SAES-422 Multistate Research Activity Accomplishments Report
Sections
Status: Approved
Basic Information
- Project No. and Title: S1096 : Selection and mating strategies to sustainably improve dairy cattle performance, efficiency, and resiliency
- Period Covered: 10/01/2024 to 10/01/2025
- Date of Report: 11/29/2025
- Annual Meeting Dates: 09/28/2025 to 09/30/2025
Participants
Basiel, Bailey - University of Vermont Bilginer, Umit - University of Wisconsin - Madison Chasco, Agustin - University of Wisconsin - Madison Cockrum, Rebecca - Virginia Tech Cole, John - Council on Dairy Cattle Breeding De Vries, Albert - University of Florida Dechow, Chad - Penn State University Fredin, Sam - University of Minnesota Gaddis, Kristin - Council on Dairy Cattle Breeding Gebeyehu, Samrawit - University of Minnesota Guinan, Fiona - Council on Dairy Cattle Breeding Haagen, Isaac - University of Minnesota Heins, Brad - University of Minnesota Huson, Heather - Cornell University Ling, Ashley - Council on Dairy Cattle Breeding Marin, Federica - University of Wisconsin - Madison Mazetti Nascimento, Barbara - University of Wisconsin - Madison Muratori, Tanya - Penn State University Peñagaricano, Francisco - University of Wisconsin - Madison Rott, Isaac - University of Minnesota Sheybani, Negin - University of Wisconsin - Madison Styer, Ben - University of Minnesota Wu, Nick - Council on Dairy Cattle Breeding Yousaf, Wasim - Penn State University
Accomplishments
Milk Fatty Acids (Commercial Herds): In a study comparing Holsteins to crossbreds (Montbéliarde, Viking Red, and Holstein) across two commercial herds, crossbred cows exhibited higher de novo fatty acids compared to Holsteins. Multiparous crossbred cows specifically showed higher de novo fatty acids and lower mixed fatty acids than their Holstein counterparts.
Milk Fatty Acids (Organic and Low-Input): In organic and low-input herds, crossbred groups (Montbéliarde/Viking Red/Holstein and Normande/Jersey/Viking Red) demonstrated higher de novo fatty acids and lower 16:0 fatty acids compared to pure Holsteins. The organic herd generally had higher preformed, 18:0, and 18:1 cis-9 fatty acids than the low-input herd.
Methane Emissions: Cows in confinement systems emitted higher methane than those in grazing systems. Grazecross cows (Normande/Jersey/Viking Red) emitted less methane and carbon dioxide than ProCross (Montbéliarde/Viking Red/Holstein) and Holstein cows. Regarding methane intensity per kilogram of dry matter intake, both ProCross and Grazecross cows produced less methane than Holstein cows.
Fly Prevalence and Coat Color: A study on grazing organic dairy cattle found that coat color significantly affects fly prevalence, with black cattle having the highest average fly scores compared to white cattle. A Genome-Wide Association Study (GWAS) identified a strong signal on chromosome 17 associated with these traits.
Beef × Dairy Growth Rates: In a comparison of calves from dairy dams sired by Angus, Charolais, Hereford, Limousin, and Simmental bulls, Hereford-sired calves achieved the highest weaning weights and average daily gains. However, there was no significant difference in final weight at harvest across the sire breeds.
Beef × Dairy Carcass Traits: Limousin-sired steers had the largest ribeye area. Angus-sired steers exhibited the highest marbling scores. Despite differences in carcass characteristics, the total revenue generated was statistically similar across all sire breeds.
Calf Trait Heritabilities: Genetic parameters calculated for Holstein calves showed high heritability for birth weight (0.72) and weaning weight (0.64), moderate heritability for average daily gain (0.39), and low heritability for serum total protein (0.13).
Reproductive Modeling: The University of Florida developed a stochastic model of dairy herd reproduction to investigate control mechanisms for hitting targets regarding the number of female dairy calf pregnancies. This project aims to use control theory to optimize the weekly assignment of sexed and conventional semen.
