Supervised Machine Learning Techniques for Breeding Value Prediction in Horses: An Example Using Gait Visual Scores.

Gait scores are widely used in the genetic evaluation of horses. However, the nature of such measurement may limit genetic progress since there is subjectivity in phenotypic information. This study aimed to assess the application of machine learning techniques in the prediction of breeding values for five visual gait scores in Campolina horses: dissociation, comfort, style, regularity, and development. The dataset contained over 5000 phenotypic records with 107,951 horses (14 generations) in the pedigree. A fixed model was used to estimate least-square solutions for fixed effects and adjusted phenotypes. Variance components and breeding values (EBV) were obtained via a multiple-trait model (MTM). Adjusted phenotypes and fixed effects solutions were used to train machine learning models (using the EBV from MTM as target variable): artificial neural network (ANN), random forest regression (RFR) and support vector regression (SVR). To validate the models, the linear regression method was used. Accuracy was comparable across all models (but it was slightly higher for ANN). The highest bias was observed for ANN, followed by MTM. Dispersion varied according to the trait; it was higher for ANN and the lowest for MTM. Machine learning is a feasible alternative to EBV prediction; however, this method will be slightly biased and over-dispersed for young animals.

Comparing algorithms to approximate accuracies for single-step genomic best linear unbiased predictor.

The exact accuracy of estimated breeding values can be calculated based on the prediction error variances obtained from the diagonal of the inverse of the left-hand side (LHS) of the mixed model equations (MME). However, inverting the LHS is not computationally feasible for large datasets, especially if genomic information is available. Thus, different algorithms have been proposed to approximate accuracies. This study aimed to: 1) compare the approximated accuracies from 2 algorithms implemented in the BLUPF90 suite of programs, 2) compare the approximated accuracies from the 2 algorithms against the exact accuracy based on the inversion of the LHS of MME, and 3) evaluate the impact of adding genotyped animals with and without phenotypes on the exact and approximated accuracies. Algorithm 1 approximates accuracies based on the diagonal of the genomic relationship matrix (G). In turn, algorithm 2 combines accuracies with and without genomic information through effective record contributions. The data were provided by the American Angus Association and included 3 datasets of growth, carcass, and marbling traits. The genotype file contained 1,235,930 animals, and the pedigree file contained 12,492,581 animals. For the genomic evaluation, a multi-trait model was applied to the datasets. To ensure the feasibility of inverting the LHS of the MME, a subset of data under single-trait models was used to compare approximated and exact accuracies. The correlations between exact and approximated accuracies from algorithms 1 and 2 of genotyped animals ranged from 0.87 to 0.90 and 0.98 to 0.99, respectively. The intercept and slope of the regression of exact on approximated accuracies from algorithm 2 ranged from 0.00 to 0.01 and 0.82 to 0.87, respectively. However, the intercept and the slope for algorithm 1 ranged from -0.10 to 0.05 and 0.98 to 1.10, respectively. In more than 80% of the traits, algorithm 2 exhibited a smaller mean square error than algorithm 1. The correlation between the approximated accuracies obtained from algorithms 1 and 2 ranged from 0.56 to 0.74, 0.38 to 0.71, and 0.71 to 0.97 in the groups of genotyped animals, genotyped animals without phenotype, and proven genotyped sires, respectively. The approximated accuracy from algorithm 2 showed a closer behavior to the exact accuracy when including genotyped animals in the analysis. According to the results, algorithm 2 is recommended for genetic evaluations since it proved more precise.

The genomic estimated breeding value (GEBV) represents an animal's genetic merit calculated using a combination of phenotypes, pedigree, and genomic information through a procedure known as single-step genomic best linear unbiased prediction (ssGBLUP). The accuracy of a GEBV reflects how closely it correlates with the true breeding value. However, calculating accuracies is not computationally feasible for large datasets with genomic information. In this context, methods for approximating accuracies have been proposed and implemented into genetic evaluations. This study aimed to compare 2 algorithms to approximate accuracies for ssGBLUP. In algorithm 1, genomic contributions are based on the diagonal of the genomic relationship matrix (G), combined with contributions from animal records and pedigrees. In turn, algorithm 2 combines accuracies with and without genomic information through effective record contributions. The data for this study were provided by the American Angus Association and included datasets of growth, carcass, and marbling traits. Genotypes were available for 1,235,930 animals, and the pedigree had 12,492,581 animals. We showed that algorithm 2 is better suited for approximating accuracies, as its approximations closely matched the exact accuracy values obtained from the inverse of the mixed model equations.

