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.

Because of the relatively high levels of genetic relationships among potential bull sires and bull dams, innovative selection tools should consider both genetic gain and genetic relationships in a long-term perspective. Optimum genetic contribution theory using official estimated breeding values for a moderately heritable trait (production index, Index-PROD), and a lowly heritable functional trait (index for somatic cell score, Index-SCS) was applied to find optimal allocations of bull dams and bull sires. In contrast to previous practical applications using optimizations based on Lagrange multipliers, we focused on semi-definite programming (SDP). The SDP methodology was combined with either pedigree (a(ij)) or genomic relationships (f(ij)) among selection candidates. Selection candidates were 484 genotyped bulls, and 499 preselected genotyped bull dams completing a central test on station. In different scenarios separately for PROD and SCS, constraints on the average pedigree relationships among future progeny were varied from a(ij)=0.08 to a(ij)=0.20 in increments of 0.01. Corresponding constraints for single nucleotide polymorphism-based kinship coefficients were derived from regression analysis. Applying the coefficient of 0.52 with an intercept of 0.14 estimated for the regression pedigree relationship on genomic relationship, the corresponding range to alter genomic relationships varied from f(ij) = 0.18 to f(ij) = 0.24. Despite differences for some bulls in genomic and pedigree relationships, the same trends were observed for constraints on pedigree and corresponding genomic relationships regarding results in genetic gain and achieved coefficients of relationships. Generally, allowing higher values for relationships resulted in an increase of genetic gain for Index-PROD and Index-SCS and in a reduction in the number of selected sires. Interestingly, more sires were selected for all scenarios when restricting genomic relationships compared with restricting pedigree relationships. For example, at constraint of f(ij)=0.185 and selection on Index-PROD, the number of selected sires was 35. In contrast, only 21 sires were selected at the comparable constraint on additive genetic relationship of a(ij)=0.09. A further reduction in relationships is possible when using SDP output (i.e., suggested genetic contributions of selected parents) and applying a simulated annealing algorithm to define specific mating plans. However, the advantage of this strategy is limited to a short-term perspective and probably not successful in the period of genomic selection allowing a substantial reduction of generation intervals.

Several arguments exist for breeding organizations to focus on cooperative herds for progeny testing, but an efficient methodology addressing herd selection strategies is lacking. In this study, a new approach based on yield deviations (YD) to identify the most informative cooperator herds in terms of genetic differentiation was evaluated. Data comprised YD from 717,377 first-lactation cows from 2 regions in East and West Germany calving between January 2003 and January 2008. Daughters were ranked and classified within sire according to their YD for protein yield, fat yield, milk yield, and somatic cell score. Cows in created YD classes were merged with respective herd-calving year (HCY) characteristics. Cows of extreme YD classes (i.e., such classes including the most extreme daughter contributions), belonged to herds characterized by a high HCY production level, a low value for HCY somatic cell count, and a low HCY age at first calving (AFC). Cows with low extremes for YD in protein yield were associated with the lowest HCY production level, a high value for HCY somatic cell count, and a late HCY AFC. Ranks of HCY and ranks of herds considering HCY over the whole analyzed period were calculated by averaging YD percentages within HCY, and within herds, respectively. The YD percentages (in absolute values so that negative and positive daughter contributions were treated equally) were derived from the rank of the YD of a daughter within sire in relation to all daughters of a sire. A further partitioning of ranks of herds into quartiles revealed the following results: herds in the first quartile had the highest average protein yield, the highest intra-herd standard deviation for the national production index, and the lowest AFC. Correlations between herd rankings for different production traits ranged between 0.64 and 0.86, and were 0.65 for West Germany and 0.62 for East Germany between HCY 2006 and the average herd rank of all calving years. Correlations between daughter yield deviations for the highest and the lowest herd quartile of 0.87 for protein yield disproved concerns regarding genotype by environment interaction between test and production environment. The suggested methodology to identify informative cooperator herds is easy to implement, holds for regions with small herd sizes, and thus, may help in implementing sustainable and competitive dairy cattle breeding programs.

The aim of the present analysis was to determine the impact of a variety of traits and effects (i.e. production, type, health, management effects, pedigree information) on prices of Holstein cows sold at auction, and to estimate genetic (co)variance components between type traits and auction price. Results were used to derive economic weights for type traits. Data of 1565 cows in first parity were collected at six monthly auction sales from August 2005 through January 2006. Seventeen linear type traits and body condition (scale 1 to 9), and four type composites (dairy character, body, feet and legs, and udder; scale 65 to 88) were scored by two classifiers in the auction hall before cows were sold. Analysis of variance revealed a highly significant impact (P b 0.001) of auction date, test day milk yield, stage of lactation, origin of sire, and miscellaneous defects on auction price. The most expensive cows were sold in August, they were from foreign proven sires, they had a high level of test day milk yield, and they were free from defects related to udder, feet and legs, or milkability. The feet and leg, udder, and body composite also had a significant effect on the price (P b 0.001), with higher scores being associated with higher prices. The opposite association was found for dairy character (P b 0.01). Utilizing results from regression analysis, economic weights per genetic standard deviation were highest for linear scored rear udder height (1.23 €), front teat placement (0.97 €), and strength (0.80 €), but were negative for dairy character (−0.69 €). Genetic parameters for linear type traits scored at the auction date were consistent with literature reports. Heritability for auction price was 0.27, and auction price was genetically positively related to the feet and leg (0.55), udder (0.55), and body composite (0.21). A relative breeding value for auction price was estimated for 27 influential sires, and correlated with official indices for production, conformation, somatic cell count, functional herd life, fertility, and the total net merit index. Correlations were 0. 15, 0.21, 0.11, 0.03, 0.05, and 0.19, respectively. Auction price in combination with type scores and information related to farm management provide valuable information for genetic analysis in dairy cattle, and results can be used to increase dairy cow profitability.

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