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The multiple-lactation autoregressive test-day (AR) model is the adopted model for the national genetic evaluation of dairy cattle in Portugal. Under this model, animals' permanent environment effects are assumed to follow a first-order autoregressive process over the long (auto-correlations between parities) and short (auto-correlations between test-days within lactation) terms. Given the relevance of genomic prediction in dairy cattle, it is essential to include marker information in national genetic evaluations. In this context, we aimed to evaluate the feasibility of applying the single-step genomic (G)BLUP to analyze milk yield using the AR model in Portuguese Holstein cattle. In total, 11,434,294 test-day records from the first 3 lactations collected between 1994 and 2017 and 1,071 genotyped bulls were used in this study. Rank correlations and differences in reliability among bulls were used to compare the performance of the traditional (A-AR) and single-step (H-AR) models. These 2 modeling approaches were also applied to reduced data sets with records truncated after 2012 (deleting daughters of tested bulls) to evaluate the predictive ability of the H-AR. Validation scenarios were proposed, taking into account young and proven bulls. Average EBV reliabilities, empirical reliabilities, and genetic trends predicted from the complete and reduced data sets were used to validate the genomic evaluation. Average EBV reliabilities for H-AR (A-AR) using the complete data set were 0.52 (0.16) and 0.72 (0.62) for genotyped bulls with no daughters and bulls with 1 to 9 daughters, respectively. These results showed an increase in EBV reliabilities of 0.10 to 0.36 when genomic information was included, corresponding to a reduction of up to 43% in prediction error variance. Considering the 3 validation scenarios, the inclusion of genomic information improved the average EBV reliability in the reduced data set, which ranged, on average, from 0.16 to 0.26, indicating an increase in the predictive ability. Similarly, empirical reliability increased by up to 0.08 between validation tests. The H-AR outperformed A-AR in terms of genetic trends when unproven genotyped bulls were included. The results suggest that the single-step GBLUP AR model is feasible and may be applied to national Portuguese genetic evaluations for milk yield., (Copyright © 2019 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.)

Ecoregional differences contribute to genetic environmental interactions and impact animal performance. These differences may become more important under climate change scenarios. Utilizing genetic diversity within a species to address such problems has not been fully explored. In this study Hereford cattle were genotyped with 50K Bead Chip or 770K Bovine Bead Chip to test the existence of genetic structure in five U.S. ecoregions characterized by precipitation, temperature and humidity and designated: cool arid (CA), cool humid (CH), transition zone (TZ), warm arid (WA), and warm humid (WH). SNP data were analyzed in three sequential analyses. Broad genetic structure was evaluated with STRUCTURE, and ADMIXTURE software using 14,312 SNPs after passing quality control variables. The second analysis was performed using principal coordinate analysis with 66 Tag SNPs associated in the literature with various aspects of environmental stressors (e.g., heat tolerance) or production (e.g., milk production). In the third analysis TreeSelect was used with the 66 SNPs to evaluate if ecoregional allelic frequencies deviated from a central frequency and by so doing are indicative of directional selection. The three analyses suggested subpopulation structures associated with ecoregions from where animals were derived. ADMIXTURE and PCA results illustrated the importance of temperature and humidity and confirm subpopulation assignments. Comparisons of allele frequencies with TreeSelect showed ecoregion differences, in particular the divergence between arid and humid regions. Patterns of genetic variability obtained by medium and high density SNP chips can be used to acclimatize a temperately derived breed to various ecoregions. As climate change becomes an important factor in cattle production, this study should be used as a proof of concept to review future breeding and conservation schemes aimed at adaptation to climatic events.

The number of follicles recruited in each estrous cycle has gained practical importance in artificial reproductive technology, as it determines the oocyte yield from ultrasound-guided ovum pickup for in vitro embryo production. We aimed to identify single nucleotide polymorphisms (SNPs) in bovine genes related to reproductive physiology and evaluate the association between the candidate SNPs and the number of oocytes collected from ultrasound-guided ovum pickup. We sequenced genomic segments of GDF9, FGF8, FGF10 and BMPR2 and identified seventeen SNPs in the Bos taurus and Bos indicus breeds. Two SNPs cause amino acid changes in the proteins GDF9 and FGF8. Three SNPs in GDF9, FGF8 and BMPR2 were genotyped in 217 Nelore cows (B. indicus), while two previously identified mutations in LHCGR and mitochondrial DNA (mtDNA) were genotyped in the same group. The polymorphisms in GDF9, FGF8, BMRP2 and LHCGR were significantly associated (P<0.01) with the number of oocytes collected by ovum pickup, whereas the SNP in the mtDNA was not. In addition, we estimated an allelic substitution effect of 1.13±0.01 (P<0.01) oocytes for the SNP in the FGF8 gene. The results we report herein provide further evidence to support the hypothesis that genetic variability is an important component of the number of antral follicles in the bovine ovary., (Copyright © 2012 Elsevier B.V. All rights reserved.)

