S1096: Selection and mating strategies to sustainably improve dairy cattle performance, efficiency, and resiliency

(Multistate Research Project)

Status: Active

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SAES-422 Reports

Annual/Termination Reports:

[11/22/2024]

Date of Annual Report: 11/22/2024

Report Information

Annual Meeting Dates: 10/21/2024 - 10/22/2024
Period the Report Covers: 10/01/2023 - 10/01/2024

Participants

Agustín Chasco, Javier (jchasco@wisc.edu) - University of Wisconsin-Madison; Basiel, Bailey (bailey.basiel@usda.gov) - USDA-AGIL; Cavani, Ligia (cavani@wisc.edu) - University of Wisconsin-Madison; Cockrum, Rebecca (rcockrum@vt.edu) - Virginia Tech; Cole, John (john.cole@uscdcb.com) - Council on Dairy Cattle Breeding; De Vries, Albert (devries@ufl.edu) - University of Florida; Dechow, Chad (cdd1@psu.edu) - Penn State University; Fredin, Sam (fredi131@umn.edu) - University of Minnesota; Gaddis, Kristen (Kristen.gaddis@uscdcb.com) - Council on Dairy Cattle Breeding; Gebeyehu, Samrawit (gebey006@umn.edu) - University of Minnesota; Haagen, Isaac (ihaagen@umn.edu) - University of Minnesota; Hansen, Les (hanse009@umn.edu) - University of Minnesota; Heins, Brad (hein0106@umn.edu ) - University of Minnesota; Marin, Federica (mmarin4@wisc.edu) - University of Wisconsin-Madison; Martinez Boggio, Guillermo (guillermo.martinezboggio@wisc.edu) - University of Wisconsin-Madison; Mazetti Nascimento, Barbara (mazettinasci@wisc.edu) - University of Wisconsin-Madison; Peñagaricano, Francisco (fpenagarican@wisc.edu) - University of Wisconsin-Madison; Rott, Isaac (rott0061@umn.edu) - University of Minnesota; Sani, Na'imatu (nsani@wisc.edu) - University of Wisconsin-Madison; Sheybani, Negin (sheybani@wisc.edu) - University of Wisconsin-Madison; VanRaden, Paul (paul.vanraden@usda.gov) - USDA-AGIL; Victoria Wu, Zhuonan (zwu375@wisc.edu) - University of Wisconsin-Madison; Weigel, Kent (kweigel@wisc.edu) - University of Wisconsin-Madison; Xu, Chang (cxu33@ncsu.edu) - North Carolina State University

Brief Summary of Minutes

The S-1096 business meeting was called to order at 9:00 am on October 22 by chair Chad Dechow

Minutes from the 2023 informal meeting in Ithaca New York were reviewed and approved with Bailey Basiel moving to approve the minutes and Rebacca Cockrum seconding the motion.

Pre-meeting business items:

Dr. Schrick congratulated us on our new project and provided background on why the multi-state research project has advantages relative to coordinating committees. We were encouraged to identify additional members. Dr. Schrick is our administrative advisor and the department head observer role is being finalized.

Dr. Van Goor is primary NIFA representative and approves our reports. Dr. Steven Smith is the secondary representative. NIFA is operating under continuing resolution which complicates award funding and review packages.

New business

Potential new members were identified, several of whom had been contacted and confirmed their interest in joining.

Station reports: We were reminded to highlight joint research efforts to justify the multi-state aspect of S-1096.

Email list: John Cole will work to clean and update the email list. It will also be renamed to reflect our new project number.

2025 meeting – we will meet September 29^th & 30^th (Monday and Tuesday of World Dairy Expo) at UW-Madison.

Future meeting locations: There is continued interest in holding a meeting in New Zealand. Chad will follow up with Heather Huson about discussions with Nicolas Lopez-Villalobos from Massey University. We will explore the potential to host a NIFA conference meeting and will reach out to Dr. Angelica VanGoor about possibilities.

Election of new secretary: Isaac Haagen was nominated by Bailey Basiel with John Cole seconding the nomination. John moved to cast a unanimous ballot which was seconded by Kristen Isaac was elected as secretary.

