Francisco Peñagaricano

Assistant Professor - Quantitative Genomics




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

A Sigdel, RS Bisinotto, and F Peñagaricano (2022) Genetic analysis of fetal loss in Holstein cattle. Journal of Dairy Science (in press)

HA Pacheco, A Rossoni, A Cecchinato, and F Peñagaricano (2022) Deciphering the genetic basis of male fertility in Italian Brown Swiss dairy cattle. Scientific Reports 12: 10575.

L Cavani, WE Brown, KL Parker Gaddis, RJ Tempelman, MJ Vandehaar, HM White, F Peñagaricano, and KA Weigel (2022) Estimates of genetic parameters for feeding behavior traits and their associations with feed efficiency in Holstein cows. Journal of Dairy Science 105: 7564-7574.

E Jara, F Peñagaricano, E Armstrong, C Menezes, L Tardiz, G Rodons, and A Iriarte (2022) Identification of long noncoding RNAs involved in eyelid pigmentation of Hereford cattle. Frontiers in Genetics 13: 864567.

E Jara, F Peñagaricano, E Armstrong, G Ciappesoni, A Iriarte, and EA Navajas (2022) Revealing the genetic basis of eyelid pigmentation in Hereford cattle. Journal of Animal Science 100: skac110.

A Sigdel, XL Wu, KL Parker Gaddis, HD Norman, JA Carrillo, JF Burchard, F Peñagaricano, and JW Dürr (2022) Genetic evaluations of stillbirth for five US dairy breeds: a data-resource feasibility study. Frontiers in Genetics 13: 819678.

LC Novo, L Cavani, P Pinedo, P Melendez, and F Peñagaricano (2022) Genomic analysis of visceral fat accumulation in Holstein cows. Frontiers in Genetics 12: 803216.

T Martins, M Sponchiado, FACC Silva, E Estrada-Cortés, PJ Hansen, F Peñagaricano, and M Binelli (2022) Progesterone-dependent and -independent modulation of luminal epithelial transcription to support pregnancy in cattle. Physiological Genomics 54: 71–85.

L Cavani, MB Poindexter, CD Nelson, JEP Santos, and F Peñagaricano (2022) Gene mapping, gene-set analysis, and genomic prediction of postpartum blood calcium in Holstein cows. Journal of Dairy Science 105: 525-534.

L Liu, R Amorín, P Moriel, N DiLorenzo, PA Lancaster, and F Peñagaricano (2021) Maternal methionine supplementation during gestation alters alternative splicing and DNA methylation in bovine skeletal muscle. BMC Genomics 22: 780.

MA Mezera, W Li, L Liu, R Meidan, F Peñagaricano, and MC Wiltbank (2021) Effect of natural pre-luteolytic prostaglandin F2α pulses on the bovine luteal transcriptome during spontaneous luteal regression. Biology of Reproduction 105: 1016-1029

HA Pacheco, M Battagin, A Rossoni, A Cecchinato, and F Peñagaricano (2021) Evaluation of bull fertility in Italian Brown Swiss dairy cattle using cow field data. Journal of Dairy Science 104: 10896-10904.

EA Palmer, F Peñagaricano, M Vedovatto, RA Oliveira, SL Field, J Laporta, and P Moriel (2021) Effects of maternal gestational diet on muscle transcriptome of beef calves following a vaccine-induced immunological challenge. PLoS ONE 16: e0253810.

A Sigdel, RS Bisinotto, and F Peñagaricano (2021) Genes and pathways associated with pregnancy loss in dairy cattle. Scientific Reports 11: 13329.

R Abdollahi-Arpanahi, HA Pacheco, and F Peñagaricano (2021) Targeted sequencing reveals candidate causal variants for dairy bull subfertility. Animal Genetics 52: 509-513.

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)