Professor Emeritus, Department of Animal Science
NRSP-8 Cattle Genome Coordinator
- Agronomist: Escuela Agrícola Panamericana, El Zamorano, Honduras. 1969 (Agriculture).
- B.S., University of California Davis, 1971 (Biochemical Animal Genetics).
- M.S., University of California Davis, 1973 (Animal Science).
- Ph.D., University of California Davis, 1975 (Genetics).
Applications of next generation sequencing and systems biology approaches to study genetic variation of complex traits. Genetics of milk composition and animal growth. Development of the new bovine genome assembly. Genomics of coffee: development of a reference genome, transcriptome sequencing and genetic diversity among varieties.
U.C. Davis Coffee Genome Project
Dairy Cattle Breeding Simulation Program (DCBSP)
Medrano, J.F., A. Ahmadi and J. Casellas 2010. Dairy Cattle Breeding Simulation Program (DCBSP v.4.9), a simulation program to teach animal breeding principles and practices. Journal of Dairy Science 93:2816-2826. PMID:20494191
The DCBSP system is a dairy cattle breeding simulation program to teach undergraduate and graduate students animal breeding principles associated with selection for multiple traits in dairy cattle. The current version of the program (DCBSP v.4.9) is written in FORTRAN 90, and a web-based interface is developed for the students to interact with the program in the teaching environment. Both the backend simulation engine and the frontend web-based interface are driven by a module written in the Visual C++ programming language that loads the input files, runs the simulation, and uploads the output files onto the proper directories for each student on the web site. This software simulates a population of dairy cattle herds and artificial insemination bulls through several generations by integrating students’ decisions about mating, culling, and selection of new heifers and bulls based on a multivariate animal mixed model evaluation and marker-assisted selection. The DCBSP simulation system is used locally, nationally, and internationally for teaching animal breeding principles and is hosted at the Department of Animal Science, University of California, Davis.
Questions on using the program should be address to email@example.com
The Program is currently being used, locally, nationally, and intrenationally, at the following universities:
- Angela Canovas
Mentored Graduate Students (Ph.D.)
- Simon Horvat, Ph.D. Genetics 1995.
- Willy Cushwa, Ph.D. Genetics 1995.
- Alison Louise Van Eenennaam, Ph.D. Genetics 1997.
- Pablo Marcelo Corva, Ph.D. Genetics, 2000.
- Marisa Lin Wong, Ph.D. Genetics, 2004.
- Charles Ronnie Farber, Ph.D. Genetics, 2005.
- Ricardo Alejandro Verdugo Salgado, Ph.D. Genetics, 2007.
- Rodrigo Gularte-Merida, Ph.D. Animal Biology, 2011.
- Saumya Wickramasinghe, Ph.D. Animal Biology, 2011.
- Rashida Lathan, Ph.D. Animal Biology, 2012.
Mentored Graduate Students (M.S.)
- Eric Douglas Aasen, M.S. Genetics, 1990.
- Alison Louise Van Eenennaam, M.S. Animal Science, 1990.
- Shelley Lynn House, M.S. Animal Science, 1993.
- Lorraine Sin-Wun Lum, M.S. Animal Science, 1993.
- La Donna Gaye Foley, M.S. Animal Science, 1994.
- Stephen Tom Fong, M.S. Animal Science, 1995.
- Andrea Michelle Johnson, M.S. Genetics, 1998.
- Deven H. Mistry, M.S. Genetics, 1999.
- Wendy Lynn Ward (Devine), M.S. Animal Science, 2003.
- Kerri Morimoto, M.S. Genetics, 2004.
- Rodrigo Jose Gularte Merida, M.S. Animal Biology, 2006.
- Lisa Goldberg, M.S. Animal Biology, 2007.
- James Chitwood, M.S. Animal Biology, 2009.
Links to External Sites
- Good Land Organics (Goleta, California)
- Mi Cafeto (Japan)
- U.C. Davis Coffee Genome Project
- U.C. Davis Coffee Center
- Coffee Education web site
- NPR-special series-Coffee Week, April 2013
- Nelson-Atkins Museum of Art, Kansas City
- Art Institute of Chicago
- Manetti Shrem Museum of Art at U.C. Davis
Medrano, J.F., A. Ahmadi and J. Casellas 2010. Dairy Cattle Breeding Simulation Program (DCBSP v.4.9), a simulation program to teach animal breeding principles and practices. Journal of Dairy Science 93:2816-2826.
