Francisco Peñagaricano

Francisco Peñagaricano
University of Wisconsin–Madison | UW · Department of Animal and Dairy Sciences

PhD

About

94
Publications
21,821
Reads
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2,033
Citations
Introduction
Francisco Peñagaricano is broadly interested in quantitative genomics and computational biology. His program focuses on the development and application of statistical and computational methods to dissect the genetic architecture of economically relevant traits in livestock. His research involves gene mapping, gene-set analysis, genomic prediction, methylome and transcriptome analysis, multi-omics data integration, and network modeling.
Additional affiliations
August 2020 - present
University of Wisconsin–Madison
Position
  • Professor (Assistant)
Description
  • http://fpenagaricano-lab.org
February 2015 - August 2020
University of Florida
Position
  • Professor (Assistant)
Description
  • http://fpenagaricano-lab.org
September 2010 - December 2014
University of Wisconsin–Madison
Position
  • Research Assistant
Education
September 2010 - May 2014
University of Wisconsin–Madison
Field of study
  • Statistics
September 2010 - December 2014
University of Wisconsin–Madison
Field of study
  • Quantitative Genetics and Genomics
January 2008 - August 2010
Universidad de la República de Uruguay
Field of study
  • Animal Genetics

Publications

Publications (94)
Article
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Background: Coexpression network analysis is a powerful tool to reveal transcriptional regulatory mechanisms, identify transcription factors, and discover gene functions. It can also be used to investigate changes in coexpression patterns in response to environmental insults or changes in experimental conditions. Maternal nutrition is considered a...
Article
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The use of information across populations is an attractive approach to increase the accuracy of genomic predictions for numerically small breeds and traits that are time-consuming and difficult to measure, such as male fertility in cattle. This study was conducted to evaluate genomic prediction of Jersey bull fertility using an across-country refer...
Article
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Background: Achieving rapid genetic progress while maintaining adequate genetic diversity is one of the main challenges facing the dairy industry. The increase in inbreeding can be used to monitor the loss of genetic diversity. Inbreeding tends to increase the proportion of homozygous loci, some of which cause homozygosity of recessive alleles that...
Article
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Heat stress negatively impacts the reproductive performance of dairy cows. The main objective of this study was to dissect the genetic basis underlying dairy cow fertility under heat stress conditions. Our first goal was to estimate genetic components of cow conception across lactations considering heat stress. Our second goal was to reveal individ...
Article
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Background: Transforming large amounts of genomic data into valuable knowledge for predicting complex traits has been an important challenge for animal and plant breeders. Prediction of complex traits has not escaped the current excitement on machine-learning, including interest in deep learning algorithms such as multilayer perceptrons (MLP) and c...
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Residual feed intake (RFI) is commonly used to measure feed efficiency but individual intake recording systems are needed. Feeding behavior may be used as an indicator trait for feed efficiency using less expensive precision livestock farming technologies. Our goal was to estimate genetic parameters for feeding behavior and the genetic correlations...
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Improving reproductive performance remains a major goal in dairy cattle worldwide. Service sire has been recognized as an important factor affecting herd fertility. The main objective of this study was to reveal the genetic basis of male fertility in Italian Brown Swiss dairy cattle. Dataset included 1102 Italian Brown Swiss bulls with sire concept...
Article
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Several ocular pathologies in cattle, such as ocular squamous cell carcinoma and infectious keratoconjunctivitis, have been associated with low pigmentation of the eyelids. The main objective of this study was to analyze the transcriptome of eyelid skin in Hereford cattle using strand-specific RNA sequencing technology to characterize and identify...
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Residual feed intake (RFI) and feed saved (FS) are important feed efficiency traits that have been increasingly considered in genetic improvement programs. Future sustainability of these genetic evaluations will depend upon greater flexibility to accommodate sparsely recorded dry matter intake (DMI) records on many more cows, especially from commer...
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Genetic selection has been an effective strategy to improve calving traits including stillbirth in dairy cattle. The primary objectives of the present study were to characterize stillbirth data and determine the feasibility of implementing routine genetic evaluations of stillbirth in five non-Holstein dairy breeds, namely Ayrshire, Guernsey, Milkin...
