A meta-analysis of genome-wide association studies to identify candidate genes associated with feed efficiency traits in pigs.

Pig production is an agricultural sector of great economic and social relevance to Brazil and global markets. Feed efficiency traits directly influence the sustainability of pig production due to the economic impact of feed costs on the production system and the environmental footprint of the industry. Therefore, breeding for improved feed efficiency has been a target of worldwide pig breeding programs.

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.

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.

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.

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.

Assessment of runs of homozygosity, heterozygosity-rich regions and genomic inbreeding estimates in a subpopulation of Guzerá (Bos indicus) dual-purpose cattle.

For decades, inbreeding in cattle has been evaluated using pedigree information. Nowadays, inbreeding coefficients can be obtained using genomic information such as runs of homozygosity (ROH). The aims of this study were to quantify ROH and heterozygosity-rich regions (HRR) in a subpopulation of Guzerá dual-purpose cattle, to examine ROH and HRR islands, and to compare inbreeding coefficients obtained by ROH with alternative genomic inbreeding coefficients.

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.

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.

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.

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.

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 -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 matrix. A total of 302 684 test-day records of 63.875 first lactation Walloon Holstein cows were used.

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 85—parturition (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 85—parturition (n = 8). At birth, newborns were euthanized and samples of the Longissimus dorsi muscle were collected and used to perform HPLC-MS/MS analysis.

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.

Assessing the effect of () (Linnaeus, 1762) control based on machine learning for predicting the spatiotemporal distribution of eggs in ovitraps.

Background: is the dominant vector of several arboviruses that threaten urban populations in tropical and subtropical countries. Because of the climate changes and the spread of the disease worldwide, the population at risk of acquiring the disease is increasing.

Methods: This study investigated the impact of the larval habitats control (CC), nebulization (NEB), and both methods (CC + NEB) using the distribution of Ae.

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.

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.

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.

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.

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.

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.

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.

Genotype by environment interaction for Holstein cattle populations using autoregressive and within- and across-country multi-trait reaction norms test-day models.

The progenies of international bulls in diverse climatic conditions and management levels may lead to different expressions of their genetic potential resulting in a re-ranking of these bulls. Therefore, evaluate the presence of genotype by environment interaction (G×E) within and across countries is important to guide the decision-making on alternative selection strategies. Thus, a two-step reaction norm (RN) approach was used to investigate the presence of G×E in Portuguese and Brazilian Holstein cattle.

Exploring the use of residual variance for uniformity of body weight in meat quail lines using Bayesian inference.

1. Uniformity in animal products is an important aspect of the production system. Several studies have reported estimates of genetics on residual variance in different species, indicating that it could be exploited to improve uniformity by selection.

Dietary nucleotide supplementation as an alternative to in-feed antibiotics in weaned piglets.

Nucleotides are important to cell growth and division and are crucial to the rapid proliferation of such cells as the intestinal mucosa and immune cells. Accordingly, the nucleotide requirements of animals are high during periods of rapid growth and periods of stress like post-weaning period. Thus, nucleotide supplementation may be a possible alternative to in-feed antibiotics as growth promoter in this phase.