Guilherme J. M. Rosa

• PhD
• Professor (Full) at University of Wisconsin–Madison

n sheep, severe anemia often results from gastrointestinal nematode infections, commonly caused by Haemonchus contortus, a blood-sucking nematode. The objective of this study was to develop a model to predict packed cell volume (PCV) in sheep through ocular conjunctiva images as a real-time anemia diagnosis approach. The dataset consisted of 3,441...

Non-contact anterior cruciate ligament (ACL) rupture is a common serious orthopaedic disease in humans and dogs. Familial risk has been recognized in both species but interactions between genetic effects and environmental risk are not understood. We investigated ACL rupture heritability, genetic architecture, selection pressure, sharing of risk gen...

Ruminants have the ability to digest human-inedible plant materials, due to the symbiotic relationship with the rumen microbiota. Rumen microbes supply short chain fatty acids, amino acids, and vitamins to dairy cows that are used for maintenance, growth, and lactation functions. The main goal of this study was to investigate gene-microbiome networ...

Haemonchus contortus is an extremely harmful blood-feeding nematode affecting small ruminants, leading to anemia, weight loss, and, in severe cases, animal death. Traditional methods of monitoring anemia in sheep, such as regular physical examinations by veterinarians and laboratory tests, can be expensive and time-consuming. In this work, we propo...

The “Precoce MS” program, established by the Brazilian government in Mato Grosso do Sul in 2017, aims to encourage beef producers to harvest animals at younger ages to enhance carcass quality. About 40% of the beef produced in the state now comes from this program, which offers tax refunds ranging from 49% to 67% based on carcass classification and...

Precision livestock farming aims to individually and automatically monitor animal activity to ensure their health, well-being, and productivity. Computer vision has emerged as a promising tool for this purpose. However, accurately tracking individuals using imaging remains challenging, especially in group housing where animals may have similar appe...

The rumen microbiome is crucial for converting feed into absorbable nutrients used for milk synthesis, and the efficiency of this process directly impacts the profitability and sustainability of the dairy industry. Recent studies have found that the rumen microbial composition explains part of the variation in feed efficiency traits, including dry...

Background Various blood metabolites are known to be useful indicators of health status in dairy cattle, but their routine assessment is time-consuming, expensive, and stressful for the cows at the herd level. Thus, we evaluated the effectiveness of combining in-line near infrared (NIR) milk spectra with on-farm (days in milk [DIM] and parity) and...

In this study, we explored the integration of machine learning (ML) techniques with feeding behavior (FB) time series data to predict mortality events (animals culled or found dead) in floor-raised broilers. Our dataset included 2,667,617 daily observations for eight FB traits from 95,711 birds across 146 feeding trials. After data cleaning, the cl...

In sheep, severe anemia often results from gastrointestinal nematodes infections, commonly caused by Haemonchus contortus, a blood-sucking nematode. The objective of the study was to develop a model to predict packed cell volume (PCV) in sheep through ocular conjunctiva images as a real-time anemia diagnosis approach. We collected 3,291 ocular conj...

Existing literature on the long-term effects of nutritional manipulation on milk production is incomplete and inconsistent as animals are typically culled before lactation. In addition, longitudinal studies are rarely conducted due to high costs and constraints related to tissue sampling; therefore, additional research is necessary to better unders...

The objective was to assess differences in productive and reproductive performance, and survival associated with vaginal discharge characteristics and fever in post-partum dairy cows located in Western and Southern states of the U.S.A. This retrospective cohort study included data from 3 experiments conducted in 9 dairies. Vaginal discharge was eva...

This study aimed to estimate genetic parameters for feeding behavior (FB) traits and to assess their genetic relationship with performance traits in group-housed broilers. In total, 99,472,151 visits were recorded for 95,711 birds between 2017 and 2022 using electronic feeders. The visits were first clustered into 2,667,617 daily observations for t...

Genomic selection (GS) offers a promising opportunity for selecting more efficient animals to use consumed energy for maintenance and growth functions, impacting profitability and environmental sustainability. Here, we compared the prediction accuracy of multi-layer neural network (MLNN) and support vector regression (SVR) against single-trait (STG...

Identifying genome-enabled methods that provide more accurate genomic prediction is crucial when evaluating complex traits such as dairy cow behavior. In this study, we aimed to compare the predictive performance of traditional genomic prediction methods and deep learning algorithms for genomic prediction of milking refusals (MREF) and milking fail...