Breeding Strategies for Sub-Saharan Africa: A simulation analysis evaluated breeding strategies using gene-edited Holstein and Gir lines (edited for heat tolerance and disease resistance). The study found that a modified crisscrossing strategy using Holstein-edited sires for two generations followed by Gir-edited sires maximized milk yield and reduced inbreeding over 20 generations.
Lab Establishment: The University of Vermont established the Sustainable Dairy Breeding and Genetics lab within the Department of Animal and Veterinary Sciences.
Software Development: Researchers at UW-Madison developed two free, open-source computational tools: EnrichKit: A multi-omics tool designed for livestock research and greenfeedr: An R-package specifically for processing and reporting GreenFeed data.
Impacts
- New traits being researched or tested for deployment related to feed efficiency, calf growth, and calf disease.
- Mentored graduate students for future careers through graduate programs, internships, and establishment of new research groups.
- Developed new open-source software (EnrichKit and greenfeedr) for use within and outside genetics research.
Publications
Basiel, B.L., T.L. Felix, and C.D. Dechow. 2025. Evaluating the predictive ability of a commercial mixed-breed genomic test for feedlot performance and carcass traits of beef × Holstein steers. J. Anim. Sci. 9(2). https://doi.org/10.1093/jas/skaf053
Basiel, B.L., J.R. Graham, and P.M. VanRaden. 2025. Quantifying the use of and the genetic progress from advanced mating strategies in US dairy herds. J. Dairy Sci. 108(9):9901–9914. https://doi.org/10.3168/jds.2025-26600
Casarotto, L.T., H.N. Jones, P. Chavatte-Palmer, J. Laporta, F. Peñagaricano, V. Ouellet, J.J. Bromfield, and G.E. Dahl. 2025. Late gestation heat stress alters placental structure and function in multiparous dairy cows. J. Dairy Sci. 108:1125–1137. https://doi.org/10.3168/jds.2024-25529
Cavani, L., K.L. Parker Gaddis, R.L. Baldwin, J.E.P. Santos, J.E. Koltes, R.J. Tempelman, M.J. VandeHaar, H.M. White, F. Peñagaricano, and K.A. Weigel. 2025. Genetic characterization of feeding patterns in lactating Holstein cows and their association with feed efficiency traits. J. Anim. Breed. Genet. 142:373–380. https://doi.org/10.1111/jbg.12911
Cavani, L., L.C. Novo, F.S. Reyes, B.M. Nascimento, M.J. VandeHaar, R.J. Tempelman, K.L. Parker Gaddis, R.L. Baldwin, J.E.P. Santos, J.E. Koltes, H.M. White, K.A. Weigel, and F. Peñagaricano. 2025. Associations between body temperature and feed efficiency traits in lactating Holstein cows. JDS Commun. 6:256–260. https://doi.org/10.3168/jdsc.2024-0701
Chasi, B., J.P. Andrade, P.L.J. Monteiro, B. Castro, E. Moreno, E. Anta, N.N. Ali, J.B. Cole, M.C. Wiltbank, F. Peñagaricano, A.Z. Balboula, and M.S. Ortega. 2025. Association of fertility traits with markers of oocyte competence in dairy cattle. J. Dairy Sci. (In press). https://doi.org/10.3168/jds.2025-26726
Coelho, W.M., H.F. Monteiro, C.C. Figueiredo, B. Mion, J.E.P. Santos, R.S. Bisinotto, F. Peñagaricano, P. Vahmani, E.S. Ribeiro, and F.S. Lima. 2025. Associations of serum fatty acids, serum urea nitrogen, and ruminal ammonia nitrogen with residual feed intake in lactating dairy cows. J. Dairy Sci. 108:4839–4850. https://doi.org/10.3168/jds.2024-25454
