Evaluation of Whole-Genome Sequence Imputation Strategies in Korean Hanwoo Cattle.

This study evaluated the accuracy of sequence imputation in Hanwoo beef cattle using different reference panels: a large multi-breed reference with no Hanwoo (n = 6269), a much smaller Hanwoo purebred reference (n = 88), and both datasets combined (n = 6357). The target animals were 136 cattle both sequenced and genotyped with the Illumina BovineSNP50 v2 (50K). The average imputation accuracy measured by the Pearson correlation (R) was 0.695 with the multi-breed reference, 0.876 with the purebred Hanwoo, and 0.887 with the combined data; the average concordance rates (CR) were 88.16%, 94.49%, and 94.84%, respectively. The accuracy gains from adding a large multi-breed reference of 6269 samples to only 88 Hanwoo was marginal; however, the concordance rate for the heterozygotes decreased from 85% to 82%, and the concordance rate for fixed SNPs in Hanwoo also decreased from 99.98% to 98.73%. Although the multi-breed panel was large, it was not sufficiently representative of the breed for accurate imputation without the Hanwoo animals. Additionally, we evaluated the value of high-density 700K genotypes (n = 991) as an intermediary step in the imputation process. The imputation accuracy differences were negligible between a single-step imputation strategy from 50K directly to sequence and a two-step imputation approach (50K-700K-sequence). We also observed that imputed sequence data can be used as a reference panel for imputation (mean R = 0.9650, mean CR = 98.35%). Finally, we identified 31 poorly imputed genomic regions in the Hanwoo genome and demonstrated that imputation accuracies were particularly lower at the chromosomal ends.

Modern livestock farming under tropical conditions using sensors in grazing systems.

The aim of this study was to evaluate a commercial sensor-a three-axis accelerometer-to predict animal behavior with a variety of conditions in tropical grazing systems. The sensor was positioned on the underjaw of young bulls to detect the animals' movements. A total of 22 animals were monitored in a grazing system, during both seasons (wet and dry), with different quality and quantity forage allowance. The machine learning (ML) methods used were random forest (RF), convolutional neural net and linear discriminant analysis; the metrics used to determine the best method were accuracy, Kappa coefficient, and a confusion matrix. After predicting animal behavior using the best ML method, a forecast for animal performance was developed using a mechanistic model: multiple linear regression to correlate intermediate average daily gain (iADG) observed versus iADG predicted. The best ML method yielded accuracy of 0.821 and Kappa coefficient of 0.704, was RF. From the forecast for animal performance, the Pearson correlation was 0.795 and the mean square error was 0.062. Hence, the commercial Ovi-bovi sensor, which is a three-axis accelerometer, can act as a powerful tool for predicting animal behavior in beef cattle production developed under a variety tropical grazing condition.

Genetic parameters for body weight and milk production of dairy Gyr herds.

The aim of this study was to estimate genetic parameters for cow weight at calving (CW) and cumulative 305-day milk yield (MY305) in dairy Gyr cattle by two-trait analysis. The study used 1,847 CW records, in which 418 females presented more than one measure, and 4,048 MY305 records, wherein 1068 females provided repeated measures, from 2,339 females belonging to three herds, which calved between 1986 and 2019. Variance components were estimated by the restricted maximum likelihood method (REML) using a two-trait animal model. The model included direct additive genetic, permanent environmental and residual effects as random effects and the fixed effects of contemporary group, formed by animals that had calved on the same farm year and season, and age of cow at calving as covariates (fitted as linear and quadratic effect). The heritability estimates for CW and MY305 were 0.21 ± 0.06 and 0.29 ± 0.04, respectively, and repeatability estimates were 0.49 ± 0.03 and 0.49 ± 0.02. The genetic correlation between CW and MY305 was positive and of low magnitude (0.33 ± 0.18), indicating that selection for MY305 will cause little genetic change in the weights of dairy Gyr animals. The genetic trends of breeding values of analyzed traits showed marked genetic gains in MY305, with little changes in CW of dairy Gyr cows over the years in the herds studied, which is an important result considering the production systems adopted in the tropics.

