Paulo Sávio Lopes

Federal University of Viçosa | UFV · Department of Animal Science

Knowledge of dominance effects should improve ge-netic evaluations, provide the accurate selection of purebred animals, and enable better breeding strategies, including the exploitation of het-erosis in crossbreeds. In this study, we combined genomic and pedi-gree data to study the relative importance of additive and dominance genetic variation in...

The objective of this study was to estimate genetic parameters and to evaluate the effects of inbreeding on productive and reproductive traits of dairy Gyr cattle. Single-trait animal models were used to estimate genetic parameters and solutions for inbreeding coefficients for milk (milk 305-d), fat (fat 305-d), protein (protein 305-d), lactose (la...

Reproductive traits as number of piglets born (NPB) and weaned (NWP) are directly related to the economic efficiency of swine production systems. Pig breeding programs seek to increase the number of weaned piglets per sow per year, and the NPB is among the factors that directly and indirectly influence the NWP. Thus, multi-trait evaluations are ess...

This study aimed to assess the effects of different cooling curves and centrifugation regimes used in cryopreservation protocols on the post-thaw viability of Piau-breed wild boar (Sus scrofa) sperm using in vitro assessment tests. Two centrifugations (800 g for 10 min and 2400 g for 3 min) and two cooling curves (conventional cooling using nitroge...

This study aimed to compare two different Genome-Wide Selection (GWS) methods (Ridge Regression BLUP - RR-BLUP and Bayesian LASSO - BL) to predict the genomic estimated breeding values (GEBV) of four phenotypes, including two boar taint compounds, i.e., the concentrations of androstenone (andro) and skatole (ska), and two carcass traits, i.e., back...

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 h...

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 ca...

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 is...

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...

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...

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 g...

We aimed to reduce the dimensionality of quantitative traits in pigs applying factor analysis. Quantitative variables were collected, and the factor analysis extracted five factors with biological meaning related to performance, carcass quality, carcass yield, meat quality, and initial pH. These factors were posteriorly used as dependent variable t...

Context. Boar taint compounds (androstenone, skatole and indole) can be measured in pig carcasses, after slaughter or, alternatively, in biopsies of subcutaneous adipose tissue from selected living pigs. Measuring these compounds via biopsy enables data collection in selected animals and high standardisation regarding tissue-collection procedures f...

We aimed to estimate genetic parameters for growth, reproductive, and carcass traits in Tabapuã cattle. Phenotypic data were collected between 1990 and 2019 in 1,218 farms, and the pedigree file had 340,868 animals. The traits evaluated were body weight at 120 (W120), 210 (W210), 365 (W365), and 550 (W550) days of age; age at first calving (AFC), s...

The Guzerá breed evolved from the introduction of breeds from India, mainly the Kankrej breed, into Brazilian livestock at the end of the 19th century. Guzerá adapted well to the climatic conditions of Brazil, where it is considered a dual-purpose breed and has been used for pasture-based beef, milk or dual-purpose production systems with the use o...

This study aimed to investigate the feasibility of genomic prediction for productive and reproductive traits in Guzerá cattle using the single-step genomic BLUP (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 days, 3...

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 m...

This study aimed to estimate genetic parameters, effective population size, inbreeding, and inbreeding depression for birth weight, weaning weight, and average pre-weaning daily weight gain (ADG) in Piau breed pigs. We used information from 3841 Piau pigs, and four linear models were fitted in single trait analyzes including or excluding maternal g...

Efficient computing techniques allow the estimation of variance components for virtually any traditional dataset. When genomic information is available, variance components can be estimated using genomic REML (GREML). If only a portion of the animals have genotypes, single-step GREML (ssGREML) is the method of choice. The genomic relationship matri...

This study aimed to evaluate the endometrial angiogenesis of pregnant commercial line and Piau gilts during early pregnancy. We used 27 gilts, divided into three groups according to the type of mating: Commercial (n = 9), commercial line females mated with commercial line males; Cross-mated (n = 9), Piau females mated with commercial line males; an...

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 aci...

The weighted single-step genome-wide association study (WssGWAS) and post-GWAS analysis may be a useful tool to identify quantitative trait loci (QTL) and candidate genes linked to economically important phenotypes, such as boar taint in pigs. The boar taint is an unpleasant taste and smell observable at uncastrated pork cooking. Therefore, we aime...

