. The EV were derived for 23 traits in terms of production, conformation and workability, dairy health, calf survival, and reproduction performance. Furthermore, the relative economic importance of the breeding traits was calculated. Relative emphasis on production was between 39.9 and 44.4% in the breeds studied. Total costs per case of ketosis and metritis ranged from €167 to €196 and €173 to €182, respectively. Highest marginal EV of direct health traits were found for mastitis (€257 to €271 per case) and lameness (€270 to €310 per case). Consequently, relative emphasis on direct health traits was between 15.7 and 17.9%. The EV of reproduction performance showed largest differences among the cattle breeds. Overall relative emphasis on reproduction was 10.5% in HOL, 10.8% in ANG, and 6.5% in RDN. The relative economic importance of cow mortality ranged from 15.5 to 16.0% across the breeds. Collectively, the study showed the high economic importance of functional traits in the cattle breeds studied.

Liability to diseases and their relation to dry matter intake and energy balance in German Holstein and Fleckvieh dairy cows.

Dairy cow efficiency is increasingly important for future breeding decisions. The efficiency is determined mostly by dry matter intake (DMI). Reducing DMI seems to increase efficiency if milk yield remains the same, but resulting negative energy balance (EB) may cause health problems, especially in early lactation. Objectives of this study were to examine relationships between DMI and liability to diseases. Therefore, cow effects for DMI and EB were correlated with cow effects for 4 disease categories throughout lactation. Disease categories were mastitis, claw and leg diseases, metabolic diseases, and all diseases. In addition, this study presents relative percentages of diseased cows per days in milk (DIM), repeatability, and cow effect correlations for disease categories across DIM. A total of 1,370 German Holstein (GH) and 287 Fleckvieh (FV) primiparous and multiparous dairy cows from 12 dairy research farms in Germany were observed over a period of 2 yr. Farm staff and veterinarians recorded health data. We modeled health and production data with threshold random regression models and linear random regression models. From DIM 2 to 305 average daily DMI was 22.1 kg/d in GH and 20.2 kg/d in FV. Average weekly EB was 2.8 MJ of NEL/d in GH and 0.6 MJ of NEL/d in FV. Most diseases occurred in the first 20 DIM. Multiparous cows were more susceptible to diseases than primiparous cows. Relative percentages of diseased cows were highest for claw and leg diseases, followed by metabolic diseases and mastitis. Repeatability of disease categories and production traits was moderate to high. Cow effect correlations for disease categories were higher for adjacent lactation stages than for more distant lactation stages. Pearson correlation coefficients between cow effects for DMI, as well as EB, and disease categories were estimated from DIM 2 to 305. Almost all correlations were negative in GH, especially in early lactation. In FV, the course of correlations was similar to GH, but correlations were mostly more negative in early lactation. For the first 20 DIM, correlations ranged from -0.31 to 0.00 in GH and from -0.42 to -0.01 in FV. The results illustrate that future breeding for dairy cow efficiency should focus on DMI and EB in early lactation to avoid health problems.

Estimation of genetic parameters and breeding values for feed intake and energy balance using pedigree relationships or single-step genomic evaluation in Holstein Friesian cows.