Estrus Prediction Models for Dairy Gyr Heifers.

Technological devices are increasingly present in livestock activities, such as identifying the reproductive status of cows. For this, predictive models must be accurate and usable in the productive context. The aims of this study were to evaluate estrus-associated changes in reticulo-rumen temperature (RRT) and activity (ACT) in Dairy Gyr heifers provided by reticulo-rumen boluses and to test the ability of different models for estrus prediction. The RRT and ACT of 45 heifers submitted to estrus synchronization were recorded using reticulo-rumen boluses. The means of RRT and ACT at different time intervals were compared between the day before and the day of estrus manifestation. An analysis of variance of RRT and ACT was performed using mixed models. A second approach employed logistic regression, random forest, and linear discriminant analysis models using RRT, ACT, time of day, and the temperature-humidity index (THI) as predictors. There was an increase in RRT and ACT at estrus (p < 0.05) compared to the same period on the day before and on the day after estrus. The random forest model provided the best performance values with a sensitivity of 51.69% and specificity of 93.1%. The present results suggest that RRT and ACT contribute to the identification of estrus in Dairy Gyr heifers.

Identification and antimicrobial susceptibility of milk pathogen isolated from dairy production systems.

Livestock has been recognized as a reservoir of antibiotic-resistant bacteria. Prevalence of resistance has been associated with herd size and intensification of animal production systems. Brazil is one of the emergent hotspots of bacterial resistance, which is also associated with animal husbandry. This study aimed to evaluate the resistance profile of pathogens that cause subclinical mastitis and the relationship between resistance status at farm level and different production systems. Milk samples from cows diagnosed with subclinical mastitis were collected from farms that adopt different husbandry systems with different production intensities, i.e., agroecological, low input, high input, Free-Stall and Compost-bedded pack barn. Etiological agents were isolated and microbiologically identified, and antibiotic susceptibility testing was conducted, using the disk diffusion method. The main isolated agents were Streptococcus spp. (n = 54, 30.5 %) and coagulase-positive Staphylococcus (CPS) (n = 54; 30.5 %). The recovered isolates displayed high antibiotic resistance against Sulfamethazine (80.2 %), Gentamicin (29.37 %), Penicillin (29.37 %), Oxacillin (28.82 %) and Ampicillin (26 %). Multidrug resistance was found for all agents and in all farming systems (39.54 %). Neither production systems (p = 0.26) nor farming systems (p = 0.24) significantly affected the resistance rates of samples. Therefore, intensive production systems may not be a root cause of increased rates of antimicrobial resistance in the milk production chain, suggesting that other environmental factors should be investigated. It is noteworthy that high levels of multidrug resistance were even found in bacteria earlier considered as minor pathogens. This development can be taken as a warning that environmental bacteria are potential transmitters of resistance genes to the environment.

Genetic evaluation for reproductive and productive traits in Brahman cattle.

Our objectives were to estimate genetic parameters for male and female reproductive traits and their genetic correlations with body weight and carcass traits, evaluate the genetic trends over the years, and verify the effect of inbreeding on the phenotypes of Brahman cattle. The traits evaluated were body weights at 120, 210, 365, and 450 days of age (W120, W210, W365, and W450); scrotal circumference at 365 and 450 days of age (SC365 and SC450), age at first calving (AFC), gestation length (GL), stayability (STAY), ribeye area (REA), backfat thickness (BFT), and rump fat thickness (RFT). Direct heritability estimates ranged from 0.10 ± 0.03 (AFC) to 0.43 ± 0.06 (GL). Maternal heritability estimates for body weights, scrotal circumferences, and GL ranged from 0.07 ± 0.02 to 0.15 ± 0.03. The proportion of the maternal permanent environment for W120 and W210 was equal to 0.11 ± 0.02. Genetic correlations varied between -0.60 ± 0.25 (STAY and BFT) to 0.97 ± 0.01 (W365 and W450). Except for AFC, all genetic trends were significant (p < 0.05) and presented favorable annual genetic gains. Unfavorable effects due to the increase of inbreeding coefficients were observed for body weights and AFC, suggesting greater attention be paid to the applied mating systems to control inbreeding. Reproductive traits, such as AFC and STAY, could be assisted indirectly by scrotal circumference selection. The emphasis applied to body weight selection, especially at W210, may assist REA. The BFT and RFT traits presented genetic variability and have responded to selection, although not included in the Brahman selection index.