Large amounts of data are routinely collected in pig production, including operational farm data and, more recently, data from digital tools such as remote and on-site sensing technologies. Furthermore, additional sources of information, such as demographic, economic, and weather variables, can be combined with farm data. Integrating and analyzing...

Animal breeding is one of the main pillars of livestock production. Statistics, computer science, and genomics have transformed productivity in the industry. Another round of breakthroughs is expected to come from harnessing the power of big data and machine learning analytics to address the complex interaction between animal genetics and the envir...

Accurate measurement of target traits in individual animals or groups of animals under different environmental conditions, such as varying diets, disease treatments, and management practices, is crucial for the progress of livestock research. While experimental studies on research farms ensure internal validity of results, observational studies on...

Leg disorders (LD) pose serious welfare issues in broiler chickens. The objective of this study was to investigate the suitability of using feeding behavior (FB) traits as potential leg health indicators in floor-raised broilers. The data used were recorded from 95,711 pure-line chickens of both sexes. The individual FB was monitored continuously o...

This study aimed to assess the predictive ability of parametric models and artificial neural network method for genomic prediction of the following indicator traits of resistance to gastrointestinal nematodes in Santa Inˆes sheep: packed cell volume (PCV), fecal egg count (FEC), and Famacha© method (FAM). After quality control, the number of genoty...

Haemonchus contortus is the most pathogenic blood-feeding parasitic in sheep, causing anemia and consequently changes in the color of the ocular conjunctiva, from the deep red of healthy sheep to shades of pink to practically white of non-healthy sheep. In this context, the Famacha method has been created for detecting sheep unable to cope with the...

Keywords Broiler chicken; genomic best linear unbiased prediction; genome-enabled prediction; marker density; marker effect sizes; minor allele frequency; predictive ability. Summary The objective was to assess goodness of fit and predictive ability of subsets of single nucleotide polymorphism (SNP) markers constructed based on minor allele frequen...

Introduction: Spontaneous rupture of tendons and ligaments is common in several species including humans. In horses, degenerative suspensory ligament desmitis (DSLD) is an important acquired idiopathic disease of a major energy-storing tendon-like structure. DSLD risk is increased in several breeds, including the Peruvian Horse. Affected horses hav...

Cloning cattle using somatic cell nuclear transfer (SCNT) is inefficient. While the rate of development of SCNT embryos in vitro is similar to that of fertilized embryos, most fail to develop into healthy calves. In this study, we aimed to identify developmentally competent embryos according to blastocyst cell composition and perform transcriptome...

Sire selection for beef on dairy crosses plays an important role in livestock systems as it may affect future performance and carcass traits of growing and finishing crossbred cattle. The phenotypic variation found in beef on dairy crosses has raised concerns from meat packers due to animals with dairy-type carcass characteristics. The use of morph...

Many studies on bovine mammary glands focus on one stage of development. Often missing in those studies are repeated measures of development from the same animals. As milk production is directly affected by amount of parenchymal tissue within the udder, understanding mammary gland growth along with visualization of its structures during development...

This study investigates non-linear kernels for multi-trait genomic prediction using support vector regression (SVR) models. We assessed the predictive ability delivered by single-trait (ST) and multi-trait (MT) models for two carcass traits (CT1 and CT2) measured in purebred broiler chickens. The MT models also included information on indicator tra...

Simple Summary Body and carcass weight are important economic characteristics for beef cattle production systems because the value of market cattle is based on weight. The possibility of predicting body and carcass weight through biometric measurements obtained from three-dimensional digital images favor the development of the production system. Pr...

Considering the economic and commercial efficiency of the beef production chain, the yield and quality of the meat produced must also be included in breeding programs. For the Nellore breed, including the polled herd, these aspects have not been much studied. The aim of this study was to estimate genetic parameters for scrotal circumference adjuste...

Subfertility represents one major challenge to enhancing dairy production and efficiency. Herein, we use a reproductive index (RI) expressing the predicted probability of pregnancy following artificial insemination with Illumina 778K genotypes to perform single and multi-locus genome-wide association analyses (GWAA) on 2,448 geographically diverse...

Simple Summary Infection by gastrointestinal nematodes is a major sanitary issue in sheep production. Therefore, improvements in the animal’s health are important to reduce losses and improve animal welfare. Thus, this study investigated the feasibility of using easy-to-measure phenotypic traits to predict sheep resistant, resilient, and susceptibl...

Here, we report the use of genome-wide association study (GWAS) for the analysis of canine whole-genome sequencing (WGS) repository data using breed phenotypes. Single-nucleotide polymorphisms (SNPs) were called from WGS data from 648 dogs that included 119 breeds from the Dog10K Genomes Project. Next, we assigned breed phenotypes for hip dysplasia...