At the beginning of lactation, high-performing dairy cows often experience a severe energy deficit, which in turn is associated with metabolic stress. Increasing feed intake (FI) or reducing the energy deficit during this period could improve the metabolic stability and thus the health of the animals. Genomic selection for the first time enables the inclusion of this hard-to-measure trait in breeding programs. The objective of the current study was the estimation of genetic parameters and genomic breeding values for FI and energy balance (EB). For this purpose, 1,374 Holstein Friesian (HF) dairy cows from 8 German research farms were phenotyped with standardized FI data protocols. After data editing, phenotypic data of HF comprised a total of 40,012 average weekly FI records with a mean of 21.8 ± 4.3 kg/d. For EB 33,376 average weekly records were available with a mean of 3.20 ± 29.4 MJ of NEL/d. With the Illumina Bovine SNP50 BeadChip (Illumina Inc., San Diego, CA) 1,128 of phenotyped cows were genotyped. Thirty-five female candidates of the HF population were genotyped but not phenotyped. Pedigree information contained sires and dams 4 generations back. The random regression animal model included the fixed effects of herd test week (alternatively, herd group test week), parity, and stage of lactation, modeled by the function according to Ali and Schaeffer (1987). For both the random permanent environmental effect across lactations and the random additive genetic effect, third-order Legendre polynomials were chosen. Additionally, a random permanent environmental cow effect within lactation was included. Analyses for heritabilities, genetic correlations between different lactation stages, and breeding values were estimated using, respectively, pedigree relationships and single-step genomic evaluation, carried out with the DMU software package (Madsen et al., 2013). This allowed for comparison of conventional reliabilities with genomic-assisted reliabilities based on real data, to evaluate the gain of genotyping. Heritability estimates ranged between 0.12 and 0.50 for FI, and 0.15 and 0.48 for EB, and increased toward the end of lactation. Genetic correlations were weak between early and late lactation, with a value of 0.05 for FI and negative with a value of -0.05 for EB. Reliabilities for genomic values of cows for FI and EB ranged between 0.33 and 0.61, and 0.27 and 0.47, respectively. For the genotyped cows without phenotypes, the inclusion of genomic relationship leads to an increase of the average reliability of the breeding value for FI by nearly 9% and for EB by 4%. The results show the possibility of combining pedigree, genotypes, and phenotypes for increasing FI or EB to reduce health and reproductive problems, especially at the beginning of lactation. Nevertheless, the reference population needs to be extended to reach higher breeding value reliabilities.

Exploration of conservation and development strategies with a limited stakeholder approach for local cattle breeds.

Many local breeds have become endangered due to their substitution by high-yielding breeds. To conserve local breeds, effective development strategies need to be investigated. The aim of this study was to explore conservation and development strategies based on quantified strengths, weaknesses, opportunities and threats (SWOT) for two local cattle breeds from Northern Germany, namely the German Angler (GA) and Red Dual-Purpose cattle (RDP). The data comprised 158 questionnaires regarding both breeds' SWOT, which were answered by 78 farmers of GA and 80 farmers of RDP. First, data were analysed using the SWOT-Analytic Hierarchy Process (AHP) method, which combines the qualitative strategic decision tool of SWOT analysis and the quantitative tool of AHP. Second, prioritised SWOT factors were discussed with stakeholders in order to form final conservation and development strategies at breed level. For GA prioritised strengths were daily gain, meat quality, milk production and the usage of new biotechnologies, weaknesses were genetic gain in milk production and inbreeding, opportunities were organic farming and breed-specific characteristics and threats were milk prices and dependency regarding the dairy business. Consequently, three conservation and development strategies were formed: (1) changing relative weights and the relevant breeding goal to drift from milk to meat, (2) increasing genetic gain and control the rate of inbreeding by the implementation of specific selection programs and (3) selection of unique and breed characteristic components on product level, that is, milk-fat and fine muscle fibers. For RDP defined strengths were robustness, high adaptability for different housing systems and a balanced dual-purpose of milk and meat, weaknesses were inbreeding, breed extinction, genomic selection with young bulls and milk yield, opportunities were organic farming and dual-purpose aspects and threats were milk and decreasing beef cattle prices. Thus, three conservation and development strategies were identified: (1) adjust relative weights and the relevant breeding goal to balance milk and meat yield, (2) increasing genetic gain and avoid extinction by implementing targeted selection programs and (3) selection of unique and breed characteristic traits on breed level, that is, environmental robustness. Quantified SWOT establish a basis for the exploration of conservation and development strategies at breed level. Explored strategies are promising even if the stakeholder approach was limited for small populations regarding a small number of stakeholder groups. The used approach reflects farmers' individual convenience better than existing quantitative strategy decision tools on their own.

Lactation curves and model evaluation for feed intake and energy balance in dairy cows.