Cortes-Hernández, J.G., A. García-Ruiz, F. Peñagaricano, H.H. Montaldo, and F.J. Ruiz-López. 2025. Uncovering the genetic basis of milk production traits in Mexican Holstein cattle based on individual markers and genomic windows. PLoS One 20:e0314888. https://doi.org/10.1371/journal.pone.0314888
Gebeyehu, S., B. Heins, T. Sonstegard, J. Sölkner, G. Mészáros, A. Traoré, and A. Soudré. 2024. Analysis of SLICK allele in African taurine and Zebu cattle breeds. Anim. Genet. 56. https://doi.org/10.1111/age.13499
Guinan, F.L., R.H. Fourdraine, F. Peñagaricano, and K.A. Weigel. 2025. Dairy cow resilience: Data driven detection and quantification of perturbations using daily milk weights. J. Dairy Sci. 108:11173–11185. https://doi.org/10.3168/jds.2025-26485
Guinan, F.L., R.H. Fourdraine, F. Peñagaricano, and K.A. Weigel. 2025. Genetic analysis of daily milk weights in U.S. Holsteins using pen-based contemporary groups. JDS Commun. 6:237–240. https://doi.org/10.3168/jdsc.2024-0635
Guinan, F.L., R.H. Fourdraine, F. Peñagaricano, and K.A. Weigel. 2025. Genetic parameters for alternative resilience phenotypes in Holstein cows. JDS Commun. (In press). https://doi.org/10.3168/jdsc.2025-0823
Houdek, E.S., A.R. Hazel, L.B. Hansen, and B.J. Heins. 2024. Lactation curves of Montbéliarde-sired and Viking Red-sired crossbred cows and their Holstein herdmates in commercial dairies. J. Dairy Sci. 107:3753–3767. https://doi.org/10.3168/jds.2023-24391
Laporta, J., B. Dado-Senn, A. Guadagnin, L. Liu, and F. Peñagaricano. 2025. Pre-weaning heat stress alters liver transcriptome and DNA methylation in dairy calves. J. Dairy Sci. 108:4390–4402. https://doi.org/10.3168/jds.2024-25975
Liu, L., and F. Peñagaricano. 2025. EnrichKit: A multi-omics tool for livestock research. Front. Genet. 16:1573374. https://doi.org/10.3389/fgene.2025.1573374
Martinez Boggio, G., P. Lutz, M. Harrison, K.A. Weigel, and F. Peñagaricano. 2025. greenfeedr: An R-package for processing and reporting GreenFeed data. JDS Commun. 6:227–230. https://doi.org/10.3168/jdsc.2024-0662
Nascimento, B.M., K.L. Parker Gaddis, J.E. Koltes, R.J. Tempelman, M.J. VandeHaar, H.M. White, F. Peñagaricano, and K.A. Weigel. 2025. Impact of heat stress on dry matter intake and residual feed intake in mid-lactation dairy cows. J. Dairy Sci. 108:7345–7353. https://doi.org/10.3168/jds.2025-26574
Portner, S.L., and B.J. Heins. 2024. Reasons for disposal and cull cow value of Holstein cows compared with Holstein, Jersey, Montbéliarde, Normande, and Viking Red crossbred cows. J. Dairy Sci. 107:9656–9665. https://doi.org/10.3168/jds.2024-24652
Townsend, J., N. Gross, Z. Peng, F. Peñagaricano, Z. Yang, N. Ahsan, and H. Khatib. 2025. The embryonic DPPA3 gene stimulates the expression of pregnancy-related genes in bovine endometrial cells. J. Dairy Sci. 108:6471–6487. https://doi.org/10.3168/jds.2024-25872
Weir, R.L., I.W. Haagen, C.E. Ambrozek, C.D. Dechow, and J.C. Hadrich. 2025. Association of sire net merit with farm profitability for Minnesota dairy farms. J. Dairy Sci. 108:7224–7234. https://doi.org/10.3168/jds.2024-25922
Yousaf, W., L.C. Hardie, I.W. Haagen, et al. 2025. Organic calf growth associations with sire breed and with milk and component yield in later life. Org. Agr. https://doi.org/10.1007/s13165-025-00509-5