Background Feed efficiency during lactation involves a set of phenotypic traits that form a complex system, with some traits exerting causal effects on the others. Information regarding such interrelationships can be used to predict the effect of external interventions on the system, and ultimately to optimize management practices and multi-trait s...

Different selection indexes (Index I [Optimal], Index II [Maternal], and Index III [Terminal]) were evaluated in a full-cycle, pasture-based production system of Nellore cattle. The economic selection indexes consisted of combinations of the traits: body weight at 120 (W120), 210 (W210), 365 (W365), and 450 days (W450) of age; age at first calving...

The association between health and pregnancy per artificial insemination, maintenance of pregnancy, and interval to pregnancy in dairy cattle is well documented. However, the understanding of the causal relationships among health and fertility traits is limited. Although information on heritabilities and genetic correlations between traits is key f...

This study was carried out to evaluate the advantage of preselecting SNP markers using Markov blanket algorithm regarding the accuracy of genomic prediction for carcass and meat quality traits in Nellore cattle. This study considered 3675, 3680, 3660 and 524 records of rib eye area (REA), back fat thickness (BF), rump fat (RF), and Warner-Bratzler...

In this study, we investigated the performance of different machine learning (ML) methods for predicting withdrawing events (culled or dead animals) according to feeding behaviors (FB) time series. The raw data comprised a total of 1,492,482 daily observations for six FB traits from 55,400 birds allocated into 88 trials. After data editing, the ove...

Body condition score (BCS) is a commonly used tool to monitor body tissue mobilization in dairy cows and manage potential health issues associated with negative energy balance. However, BCS is a subjective measurement that requires a trained evaluator and is time-consuming. Consequently, the development of a computer vision system to assess BCS in...

The notion of contemporary groups (CG) is routinely used in beef cattle breeding programs for adjusting phenotypic observations for environmental effects. Although CG include the effect of farms, they do not allow information borrowing across farms as the CG are generally modeled either as fixed effects or as statistically independent random effect...

The Famacha© method has been created for detecting sheep unable to cope with the infection by Haemonchus contortus, through visual assessment of ocular conjunctiva coloration. The objective of this study was to develop a computer vision system (CVS) for prediction of Famacha© degree (FAM) from ocular conjunctiva images. The dataset consisted of 475...

This study aimed to assess the genetic relationship among feeding behavior (FB), feed efficiency (FE), and production traits in broilers. A total of 44,234,350 feeders visit logs from 55,400 birds allocated into 88 trials were recorded by radio-frequency identification system. The daily data were averaged per animal for FB traits, considering the e...

The objective was to investigate the feasibility of using easy-to-measure phenotypic traits to predict resistant, resilient and susceptible sheep to gastrointestinal nematodes via multinomial logistic regression (MLR). The database comprised 3,654 records on 1,250 Santa Ines sheep from six farms. The animals were classified into three responses to...

The objective of this observational prospective cohort study was to evaluate the combined effect of purulent vaginal discharge (PVD) and anovulation (ANOV) on the reproductive performance of a large multi-state population of Holstein cows. Data were prospectively collected from 11,729 cows in 16 herds located in 4 regions in the United States [Nort...

Abstract This study aimed to explore the effects of additive and non-additive genetic effects on the prediction of complex traits using Bayesian regularized artificial neural network (BRANN). The data sets were simulated for two hypothetical pedigrees with five different fractions of total genetic variance accounted by additive, additive x additive...

Abstract This study aimed to explore the effects of additive and non-additive genetic effects on the prediction of complex traits using Bayesian regularized artificial neural network (BRANN). The data sets were simulated for two hypothetical pedigrees with five different fractions of total genetic variance accounted by additive, additive x additive...

We fit the Wood's lactation model to an extensive database of test-day milk production records of US Holstein cows to obtain lactation-specific parameter estimates and investigated the effects of temporal, spatial, and management factors on lactation curve parameters and 305-d milk yield. Our approach included 2 steps as follows: (1) individual ani...

Advances in machine learning techniques have allowed the development of computer vision systems (CVS) that can accurately predict several phenotypes of interest for livestock operations. In this context, 3D images taken from a top-down view are particularly useful for estimating body condition score, growth development, and body biometrics in cattl...

Degenerative suspensory ligament (SL) desmitis (DSLD) is a progressive idiopathic condition that leads to scarring and rupture of SL fibers in multiple limbs in horses. Prevalence of DSLD is breed-related. Risk is high in the Peruvian Horse (PH), whereas pony and draft breeds have low breed risk. DSLD occurs in families of PHs, but its genetic arch...