Genome-Wide Association Study Provides Insights into Important Genes for Reproductive Traits in Nelore Cattle.

The identification of genomic regions associated with reproductive traits as well as their biological processes allows a better understanding of the phenotypic variability of these traits. This information could be applied to animal breeding programs to accelerate genetic gain. The aim of this study was to evaluate the association between single nucleotide polymorphisms (SNP) with a scrotal circumference at 365 days of age (SC365) and at 450 days of age (SC450), gestation length (GL) as a calf trait, age at first calving (AFC), accumulated productivity (ACP), heifer early calving until 30 months (HC30), and stayability (STAY) traits, in order to identify candidate genes and biological pathways associated with reproductive traits in Nelore cattle. The data set consisted of pedigree, phenotypes, and genotypes of Nelore cattle from the "Associação Nacional de Criadores e Pesquisadores" (ANCP). The association analyses were performed using the Weighted Single-Step Genome-Wide Association method; the regions, consisting of 10 consecutive SNP, which explained more than 0.5% of additive genetic variance, were considered as a significant association. A total of 3, 6, 7, 5, 10, 25, and 12 windows were associated with SC355, SC450, GL, AFC, ACP, HC30, and STAY, respectively. The results revealed genes with important functions for reproductive traits, such as fertility and precocity. Some genes were associated with more than one trait, among them CAMK1D, TASP1, ACOXL, RAB11FIP5, and SFXN5. Moreover, the genes were enriched in functional terms, like negative regulation of fat cell differentiation, fatty acid alpha-oxidation, and sphingolipids signaling pathway. The identification of the genes associated with the traits, as well as genes enriched in the terms and pathway mentioned above, should contribute to future biological validation studies and may be used as candidate genes in Nelore breeding programs.

Predictive potential of activity and reticulo-rumen temperature variation for calving in Gyr heifers (Bos taurus indicus).

Factors related to the thermal physiology and activity of Zebu animals close to calving are still unknown. The aims of this study were 1) to describe the pattern of reticulo-rumen temperature and activity variation in nulliparous Gyr heifers close to calving, and 2) to evaluate the predictive potential of these traits for calving in Gyr heifers. Forty pregnant Gyr heifers that had calved between August and December 2017 at the Getúlio Vargas Experimental Station, Empresa de Pesquisa Agropecuária de Minas Gerais (Epamig), Brazil, were used. The animals received a rumen bolus to monitor reticulo-rumen temperature (Trr) and activity (Act) at intervals of 10 min. Mixed linear models were used. A decrease in Trr and an increase in Act were observed on the days preceding calving. Differences in Trr and Act were more evident during the final 21 and 11 h previous to calving compared to 14 days before calving, measured at the same time of day. There was a decrease of about 0.20 °C in Trr at the time of calving when compared to baseline (14 days before calving measured at the same time of day). Environmental variables, such as temperature and air humidity, as well as biological factors such as circadian rhythm, may influence the interpretation of the data. In conclusion, variations exist in the Trr and Act of Gyr heifers in the hours before calving, which is preceded by a decrease in Trr and an increase in Act. Particularities in the thermal physiology of Zebu cattle must be considered when prediction devices previously validated only for European breeds are used.

