Estimation of genetic parameters for feed efficiency traits using random regression models in dairy cattle.

Feed efficiency has become an increasingly important research topic in recent years. As feed costs rise and the environmental impacts of agriculture become more apparent, improving the efficiency with which dairy cows convert feed to milk is increasingly important. However, feed intake is expensive to measure accurately on large populations, making the inclusion of this trait in breeding programs difficult. Understanding how the genetic parameters of feed efficiency and traits related to feed efficiency vary throughout the lactation period is valuable to gain understanding into the genetic nature of feed efficiency. This study used 121,226 dry matter intake (DMI) records, 120,500 energy-corrected milk (ECM) records, and 98,975 metabolic body weight (MBW) records, collected on 7,440 first-lactation Holstein cows from 6 countries (Canada, Denmark, Germany, Spain, Switzerland, and the United States), from January 2003 to February 2022. Genetic parameters were estimated using a multiple-trait random regression model with a fourth-order Legendre polynomial for all traits. Weekly phenotypes for DMI were re-parameterized using linear regressions of DMI on ECM and MBW, creating a measure of feed efficiency that was genetically corrected for ECM and MBW, referred to as genomic residual feed intake (gRFI). Heritability (SE) estimates varied from 0.15 (0.03) to 0.29 (0.02) for DMI, 0.24 (0.01) to 0.29 (0.03) for ECM, 0.55 (0.03) to 0.83 (0.05) for MBW, and 0.12 (0.03) to 0.22 (0.06) for gRFI. In general, heritability estimates were lower in the first stage of lactation compared with the later stages of lactation. Additive genetic correlations between weeks of lactation varied, with stronger correlations between weeks of lactation that were close together. The results of this study contribute to a better understanding of the change in genetic parameters across the first lactation, providing insight into potential selection strategies to include feed efficiency in breeding programs.

Comparison of a single-step with a multistep single nucleotide polymorphism best linear unbiased predictor model for genomic evaluation of conformation traits in German Holsteins.

Genomic evaluation based on a single-step model uses all available data of phenotype, genotype, and pedigree; therefore, it should provide unbiased genomic breeding values with a higher correlation of prediction than the current multistep genomic model. Since 2019, a mixed reference population of cows and bulls has been applied to the routine multistep genomic evaluation in German Holsteins. For a fair comparison between the single-step and multistep genomic models, the same phenotype, genotype, and pedigree data were used. Because of its simple structure of the standard multitrait animal model used for German Holstein conventional evaluation, conformation traits were chosen as the first trait group to test a single-step SNP BLUP model for the large, genotyped population of German Holsteins. Genotype, phenotype, and pedigree data were taken from the official August 2020 conventional and genomic evaluation. Because of the same trait definition in national and multiple across-country evaluation for the conformation traits, deregressed multiple across-country evaluation estimated breeding value (EBV) of foreign bulls were treated as a new source of data for the same trait in the genomic evaluations. Due to a short history of female genotyping in Germany, the last 3 yr of youngest cows and bulls were deleted, instead of 4 yr, to perform a genomic validation. In comparison to the multistep genomic model, the single-step SNP BLUP model resulted in a higher correlation and greater variance of genomic EBV according to 798 national validation bulls. The regression of genomic prediction of the current, full evaluation on the earlier, truncated evaluation was slightly closer to 1 than the multistep model. For the validation bulls or youngest genomic artificial insemination bulls, correlation of genomic EBV between the 2 models was, on average, 0.95 across all the conformation traits. We did not find overprediction of young animals by the single-step SNP BLUP model for the conformation traits in German Holsteins.

Genetic selection for bovine chromosome 18 haplotypes associated with divergent somatic cell score affects postpartum reproductive and metabolic performance.