Article
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Ocular squamous cell carcinoma and infectious keratoconjunctivitis are common ocular pathologies in Hereford cattle with considerable economic impact. Both pathologies have been associated with low eyelid pigmentation, and thus, genetic selection for higher eyelid pigmentation could reduce their incidence. The objective of the present study was to...
Article
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Serotonin is a key regulator of mammary gland homeostasis during lactation. Selective serotonin reuptake inhibitors (SSRIs) are commonly used to treat peripartum depression, but also modulates mammary gland serotonin concentrations and signaling in part through DNA methylation. The objective of this study was to determine mouse mammary transcriptom...
Article
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The transition of courses from in-person to an online format due to the COVID-19 pandemic could have potentially affected overall student performance in lecture-based courses. The objective of this case study was to determine the impact of course format, as well as the effects of student sex, time of year at which the course was taken, and the inst...
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Visceral fat is related to important metabolic processes, including insulin sensitivity and lipid mobilization. The goal of this study was to identify individual genes, pathways, and molecular processes implicated in visceral fat deposition in dairy cows. Data from 172 genotyped Holstein cows classified at slaughterhouse as having low (n 77; omenta...
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In cattle, starting 4-5 days after estrus, pre-implantation embryonic development occurs in the confinement of the uterine lumen. Cells in the endometrial epithelial layer control the molecular traffic to and from the lumen and, thereby determine luminal composition. Starting early post-estrus, endometrial function is regulated by sex-steroids, but...
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Background The evaluation of alternative splicing, including differential isoform expression and differential exon usage, can provide some insights on the transcriptional changes that occur in response to environmental perturbations. Maternal nutrition is considered a major intrauterine regulator of fetal developmental programming. The objective of...
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The onset of lactation results in a sudden irreversible loss of Ca for colostrum and milk synthesis. Some cows are unable to quickly adapt to this demand and succumb to clinical hypocalcemia, whereas a larger proportion of cows develop subclinical hypocalcemia that predisposes them to other peripartum diseases. The objective of this study was to pe...
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Dairy bull fertility is traditionally evaluated using semen production and quality traits; however, these attributes explain only part of the differences observed in fertility among bulls. Alternatively, bull fertility can be directly evaluated using cow field data. The main objective of this study was to investigate bull fertility in the Italian B...
Article
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The massive improvement in food production, as a result of effective genetic selection combined with advancements in farming practices, has been one of the greatest achievements of modern agriculture. For instance, the dairy cattle industry has more than doubled milk production over the past five decades, while the total number of cows has been red...
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In general, Fourier-transform infrared (FTIR) predictions are developed using a single-breed population split into a training and a validation set. However, using populations formed of dif-ferent breeds is an attractive way to design cross-validation scenarios aimed at increasing pre-diction for difficult-to-measure traits in the dairy industry. Th...
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Pregnancy loss directly impairs reproductive performance in dairy cattle. Here, we investigated genetic factors associated with pregnancy loss following detection of a viable embryo around 42 days of gestation. The objectives of this study were to perform whole-genome scans and subsequent gene-set analyses for identifying candidate genes, functiona...
Article
The pulsatile pattern of prostaglandin F2alpha (PGF) secretion during spontaneous luteolysis is well-documented, with multiple pulses of exogenous PGF necessary to induce regression using physiologic concentrations of PGF. However, during spontaneous regression, the earliest pulses of PGF are small and not associated with detectable changes in circ...
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Maternal nutrition during gestation can cause epigenetic effects that translate to alterations in gene expression in offspring. This 2-year study employed RNA-sequencing technology to evaluate the pre- and post-vaccination muscle transcriptome of early-weaned Bos indicus -influenced beef calves born from dams offered different supplementation strat...
Article
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Bull fertility is a key factor for successful reproductive performance in dairy cattle. Since the semen from a single bull can be used to inseminate hundreds of cows, one subfertile bull could have a major impact on herd reproductive efficiency. We have previously identified five genomic regions, located on BTA8 (72.2 Mb), BTA9 (43.7 Mb), BTA13 (60...