A good health status of high-performing dairy cows is essential for successful production. Feed intake affects the metabolic stability of dairy cows and can be used as a measurement for energy balance. By implementing feed intake and energy balance into the breeding goal, these traits provide great potential for an improvement in the health of dairy cows by breeders. In this study, fixed and random regression models were tested to establish appropriate models for a further analysis of this approach. A total of 1,374 Holstein-Friesian cows and 327 Simmental cows (SI) from 12 German research farms participating in a collaboration called optiKuh were phenotyped. Feed intake data recording was standardized across farms, and energy balance was calculated using phenotypic information on milk yield, milk ingredients, live weight, gestation stage, and feed intake. The phenotypic data set consisted of a total of 40,012 Holstein-Friesian and 16,996 SI with average weekly dry matter intakes of 21.8 ± 4.3 and 20.2 ± 3.6 kg/d, respectively. Observations of days in milk 1 to 350 were used to evaluate the best-fitting models and to estimate the repeatability and correlations between cow effects at different stages for feed intake and energy balance. Four parametric functions (Ali and Schaeffer and Legendre polynomials of second, third, and fourth degree) were compared to model the lactation curves. Based on the corrected Akaike information criterion and the Bayesian information criterion, the goodness of fit was evaluated to choose the best-fitting model for the finest description of lactation curves for the traits energy balance and feed intake. Legendre polynomial fourth degree was the best-fitting model for random regression models. In contrast, Ali and Schaeffer was the best choice for fixed regression models. Feed intake and energy balance acted as expected: the feed intake increased slowly at the beginning of lactation and the negative energy balance switched to a positive range around 40 to 80 d of lactation. The repeatabilities of both traits were quite similar and the repeatabilities for SI were the highest for both traits. Additionally, correlations between cow effects were closest between early days in milk. These results emphasize the possibility that the unique optiKuh data set can be used for further genetic analyses to enable genomic selection for feed intake or energy balance.

Analysis of the genetic architecture of energy balance and its major determinants dry matter intake and energy-corrected milk yield in primiparous Holstein cows.

The focus of modern dairy cow breeding programs has shifted from being mainly yield based toward balanced goals that increasingly consider functional traits such as fertility, metabolic stability, and longevity. To improve these traits, a less pronounced energy deficit postpartum is considered a key challenge. On the other hand, feed efficiency and methane emissions are gaining importance, possibly leading to conflicts in the design of breeding goals. Dry matter intake (DMI) is one of the major determinants of energy balance (EB), and recently some efforts were undertaken to include DMI in genomic breeding programs. However, there is not yet a consensus on how this should be achieved as there are different goals in the course of lactation (i.e., reducing energy deficit postpartum vs. subsequently improving feed efficiency). Thus, the aim of this study was to gain more insight into the genetic architecture of energy metabolism across lactation by genetically dissecting EB and its major determinants DMI and energy-corrected milk (ECM) yield at different lactation stages applying random regression methodology and univariate and multivariate genomic analyses to data from 1,174 primiparous Holstein cows. Daily heritability estimates ranged from 0.29 to 0.49, 0.26 to 0.37, and 0.58 to 0.68 for EB, DMI, and ECM, respectively, across the first 180 d in milk (DIM). Genetic correlations between ECM and DMI were positive, ranging from 0.09 (DIM 11) to 0.36 (DIM 180). However, ECM and EB were negatively correlated (rg = -0.26 to -0.59). The strongest relationship was found at the onset of lactation, indicating that selection for increased milk yield at this stage will result in a more severe energy deficit postpartum. The results also indicate that EB is more affected by DMI (rg = 0.71 to 0.81) than by its other major determinant, ECM. Thus, breeding for a higher DMI in early lactation seems to be a promising strategy to improve the energy status of dairy cows. We found evidence that genetic regulation of energy homeostasis is complex, with trait- and lactation stage-specific quantitative trait loci suggesting that the trajectories of the analyzed traits can be optimized as mentioned above. Especially from the multivariate genomic analyses, we were able to draw some conclusions on the mechanisms involved and identified the genes encoding fumarate hydratase and adiponectin as highly promising candidates for EB, which will be further analyzed.

