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Background: Commercial cuts yield is an important trait for beef production, which affects the final value of the products, but its direct determination is a challenging procedure to be implemented in practice. The measurement of ribeye area (REA) and backfat thickness (BFT) can be used as indirect measures of meat yield. REA and BFT are important traits studied in beef cattle due to their strong implication in technological (carcass yield) and nutritional characteristics of meat products, like the degree of muscularity and total body fat. Thus, the aim of this work was to study the Longissimus dorsi muscle transcriptome of Nellore cattle, associated with REA and BFT, to find differentially expressed (DE) genes, metabolic pathways, and biological processes that may regulate these traits. Results: By comparing the gene expression level between groups with extreme genomic estimated breeding values (GEBV), 101 DE genes for REA and 18 for BFT (false discovery rate, FDR 10%) were identified. Functional enrichment analysis for REA identified two KEGG pathways, MAPK (Mitogen-Activated Protein Kinase) signaling pathway and endocytosis pathway, and three biological processes, response to endoplasmic reticulum stress, cellular protein modification process, and macromolecule modification. The MAPK pathway is responsible for fundamental cellular processes, such as growth, differentiation, and hypertrophy. For BFT, 18 biological processes were found to be altered and grouped into 8 clusters of semantically similar terms. The DE genes identified in the biological processes for BFT were ACHE, SRD5A1, RSAD2 and RSPO3. RSAD2 has been previously shown to be associated with lipid droplet content and lipid biosynthesis. Conclusion: In this study, we identified genes, metabolic pathways, and biological processes, involved in differentiation, proliferation, protein turnover, hypertrophy, as well as adipogenesis and lipid biosynthesis related to REA and BFT. These results enlighten some of the molecular processes involved in muscle and fat deposition, which are economically important carcass traits for beef production. [ABSTRACT FROM AUTHOR]

Background: The availability of dense genotypes and whole-genome sequence variants from various sources offers the opportunity to compile large datasets consisting of tens of thousands of individuals with genotypes at millions of polymorphic sites that may enhance the power of genomic analyses. The imputation of missing genotypes ensures that all individuals have genotypes for a shared set of variants. Results: We evaluated the accuracy of imputation from dense genotypes to whole-genome sequence variants in 249 Fleckvieh and 450 Holstein cattle using Minimac and FImpute. The sequence variants of a subset of the animals were reduced to the variants that were included on the Illumina BovineHD genotyping array and subsequently inferred in silico using either within- or multi-breed reference populations. The accuracy of imputation varied considerably across chromosomes and dropped at regions where the bovine genome contains segmental duplications. Depending on the imputation strategy, the correlation between imputed and true genotypes ranged from 0.898 to 0.952. The accuracy of imputation was higher with Minimac than FImpute particularly for variants with a low minor allele frequency. Using a multi-breed reference population increased the accuracy of imputation, particularly when FImpute was used to infer genotypes. When the sequence variants were imputed using Minimac, the true genotypes were more correlated to predicted allele dosages than best-guess genotypes. The computing costs to impute 23,256,743 sequence variants in 6958 animals were ten-fold higher with Minimac than FImpute. Association studies with imputed sequence variants revealed seven quantitative trait loci (QTL) for milk fat percentage. Two causal mutations in the DGAT1 and GHR genes were the most significantly associated variants at two QTL on chromosomes 14 and 20 when Minimac was used to infer genotypes. Conclusions: The population-based imputation of millions of sequence variants in large cohorts is computationally feasible and provides accurate genotypes. However, the accuracy of imputation is low in regions where the genome contains large segmental duplications or the coverage with array-derived single nucleotide polymorphisms is poor. Using a reference population that includes individuals from many breeds increases the accuracy of imputation particularly at low-frequency variants. Considering allele dosages rather than best-guess genotypes as explanatory variables is advantageous to detect causal mutations in association studies with imputed sequence variants. [ABSTRACT FROM AUTHOR]