Genomic regions, candidate genes, and pleiotropic variants associated with physiological and anatomical indicators of heat stress response in lactating sows.

BACKGROUND: Heat stress (HS) poses significant threats to the sustainability of livestock production. Genetically improving heat tolerance could enhance animal welfare and minimize production losses during HS events. Measuring phenotypic indicators of HS response and understanding their genetic background are crucial steps to optimize breeding schemes for improved climatic resilience. The identification of genomic regions and candidate genes influencing the traits of interest, including variants with pleiotropic effects, enables the refinement of genotyping panels used to perform genomic prediction of breeding values and contributes to unraveling the biological mechanisms influencing heat stress response. Therefore, the main objectives of this study were to identify genomic regions, candidate genes, and potential pleiotropic variants significantly associated with indicators of HS response in lactating sows using imputed whole-genome sequence (WGS) data. Phenotypic records for 18 traits and genomic information from 1,645 lactating sows were available for the study. The genotypes from the PorcineSNP50K panel containing 50,703 single nucleotide polymorphisms (SNPs) were imputed to WGS and after quality control, 1,622 animals and 7,065,922 SNPs were included in the analyses. RESULTS: A total of 1,388 unique SNPs located on sixteen chromosomes were found to be associated with 11 traits. Twenty gene ontology terms and 11 biological pathways were shown to be associated with variability in ear skin temperature, shoulder skin temperature, rump skin temperature, tail skin temperature, respiration rate, panting score, vaginal temperature automatically measured every 10 min, vaginal temperature measured at 0800 h, hair density score, body condition score, and ear area. Seven, five, six, two, seven, 15, and 14 genes with potential pleiotropic effects were identified for indicators of skin temperature, vaginal temperature, animal temperature, respiration rate, thermoregulatory traits, anatomical traits, and all traits, respectively. CONCLUSIONS: Physiological and anatomical indicators of HS response in lactating sows are heritable but highly polygenic. The candidate genes found are associated with important gene ontology terms and biological pathways related to heat shock protein activities, immune response, and cellular oxidative stress. Many of the candidate genes with pleiotropic effects are involved in catalytic activities to reduce cell damage from oxidative stress and cellular mechanisms related to immune response.

Genomic analysis of feed efficiency traits in beef cattle using random regression models.

Feed efficiency plays a major role in the overall profitability and sustainability of the beef cattle industry, as it is directly related to the reduction of the animal demand for input and methane emissions. Traditionally, the average daily feed intake and weight gain are used to calculate feed efficiency traits. However, feed efficiency traits can be analysed longitudinally using random regression models (RRMs), which allow fitting random genetic and environmental effects over time by considering the covariance pattern between the daily records. Therefore, the objectives of this study were to: (1) propose genomic evaluations for dry matter intake (DMI), body weight gain (BWG), residual feed intake (RFI) and residual weight gain (RWG) data collected during an 84-day feedlot test period via RRMs; (2) compare the goodness-of-fit of RRM using Legendre polynomials (LP) and B-spline functions; (3) evaluate the genetic parameters behaviour for feed efficiency traits and their implication for new selection strategies. The datasets were provided by the EMBRAPA-GENEPLUS beef cattle breeding program and included 2920 records for DMI, 2696 records for BWG and 4675 genotyped animals. Genetic parameters and genomic breeding values (GEBVs) were estimated by RRMs under ssGBLUP for Nellore cattle using orthogonal LPs and B-spline. Models were compared based on the deviance information criterion (DIC). The ranking of the average GEBV of each test week and the overall GEBV average were compared by the percentage of individuals in common and the Spearman correlation coefficient (top 1%, 5%, 10% and 100%). The highest goodness-of-fit was obtained with linear B-Spline function considering heterogeneous residual variance. The heritability estimates across the test period for DMI, BWG, RFI and RWG ranged from 0.06 to 0.21, 0.11 to 0.30, 0.03 to 0.26 and 0.07 to 0.27, respectively. DMI and RFI presented within-trait genetic correlations ranging from low to high magnitude across different performance test-day. In contrast, BWG and RWG presented negative genetic correlations between the first 3 weeks and the other days of performance tests. DMI and RFI presented a high-ranking similarity between the GEBV average of week eight and the overall GEBV average, with Spearman correlations and percentages of individuals selected in common ranging from 0.95 to 1.00 and 93 to 100, respectively. Week 11 presented the highest Spearman correlations (ranging from 0.94 to 0.98) and percentages of individuals selected in common (ranging from 85 to 94) of BWG and RWG with the average GEBV of the entire period of the test. In conclusion, the RRM using linear B-splines is a feasible alternative for the genomic evaluation of feed efficiency. Heritability estimates of DMI, RFI, BWG and RWG indicate enough additive genetic variance to achieve a moderate response to selection. A new selection strategy can be adopted by reducing the performance test to 56 days for DMI and RFI selection and 77 days for BWG and RWG selection.

