Francisco Peñagaricano

Penagaricano Lab

Assistant Professor - Quantitative Genomics

Research, Teaching



Office Location

1675 Observatory Dr
436 Animal Sciences
Madison, WI 53706

Francisco Peñagaricano is originally from Uruguay, where he earned his BS (2005) in Biology and Biochemistry and his MS (2010) in Animal Science, all from Universidad de la República. He continued his graduate studies at the University of Wisconsin where he earned his MS (2014) in Statistics and Ph.D. (2014) in Animal Science. Before joining UW, Francisco was a faculty member (2015-2020) in the Department of Animal Sciences at the University of Florida. 

His research interests are in quantitative genomics and computational biology. His research program focuses on the development and application of methods to dissect the genetic architecture of economically relevant traits in livestock. He typically combines large, nationwide phenotypic datasets or field experiments, with highthroughput genomic technologies, and advanced statistical and computational methods in order to elucidate the connection between genome and phenotype. His research involves gene mapping, gene-set analysis, genomic prediction, methylome and transcriptome analysis, multi-omics data integration, and network modeling. 

Selected Peer-Reviewed Articles

FL Guinan, RH Fourdraine, F Peñagaricano, and KA Weigel (2023) Genetic analysis of lactation consistency in U.S. Holsteins using temporal variation in daily milk weights. Journal of Dairy Science. In press

L Cavani, KL Parker Gaddis, RL Baldwin, JEP Santos, JE Koltes, RJ Tempelman, MJ VandeHaar, HM White, F Peñagaricano, and KA Weigel (2023) Consistency of dry matter intake in Holstein cows: heritability estimates and associations with feed efficiency. Journal of Dairy Science. In press

F Peñagaricano (2023) Genomics and dairy bull fertility. Veterinary Clinics of North America: Food Animal Practice. In press

K Houlahan, FS Schenkel, F Miglior et al. (2023) Estimation of genetic parameters for feed efficiency traits using random regression models in dairy cattle. Journal of Dairy Science. In press

RB Stephansen, P Martin, CIV Manzanilla-Pech, et al. (2023) Novel genetic parameters for residual feed intake in dairy cattle using time series data from multiple parities and countries in North America and Europe. Journal of Dairy Science. In press

HA Pacheco, A Rossoni, A Cecchinato, and F Peñagaricano (2023) Identification of runs of homozygosity associated with male fertility in Italian Brown Swiss cattle. Frontiers in Genetics 14: 1227310.

FACC Silva, T Martins, M Sponchiado, CC Rocha, N Ashrafi, SF Graham, KG Pohler, F Peñagaricano, AM Gonella-Diaza, and M Binelli (2023) Pre-estrus progesterone does not affect post-estrus luminal metabolome in cross-bred beef cows. Reproduction 166: 99-116.

JA de los Santos, JPN Andrade, LR Cangiano, A Iriarte, F Peñagaricano, and JJ Parrish (2023) Transcriptomic analysis reveals gene expression changes in peripheral white blood cells of cows after embryo transfer: implications for pregnancy tolerance. Reproduction in Domestic Animals 58: 946–954.

FACC Silva, T Martins, M Sponchiado, CC Rocha, KG Pohler, F Peñagaricano, and M Binelli (2023)
Hormonal profile prior to luteolysis modulates the uterine luminal transcriptome in the subsequent cycle in beef cross-bred cows. Biology of Reproduction 108: 922-935.

B Hatew, F Peñagaricano, M Gebremikael, CS Jones, GE Dahl, and AT Adesogan (2023) Synergies of feed, management trainings, and genetics on milk production of dairy cows in the tropics: the case of Ethiopian smallholder farmers. Frontiers in Animal Science 4:1119786.

R Amorín, L Liu, P Moriel, N DiLorenzo, PA Lancaster, and F Peñagaricano (2023) Maternal diet induces persistent DNA methylation changes in the muscle of beef calves. Scientific Reports 13:1587.

BM Nascimento, CW Wolfe, KA Weigel, and F Peñagaricano (2023) Effects of type traits, inbreeding, and production on survival in US Jersey cattle. Journal of Dairy Science 106: 4825-4835.

MR Lauber, F Peñagaricano, RH Fourdraine, JS Clay, and PM Fricke (2023) Characterization of semen type prevalence and allocation in Holstein and Jersey females in the United States. Journal of Dairy Science 106: 3748-3760.

L Cavani, KL Parker Gaddis, RL Baldwin, JEP Santos, JE Koltes, RJ Tempelman, MJ VandeHaar, MJM Caputo, HM White, F Peñagaricano, and KA Weigel (2023) Impact of parity differences on residual feed intake estimation in Holstein cows. JDS Communications 4: 201-204.

A Mirzaei, VR Merenda, LF Ferraretto, RD Shaver, F Peñagaricano, and RC Chebel (2023) Individual animal variability in rumination, activity, and lying behavior during the periparturient period of dairy cattle. JDS Communications 4: 205-209.

Selected Book Chapters

JE Koltes and F Peñagaricano (2019) Linking genotype to phenotype: functional annotation as a tool to advance dairy cattle breeding. In: Advances in Breeding of Dairy Cattle. Chapter 16. Burleigh Dodds Science. 

F Peñagaricano (2019) Genetics and genomics of dairy cattle. In: Animal Agriculture: Challenges, Innovations, and Sustainability. pp 101-119. Elsevier.  

F Peñagaricano, A De Vries, and DT Bennink (2017) Genomic selection and reproductive technologies to optimize herd replacements. In: Large Dairy Herd Management, 3rd ed. pp 379-388. ADSA® Foundation. 

GJM Rosa, VPS Felipe, and F Peñagaricano (2016) Applications of Graphical Models in Quantitative Genetics and Genomics. In: Systems Biology in Animal Production and Health, Vol. 1. pp 95-116. Springer International Publishing. 

AN SCI 366 Concepts in Genomics (3 credits, Fall)
Description: Basic overview of the latest concepts in genomics, including genome organization, the importance of genome annotation, the use of genomic testing in plant and animal breeding, the potential of genomic prediction on human medicine, and the latest advances in omics integration.

AN SCI 865 Design and Analysis of Biological Studies (4 credits, Spring)
Description: The fundamentals of linear models, generalized linear models, experimental design, and data analysis using common examples from biological studies.

Associate Editor BMC Genomics

Associate Editor Frontiers in Genetics

Associate Editor Animal The international journal of animal biosciences

Editorial Board Journal of Dairy Science

Excellence Award for Assistant Professors, University of Florida (2019)