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In mammals, peripheral serotonin is involved in regulating energy balance. Herein, we characterized the transcriptomic profile and microstructure of adipose and muscle in pre-weaned calves with increased circulating serotonin. Holstein bull calves (21 ± 2 days old) were fed milk replacer supplemented with saline (CON, 8 mL/day n = 4) or 5-hydroxytr...
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Fourier-transform infrared (FTIR) spectroscopy is a powerful high-throughput phenotyping tool for predicting traits that are expensive and difficult to measure in dairy cattle. Calibration equations are often developed using standard methods, such as partial least squares (PLS) regression. Methods that employ penalization, rank-reduction, and varia...
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Background: Over the past decade, Fourier transform infrared (FTIR) spectroscopy has been used to predict novel milk protein phenotypes. Genomic data might help predict these phenotypes when integrated with milk FTIR spectra. The objective of this study was to investigate prediction accuracy for milk protein phenotypes when heterogeneous on-farm,...
Article
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The gut microbiota is a complex ecological community that plays multiple critical roles within a host. Known intrinsic and extrinsic factors affect gut microbiota structure, but the influence of host genetics is understudied. To investigate the role of host genetics upon the gut microbiota structure, we performed a longitudinal study in which we ev...
Article
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Objectives were to evaluate the associations between residual dry matter (DM) intake (RFI) and residual N intake (RNI) in early lactation, from 1 to 5 wk postpar- tum, and in mid-lactation, from 9 to 15 wk postpartum, and assess production performance and risk of diseases in cows according to RFI in mid-lactation. Data from 4 experiments including...
Article
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The study of skin color in cattle holds both economic and scientific interest. Several ocular diseases of cattle have been associated with low pigmentation of the eyelids, including ocular squamous cell carcinoma and infectious keratoconjunctivitis, the two most common ocular diseases affecting cattle production. Although low eyelid pigmentation is...
Article
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Tenderness is a major quality attribute for fresh beef steaks in the United States, and meat quality traits in general are suitable candidates for genomic research. The objectives of the present analysis were to (1) perform genome-wide association (GWA) analysis for marbling, Warner-Bratzler shear force (WBSF), tenderness, and connective tissue usi...
Article
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Predicting bull fertility prior to breeding is a current challenge for the dairy industry. The use of molecular biomarkers has been previously assessed. However, the integration of this information has not been performed to extract biologically relevant markers. The goal of this study was to integrate DNA methylation data with previously published...
Article
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Service sire has been recognized as an important factor affecting dairy herd fertility. Our group has reported promising results on gene mapping and genomic prediction of dairy bull fertility using autosomal SNP markers. Little is known, however, about the genetic contribution of sex chromosomes, which are enriched in genes related to sexual develo...
Article
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The use of genomic testing for selecting replacement heifers in commercial farms has recently attracted much attention. Fertility traits are among the most complex, hard to measure, and lowly heritable traits, and hence they can benefit the most from genomic testing. The objectives of this study were to assess the relationship between early genomic...
Article
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Background: Reproductive capacity can be altered by challenges experienced during critical periods of development, including fetal development and early neonatal life. Gossypol is a polyphenolic compound, commonly found in cotton seeds, that impairs male reproduction. Here, we investigated whether the exposure to gossypol in utero and during lactat...
Article
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Embryos utilize oocyte-donated RNAs until they become capable of producing RNAs through embryonic genome activation (EGA). The sperm’s influence over pre-EGA RNA content of embryos remains unknown. Recent studies have revealed that sperm donate non-genomic components upon fertilization. Thus, sperm may also contribute to RNA presence in pre-EGA emb...
Chapter
Dairy cattle selection programs aim to improve the profitability and sustainability of the dairy industry, either by targeting traits that increase revenues or traits that reduce expenses. These breeding objectives are typically addressed using selection indices, in which relevant traits are combined and weighted according to their economic importa...
Article
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Heat stress represents a major environmental factor that negatively affects the health and performance of dairy cows, causing huge economic losses to the dairy industry. Identifying and selecting animals that are thermotolerant is an attractive alternative for reducing the negative effects of heat stress on dairy cattle performance. As such, the ob...
Article
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The objective of this study was to investigate whether health, survival, and performance of dairy heifers from birth through first lactation are associated with parity and health status of their dams. Holstein heifers (n = 1,811) derived from artificial insemination were categorized as (1) daughters of primiparous cows that, consequently, were nonl...