Investigating the impact of non-additive genetic effects in the estimation of variance components and genomic predictions for heat tolerance and performance traits in crossbred and purebred pig populations.

BACKGROUND: Non-additive genetic effects are often ignored in livestock genetic evaluations. However, fitting them in the models could improve the accuracy of genomic breeding values. Furthermore, non-additive genetic effects contribute to heterosis, which could be optimized through mating designs. Traits related to fitness and adaptation, such as heat tolerance, tend to be more influenced by non-additive genetic effects. In this context, the primary objectives of this study were to estimate variance components and assess the predictive performance of genomic prediction of breeding values based on alternative models and two independent datasets, including performance records from a purebred pig population and heat tolerance indicators recorded in crossbred lactating sows. RESULTS: Including non-additive genetic effects when modelling performance traits in purebred pigs had no effect on the residual variance estimates for most of the traits, but lower additive genetic variances were observed, especially when additive-by-additive epistasis was included in the models. Furthermore, including non-additive genetic effects did not improve the prediction accuracy of genomic breeding values, but there was animal re-ranking across the models. For the heat tolerance indicators recorded in a crossbred population, most traits had small non-additive genetic variance with large standard error estimates. Nevertheless, panting score and hair density presented substantial additive-by-additive epistatic variance. Panting score had an epistatic variance estimate of 0.1379, which accounted for 82.22% of the total genetic variance. For hair density, the epistatic variance estimates ranged from 0.1745 to 0.1845, which represent 64.95-69.59% of the total genetic variance. CONCLUSIONS: Including non-additive genetic effects in the models did not improve the accuracy of genomic breeding values for performance traits in purebred pigs, but there was substantial re-ranking of selection candidates depending on the model fitted. Except for panting score and hair density, low non-additive genetic variance estimates were observed for heat tolerance indicators in crossbred pigs.

Genomic Prediction and Genome-Wide Association Study for Boar Taint Compounds.

With a perspective future ban on surgical castration in Europe, selecting pigs with reduced ability to accumulate boar taint (BT) compounds (androstenone, indole, skatole) in their tissues seems a promising strategy. BT compound concentrations were quantified in the adipose tissue of 1075 boars genotyped at 29,844 SNPs. Traditional and SNP-based breeding values were estimated using pedigree-based BLUP (PBLUP) and genomic BLUP (GBLUP), respectively. Heritabilities for BT compounds were moderate (0.30-0.52). The accuracies of GBLUP and PBLUP were significantly different for androstenone (0.58 and 0.36, respectively), but comparable for indole and skatole (~0.43 and ~0.47, respectively). Several SNP windows, each explaining a small percentage of the variance of BT compound concentrations, were identified in a genome-wide association study (GWAS). A total of 18 candidate genes previously associated with BT (MX1), reproduction traits (TCF21, NME5, PTGFR, KCNQ1, UMODL1), and fat metabolism (CTSD, SYT8, TNNI2, CD81, EGR1, GIPC2, MIGA1, NEGR1, CCSER1, MTMR2, LPL, ERFE) were identified in the post-GWAS analysis. The large number of genes related to fat metabolism might be explained by the relationship between sexual steroid levels and fat deposition and be partially ascribed to the pig line investigated, which is selected for ham quality and not for lean growth.

NASA POWER satellite meteorological system is a good tool for obtaining estimates of the temperature-humidity index under Brazilian conditions compared to INMET weather stations data.