Background: Bovine progressive degenerative myeloencephalopathy (Weaver syndrome) is a neurodegenerative disorder in Brown Swiss cattle that is characterized by progressive hind leg weakness and ataxia, while sensorium and spinal reflexes remain unaffected. Although the causal mutation has not been identified yet, an indirect genetic test based on six microsatellite markers and consequent exclusion of Weaver carriers from breeding have led to the complete absence of new cases for over two decades. Evaluation of disease status by imputation of 41 diagnostic single nucleotide polymorphisms (SNPs) and a common haplotype published in 2013 identified several suspected carriers in the current breeding population, which suggests a higher frequency of the Weaver allele than anticipated. In order to prevent the reemergence of the disease, this study aimed at mapping the gene that underlies Weaver syndrome and thus at providing the basis for direct genetic testing and monitoring of today's Braunvieh/Brown Swiss herds. Results: Combined linkage/linkage disequilibrium mapping on Bos taurus chromosome (BTA) 4 based on Illumina Bovine SNP50 genotypes of 43 Weaver-affected, 31 Weaver carrier and 86 Weaver-free animals resulted in a maximum likelihood ratio test statistic value at position 49,812,384 bp. The confidence interval (0.853 Mb) determined by the 2-LOD drop-off method was contained within a 1.72-Mb segment of extended homozygosity. Exploitation of wholegenome sequence data from two official Weaver carriers and 1145 other bulls that were sequenced in Run4 of the 1000 bull genomes project showed that only a non-synonymous SNP (rs800397662) within the PNPLA8 gene at position 49,878,773 bp was concordant with the Weaver carrier status. Targeted SNP genotyping confirmed this SNP as a candidate causal mutation for Weaver syndrome. Genotyping for the candidate causal mutation in a random sample of 2334 current Braunvieh animals suggested a frequency of the Weaver allele of 0.26 %. Conclusions: Through combined use of exhaustive sequencing data and SNP genotyping results, we were able to provide evidence that supports the non-synonymous mutation at position 49,878,773 bp as the most likely causal mutation for Weaver syndrome. Further studies are needed to uncover the exact mechanisms that underlie this syndrome. [ABSTRACT FROM AUTHOR]

Background Atypical bovine spongiform encephalopathies (BSEs), classified as H-type and L-type BSE based on the Western immunoblot profiles, are naturally occurring diseases in cattle, which are phenotypically different to classical BSE. Transmission studies in cattle using the intracerebral route resulted in disease where the phenotypes were maintained irrespective of BSE type but clinically affected cattle with a shorter survival time displayed a nervous form whereas cattle with a longer survival time displayed a dull form. A second transmission study is reported here where four cattle were intracerebrally inoculated with brain tissue from experimentally infected cattle presenting with either the nervous or dull form of H- or L-type BSE to determine whether the phenotype is maintained. Results The four inoculated cattle were culled at 16.5-19.5 months post inoculation after presenting with difficulty getting up, a positive scratch response (all) and dullness (three cattle), which was not observed in two non-inoculated control cattle, each housed with either group of inoculated cattle. Only the inoculated cattle had detectable prion protein in the brain based on immunohistochemical examination, and the Western immunoblot profile was consistent with the H-type or L-type BSE of the respective donor cattle. Conclusions Second passage of H-type and L-type BSE in cattle produced a TSE where the majority of cattle displayed the dull form regardless of clinical disease form of the donor cattle. The pathological and molecular phenotypes of H- and L-type BSE were maintained. [ABSTRACT FROM AUTHOR]

Background Perosomus elumbis (PE) is a congenital defect that has been observed sporadically in Holstein cattle for many years. However, several cases have been reported in recent years and this may indicate an unrecognised spread of a mutant allele in the Holstein population worldwide. Two cases in Danish Holstein calves are reported to provide details on the phenotype. Case presentation Two full-term Holstein calves were born after assisted delivery due to dystocia with breech presentation. External morphological examination indicated that the lumbar, sacral and coccygeal vertebrae were absent and the abdominal region was just present as a floppy sac covered by skin and enclosing the abdominal organs. The hind limbs were hypoplastic with bilateral symmetric arthrogryposis and muscular atrophy. Radiographs, computed tomography scan and necropsy confirmed these findings. The caudal part of the thoracic spinal cord showed myelodysplasia. A range of abdominal organ malformations were found at necropsy. Inbreeding was not found during genealogical examination, but remote shared ancestors were present in the pedigrees. Conclusion The addition of these further cases of PE to the in recent years reported record of cases should draw more attention to this defect in the Holstein breed. PE may be an emerging genetic defect in the Holstein population worldwide and cases should be sampled to enable genetic mapping of the gene possibly underlying the disease. PE cases seem to be associated with a high risk of dystocia due to increased rate of breech presentation. [ABSTRACT FROM AUTHOR]