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Two retrospective studies examining data of 7,500 lactating cows from a single herd were performed with the objective of evaluating the long-term effects of clinical disease during the early postpartum period on milk production, reproduction, and culling of dairy cows through 305 days in milk (DIM). In the first study, data regarding health, milk p...
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Elongation of the preimplantation conceptus is a requirement for pregnancy success in ruminants, and failures in this process are highly associated with subfertility in dairy cattle. Identifying genetic markers that are related to early conceptus development and survival and utilizing these markers in selective breeding can improve the reproductive...
Article
Fertility traits were recently added to the evaluation of genetic merit, allowing for the selection of Holstein cattle with improved reproductive performance. In the current study, we investigated the associations among genomic merit for daughter pregnancy rate (GDPR) and heifer conception rate (GHCR) and physiological responses during proestrus an...
Article
Genetic selection of dairy cattle in the United States has included reproductive traits (daughter pregnancy rate, DPR; heifer conception rate, HCR), which is believed to have partly contributed to halting the decline in reproductive performance. The objectives of the current study were to evaluate the association among genomic merit for DPR (GDPR)...
Article
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Background: Fertility is among the most important economic traits in dairy cattle. Genomic prediction for cowfertility has received much attention in the last decade, while bull fertility has been largely overlooked. The goal ofthis study was to assess genomic prediction of dairy bull fertility using markers with large effect and functionalannotati...
Article
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Service sire has a major effect on reproductive success in dairy cattle. Recent studies have reported accurate predictions for Holstein bull fertility using genomic data. The objective of this study was to assess the feasibility of genomic prediction of sire conception rate (SCR) in US Jersey cattle using alternative predictive models. Data set con...
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Structural equation models involving latent variables are useful tools for formulating hypothesized models defined by theoretical variables and causal links between these variables. The objectives of this study were: (1) to identify latent variables underlying carcass and meat quality traits and (2) to perform whole-genome scans for these latent va...
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Milk fever is an important metabolic disorder that affects dairy cows around parturition. It is associated with a breakdown in the mechanisms of calcium homeostasis, resulting in very low blood calcium levels (hypocalcemia). The main objective of this study was to dissect the genetic basis underlying milk fever incidence in Holstein cattle. Data co...
Article
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Exposure to intrauterine heat stress during late gestation affects offspring performance into adulthood. However, underlying mechanistic links between thermal insult in fetal life and postnatal outcomes are not completely understood. We examined morphology, DNA methylation, and gene expression of liver and mammary gland for bull calves and heifers...
Article
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The service sire has been recognized as an important factor affecting herd fertility in dairy cattle. Recent studies suggest that genetic factors explain part of the difference in fertility among Holstein sires. The main objective of this study was to dissect the genetic architecture of sire fertility in US Jersey cattle. The dataset included 1.5 K...
Article
Transcriptome deep sequencing is a powerful tool for exploring the genetic architecture of complex traits. Gene expression patterns may explain a high degree of the observed phenotypic differences in histochemical and metabolic parameters related to meat quality among different muscles. In this study, we sequenced by RNA-Seq the whole transcriptome...
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The bovine dry period is a dynamic non-lactating phase where the mammary gland undergoes extensive cellular turnover. Utilizing RNA sequencing, we characterized novel genes and pathways involved in this process and determined the impact of dry period heat stress. Mammary tissue was collected before and during the dry period (−3, 3, 7, 14, and 25 da...
Article
The aim of this study was to estimate the genetic parameters of performance in a 750‐km, 15‐day ride in Criollo horses. Heritability (h2) and maternal lineage effects (mt2) were obtained for rank, a relative placing measure of performance. Additive genetic and maternal lineage (rmt) correlations among five medium‐to‐high intensity phase ranks (pRK)...
Article
In ruminants, uterine pulses of prostaglandin (PG) F2α characterize luteolysis, while increased PGE2/PGE1 distinguish early pregnancy. This study evaluated intrauterine (IU) infusions of PGF2α and PGE1 pulses on CL function and gene expression. Cows on day 10 of estrous cycle received 4 IU infusions (every 6h; n = 5/treatment) of saline, PGE1 (2 mg...