Our objective was to estimate Bos primigenius taurus introgression in American Zebu cattle. One hundred and four American Zebu (Nellore) cattle were submitted to mtDNA, microsatellite and satellite analysis. Twenty-three alleles were detected in microsatellite analysis, averaging 4.6 ± 1.82/locus. Variance component comparisons of microsatellite allele sizes allowed the construction of two clusters separating taurus and indicus. No significant variation was observed when indicus and taurus mtDNA were compared. Three possible genotypes of 1711b satellite DNA were identified. All European animals showed the same restriction pattern, suggesting a Zebu-specific restriction pattern. The frequencies of B. primigenius indicus-specific microsatellite alleles and 1711b satellite DNA restriction patterns lead to an estimate of 14% taurine contribution in purebred Nellore.

The ultimate goal of in vitro embryo culture systems is to perfectly mimic the condition of oocyte maturation, fertilization and embryo development. These systems are far more complex than standard in vitro cell culture because of the various environments through which the gametes and embryos pass during in vivo development. Improvement of the medium and other culture conditions has allowed for full development of a percentage of the fertilized oocytes but the great majority of bovine zygotes stop developing within a few cell cycles after initiating cleavage. This developmental block arises in the bovine embryo at the eight-cell-stage and is likely correlated with the cytoplasmic quality of the oocyte. Oocytes harbor all mRNAs and proteins needed to reach the fourth or fifth cell cycle, however, embryos that fail to transcribe their own genome fail to further develop. In this article, we review some of the advances in developmental block knowledge and describe a possible role of active embryo transcription that drives incompetent embryos to block and death.

Background: The existence of moderate to high levels of linkage disequilibrium (LD) between genetic markers and quantitative trait loci (QTL) affecting traits of interest is fundamental for the success of genome-wide association (GWAS) and genomic selection (GS) studies. Knowledge about the extent and the pattern of LD in livestock populations is essential to determine the density of single nucleotide polymorphisms (SNP) required for accurate GWAS and GS. Moreover, observed LD is related to historical effective population sizes (Ne), and can provide insights into the genetic diversity history of populations. Estimates of the consistency of linkage phase across breeds (RH,B) can be used to determine if there is sufficient relationship to use pooled reference populations in multi-breed GS programs. The objective of this study was to estimate LD levels, persistence of phase and effective population size in Hereford and Braford cattle populations sampled in Brazil. Results: Mean LD estimates, measured using the squared correlation of alleles at two loci (r²), obtained between adjacent SNP across all chromosomes were 0.21 ± 0.27 for Herefords (391 samples with 41,241 SNP) and 0.16 ± 0.22 for Brafords (2044 samples and 41,207 SNP). Estimated r² was > 0.2 and 0.3, respectively, for 34 and 25% of adjacent markers in Herefords, and 26 and 17% in Brafords. Estimated Ne for Brafords and Herefords at the current generation was 220 and 153 individuals, respectively. The two breeds demonstrated moderate to strong persistence of phase at all distances (RH,B = 0.53 to 0.97). The largest phase correlations were found in the 0 to 50 Kb bins (RH,B = 0.92 to 0.97). Estimated LD decreased rapidly with increasing distance between SNP, however, useful linkage for GWAS and GS (r²>0.2) was found spanning to ~50 Kb. Conclusions: Panels containing about 50,000 and 150,000 SNP markers are necessary to detect minimal levels of LD between adjacent markers that would be useful for GWAS and GS studies to Hereford and Braford breeds, respectively. Markers are expected to be linked to the same QTL alleles in distances < 50 Kb in both populations due to observed high persistence of phase levels. [ABSTRACT FROM AUTHOR]

Tick and tick-borne diseases, including babesiosis (B. bovis), constitute a major drawback to improve productivity of beef cattle in the tropics, especially for systems where Bos taurus cattle animals and their crosses are used. This study aimed to estimate genetic parameters for tick counts (TC) and infection level of Babesia bovis (IB) using Bayesian inference. Tick counts on one side of each animal were obtained from 717 Braford and 43 Hereford cattle in farms located at Rio Grande do Sul State, Brazil. The tick counts were collected when average individual infestation exceeded 20 engorged tick females with at least 4.5 mm in length. Blood samples were collected in tubes containing EDTA for DNA extraction. B. bovis quantification was performed using both the qPCR technique from genomic DNA of each animal with specific primers for this protozoan and the absolute quantification method. The TC and IB records were transformed in log base 10 (x + 1), and the means were 1.334 and 1.511 for TC and IB, respectively. The model included fixed effects, random effects that represented additive genetic direct effects of each animal, and residuals. The fixed effects were composed by contemporary group (same farm, sex, year and season of birth, management, and tick count date). Also, the effects of Nelore breed proportion, heterozygosity, recombination loss, and linear and quadratic coefficients for animal age at counting in days (358 to 697) were included in the model as covariates. Contemporary groups with less than 4 individuals were excluded from analyzes. The Gibbs sampler in a bivariate animal model analysis using GIBBSF90 software was run for 500,000 iterations (burn-in period of 50,000). Moreover, the convergence of the Markov chains was checked based on tests by using the coda package of R software. The mean additive genetic variances were 0.018 and 0.080 for TC and IB, respectively. The mean residual variances were 0.144 and 0.356 for TC and IB, respectively. The mean h2 were 0.109 and 0.182 for TC and IB, respectively. The genetic correlation was 0.38 between TC and IB. The selection response of Braford and Hereford cattle for IB trait will have greater magnitude than for TC, and moderate correlated response between these two traits would be expected. [ABSTRACT FROM AUTHOR]