The susceptibility of animals to periparturient diseases has a great effect on the economic efficiency of dairy industries, on the frequency of antibiotic treatment, and on animal welfare. The use of selection for breeding cows with reduced susceptibility to diseases offers a sustainable tool to improve dairy cattle farming. Several studies have focused on the association of distinct bovine chromosome 18 genotypes or haplotypes with performance traits. The aim of this study was to test whether selection of Holstein Friesian heifers via SNP genotyping for alternative paternal chromosome 18 haplotypes associated with favorable (Q) or unfavorable (q) somatic cell scores influences postpartum reproductive and metabolic diseases. Thirty-six heifers (18 Q and 18 q) were monitored from 3 wk before calving until necropsy on d 39 (± 4 d) after calving. Health status and rectal temperature were measured daily, and body condition score and body weight were assessed once per week. Blood samples were drawn twice weekly, and levels of insulin, nonesterified fatty acids, insulin-like growth factor-I, growth hormone, and ß-hydroxybutyrate were measured. Comparisons between the groups were performed using Fisher's exact test, chi-squared test, and the GLIMMIX procedure in SAS. Results showed that Q-heifers had reduced incidence of metritis compared with q-heifers and were less likely to develop fever. Serum concentrations of ß-hydroxybutyrate were lower and insulin-like growth factor-I plasma concentrations were higher in Q- compared with q-heifers. However, the body condition score and withers height were comparable between haplotypes, but weight loss tended to be lower in Q-heifers compared with q-heifers. No differences between the groups were detected concerning retained fetal membranes, uterine involution, or onset of cyclicity. In conclusion, selection of chromosome 18 haplotypes associated with a reduced somatic cell score resulted in a decreased incidence of postpartum reproductive and metabolic diseases in this study. The presented data add to the existing knowledge aimed at avoiding negative consequences of genetic selection strategies in dairy cattle farming. The underlying causal mechanisms modulated by haplotypes in the targeted genomic region and immune competence necessitate further investigation.

Rapid Discovery of De Novo Deleterious Mutations in Cattle Enhances the Value of Livestock as Model Species.

In humans, the clinical and molecular characterization of sporadic syndromes is often hindered by the small number of patients and the difficulty in developing animal models for severe dominant conditions. Here we show that the availability of large data sets of whole-genome sequences, high-density SNP chip genotypes and extensive recording of phenotype offers an unprecedented opportunity to quickly dissect the genetic architecture of severe dominant conditions in livestock. We report on the identification of seven dominant de novo mutations in CHD7, COL1A1, COL2A1, COPA, and MITF and exploit the structure of cattle populations to describe their clinical consequences and map modifier loci. Moreover, we demonstrate that the emergence of recessive genetic defects can be monitored by detecting de novo deleterious mutations in the genome of bulls used for artificial insemination. These results demonstrate the attractiveness of cattle as a model species in the post genomic era, particularly to confirm the genetic aetiology of isolated clinical case reports in humans.

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.

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.

Reliability of genomic prediction for German Holsteins using imputed genotypes from low-density chips.

With the availability of single nucleotide polymorphism (SNP) marker chips, such as the Illumina BovineSNP50 BeadChip (50K), genomic evaluation has been routinely implemented in dairy cattle breeding. However, for an average dairy producer, total costs associated with the 50K chip are still too high to have all the cows genotyped and genomically evaluated. To study the accuracy of cheaper low-density chips, genotypes were simulated for 2 low-density chips, the Illumina Bovine3K BeadChip (3K) and BovineLD BeadChip (6K), according to their original marker maps. Simulated missing genotypes of the 50K chip were imputed using the programs Beagle and Findhap. Three genotype data sets were used to study imputation accuracy: the EuroGenomics data set, with 14,405 reference bulls (data set I); the smaller EuroGenomics data set, with 11,670 older reference bulls (data set II); and the data set of all genotyped German Holsteins, with 31,597 reference animals (data set III). Imputed genotypes were compared with their original ones to calculate allele error rate for validation animals in the 3 data sets. To evaluate the loss in accuracy of genomic prediction when using imputed genotypes, a genomic evaluation was conducted only for EuroGenomics data set II. Furthermore, combined genome-enhanced breeding values calculated from the original and imputed genotypes were compared. Allele error rate for EuroGenomics data set II was highest for the Findhap program on the 3K chip (3.3%) and lowest for the Beagle program on the 6K chip (0.6%). Across the data sets, Beagle was shown to be about 2 times as accurate as Findhap. Compared with the real 50K genotypes, the reduction in reliability of the genomic prediction when using the imputed genotypes was highest for Findhap on the 3K chip (5.3%) and lowest for Beagle on the 6K chip (1%) when averaged over the 12 evaluated traits. Differences in genome-enhanced breeding values of the original and imputed genotypes were largest for Findhap on the 3K chip, whereas Beagle on the 6K chip had the smallest difference. The low-density chip, 6K, gave markedly higher imputation accuracy and more accurate genomic prediction than the 3K chip. On the basis of the relatively small reduction in accuracy of genomic prediction, we would recommend the BovineLD 6K chip for large-scale genotyping as long as its costs are acceptable to breeders.