Heat stress negatively affects livestock, with undesirable effects on animals' production and reproduction. Temperature and humidity index (THI) is a climatic variable used worldwide to study the effect of heat stress on farm animals. Temperature and humidity data can be obtained in Brazil through the National Institute of Meteorology (INMET), but complete data may not be available due to temporary failures on weather stations. An alternative to obtaining meteorological data is the National Aeronautics and Space Administration Prediction of Worldwide Energy Resources (NASA POWER) satellite-based weather system. We aimed to compare THI estimates obtained from INMET weather stations and NASA POWER meteorological information sources using Pearson correlation and linear regression. After quality check, data from 489 INMET weather stations were used. The hourly, average daily and maximum daily THI were evaluated. We found greater correlations and better regression evaluation metrics when average daily THI values were considered, followed by maximum daily THI, and hourly THI. NASA POWER satellite-based weather system is a suitable tool for obtaining the average and maximum THI values using information collected from Brazil, showing high correlations with THI estimates from INMET and good regression evaluation metrics, and can assist studies that aim to analyze the impact of heat stress on livestock production in Brazil, providing additional data to complement the existing information available in the INMET database.

Genomic prediction in Brazilian Guzerá cattle: application of a single-step approach to productive and reproductive traits.

This study aimed to investigate the feasibility of genomic prediction for productive and reproductive traits in Guzerá cattle using single-step genomic best linear unbiased prediction (ssGBLUP). Evaluations included the 305-day cumulative yields (first lactation, in kg) of milk, lactose, protein, fat, and total solids; adjusted body weight (kg) at the ages of 450, 365, and 210 days; and age at first calving (in days), from a database containing 197,283 measurements from Guzerá males and females born between 1954 and 2018. The pedigree included 433,823 animals spanning up to 14 overlapping generations. A total of 1618 animals were genotyped. The analyses were performed using ssGBLUP and traditional BLUP methods. Predictive ability and bias were accessed using cross-validation: predictive ability was similar between the methods and ranged from 0.27 to 0.47 for the genomic-based model and from 0.30 to 0.45 for the pedigree-based model; the bias was also similar between the methods, ranging from 0.88 to 1.35 in the genomic-based model and from 0.96 to 1.41 in the pedigree-based model. The individual accuracies of breeding values were evidently increased in the genomic evaluation, with values ranging from 0.41 to 0.56 in the genomic-based model and from 0.26 to 0.54 in the pedigree-based model. Even based on a small number of genotyped animals and a small database for some traits, the results suggest that ssGBLUP is feasible and may be applied to national genetic evaluation of the breed to increase the accuracy of breeding values without greatly impacting predictive ability and bias.

Estimation of genetic parameters and inbreeding depression in Piau pig breed.

This study is aimed at estimating genetic parameters, effective population size, inbreeding, and inbreeding depression for birth weight, weaning weight, and average pre-weaning daily weight gain (ADG) in Piau pigs. We used information from 3841 Piau pigs, and four linear models were fitted in single-trait analyses, including or excluding maternal genetic effect, common litter effect, or a combination. The adjustments of the models were compared using the likelihood ratio test, in which the model that presented the best fit for each trait was used to estimate the (co)variance components. The inbreeding depression effect was evaluated using a linear model that included the fixed effects of sex, parity order, contemporary group, and inbreeding coefficient as a fixed covariate. The weights at birth and weaning showed low direct heritabilities (0.08 and 0.05, respectively), while the ADG showed moderate heritability (0.20). The weight at birth showed high genetic correlations with the weight at weaning (0.90) and the ADG (0.82). The weight at weaning and the ADG also showed a high genetic correlation (0.99). There was an inbreeding increase over the generations and a reduction in the effective population size. In the last generation evaluated, all the animals were inbred, the average inbreeding coefficient was 0.07, and the effective population size was 20.8. A significant inbreeding effect on ADG was observed, where an increase of 1% in the inbreeding coefficient resulted in a decrease of 0.005 g in the ADG. Thus, increasing effective population size is mandatory for controlling inbreeding and reducing the loss of variability in this Piau pig population.

Genomic prediction and genetic correlations estimated for milk production and fatty acid traits in Walloon Holstein cattle using random regression models.