Comprehensive characterization of horse genome variation by whole-genome sequencing of 88 horses.

Whole-genome sequencing studies are vital to gain a thorough understanding of genomic variation. Here, we summarize the results of a whole-genome sequencing study comprising 88 horses and ponies from diverse breeds at 19.1× average coverage. The paired-end reads were mapped to the current EquCab3.0 horse reference genome assembly, and we identified approximately 23.5 million single nucleotide variants and 2.3 million short indel variants. Our dataset included at least 7 million variants that were not previously reported. On average, each individual horse genome carried ∼5.7 million single nucleotides and 0.8 million small indel variants with respect to the reference genome assembly. The variants were functionally annotated. We provide two examples for potentially deleterious recessive alleles that were identified in a heterozygous state in individual genome sequences. Appropriate management of such deleterious recessive alleles in horse breeding programs should help to improve fertility and reduce the prevalence of heritable diseases. This comprehensive dataset has been made publicly available, will represent a valuable resource for future horse genetic studies and supports the goal of accelerating the rates of genetic gain in domestic horse.

Linkage disequilibrium pattern and genome-wide association mapping for meat traits in multiple porcine F2 crosses.

In the present study, data from four F2 crosses were analysed and used to study the linkage disequilibrium (LD) structure within and across the crosses. Genome-wide association analyses (GWASes) for conductivity and dressing out meat traits were conducted using single-marker and Bayesian multi-marker models using the pooled data from all F2 crosses. Porcine F2 crosses generated from the distantly related founder breeds Wild Boar, Piétrain and Meishan, as well as from a porcine F2 cross from the closely related founder breed Piétrain and an F1 Large White × Landrace cross were pooled. A total of 2572 F2 animals were genotyped using a 62K SNP chip. The positions of the SNPs were based on genome assembly Sscrofa11.1. After post-alignment and genotype filtering, approximately 50K SNPs were usable for LD studies and GWASes. The main findings of the present study are that the breakdown of LD was faster in crosses from closely related founder breeds compared to crosses from distantly related founders. The fastest breakdown of LD was observed by pooling the data. Based on the single-marker results and LD structure, clusters and windows were built for 1-Mb intervals. For conductivity and dressing out, 183 and 191 nominal significant associations respectively and six and five clusters respectively were found. Dominance was important for conductivity, and considering dominance in GWASes improved the mapping signals. Most clear signals were found for conductivity on SSC6, 8 and 15 and for dressing out on SSC2 and 7. Considering dominance might contribute to the accuracy of genomic selection and serve as a guide for choosing mating pairs with good combining abilities. However, further research is needed to investigate if dominance is also important in crossbreed pig breeding schemes.

Genome-wide mapping of 10 calving and fertility traits in Holstein dairy cattle with special regard to chromosome 18.

Over the last decades, a dramatic decrease in reproductive performance has been observed in Holstein cattle and fertility problems have become the most common reason for a cow to leave the herd. The premature removal of animals with high breeding values results in both economic and breeding losses. For efficient future Holstein breeding, the identification of loci associated with low fertility is of major interest and thus constitutes the aim of this study. To reach this aim, a genome-wide combined linkage disequilibrium and linkage analysis (cLDLA) was conducted using data on the following 10 calving and fertility traits in the form of estimated breeding values: days from first service to conception of heifers and cows, nonreturn rate on d 56 of heifers and cows, days from calving to first insemination, days open, paternal and maternal calving ease, paternal and maternal stillbirth. The animal data set contained 2,527 daughter-proven Holstein bulls from Germany that were genotyped with Illumina's BovineSNP50 BeadChip (Illumina Inc., San Diego, CA). For the cLDLA, 41,635 sliding windows of 40 adjacent single nucleotide polymorphisms (SNP) were used. At each window midpoint, a variance component analysis was executed using ASReml. The underlying mixed linear model included random quantitative trait locus (QTL) and polygenic effects. We identified 50 genome-wide significant QTL. The most significant peak was detected for direct calving ease at 59,179,424 bp on chromosome 18 (BTA18). Next, a mixed-linear model association (MLMA) analysis was conducted. A comparison of the cLDLA and MLMA results with special regard to BTA18 showed that the genome-wide most significant SNP from the MLMA was associated with the same trait and located on the same chromosome at 57,589,121 bp (i.e., about 1.5 Mb apart from the cLDLA peak). The results of 5 different cLDLA and 2 MLMA models, which included the fixed effects of either SNP or haplotypes, suggested that the cLDLA method outperformed the MLMA in accuracy and precision. The haplotype-based cLDLA method allowed for a more precise mapping and the definition of ancestral and derived QTL alleles, both of which are essential for the detection of underlying quantitative trait nucleotides.