Resolution committee report

Whereas, the renewal of a Multistate Research Project requires considerable time, including drafting, review, and revision of the project plan; and

Whereas, all the members of Multistate Research Project S1096 and their guests benefit from the collaboration enabled by joint membership in said project;

Therefore, the Resolutions Committee, on behalf of the members of Multistate Research Project S1096 and their guests, does hereby tender to Drs. Chad Dechow, Albert de Vries, and Bradley Heins its appreciation for their work in rewriting the project and shepherding it through the review and revision process.

Whereas, the organization and planning of the October 2024 meeting of Multistate Research Project S1096 resulted in a successful gathering characterized by open discussion and vigorous debate, to the mutual benefit of all participants;

Therefore, the Resolutions Committee, on behalf of the members of Multistate Research Project S1096 and their guests, does hereby tender to the University of Minnesota Department of Animal Science and Drs. Bradley Hein and Isaac Haagen its appreciation for their hospitality and a job well done in the planning and execution of the October 2024 meeting.

Whereas, Dr. Leslie B. Hansen is retiring from his position as the Morse Alumni Distinguished Teaching Professor in the Department of Animal Science at the University of Minnesota at the end of 2024; and

Whereas, Les has been a passionate advocate of dairy cattle improvement, dedicated undergraduate educator, mentor of graduate students, and successful coach of Intercollegiate Dairy Judging teams; and

Whereas, Les has advanced the progress of dairy cattle genetics through his training of industry professionals, education of researchers, and vigorous participation in S1096 and its predecessor multistate projects for almost 40 years;

Therefore, the Resolutions Committee, on behalf of the members of Multistate Research Project S1096 and their guests, would like to congratulate Dr. Hansen on his retirement and wish him well in all his future endeavors. His enthusiasm and dedication will be missed by all.

Whereas, Dr. Anthony J. (Tony) Seykora, is retiring from his position as Professor and Director of Undergraduate Studies in the Department of Animal Science at the University of Minnesota in the spring of 2025; and

Whereas, Tony has been a committed educator and mentor to students at both the Twin Cities and Waseca campuses; and

Whereas, Tony has contributed to the evolution and improvement of economic selection indices through his active participation in S1096 and its predecessor multistate projects;

Therefore, the Resolutions Committee, on behalf of the members of Multistate Research Project S1096 and their guests, would like to congratulate Dr. Seykora on his retirement and wish him well in all his future endeavors.

Whereas, Dr. Paul M. VanRaden, is retiring from his position as Research Geneticist (Animals) in the USDA Animal Genomics and Improvement Laboratory in May 2025 after a distinguished 37-year career; and

Whereas, Paul is a highly recognized international expert who investigates differences among dairy cattle for many traits; estimates trait economic values in genetic merit indexes; and develops efficient statistical methods to process phenotype, genotype, pedigree, and DNA sequence data for very large national and international populations; and

Whereas, Paul always shares generously of his time and expertise with students, researchers, and industry personnel;

Therefore, the Resolutions Committee, on behalf of the members of Multistate Research Project S1096 and their guests, would like to congratulate Dr. VanRaden on his retirement and wish him well in all his future endeavors.

Whereas, Dr. Dan Carlson, Chief Scientific Officer and Senior Vice President of Research and Development of Recombinetics, contributed to the success of the October 2024 meeting by sharing his knowledge of precision breeding and opportunities to apply those tools to dairy production worldwide;

Therefore, the Resolutions Committee, on behalf of the members of Multistate Research Project S1096 and their guests, would like to thank Dr. Carlson for his contribution to the meeting.

Whereas, external attendees from the CDCB add valued input and collaboration with Multistate Research Project S1096;

Therefore, we thank our external attendees for their valuable contributions to the project.

Respectfully submitted,

Bailey Basiel, USDA-ARS-AGIL

Rebecca Cockrum, Virginia Tech

John B. Cole, CDCB

Kristen L. Gaddis, CDCB

The resolutions were unanimously approved.