The aims of this study were to: (1) estimate genetic correlation for milk production traits (milk, fat and protein yields and fat and protein contents) and fatty acids (FA: C16:0, C18:1 cis-9, LCFA, SFA, and UFA) over days in milk, (2) investigate the performance of genomic predictions using single-step GBLUP (ssGBLUP) based on random regression models (RRM), and (3) identify the optimal scaling and weighting factors to be used in the construction of the H matrix. A total of 302 684 test-day records of 63.875 first lactation Walloon Holstein cows were used. Positive genetic correlations were found between milk yield and fat and protein yield (rg from 0.46 to 0.85) and between fat yield and milk FA (rg from 0.17 to 0.47). On the other hand, negative correlations were estimated between fat and protein contents (rg from -0.22 to -0.59), between milk yield and milk FA (rg from -0.22 to -0.62), and between protein yield and milk FA (rg from -0.11 to -0.19). The selection for high fat content increases milk FA throughout lactation (rg from 0.61 to 0.98). The test-day ssGBLUP approach showed considerably higher prediction reliability than the parent average for all milk production and FA traits, even when no scaling and weighting factors were used in the H matrix. The highest validation reliabilities (r2 from 0.09 to 0.38) and less biased predictions (b1 from 0.76 to 0.92) were obtained using the optimal parameters (i.e., ω = 0.7 and α = 0.6) for the genomic evaluation of milk production traits. For milk FA, the optimal parameters were ω = 0.6 and α = 0.6. However, biased predictions were still observed (b1 from 0.32 to 0.81). The findings suggest that using ssGBLUP based on RRM is feasible for the genomic prediction of daily milk production and FA traits in Walloon Holstein dairy cattle.

Impact of Maternal Feed Restriction at Different Stages of Gestation on the Proteomic Profile of the Newborn Skeletal Muscle.

We aimed to investigate the effects of the maternal plane of nutrition during gestation on the proteome profile of the skeletal muscle of the newborn. Pregnant goats were assigned to the following experimental treatments: restriction maintenance (RM) where pregnant dams were fed at 50% of their maintenance requirements from 8−84 days of gestation, and then feed of 100% of the maintenance requirements was supplied from 85­parturition (n = 6); maintenance restriction (MR) where pregnant dams were fed at 100% of their maintenance requirements from 8−84 days of gestation, and then experienced feed restriction of 50% of the maintenance requirements from 85­parturition (n = 8). At birth, newborns were euthanized and samples of the Longissimus dorsi muscle were collected and used to perform HPLC-MS/MS analysis. The network analyses were performed to identify the biological processes and KEGG pathways of the proteins identified as differentially abundant protein and were deemed significant when the adjusted p-value (FDR) < 0.05. Our results suggest that treatment RM affects the energy metabolism of newborns' skeletal muscle by changing the energy-investment phase of glycolysis, in addition to utilizing glycogen as a carbon source. Moreover, the RM plane of nutrition may contribute to fatty acid oxidation and increases in the cytosolic α-KG and mitochondrial NADH levels in the skeletal muscle of the newborn. On the other hand, treatment MR likely affects the energy-generation phase of glycolysis, contributing to the accumulation of mitochondrial α-KG and the biosynthesis of glutamine.

Random regression test-day models to describe milk production and fatty acid traits in first lactation Walloon Holstein cows.

We investigated the use of different Legendre polynomial orders to estimate genetic parameters for milk production and fatty acid (FA) traits in the first lactation Walloon Holstein cows. The data set comprised 302,684 test-day records of milk yield, fat and protein contents, and FAs generated by mid-infrared (MIR) spectroscopy, C16:0 (palmitic acid), C18:1 cis-9 (oleic acid), LCFAs (long-chain FAs), SFAs (saturated FAs) and UFAs (unsaturated FAs) were studied. The models included random regression coefficients for herd-year of calving (h), additive genetic (a) and permanent environment (p) effects. The selection of the best random regression model (RRM) was based on the deviance information criterion (DIC), and genetic parameters were estimated via a Bayesian approach. For all analysed random effects, DIC values decreased as the order of the Legendre polynomials increased. Best-fit models had fifth-order (degree 4) for the p effect and ranged from second- to fifth-order (degree 1-4) for the a and h effects (LEGhap: LEG555 for milk yield and protein content; LEG335 for fat content and SFA; LEG545 for C16:0 and UFA; and LEG535 for C18:1 cis-9 and LCFA). Based on the best-fit models, an effect of overcorrection was observed in early lactation (5-35 days in milk [DIM]). On the contrary, third-order (LEG333; degree 2) models showed flat residual trajectories throughout lactation. In general, the estimates of genetic variance tended to increase over DIM, for all traits. Heritabilities for milk production traits ranged from 0.11 to 0.58. Milk FA heritabilities ranged from low-to-high magnitude (0.03-0.56). High Spearman correlations (>0.90 for all bulls and >0.97 for top 100) were found among breeding values for 155 and 305 DIM between the best RRM and LEG333 model. Therefore, third-order Legendre polynomials seem to be most parsimonious and sufficient to describe milk production and FA traits in Walloon Holstein cows.