Genomic selection in the German Landrace population of the Bavarian herdbook.

The aim of our study was to compare different validation methods with respect to their impact on validation results and to evaluate the feasibility of genomic selection in the German Landrace population of the Bavarian herdbook. For this purpose, a sample of 337 boars and 1,676 sows was genotyped with the Illumina PorcineSNP60 BeadChip. Conventional BLUP breeding values for fertility, growth, carcass, and quality traits were deregressed and used as phenotypes in genomic BLUP. The resulting genomic breeding values were also blended with information from the full conventional breeding value estimation to include information from nongenotyped parents. Subsequent validation used forward prediction, realized reliabilities, and theoretical reliabilities. The results indicate that the validation methods showed a relatively large effect on in the displayed reliability levels in our study: forward prediction reliabilities were found to be much lower than the conventional parent-average reliabilities whereas corresponding realized and theoretical reliabilities were found substantially greater. Theoretical reliabilities appear to be the most consistent validation approach tested in our study, because they avoid the use of proxy variables. Generally, our results suggest a substantial potential for a genomic selection implementation for the Bavarian herdbook by using both sows and boars. Theoretical genomic reliabilities of direct genomic values of selection candidates were, on average, 31 to 36% greater than the conventional parent average reliabilities. However, the inclusion of residual information from conventional breeding values had only a marginal effect on reliabilities.

Technical note: Analytical refinements of the methane indicator archaeol in bovine feces, rumen fluid, and feedstuffs.

Archaeol (1,2-di-O-phytanyl-sn-glycerol) is a cell membrane lipid component of methanogens that has the potential to be used as a biomarker for methane production in ruminants. However, its analysis via gas chromatography-mass spectrometry (GC-MS) is challenging because of its molecular size and structure. In this study, 2 different sample preparation methods were tested, Soxhlet and sonication-aided extraction, and the methods were compared for extraction efficiency using the internal standard (IS; 1,2-di-o-hexadecyl-rac-glycerol). The extraction efficiency of the Soxhlet method for fecal archaeol was twice that of sonication. With the use of a high-temperature GC column, the retention times of IS and archaeol were 17.6 and 19.4 min, respectively, with a total run time of only 25 min. The molecule ions m/z 611.4 (IS) and m/z 725.8 (archaeol), or alternatively the fragment ion of the glycerol moiety m/z 130.0, were used for identification and quantification via GC-MS in positive chemical ionization mode. The intra-assay coefficients of variation for fecal archaeol measurements were 1.3% (m/z 725.8) and 2.1% (m/z 130.0) (n=3), respectively. Fecal archaeol quantifications did not differ between the use of the molecule or glycerol moiety ions (paired t-test, n=156). Archaeol concentrations tended to be 3.3% greater in samples stored at -20°C before drying compared with samples that were immediately dried after collection (paired t-test, n=5). The detection limit of archaeol was 0.5 µg/g of fecal dry matter (DM); no archaeol could be detected in feed samples. In different fractions of rumen fluid, archaeol levels ranged from 1.9 to 24.0 µg/g of DM. In 10 cows fed the same grass and corn silage/hay-based ration, diurnal variations of fecal archaeol levels (5 time points over 2 d) were cow dependent and ranged from 26.2 to 77.2 µg/g of DM (mean 48.4 µg/g of DM). Thus, within-animal variation in cows on the same diet was between 4 and 27%. We suggest that this finding is related to the amount and time of the latest feed intake event before the fecal sampling. Feeding pattern can determine the passage rate of digesta through the alimentary tract and thus the duration of contact time of archaea with their substrate.