Bailey Basiel moved to adjourn the meeting. The meeting was adjourned at 9:31

Submitted by Chad Dechow, 11/22/24

Accomplishments

Research stations made significant progress toward meeting milestones of evaluating the quality of field data used in genetic assessments concerning reproduction, health, and survival in dairy cattle (2025 milestone) and estimating genetic parameters using such data as well as methane and feed efficiency data (2026 milestone). Collaborative research efforts across stations (WI, FL, IA, MI, PA, USDA, CDCB) have facilitated improved genetic parameter estimates for feed efficiency. Datasets have been developed to explore effects on feed efficiency from feeding pattern variation (WI), body temperature (WI), heat stress (WI), methane (WI, MN), and growth based on dam diet (WI). PA developed a method to determine diet digestibility that can be obtained from commercial cattle breeders. CDCB is developing reports on farm sustainability, and MN is developing feed efficiency comparisons across breed groups in grazing and organic herds. Whole farm systems modelling using the Integrated Farm System Model developed by USDA was used to genetic and environmental trends from 1970 to 2020 on dairy farm efficiency. Genetic selection increased economic efficiency by $843 per cow annually, with most change arising because of increased fat and protein yields. Improved farm management and nutrition increased efficiency by $666.  Crop yield increases improved efficiency by $711, the majority of which was due to rising CO2 levels and associated increases in the rate of plant growth. Higher milk fluid volume after removal of fat and protein, increased body size, and changes in fertility had negative effects on economic efficiency. A 10-year study compared cows from a 3-breed rotational crossbreeding program using the Holstein, Viking Red, and Montbéliarde breeds with their pure Holstein herdmates. Health treatment cost was 23% lower for the 2-breed crossbreds and 17% lower for 3-breed crossbreds than their Holstein herdmates. Lifetime death loss was 4% lower for both the 2-breed crossbreds and the 3-breed crossbreds than their Holstein herdmates. Daily profit was 13% higher for the 2-breed crossbreds and 9% higher for the 3-breed crossbreds than their Holstein herdmates. An ongoing crossbreeding research study at the University of Minnesota West Central Research and Outreach Center, Morris, Minnesota, dairy will evaluate the production, health, and most importantly, the economic performance of crossbred dairy cattle compared with their Holstein herdmates. Organic dairy operations account for approximately 3% of dairy cows in the United States. The organic market demands that products come from healthy animals and are produced sustainably, all while maintaining herd profit. However, in the United States, genetic evaluations are largely based upon conventional production systems from herds participating in Dairy Herd Improvement testing, and organic dairy producers are less likely to participate in milk recording than conventional producers. Currently there are approximately 50 genetic traits evaluated in the United States. Research suggests that current US national selection indexes, such as Net Merit, will produce positive changes related to production, health, efficiency, and sustainability in organic production systems. Further, several selection indexes have been developed for alternative production systems, such as Grazing Merit, which places greater emphasis on fertility traits. However, while genetic correlation estimates between conventional and organic production systems are generally favorable, many estimates are less than unity suggesting there is reranking of sires across systems. Additionally, there are considerations for organic producers that may not be fully accounted for in current national evaluation systems. For instance, our research suggests that increased selection emphasis should be put on youngstock stayability and disease resistance in organic production compared with conventional production systems. While current national selection decisions are driving improvements in dairy production efficiency and sustainability, organic dairy producers must consider if current national breeding goals fully meet the needs of their operations. Age, parity and season adjustment factors for yield traits have been revised to replace the adjustments from 30 years ago. Standardized yield records are now adjusted to 36-months instead of