Genetic study of quantitative traits supports the use of Guzerá as dual-purpose cattle.

OBJECTIVE: The aim of this study was to estimate genetic parameters for 305-day cumulative milk yield and components, growth, and reproductive traits in Guzerá cattle. METHODS: The evaluated traits were 305-day first-lactation cumulative yields (kg) of milk (MY305), fat (FY305), protein (PY305), lactose (LY305), and total solids (SY305); age at first calving (AFC) in days; adjusted scrotal perimeter (cm) at the ages of 365 (SP365) and 450 (SP450) days; and adjusted body weight (kg) at the ages of 210 (W210), 365 (W365), and 450 (W450) days. The (co)variance components were estimated using the restricted maximum likelihood method for single-trait, bi-trait and tri-trait analyses. Contemporary groups and additive genetic effects were included in the general mixed model. Maternal genetic and permanent environmental effects were also included for W210. RESULTS: The direct heritability estimates ranged from 0.16 (W210) to 0.32 (MY305). The maternal heritability estimate for W210 was 0.03. Genetic correlation estimates among milk production traits and growth traits ranged from 0.92 to 0.99 and from 0.92 to 0.99, respectively. For milk production and growth traits, the genetic correlations ranged from 0.33 to 0.56. The genetic correlations among AFC and all other traits were negative (-0.43 to -0.27). Scrotal perimeter traits and body weights showed genetic correlations ranging from 0.41 to 0.46, and scrotal perimeter and milk production traits showed genetic correlations ranging from 0.11 to 0.30. The phenotypic correlations were similar in direction (same sign) and lower than the corresponding genetic correlations. CONCLUSION: These results suggest the viability and potential of joint selection for dairy and beef traits in Guzerá cattle, taking into account reproductive traits.

Searching for causal relationships among latent variables concerning performance, carcass, and meat quality traits in broilers.

In causal relationship studies, the latent variables may summarize the phenotypes in theoretical traits according to their phenotypic correlations, improving the understanding of causal relationships between broilers phenotypes. In this study, we aimed to investigate potential causal relationships among latent variables in broilers using a structural equation model in the context of genetic analysis. The data used in this study comprised 14 traits in broilers with 2,017 records each, and 104,154 animals in pedigree. Four latent variables (WEIGHT, LOSSES, COLOUR, and VISCERA) were defined and validated using Bayesian Confirmatory Factor Analysis. Subsequently, a search for causal linkage structures was performed, obtaining a single causal link structure between the latent variables. Then, this information was used to fit the structural equation model (SEM). The results from the SEM indicated positive causal effects of the variables WEIGHT and LOSSES on the variables VISCERA and COLOUR, respectively, with structural coefficient estimates of 1.006 and 0.040, respectively. On the other hand, an antagonist causal effect of the variable WEIGHT on the variable LOSSES was verified, with a structural coefficient estimate of -4.333. These results highlight the causal relationship between performance and meat quality traits, which may be associated with the natural processes involved in the conversion of muscle into meat and the structural changes in muscle tissues due to intense selection for high growth rates in broilers.

A Comprehensive Comparison of Haplotype-Based Single-Step Genomic Predictions in Livestock Populations With Different Genetic Diversity Levels: A Simulation Study.