Identification of a haplotype associated with cholesterol deficiency and increased juvenile mortality in Holstein cattle.

Over the last decades, several genetic disorders have been discovered in cattle. However, the genetic background of disorders in calves is less reported. Recently, German cattle farmers reported on calves from specific matings with chronic diarrhea and retarded growth of unknown etiology. Affected calves did not respond to any medical treatment and died within the first months of life. These calves were underdeveloped in weight and showed progressive and severe emaciation despite of normal feed intake. Hallmark findings of the blood biochemical analysis were pronounced hypocholesterolemia and deficiency of fat-soluble vitamins. Results of the clinical and blood biochemical examination had striking similarities with findings reported in human hypobetalipoproteinemia. Postmortem examination revealed near-complete atrophy of the body fat reserves including the spinal canal and bone marrow. To identify the causal region, we performed a genome-wide association study with 9 affected and 21,077 control animals genotyped with the Illumina BovineSNP50 BeadChip (Illumina Inc., San Diego, CA), revealing a strong association signal on BTA 11. Subsequent autozygosity mapping identified a disease-associated haplotype encompassing 1.01 Mb. The segment of extended homozygosity contains 6 transcripts, among them the gene APOB, which is causal for cholesterol disorders in humans. However, results from multi-sample variant calling of 1 affected and 47 unaffected animals did not detect any putative causal mutation. The disease-associated haplotype has an important adverse effect on calf mortality in the homozygous state when comparing survival rates of risk matings vs. non-risk matings. Blood cholesterol values of animals are significantly associated with the carrier status indicating a codominant inheritance. The frequency of the haplotype in the current Holstein population was estimated to be 4.2%. This study describes the identification and phenotypic manifestation of a new Holstein haplotype characterized by pronounced hypocholesterolemia, chronic emaciation, growth retardation, and increased mortality in young cattle, denominated as cholesterol deficiency haplotype. Our genomic investigations and phenotypic examinations provide additional evidence for a mutation within the APOB gene causing cholesterol deficiency in Holstein cattle.

Genetic variability of the equine casein genes.

The casein genes are known to be highly variable in typical dairy species, such as cattle and goat, but the knowledge about equine casein genes is limited. Nevertheless, mare milk production and consumption is gaining importance because of its high nutritive value, use in naturopathy, and hypoallergenic properties with respect to cow milk protein allergies. In the current study, the open reading frames of the 4 casein genes CSN1S1 (αS1-casein), CSN2 (ß-casein), CSN1S2 (αS2-casein), and CSN3 (κ-casein) were resequenced in 253 horses of 14 breeds. The analysis revealed 21 nonsynonymous nucleotide exchanges, as well as 11 synonymous nucleotide exchanges, leading to a total of 31 putative protein isoforms predicted at the DNA level, 26 of which considered novel. Although the majority of the alleles need to be confirmed at the transcript and protein level, a preliminary nomenclature was established for the equine casein alleles.

Developing a multi-Kinect-system for monitoring in dairy cows: object recognition and surface analysis using wavelets.