Evaluation of imputation accuracy using the combination of two high-density panels in Nelore beef cattle.

This study compared imputation from lower-density commercial and customized panels to high-density panels and a combined panel (Illumina and Affymetrix) in Nelore beef cattle. Additionally, linkage disequilibrium and haplotype block conformation were estimated in individual high-density panels and compared with corresponding values in the combined panel after imputation. Overall, 814 animals were genotyped using BovineHD BeadChip (IllumHD), and 93 of these animals were also genotyped using the Axion Genome-Wide BOS 1 Array Plate (AffyHD). In general, customization considering linkage disequilibrium and minor allele frequency had the highest accuracies. The IllumHD panel had higher values of linkage disequilibrium for short distances between SNPs than AffyHD and the combined panel. The combined panel had an increased number of small haplotype blocks. The use of a combined panel is recommended due to its increased density and number of haplotype blocks, which in turn increase the probability of a marker being close to a quantitative trait locus of interest. Considering common SNPs between IllumHD and AffyHD for the customization of a low-density panel increases the imputation accuracy for IllumHD, AffyHD and the combined panel.

Feedlot of lambs fed biodiesel co-products: performance, commercial cuts and economic evaluation.

The aim of this study was to evaluate the animal performance, commercial cuts, and their yields within the production system, and economics of sheep production, of lambs finished in feedlots and fed with or without biodiesel co-products. A total of 40 lambs were divided into four biodiesel co-product treatment groups: a no-treatment control; peanut meal; crude glycerin; and peanut meal + crude glycerin. Animal performance did not differ (P > 0.05) among the treatment groups, where the average daily gain was close to 0.26 kg/day. Likewise, the quantitative carcass characteristics did not differ (P > 0.05) and the biological mean yield was 54.92%. Similarly, the commercial cuts and their yields did not differ (P ≥ 0.09) among the treatments. These results took into consideration the standard, age, and slaughter body weight of the animals. The economic evaluation determined that peanut meal was the best co-product for use in finishing lambs in a feedlot. Hence, all the biodiesel co-products evaluated can be used at feedlots to finish lambs without changing the variables measured.

Study on the introgression of beef breeds in Canchim cattle using single nucleotide polymorphism markers.

The aim of this study was to evaluate the level of introgression of breeds in the Canchim (CA: 62.5% Charolais-37.5% Zebu) and MA genetic group (MA: 65.6% Charolais-34.4% Zebu) cattle using genomic information on Charolais (CH), Nelore (NE), and Indubrasil (IB) breeds. The number of animals used was 395 (CA and MA), 763 (NE), 338 (CH), and 37 (IB). The Bovine50SNP BeadChip from Illumina panel was used to estimate the levels of introgression of breeds considering the Maximum likelihood, Bayesian, and Single Regression method. After genotype quality control, 32,308 SNPs were considered in the analysis. Furthermore, three thresholds to prune out SNPs in linkage disequilibrium higher than 0.10, 0.05, and 0.01 were considered, resulting in 15,286, 7,652, and 1,582 SNPs, respectively. For k = 2, the proportion of taurine and indicine varied from the expected proportion based on pedigree for all methods studied. For k = 3, the Regression method was able to differentiate the animals in three main clusters assigned to each purebred breed, showing more reasonable according to its biological viewpoint. Analyzing the data considering k = 2 seems to be more appropriate for Canchim-MA animals due to its biological interpretation. The usage of 32,308 SNPs in the analyses resulted in similar findings between the estimated and expected breed proportions. Using the Regression approach, a contribution of Indubrasil was observed in Canchim-MA when k = 3 was considered. Genetic parameter estimation could account for this breed composition information as a source of variation in order to improve the accuracy of genetic models. Our findings may help assemble appropriate reference populations for genomic prediction for Canchim-MA in order to improve prediction accuracy. Using the information on the level of introgression in each individual could also be useful in breeding or crossing design to improve individual heterosis in crossbred cattle.