The level of genetic diversity in a population is inversely proportional to the linkage disequilibrium (LD) between individual single nucleotide polymorphisms (SNPs) and quantitative trait loci (QTLs), leading to lower predictive ability of genomic breeding values (GEBVs) in high genetically diverse populations. Haplotype-based predictions could outperform individual SNP predictions by better capturing the LD between SNP and QTL. Therefore, we aimed to evaluate the accuracy and bias of individual-SNP- and haplotype-based genomic predictions under the single-step-genomic best linear unbiased prediction (ssGBLUP) approach in genetically diverse populations. We simulated purebred and composite sheep populations using literature parameters for moderate and low heritability traits. The haplotypes were created based on LD thresholds of 0.1, 0.3, and 0.6. Pseudo-SNPs from unique haplotype alleles were used to create the genomic relationship matrix ( G ) in the ssGBLUP analyses. Alternative scenarios were compared in which the pseudo-SNPs were combined with non-LD clustered SNPs, only pseudo-SNPs, or haplotypes fitted in a second G (two relationship matrices). The GEBV accuracies for the moderate heritability-trait scenarios fitting individual SNPs ranged from 0.41 to 0.55 and with haplotypes from 0.17 to 0.54 in the most (Ne ≅ 450) and less (Ne < 200) genetically diverse populations, respectively, and the bias fitting individual SNPs or haplotypes ranged between -0.14 and -0.08 and from -0.62 to -0.08, respectively. For the low heritability-trait scenarios, the GEBV accuracies fitting individual SNPs ranged from 0.24 to 0.32, and for fitting haplotypes, it ranged from 0.11 to 0.32 in the more (Ne   ≅ 250) and less (Ne   ≅ 100) genetically diverse populations, respectively, and the bias ranged between -0.36 and -0.32 and from -0.78 to -0.33 fitting individual SNPs or haplotypes, respectively. The lowest accuracies and largest biases were observed fitting only pseudo-SNPs from blocks constructed with an LD threshold of 0.3 (p < 0.05), whereas the best results were obtained using only SNPs or the combination of independent SNPs and pseudo-SNPs in one or two G matrices, in both heritability levels and all populations regardless of the level of genetic diversity. In summary, haplotype-based models did not improve the performance of genomic predictions in genetically diverse populations.

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.

Effects of Ambient Temperature on the Performance and Thermoregulatory Responses of Commercial and Crossbred (Brazilian Piau Purebred Sires × Commercial Dams) Growing-Finishing Pigs.

The study aimed at evaluating the effects of high ambient temperature (HT: 30 °C) on the thermoregulatory responses and performance of commercial and Piau crossbred (Brazilian Piau breed sires × commercial genotype dams) growing pigs. Commercial and Piau crossbred pigs were reared under thermoneutral (TN: 22 °C) or HT conditions during a 14-day experimental period. Feeding (daily) and animals (beginning and end) were weighted to obtain performance parameters. Skin and rectal temperatures, respiratory rate, and blood parameters were also measured. At the end of the trial (day 15), the animal's backfat thickness (BF) and loin eye area (LEA) were measured. No interaction (p > 0.05) between the genetic group and ambient temperature was observed for any performance trait. Irrespective of ambient temperature, Piau crossbred pigs had a similar feed intake (ADFI, 2615 g/day, on average; p > 0.05), lower daily weight gain (ADG, -234 g/day; p < 0.01), and a higher feed conversion ratio (FCR, +0.675 g/g; p < 0.01). There was interaction (p = 0.01) between genotype and ambient temperature for the LEA that decreased significantly in response to HT in commercial pigs (-6.88 cm2) and did not differ in response to ambient temperature in Piau crossbred pigs (29.14 cm2, on average; p > 0.05). Piau crossbred pigs had greater BF (+7.2 mm; p < 0.01) than commercial pigs. Regardless of the genetic group, exposure of pigs to HT resulted in decreased ADFI (-372 g/day; p < 0.01), ADG (-185 g/day; p < 0.01), and a higher FCR (+0.48 g/g; p = 0.01). Ambient temperature did not affect lipid deposition. Pigs at HT had an increased respiratory rate (+38 bpm; p < 0.01) and a long-lasting increase in skin and rectal temperatures compared to TN pigs. Total concentrations of triiodothyronine (T3) and thyroxine (T4) were not affected by ambient temperature in commercial pigs, whereas Piau crossbred pigs kept at 30 °C had a transient decrease in both hormones at day 2 (p < 0.01). Serum cortisol concentrations were not affected (p > 0.05) by genotype nor ambient temperature. In summary, Piau crossbred pigs had lower efficiency using nutrients for growth in association with increased lipid deposition when compared to commercial pigs. In response to HT, commercial pigs had a decreased LEA, whereas no effect was observed for Piau crossbred pigs. Apart from that, commercial and Piau crossbred pigs had a similar magnitude of thermoregulatory responses activation in response to HT, evidencing their innate survival-oriented function.

Effects of heat stress on performance and thermoregulatory responses of Piau purebred growing pigs.