This study aimed to perform a genome-wide association analysis (GWAS) using the Random Forest (RF) approach for scanning candidate genes for age at first calving (AFC) in Nellore cattle. Additionally, potential epistatic effects were investigated using linear mixed models with pairwise interactions between all markers with high importance scores wi...

To devise better selection strategies in dairy cattle breeding programs, a deeper knowledge of the role of the major genes encoding for milk protein fractions is required. The aim of the present study was to assess the effect of the CSN2, CSN3, and BLG genotypes on individual protein fractions (α S1-CN, α S2-CN, β-CN, κ-CN, β-LG, α-LA) expressed qu...

Genetic parameters were estimated for scrotal circumference adjusted to 365 (SC365) and 450 (SC450) days of age, age at first calving (AFC), accumulated productivity (AP), stayability (STAY), loin eye area (LMA), thickness of subcutaneous fat over the 12 th -13 th ribs (BF), thickness of subcutaneous fat over the rump (RF), and shear force measured...

The objective of this study was to investigate potential causal relationships among hot carcass weight (HCW), longissimus muscle area (LMA), backfat thickness (BF), Warner-Bratzler shear force (WBSF), and marbling score (MB) traits in Nellore cattle using structural equation models (SEM). The SEM fitted comprises the following links between traits:...

Single-step GBLUP (ssGBLUP) to obtain genomic prediction was proposed in 2009. Many studies have investigated ssGBLUP in genomic selection in animals and plants using a standard linear kernel (similarity matrix) called genomic relationship matrix (G). More general kernels should allow capturing non-additive effects as well, whereas GBLUP is based o...

A bioeconomic model was developed to calculate the economic value (ev) of reproductive and growth performance, feed efficiency and carcass traits of a seedstock Nellore herd. Data from a full-cycle cattle operation (1,436 dams) located in the Brazilian Cerrado were assessed. The ev was calculated by the difference in profit before and after one-uni...

Computer vision has been proposed as an alternative to monitor livestock growth, for example using 3D cameras to estimate body weight and condition. However, implementing this technology outdoors and with unrestrained animals poses a great challenge, because of harsh conditions for the equipment, as well as varying lighting and animal movement. Her...

Body condition score (BCS) and disease records are commonly available in dairy operations. However, the effect of BCS changes (ΔBCS) considering specific health profiles has not been investigated extensively. The objective of this study was to assess the effects of different levels of ΔBCS on fertility, milk yield, and survival of Holstein cows dia...

The protein profile of milk includes several caseins, whey proteins, and nonprotein nitrogen compounds, which influence milk's value for human nutrition and its cheesemaking properties for the dairy industry. To fill in the gap in current knowledge of the patterns of these individual nitrogenous compounds throughout lactation, we tested the ability...

Wearable sensors have been explored as an alternative for real-time monitoring of cattle feeding behavior in grazing systems. To evaluate the performance of predictive models such as machine learning (ML) techniques, data cross-validation (CV) approaches are often employed. However, due to data dependencies and confounding effects, poorly performed...

Although more than 3 million head of dairy cows enter the food supply chain in the U.S. every year, research on this topic remains limited and scarce. Meat production from dairy cows is a significant component of beef production, accounting for almost 10% of U.S. commercial beef production. Thus, the purpose of this review is to demonstrate the imp...

The aims of this study were to investigate potential functional relationships among milk protein fractions in dairy cattle and to carry out a structural equation model (SEM) GWAS to provide a decomposition of total SNP effects into direct effects and effects mediated by traits that are upstream in a phenotypic network. To achieve these aims, we fir...

The objective of this study was to estimate the cost of metritis in dairy herds. Data from 11,733 dairy cows from 16 different farms located in 4 different regions of the United States were compiled for up to 305 d in milk, and 11,581 cows (2,907 with and 8,674 without metritis) were used for this study. Metritis was defined as fetid, watery, red-b...

Key message We propose the application of enviromics to breeding practice, by which the similarity among sites assessed on an “omics” scale of environmental attributes drives the prediction of unobserved genotype performances. Abstract Genotype by environment interaction (GEI) studies in plant breeding have focused mainly on estimating genetic par...

Cull dairy cows contribute almost 10% of national beef production in the United States. However, different factors throughout the life of dairy cows affect their weight and overall body condition as well as carcass traits, and consequently affect their market price. Therefore, the objectives of this study were: 1) to assess relationships between pr...