Efficient computing techniques allow the estimation of variance components for virtually any traditional dataset. When genomic information is available, variance components can be estimated using genomic REML (GREML). If only a portion of the animals have genotypes, single-step GREML (ssGREML) is the method of choice. The genomic relationship matri...

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 fir...

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 fir...

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 structur...

Objetivamos estimar parâmetros genéticos para os parâmetros da curva de crescimento não-linear de Gompertz com base no método em duas etapas e em dados simulados de uma população de suínos. Dados de valores genéticos reais, dos parâmetros da curva de crescimento (a, b e k) e dos pesos corporais aos 1, 90, 210, 360 e 540 dias de idade foram simulado...

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. Nevertheless, there are no reports about the possibilities of such a selection strategy in meat qua...

Reproductive efficiency is major determinant of the dairy herd profitability. Thus, reproductive traits have been widely used as selection objectives in the current dairy cattle breeding programs. We aimed to evaluate strategies to model days open (DO), calving interval (CI), and daughter pregnancy rate (DPR) in Brazilian Holstein cattle. These rep...

Biological information regarding markers and gene association may be used to attribute different weights for single nucleotide polymorphism (SNP) in genome‐wide selection. Therefore, we aimed to evaluate the predictive ability and the bias of genomic prediction using models that allow SNP weighting in the genomic relationship matrix (G) building, w...

Pedigree information is incomplete by nature and commonly not well-established because many of the genetic ties are not known a priori or can be wrong. The genomic era brought new opportunities to assess relationships between individuals. However, when pedigree and genomic information are used simultaneously, which is the case of single-step genomi...

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 alte...

The profitability of dairy activity is influenced by the genetic selection of economically important traits. In this context, the correct estimation of genetic parameters and the knowledge regarding candidate genes involved in the expression of genetically associated traits may help develop appropriate breeding strategies for the Guzerá breed. In t...

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), ca...

Reproductive performance is one of the most important factors for the productive efficiency in beef cattle production. Biometric testicular and physical and morphological traits of the ejaculate are used to evaluate the reproductive performance of bulls. The phenotypic data of semen physical and morphological traits are expressed in percentage or n...

This study aimed to estimate the genetic parameters of milk (305-day milk yield (MY305)), growth (weaning weight (WW), yearling weight (YW), and weight at 550 days (W550)), and reproductive (age at first calving (AFC)) traits in Guzerá cattle by using Bayesian multiple-trait models. Systematic effects included sex and age at calving for the growth...

This study focused on the identification of QTL regions, candidate genes, and network related genes based on the first 3 lactations (LAC3) of milk, fat, and protein yields, and somatic cell score (SCS) in Portuguese Holstein cattle. Additionally, the results were compared with those from only first lactation (LAC1) data. The analyses were performed...

We aimed to estimate litter size and litter uniformity genetic parameters and genetic trends of Landrace pigs at birth and at three weeks by using multitrait analyses for 2,787 litters. The following litter traits were evaluated: number of piglets born alive (NBA), within-litter weight mean at birth (MBW), within-litter weight standard deviation at...

As crossbreeding is extensively used in some livestock species, we aimed to evaluate the performance of single-step GBLUP (ssGBLUP) and weighted ssGBLUP (WssGBLUP) methods to predict Genomic Estimated Breeding Values (GEBVs) of crossbred animals. Different training population scenarios were evaluated: (SC1) ssGBLUP based on a single-trait model con...

Scrotal circumference of bulls is correlated with pubertal age of female offspring. Hormonal control of reproductive function is similar in males and females, which may result in genetic correlation among different reproductive traits measured in the two sexes. The estimation of heritability and genetic correlations allows for the computation of di...

We investigated the efficiency of the autoregressive repeatability model (AR) for genetic evaluation of longitudinal reproductive traits in Portuguese Holstein cattle and compared the results with those from the conventional repeatability model (REP). The data set comprised records taken during the first four calving orders, corresponding to a tota...