Camera-based systems in dairy cattle were intensively studied over the last years. Different from this study, single camera systems with a limited range of applications were presented, mostly using 2D cameras. This study presents current steps in the development of a camera system comprising multiple 3D cameras (six Microsoft Kinect cameras) for monitoring purposes in dairy cows. An early prototype was constructed, and alpha versions of software for recording, synchronizing, sorting and segmenting images and transforming the 3D data in a joint coordinate system have already been implemented. This study introduced the application of two-dimensional wavelet transforms as method for object recognition and surface analyses. The method was explained in detail, and four differently shaped wavelets were tested with respect to their reconstruction error concerning Kinect recorded depth maps from different camera positions. The images' high frequency parts reconstructed from wavelet decompositions using the haar and the biorthogonal 1.5 wavelet were statistically analyzed with regard to the effects of image fore- or background and of cows' or persons' surface. Furthermore, binary classifiers based on the local high frequencies have been implemented to decide whether a pixel belongs to the image foreground and if it was located on a cow or a person. Classifiers distinguishing between image regions showed high (⩾0.8) values of Area Under reciever operation characteristic Curve (AUC). The classifications due to species showed maximal AUC values of 0.69.

Considering genetic characteristics in German Holstein breeding programs.

Recently, several research groups have demonstrated that several haplotypes may cause embryonic loss in the homozygous state. Up to now, carriers of genetic disorders were often excluded from mating, resulting in a decrease of genetic gain and a reduced number of sires available for the breeding program. Ongoing research is very likely to identify additional genetic defects causing embryonic loss and calf mortality by genotyping a large proportion of the female cattle population and sequencing key ancestors. Hence, a clear demand is present to develop a method combining selection against recessive defects (e.g., Holstein haplotypes HH1-HH5) with selection for economically beneficial traits (e.g., polled) for mating decisions. Our proposed method is a genetic index that accounts for the allele frequencies in the population and the economic value of the genetic characteristic without excluding carriers from breeding schemes. Fertility phenotypes from routine genetic evaluations were used to determine the economic value per embryo lost. Previous research has shown that embryo loss caused by HH1 and HH2 occurs later than the loss for HH3, HH4, and HH5. Therefore, an economic value of € 97 was used against HH1 and HH2 and € 70 against HH3, HH4, and HH5. For polled, € 7 per polled calf was considered. Minor allele frequencies of the defects ranged between 0.8 and 3.3%. The polled allele has a frequency of 4.1% in the German Holstein population. A genomic breeding program was simulated to study the effect of changing the selection criteria from assortative mating based on breeding values to selecting the females using the genetic index. Selection for a genetic index on the female path is a useful method to control the allele frequencies by reducing undesirable alleles and simultaneously increasing economical beneficial characteristics maintaining most of the genetic gain in production and functional traits. Additionally, we applied the genetic index to real data and found a decrease of the genetic trend for the birth years 1990 to 2006. Since 2010 the genetic index has increased due to a strong increase in the polled frequency. However, further investigation is needed to better understand the biology to determine the correct time of embryo loss and the economic value of fertility disorders.

Methyl-coenzyme M reductase A as an indicator to estimate methane production from dairy cows.

The evaluation of greenhouse gas mitigation strategies requires the quantitative assessment of individual methane production. Because methane measurement in respiration chambers is highly accurate, but also comprises various disadvantages such as limited capacity and high costs, the establishment of an indicator for estimating methane production of individual ruminants would provide an alternative to direct methane measurement. Methyl-coenzyme M reductase is involved in methanogenesis and the subunit α of methyl-coenzyme M reductase is encoded by the mcrA gene of rumen archaea. We therefore examined the relationship between methane emissions of Holstein dairy cows measured in respiration chambers with 2 different diets (high- and medium-concentrate diet) and the mcrA DNA and mcrA cDNA abundance determined from corresponding rumen fluid samples. Whole-body methane production per kilogram of dry matter intake and mcrA DNA normalized to the abundance of the rrs gene coding for 16S rRNA correlated significantly when using qmcrA primers. Use of qmcrA primers also revealed linear correlation between mcrA DNA copy number and methane yield. Regression analyses based on normalized mcrA cDNA abundances revealed no significant linear correlation with methane production per kilogram of dry matter intake. Furthermore, the correlations between normalized mcrA DNA abundance and the rumen fluid concentration of acetic and isobutyric acid were positive, whereas the correlations with propionic and lactic acid were negative. These data suggest that the mcrA DNA approach based on qmcrA primers could potentially be a molecular proxy for methane yield after further refinement.