mature equivalent, which was the standard from 1935 to June 2024. The revised records are referred to as 305-AA (average age of 36 months) instead of 305d-2X-ME (mature equivalent) records, or more simply, standardized records. Season adjustments are now calculated across five U.S. climate regions, compared to the previous three geographical regions, which more accurately reflects environmental differences. The new factors are breed-specific, meaning each breed experienced different impacts from this change. This change enables fairer phenotypic comparisons of standardized records for cows of different ages, parities and seasons of calving, based on recent analysis in the modern dairy environment. Traditional and genomic evaluations for Brown Swiss rear teat placement (RTP) were introduced in August 2024. In January 2024, nearly 15,000 appraisals were used to estimate the parameters for this trait and run a first evaluation. Of these appraisals, nearly 80 percent are between 25 and 35 points on the 50-point linear scale. The heritability estimate for RTP was 0.21, in line with similar traits, such as Front Teat Placement at 0.22 heritability. Repeatability for RTP was 0.33. Since the 2018 debut of CDCB evaluations for disease resistance, the number of health records in the National Cooperator Database has tripled or quadrupled – depending on the trait. With this data surge, the trait model has been adjusted with new variance component estimates and adjusted weights, effective with the April 2024 evaluations. This follows a typical progression and evolution of newer traits.  The set of 78,964 genetic markers, gene tests and quantitative trait loci used in genomic predictions since August 2021 was updated to a new list of 69,200 SNPs, effective in August 2024. The 9,769 markers removed had small effects on all traits, were not on recent chips, or had poorer genotype quality. This revision had very limited impact on evaluations. Removing some extra SNPs improved processing time, which is beneficial given the ongoing, large additions of animals in the database each year. Holstein HH6 and Jersey Neuropathy with Splayed Forelimbs (JNS) now include direct gene test information in their haplotype calculation. Neogen regularly shares gene tests in their genotype submissions with CDCB for their use in haplotype calculation. Also, the American Jersey Cattle Association has been submitting gene test results for JNS from multiple providers to CDCB. Both these sources of information will now be included directly in imputation and will be used in haplotype calculation. Test run results show improved performance and higher correspondence for both haplotypes on animals with gene test information and their progeny. The December 5, 2023, dairy cattle genetic evaluations included a new haplotype call for Early Onset Muscle Weakness Syndrome in Holsteins. Abbreviated HMW, U.S. genetic evaluations now include the reporting of noncarrier (0), carrier (1), homozygous (2), probable carrier (3), or probable homozygous (4) status of an animal for Early Onset Muscle Weakness Syndrome (MW). In a November 2023 test run, 87.7% of Holsteins were reported as noncarriers (0), 2.3% as carriers (1), 0.02% as homozygous (2), 9.6% as probable carriers (3), and 0.4% as probable homozygous (4). The haplotype for muscle weakness (HMW) is now reported for all genotyped Holsteins and includes gene tests collected by the breed association. The Net Merit index was revised in 2021 to better account for preliminary estimates of feed intake needed for milk components and measures of body size and will be revised again in 2025 for the published estimates that included more data. Use of the revised indexes will make dairy cows more profitable by selecting for smaller size, improved feed efficiency, and higher milk production. The research to validate cow PTAs was presented to international scientists, published, and sheds light on the advantages of using genomic predictions for cow selection and management. Milking speed genetic evaluations were developed by AGIL using data from NC State, are being tested by CDCB, and are likely to become public in April 2025. In terms of milestones for 2027 and beyond, PA and MN have begun assembling records on parasite resistance in pure and crossbred organic dairy cattle. To date, fecal samples from several hundred calves, heifers, and cows have been collected and evaluated for the presence of parasites. This database building will continue into future years.