Several methods have been used for genome-enabled prediction (or genomic selection) of complex traits, for example, multiple regression models describing a target trait with a linear function of a set of genetic markers. Genomic selection studies have been focused mostly on single-trait analyses. However, most profitability traits are genetically c...

In this presentation we will discuss our current research on computer vision techniques for optimized management of feed bunks and prediction of live weight in beef cattle. The combination of these two techniques allows not only an enhanced nutritional management in feedlots, but also the determination of economically optimal harvest time for maxim...

Best production practices for Beef Cattle (BPP) is a protocol created by Embrapa Beef Cattle in Brazil, to guide farmers towards more sustainable production. The protocol includes checkpoints to the whole production system (management, nutrition, animal health and welfare, pasture, reproduction, environmental, etc.). Despite the benefits of the BPP...

Currently, the amount of feed delivered daily in feedlots is based on the previous day’s consumption and the estimated animal growth. Nevertheless, factors such as weather variables may influence feed consumption. The objective of this study was to evaluate the effect of weather on dry matter intake (DMI) in beef cattle finished in a commercial fee...

Wearable sensors have been adopted as an alternative for real-time monitoring of cattle feeding behavior in grazing systems. However, even using machine learning (ML) techniques confounding effects such as cross-validation strategy may inflate the prediction quality. Our objective was to evaluate the effect of different cross-validation strategies...

Cull dairy cows comprise almost 10% of the national beef production in the United States and contribute with an important additional income source for farmers. However, cull dairy cows present high variation due to many reasons, which affect live animal characteristics, carcass traits, and market price. The objectives of this study were 1) to asses...

The measurement of carcass traits in live pigs, such as muscle depth (MD) and backfat thickness (BF), is a topic of great interest for breeding companies and production farms. Breeding companies currently measure MD and BF using medical imaging technologies such as ultrasound (US). However, US is costly, requires trained personnel, and involves dir...

Poultry is the second largest livestock in Benin (contributing to 22% of the total meat produced), and chickens are the most reared poultry in the country. The objective of this study was to assess the current trends of local chicken breeding and factors that influence their production performance, and thereby to deliver information for production...

Background Deep neural networks (DNN) are a particular case of artificial neural networks (ANN) composed by multiple hidden layers, and have recently gained attention in genome-enabled prediction of complex traits. Yet, few studies in genome-enabled prediction have assessed the performance of DNN compared to traditional regression models. Strikingl...

Worms and ticks are important parasites in beef cattle, especially in tropical areas, causing significant economic and production losses. Understanding animal-to-animal variation on infestation for these parasites might guide genetic selection and improvement of management practices to attenuate its detrimental effects. Statistical models used to a...

Genomic breed composition (GBC) of an individual animal refers to the partition of its genome according to the inheritance from its ancestors or ancestral breeds. For crossbred or composite animals, knowing their GBC is useful to estimate heterosis, to characterize their actual inheritance from foundation breeds, and to make management decisions fo...

Computer Vision, Digital Image Processing, and Digital Image Analysis can be viewed as an amalgam of terms that very often are used to describe similar processes. Most of this confusion arises because these are interconnected fields that emerged with the development of digital image acquisition. Thus, there is a need to understand the connection be...

The objective of this study was to characterize incidences of health disorders during early lactation in a large population of Holstein cows calving in 2 seasons across multiple US dairy herds. In addition, cumulative effects of combinations of health-related events on fertility and survival by season of calving and parity number were tested. Data...

An important economic reason for the loss of local breeds is that they tend to be less productive, and hence having less market value than commercial breeds. Nevertheless, local breeds often have irreplaceable values, genetically and sociologically. In the breeding programs with local breeds, it is crucial to balance the selection for genetic gain...

Computer vision systems (CVS) have been shown to be a powerful tool for the measurement of live pig body weight with no animal stress. With advances in precision farming, it is now possible to evaluate the growth performance of individual pigs more accurately. However, important traits such as muscle and fat deposition can still be evaluated only v...

A variety of statistical methods, such as admixture models, have been used to estimate genomic breed composition (GBC). These methods, however, tend to produce non-zero components to reference breeds that shared some genomic similarity with a test animal. These non-essential GBC components, in turn, offset the estimated GBC for the breed to which i...

Milk production is one of the most important characteristics of dairy sheep, and the identification of genes affecting milk production traits is critical to understanding the genetics and improve milk production in future generations. Three statistical techniques, namely GWAS, ridge‐regression BLUP and BayesC π , were used to identify SNPs in signi...