Cánovas, A, G. Rincón, A.D. Islas, S. Wickramasinghe, and J. F. Medrano 2010. SNP Discovery in the bovine milk transcriptome using RNA-Seq technology. Mammalian Genome 21:592-598.
Wickramasinghe, S., G. Rincon, A. Islas-Trejo, J.F. Medrano 2012. Transcriptional profiling of bovine milk using RNA sequencing. BMC Genomics 13:45
Medrano, J.F. 2012. Genetic sustainability and biodiversity: Challenges to the California Dairy Industry. In: Biodiversity in Agriculture: Domestication, Evolution and Sustainability (Chap 27). Editors: P. Gepts, T.R. Famula, R.L. Bettinger, S.B. Brush, A.B. Damania, P.E. McGuire and C.O. Qualset. Cambridge University, Press, Cambridge, UK., 606pp.
Cánovas, A., G. Rincón, A. Islas-Trejo, R. Jimenez-Flores, A. Laubscher and J. F. Medrano 2013. RNA-Sequencing to study gene expression and SNP variation associated with citrate content in cow’s milk. Journal of Dairy Science 96:2637-2648.
Lemay, D.G., R.C. Hovey, S.R. Hartono, K. Hinde, J.T. Smilowitz, F. Ventimiglia, K.A. Schmidt, J.W. Lee, A. Islas-Trejo, P.I. Silva, I. Korf, J.F. Medrano, P.A. Barry, J.B. German 2013. Sequencing the transcriptome of milk production: milk trumps mammary tissue. BMC Genomics. 14:872.
Cánovas, A., A. Reverter, K.L. DeAtley, R.L. Ashley, M.L. Colgrave, M.R. Fortes, A. Islas-Trejo, S. Lehnert, L. Porto-Neto, G. Rincón, G.A. Silver, W.M. Snelling, J.F. Medrano, M.G. Thomas 2014. Multi-Tissue Omics Analyses Reveal Molecular Regulatory Networks for Puberty in Composite Beef Cattle. PLoS One. 9(7):e102551
Casellas, J., D. Gianola and J.F. Medrano 2014. Bayesian analysis of additive epistasis arising from new mutation in mice. Genetic Res. 96:e008.
Gularte-Merida, R, L.M. DiCarlo, G. Robertson, J. Simon, W.D. Johnson, C. Kappen, J.F. Medrano, B.K. Richards 2014. High-Resolution Mapping of a Genetic Locus Regulating Preferential Carbohydrate Intake, Total Kilocalories, and Food Volume on Mouse Chromosome 17. PLoSOne 9(10):e110424 doi: 10.1371/journal.pone.0110424.
Cronin, M.A., A. Cánovas, A. Islas-Trejo, D.L. Bannasch, A.M. Oberbauer, J.F. Medrano 2015. Single nucleotide polymorphism loci (SNP) variation of wolves (Canis lupus) in Southeast Alaska and comparison with wolves and coyotes in North America. J of Heredity, 106 (1): 26-36
Bailey, D.B., S. Lunt, A. Lipka, M.G. Thomas, J.F. Medrano, A. Cánovas, G. Rincon, and M.B. Stephenson 2015. Genetic Influences on Cattle Grazing Distribution: Association of Genetic Markers with Terrain Use in Cattle. Rangeland Ecology Management 68:142-149
Zhou, S., S. Goldstein, M. Place, M. Bechner, D. Patino, K. Potamousis, P. Ravindran, L. Pape, G. Rincon, J. Hernandez-Ortiz, J.F. Medrano, D.C. Schwartz 2015. A Clone-free, Single Molecule Map of the Domestic Cow (Bos taurus) Genome 16:644.
Welly, B.T., M.R. Miller, J.L. Stott, M.T. Blanchard, A.D. Islas-Trejo, S.M. O Rourke, A.E. Young, J.F. Medrano and A.L. Van Eenennaam 2016. Genome Report: Identification and Validation of Antigenic Proteins from Pajaroellobacter abortibovis Using De Novo Genome Sequence Assembly and Reverse Vaccinology. G3 doi: 10.1534/g3.116.036673. [Epub ahead of print]