Publications

<ul> <li> Al-Khudhair, A., VanRaden, P.M., Null, D.J., Neupane, M., McClure, M.C., & Dechow, C.D. (2024). New mutation within a common haplotype is associated with calf muscle weakness in Holsteins. Journal of Dairy Science, 107(6), 3768–3779. DOI: 10.3168/jds.2023-24121. </li> <li> Arens, S.C., Sharpe, K.T., Schutz, M.M., Hardie, L.C., Dechow, C.D., & Heins, B.J. (2023). Relationships of beta-casein genetics with production, fertility, and survival of purebred organic Holstein dairy cows. JDS Communications, 4(6), 458–463. DOI: 10.3168/jdsc.2022-0367. </li> <li> Arens, S.C., Sharpe, K.T., Schutz, M.M., & Heins, B.J. (2023). Response to ad libitum milk allowance by crossbred dairy and dairy-beef calves in an automated feeding system. Translational Animal Science, 7, txad063. DOI: 10.1093/tas/txad063. </li> <li> Basiel, B.L., Barragan, A., Felix, T., & Dechow, C.D. (2024). The impact of beef sire breed on dystocia, stillbirth, gestation length, health, and lactation performance of cows that carry beef × dairy calves. Journal of Dairy Science, 107(4), 2241–2252. DOI: 10.3168/jds.2023-24112. </li> <li> Basiel, B.L., Campbell, J., Dechow, C.D., & Felix, T. (2024). The impact of sire breed on feedlot performance and carcass characteristics of beef × Holstein steers. Translational Animal Science, 8. DOI: 10.1093/tas/txae043. </li> <li> Bierly, S.A., Van Syoc, E., Westphalen, M.F., Miles, A.M., Gaeta, N.C., Felix, T.L., Hristov, A.N., & Ganda, E.K. (2024). Alterations of rumen and fecal microbiome in growing beef and dairy steers fed rumen protected Capsicum oleoresin. Journal of Animal Science. DOI: 10.1093/jas/skae014. </li> <li> Cesarani, A., Lourenco, D., Bermann, M., Nicolazzi, E.L., VanRaden, P.M., Misztal, I. (2024). Single-step genomic predictions for crossbred Holstein and Jersey cattle in the United States. Journal of Dairy Science Communications, 5(2), 124–128. DOI: 10.3168/jdsc.2023-0399. </li> <li> De Vries, A. (2024). Challenging the norm - Cull rates and farm economics. Proceedings of Annual Meeting of the American Association of Bovine Practitioners, Columbus, OH. In press. </li> <li> Deru, V., Tiezzi, F., Van Raden, P.M., Lozada-Soto, E.L., Toghiani, S., & Maltecca, C. (2024). Imputation accuracy from low- to medium-density SNP chips for US crossbred dairy cattle. Journal of Dairy Science, 107(1), 398–411. DOI: 10.3168/jds.2023-23250. </li> <li> Donnelly, M.R., Hazel, A.R., Hansen, L.B., & Heins, B.J. (2023). Genetic selection for reduced health treatment costs in Holstein cows: implications from a long-term study. Frontiers in Genetics, 14, 1254183. DOI: 10.3389/fgene.2023.1254183. </li> <li> Donnelly, M.R., Hazel, A.R., Hansen, L.B., & Heins, B.J. (2023). Health treatment cost of Holsteins in eight high-performance herds. Animals, 13(11), 2061. DOI: 10.3390/ani13132061. </li> <li> Hardie, L.C., Haagen, I.W., Heins, B.J., & Dechow, C.D. (2023). Genetic evaluation of health costs in US organic Holstein calves and cows. JDS Communications, 4, 464–468. DOI: 10.3168/jdsc.2023-0377. </li> <li> Heins, B.J., Pereira, G.M., & Sharpe, K.T. (2023). Precision technologies to improve dairy grazing systems. JDS Communications, 4, 318–323. DOI: 10.3168/jdsc.2022-0308. </li> <li> Houdek, E.S., Hazel, A.R., Hansen, L.B., & Heins, B.J. (2024). Lactation curves of Montbéliarde-sired and Viking Red-sired crossbred cows and their Holstein herdmates in commercial dairies. Journal of Dairy Science, 107(6), 3753–3767. DOI: 10.3168/jds.2023-24391. </li> <li> Kowalski, Z.M., Sabatowicz, M., Vansaun, R.J., Młocek, W., Jagusiak, W., Spanghero, M., & Dechow, C.D. (2023). Association between hyperketolactia and production in early-lactating dairy cows. Journal of Dairy Science, 106(12), 9532–9551. DOI: 10.3168/jds.2022-23081. </li> <li> Liang, Z., Prakapenka, D., Van Raden, P.M., Jiang, J., Ma, L., & Da, Y. (2023). A million-cow genome-wide association study of three fertility traits in U.S. Holstein cows. International Journal of Molecular Sciences, 24(13), 10496. DOI: 10.3390/ijms241310496. </li> <li> Lozada-Soto, E.A., Gaddis, K.L.P., Tiezzi, F., Jiang, J., Ma, L., Toghiani, S., VanRaden, P.M., Maltecca, C. (2024). Inbreeding depression for producer-recorded udder, metabolic, and