We aimed to evaluate multiple-trait Bayesian models for handling censored records in genetic evaluations of age at first calving (AFC) and stayability (STAY) in Nellore cattle. Phenotypic and pedigree datasets were provided by Brazilian Association of Zebu Breeders. Four models were evaluated: linear-threshold model (LTM), penalty-threshold model (...

Autoregressive (AR) and random regression (RR) models were fitted to test‐day records from the first three lactations of Brazilian Holstein cattle with the objective of comparing their efficiency for national genetic evaluations. The data comprised 4,142,740 records of milk yield (MY) and somatic cell score (SCS) from 274,335 cows belonging to 2,32...

• The aim of this study was to investigate the associations between several carcass, performance and meat quality traits in broilers through factor analysis and use the latent variables (i.e. factors) as pseudo-phenotypes in genetic evaluations. • Factors were extracted using the principal components method and varimax rotation algorithm. Genetic p...

Nellore is the main cattle breed used in Brazil, being the largest commercial herd in the world. Beyond the importance of male reproductive efficiency for farm profit, the use of reproductive techniques, mainly artificial insemination, turns the evaluation of male reproductive traits even more important. Estimation of genetic parameters increases t...

Although several studies have investigated the factors affecting imputation accuracy, most of these studies involved a large number of genotyped animals. Thus, results from these studies cannot be directly applied to small populations, since the population structure affects imputation accuracy. In addition, factors affecting imputation accuracy may...

O melhoramento animal é uma ciência preditiva que tem na variabilidade genética do rebanho a sua base e na seleção uma importante ferramenta de ação, cuja eficiência é ponderada pela herdabilidade das características de importância econômica, que é um parâmetro específico de cada rebanho. Por ser bom indicador das consequências do manejo genético n...

We aimed to evaluate the effects of paternal genotypes (Piau, Duroc-based, and Pietrain) and nutritional plans with different digestible lysine contents (Low, Medium, and High) on performance, carcass, and meat quality traits of pigs. Pietrain and Duroc crossbred barrows and gilts were similar in performance and carcass traits and had the greatest...

Objetivou-se avaliar metodologias para a predição genômica de animais cruzados por meio de dados simulados. Foram simuladas populações Bos indicus (L1), Bos taurus (L2) e animais provenientes do cruzamento dessas duas populações (F1). A característica simulada foi o consumo alimentar residual (herdabilidade = 0,33 e variância fenotípica = 12,5). Qu...

Resumo: A caracterização de raças naturalizadas é importante para que se possa traçar estratégias de conservação eficientes. Objetivou-se estimar parâmetros genéticos para peso ao nascimento e peso ao desmame para suínos da raça Piau. Foram utilizadas 3813 pesagens de leitões provenientes do programa de conservação de suínos da raça Piau da Unidade...

We aimed to characterize the expression of angiogenesis-related genes in corpus luteum (CL) and cumulus cells (CC) during estrous cycle in gilts of different genetic groups, as well as to study the relation between gene expression and phenotypic data. Forty five gilts were used as follows: L1, Commercial Line 1 (Large White x Landrace x Duroc) (n =...

Feed efficiency (FE) is one of the most important traits in pig production. However, it is difficult and costly to measure it, limiting the collection of large amount of data for an accurate selection for better FE. Therefore, the identification of single-nucleotide polymorphisms (SNPs) associated with FE-related traits to be used in the genetic ev...

We evaluated the inclusion of information on genetic relationship into the analysis of crude protein requirement in diets for pigs of Brazilian Piau breed, using Bayesian inference. The animals were assigned to treatments in a completely randomized design in factorial scheme 4 × 2 (crude protein levels × sex) with 12 repetitions per treatment. The...

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 te...

We compared Hurdle Poisson (Hupoisson), Zero Inflated Poisson (Zipoisson), Poisson and Gaussian Bayesian mixed models for genetic evaluation of litter traits in pigs (number of piglets born alive – NBA; number of piglets weaned – NW; and mortality during the suckling period – MORT). The models’ goodness-of-fit was based on Deviance Information Crit...

A epigenética é definida como mudanças na expressão gênica que podem ser herdadas e que não alteram a sequência do DNA. Existem dois mecanismos epigenéticos principais, a metilação do DNA e a modificação de histonas. Também se destaca o imprinting genômico, o qual está relacionado com a regulação gênica quando apenas um alelo (herdado do pai ou da...