The study of how different breeds adapt to heat stress and the further understanding of mechanisms underlying pigs thermotolerance is of utmost importance to attenuate the negative effects of heat stress on pigs welfare, physiology, and performance. Therefore, this study aimed at evaluating the effects of ambient temperature on performance and thermoregulatory responses of Piau purebred pigs. The Brazilian native pig breed Piau is a fat-type breed characterized by adaptability and resistance to diseases. To achieve our goal, Piau purebred pigs (65 kg initial BW) were allocated to one of the two constant ambient temperature conditions: thermoneutral (22 °C; n = 11) and heat stress (30 °C; n = 11). The experimental period lasted 15 days (days 1 to 15). Pigs were individually weighed at the beginning and end of the experimental period. Body and rectal temperatures, respiratory rate and blood indicators of stress and metabolism were measured throughout the experiment. Piau purebred pigs exposed to 30 °C had lower (p < 0.05) feed intake, body weight gain and final body weight than pigs at 22 °C. Feed conversion rate was not affected (p > 0.05) by ambient temperature. Irrespective of ambient temperature, pigs had similar (p > 0.05) backfat thickness and loin eye area. Piau pigs at 30 °C had increased (p < 0.05) nape, dorsal, flank, and rectal temperatures and increased respiratory rate than their counterparts reared at 22 °C. In summary, our results show that Piau purebred pigs acclimation to 30 °C of ambient temperature is characterized by increased body skin temperature to optimize sensible heat loss to the environment; increased respiratory rate to promote latent heat loss; and by a concomitant reduced voluntary feed intake to reduce heat production associated with digestion and metabolic processes with negative effects on body weight gain.

Proteomic Analysis of Liver from Finishing Beef Cattle Supplemented with a Rumen-Protected B-Vitamin Blend and Hydroxy Trace Minerals.

Vitamin B and trace minerals are crucial molecular signals involved in many biological pathways; however, their bioavailability is compromised in high-producing ruminant animals. So far, studies have mainly focused on the effects of these micronutrients on animal performance, but their use in a rumen-protected form and their impact on liver metabolism in finishing beef cattle is poorly known. We used a shotgun proteomic approach combined with biological network analyses to assess the effects of a rumen-protected B-vitamin blend, as well as those of hydroxy trace minerals, on the hepatic proteome. A total of 20 non-castrated Nellore males with 353 ± 43 kg of initial body weight were randomly assigned to one of the following treatments: CTRL-inorganic trace minerals without supplementation of a protected vitamin B blend, or SUP-supplementation of hydroxy trace minerals and a protected vitamin B blend. All animals were fed the same amount of the experimental diet for 106 days, and liver biopsies were performed at the end of the experimental period. Supplemented animals showed 37 up-regulated proteins (p < 0.10), and the enrichment analysis revealed that these proteins were involved in protein folding (p = 0.04), mitochondrial respiratory chain complex I (p = 0.01) and IV (p = 0.01), chaperonin-containing T-complex 2 (p = 0.01), glutathione metabolism (p < 0.01), and other aspects linked to oxidative-stress responses. These results indicate that rumen-protected vitamin B and hydroxy trace mineral supplementation during the finishing phase alters the abundance of proteins associated with the electron transport chain and other oxidation-reduction pathways, boosting the production of reactive oxygen species, which appear to modulate proteins linked to oxidative-damage responses to maintain cellular homeostasis.

Autoregressive single-step model for genomic evaluation of longitudinal reproductive traits in portuguese holstein cattle.

We investigated the applicability of ssGBLUP methodology under the autoregressive model (H-AR) for genomic evaluation of longitudinal reproductive traits in Portuguese Holstein cattle. The genotype data of 1,230 bulls and 1,645 cows were considered in our study. The reproductive traits evaluated were interval from calving to first service (ICF), calving interval (CI) and daughter pregnancy rate (DPR) measured during the first four parities. Reliability and rank correlation were used to compare the H-AR with the traditional pedigree-based autoregressive models (A-AR). In addition, a validation study was performed considering different scenarios. Higher genomic estimated breeding values (GEBV) reliabilities were obtained for genotyped bulls when evaluated under the H-AR model, with emphasis on bulls with less than 9 daughters. For this group, the averages of GEBV reliabilities corresponded to 0.62, 0.69 and 0.62 for ICF, CI and DPR, respectively, while the averages obtained by the A-AR model were 0.27, 0.15 and 0.16. The validation study was favourable to H-AR. The best results were observed in the scenario where genotyped cows were combined with contributing bulls (genotyped bulls with daughter or relationship information in the population). Overall, the results suggest that ssGBLUP methodology under the autoregressive model is a feasible and applicable approach to be used in genomic analyses of longitudinal reproductive traits in Portuguese Holstein cattle.