reproductive diseases in US dairy cattle. Journal of Dairy Science, 107(5), 3032–3046. DOI: 10.3168/jds.2023-23909. </li> <li> Matamoros, C., Dechow, C.D., & Harvatine, K.J. (2023). Interaction of DGAT1 polymorphism, parity, and acetate supplementation on feeding behavior, milk synthesis, and plasma metabolites. Journal of Dairy Science, 106(11), 7613–7629. DOI: 10.3168/jds.2022-23209. </li> <li> Prakapenka, D., Liang, Z., Zaabza, H.B., Van Raden, P.M., Van Tassell, C.P., & Da, Y. (2024). Large-sample genome-wide association study of resistance to retained placenta in U.S. Holstein cows. International Journal of Molecular Sciences, 25(10), 5551. DOI: 10.3390/ijms25105551. </li> <li> Prakapenka, D., Liang, Z., Zaabza, H.B., Jiang, J., Ma, L., Van Raden, P.M., Van Tassell, C.P., & Da, Y. (2024). A million-cow validation of a chromosome 14 region interacting with all chromosomes for fat percentage in U.S. Holstein cows. International Journal of Molecular Sciences, 25, 674. DOI: 10.3390/ijms25010674. </li> <li> Portner, S.L., & Heins, B.J. (2024). Reasons for disposal and cull cow value of Holstein cows compared with Holstein, Jersey, Montbéliarde, Normande, and Viking Red crossbred cows. Journal of Dairy Science, DOI: 10.3168/jds.2024-24652. </li> <li> Schmidt, P., Mota, L., Fonseca, L., Dos Santos Silva, D., Frezzarim, G., Arikawa, L., De Abreu Santos, D., Magalhaes, A., Cole, J., Carvalheiro, R., De Oliveira, H., Null, D.J., Van Raden, P.M., Ma, L., & De Albuquerque, L. (2023). Identification of candidate lethal haplotypes and genomic association with post-natal mortality and reproductive traits in Nellore cattle. Scientific Reports, 13, 10399. DOI: 10.1038/s41598-023-37586-z. </li> <li> Sharpe, K.T., & Heins, B.J. (2023). Evaluation of a Forefront Weight Scale from an Automated Calf Milk Feeder for Holstein and Crossbred Dairy and Dairy–Beef Calves. Animals, 13(11), 1752. DOI: 10.3390/ani13111752. </li> <li> Toghiani, S., Van Raden, P.M., Baldwin, R.L., Weigel, K., White, H., Penagaricano, F., Koltes, J.E., Santos, J.P., Parker Gaddis, K.L., Vandehaar, M.J., & Tempelman, R.J. (2024). Dry matter intake in US Holstein cows: Exploring the genomic and phenotypic impact of milk components and body weight composite. Journal of Dairy Science. DOI: 10.3168/jds.2023-24296. </li> <li> Wu, X.-L., Wiggans, G.R., Norman, H.D., Caputo, M., Miles, A.M., Van Tassell, C.P., Baldwin, R.L., Sievert, S., Mattison, J., Burchard, J., & Durr, J. (2023). Updating test-day milk yield factors for use in genetic evaluations and dairy production systems: A comprehensive review. Frontiers in Genetics, 14, 1298114. DOI: 10.3389/fgene.2023.1298114. </li> <li> Wu, X., Wiggans, G.R., Norman, H.D., Enzenauer, H.A., Miles, A.M., Van Tassell, C.P., Baldwin, R.L., Burchard, J., & Durr, J. (2023). Estimating test day milk yields by modeling proportional daily yields: Going beyond linearity. Journal of Dairy Science, 106(12), 8979–9005. DOI: 10.3168/jds.2023-23479. </li> <li> Wu, X., Miles, A.M., Van Tassell, C.P., Wiggans, G.R., Norman, H.D., Baldwin, R.L., Burchard, J., & Durr, J. (2023). Does modeling causal relationships improve the accuracy of estimating lactation milk yields? Journal of Dairy Science Communications. DOI: 10.3168/jdsc.2022-0343. </li> </ul>

Impact Statements

The launch of KeepOrBeef by Dairy Records Management Systems, Raleigh, NC, occurred in October of 2023 and is licensed from the University of Florida. KeepOrBeef ranks cows for culling and insemination decisions.
A genetic test for early onset muscle weakness is now commercially licensed from Penn State to four US and one international genetic testing company.
The December 5, 2023, dairy cattle genetic evaluations included a new haplotype call for Early Onset Muscle Weakness Syndrome in Holsteins and an update to the haplotype call for Cholesterol Deficiency (HCD) in Holsteins.
In the summer of 2024, the Council on Dairy Cattle Breeding hosted three paid summer interns in Bowie, MD.
Milking speed genetic evaluations were developed by AGIL using data from NC State, are being tested by CDCB, and are likely to become public in April 2025.
Traditional and genomic evaluations for Brown Swiss rear teat placement (RTP) were introduced in August 2024.