Test-day milk, fat and protein yields and somatic cell score (SCS) of Brazilian Holstein cattle were used to study the effect of fixed (HTDF) vs random (HTDR) contemporary groups (herd-test-date) with or without unknown parent groups (UPG) using an autoregressive test-day animal model for genetic evaluations. Therefore, four models were used in thi...

We compared different Bayesian models to handle censored data for genetic parameters estimation of age at first calving (AFC) in Brazilian Brahman cattle. Data from females with AFC above 1825 days of age were assumed to have failed to calve and were considered as censored records. Data including information of 53,703 cows were analyzed through the...

The objective of this work was to evaluate the use of regularized quantile regression (RQR) to predict the genetic merit of pigs for asymmetric carcass traits, compared with the Bayesian lasso (Blasso) method. The genetic data of the traits carcass yield, bacon thickness, and backfat thickness from a F2 population composed of 345 individuals, gener...

• The aim of the following experiment was to estimate transgenerational epigenetic variance for egg quality traits using genealogical and phenotypic information in meat-type quail. Measured traits included egg length (EL) and width (EWD), albumen weight (AW), shell weight (SW), yolk weight (YW), and egg weight (EW). • A total of 391 birds were eval...

Background: In recent years, there has been increased interest in the study of the molecular processes that affect semen traits. In this study, our aim was to identify quantitative trait loci (QTL) regions associated with four semen traits (motility, progressive motility, number of sperm cells per ejaculate and total morphological defects) in two...

We aimed to evaluate the impact of using embryo transfer (ET) information on weaning weight estimated breeding values (EBV) and its accuracy. Data from Hereford and Braford cattle, raised under extensive conditions in Southern Brazil, were used. A model that included ET information in addition to maternal (genetic and permanent environmental) effec...

Expression of lipid metabolism and myosin heavy chain genes was evaluated in skeletal muscle of pig’s genotypes submitted to different dietary digestible lysine contents. Fifty-two barrows and fifty gilts from three genotypes (G: Piau, Duroc and Pietrain crossbreds) were assigned to three dietary digestible lysine contents (DL: Low, Medium and High...

Selection for feed efficiency (FE) is a strategy to reduce the production costs per unit of animal product, which is one of the major objectives of current animal breeding programs. In pig breeding, selection for FE and other traits traditionally takes place based on purebred pig (PB) performance at the nucleus level, while pork production typicall...

In view of the importance of the genetic material of local breeds in the swine industry and the lack of information about reproductive performance of Piau females, two experiments were conducted to evaluate puberty and sexual maturity as well as the morphometry of embryos/fetuses, placenta and uterus during the first 90 days of gestation in Piau br...

We combined linkage (LA) and linkage disequilibrium (LDA) analyses (emerging the term ‘LALDA’) for genomic selection (GS) purposes. The models were fitted to a simulated dataset and to a real data of feed conversion ratio in pigs. Firstly, the significant QTLs (quantitative trait locus) were identified through LA-based mixed models considering the...

Contents The objective was to study the use of ultrasound as a complementary test in the breeding soundness evaluation in male pigs and study the pattern of echogenicity of the testicular parenchyma in boars of different racial groups. Twenty‐six adult boars from four different racial groups were used, 10 from the Piau breed (group 1), four from th...

Age at first calving (AFC) is characterized as a censored trait due to missing values provided by recording mistakes and non-occurrence or delay in calving communication. In this context, we aimed to compare several statistical methods for genetic evaluation of AFC in Guzerá beef cattle under a Bayesian approach. Seven different methods were used f...

We aimed to estimate genetic parameters for semen quality and quantity traits as well as for within-boar variation of these traits to evaluate their inclusion in breeding goals. Genetic parameters were estimated within line using a multiple-trait (4 × 4) repeatability animal model fitted for 5 pig lines, considering 4 semen traits: sperm motility (...

For reproductive traits such as total number born (TNB), variance due to different environments is highly relevant in animal breeding. In this study, we aimed to perform a gene-network analysis for TNB in pigs across different environments using genomic reaction norm models. Thus, based on relevant single-nucleotide polymorphisms and linkage disequ...