SAES-422 Multistate Research Activity Accomplishments Report

Sections

Basic Information
Additional Info

Status: Approved

Basic Information

Project No. and Title: SCC84 : Selection and mating strategies to improve dairy cattle performance, efficiency, and longevity
Period Covered: 10/01/2021 to 09/30/2022
Date of Report: 12/21/2022
Annual Meeting Dates: 10/17/2022 to 10/19/2022

Participants Members: Tasia Kendrick, Michigan State University, taxistas@msu.edu Heather Huson, Cornell University, hjh3@cornell.edu Luiz Brito, Purdue University, britol@purdue.edu Ignacy Misztal, University of Georgia, ignacy@uga.edu Albert De Vries, University of Florida, devries@ufl.edu Bradley Heins, University of Minnesota WCROC, hein0106@umn.edu Francisco Penagaricano, University of Wisconsin, shelley.prudom@wisc.edu Kent Weigel, University of Wisconsin, kweigel@wisc.edu Students/postdocs: Samrawit Gebeyehu, University of Minnesota Kathryn Bosley, University of Minnesota Tanya Muratori, Penn State Wasim Yousaf, Penn State Emmanuel Lozada-Soto, North Carolina State University Srikanth Krishnamoorthy, Cornell University Azwan Jaafar, Cornell University Sydney Jewell, Cornell University Maddy Sokacz, Michigan State University Ligia Cavani, UW Madison Barbara Nascimento, UW Madison Larissa Novo, UW Madison Hendyel Pacheco, UW Madison Fiona Louise Guinan, UW Madison Barbara Mazetti Nascimento, UW Madison Partners: Sajjad Toghiani, USDA-ARS-AGIL, sajjad.toghiani@usda.gov Ahmed Al-Khudhair, USDA-ARS-AGIL, ahmed.al-khudhair@usda.gov Kristen Gaddis, CDCB, kristen.gaddis@uscdcb.com Xiao-Lin (Nick) Wu, CDCB, nick.wu@uscdcb.com Virtual reports: Neal Schrick, Administrative Advisor, fschrick@utk.edu Frank Siewerdt, USDA-NIFA, Frank.Siewerdt@USDA.gov

Brief Summary of Minutes of Annual Meeting

AGENDA

Monday, October 17, 2022

Meet at Kellogg Hotel and Conference Center Lobby, Michigan State University

Tour Sand Creek Dairy

Tour and Lunch at MooVille Creamery

Tour CentralStar Cooperative Diagnostic Laboratory

Return to Kellogg Hotel and Conference Center

Dinner at Harrison Roadhouse (networking with industry supporters)

Tuesday, October 18, 2022

Meet in private dining room in the Brody Café, Michigan State University

Administrative Advisor update

USDA-NIFA update

SCC-84 Project rewrite discussion

Station Reports

Lunch at Brody Square

Station Reports

Dinner at Lansing Brewing Company (networking with MSU affiliated individuals)

Wednesday, October 19, 2022

Meet in private dining room in the Brody Café, Michigan State University

Business meeting: 2023 host will be Heather Huson, Cornell University. Albert De Vries will repeat as chair. The group thanked Tasia Kendrick for the excellent organization of the meeting.

Station Reports

SCC-84 Project rewrite discussion: Brad Heins will lead the rewrite. Aim is a full multi-state project (S-1096)

Conference Concludes at noon

Submitted by Albert De Vries, Chair and acting secretary

Accomplishments

Outcomes, outputs, activities and milestones reported by the following stations:

Objective 1: Recommend breeding strategies for optimal use of breed resources, maintenance and(or) exploitation of within-breed (additive and non-additive) genetic variation

Reasons for disposal and cull cow value of Holstein and crossbred dairy cattle (UMN)
Fatty Acids of Holsteins and Crossbred Cows (UMN)
RFI of Pre-Weaned Holstein Calves (UMN)
Development of insemination values to assist dairy producers making breeding decisions (UFL)
Managing Bovine Leukemia Virus by Integrating Surveillance of Youngstock and Monitoring of the Milking Herd (MSU)
Assessment of inbreeding and strategies to safeguard genetic diversity in US dairy cattle (NCSU)
Strategies for accuracy of imputation from 7K to 50K single nucleotide polymorphism chips in US crossbred dairy cattle (NCSU)

Objective 2: Capture phenotypic data for novel and economically important traits to elucidate their genetic regulation and potential for genomic selection

Milk microbiome analysis (Cornell)
The effect of selection on the genome architecture of crossbred dairy cattle (Cornell)
Local Ancestry Inference (Cornell)
Investigating epigenetic inheritance and associations with development, disease, and performance (Cornell)
Diet digestibility (PSU)
Organic calf growth (PSU)
Calf recumbency (PSU)
Beef x Dairy (PSU)
Telomere length (PSU)
Lost Y chromosome lineages (PSU)
Precision Dairy Research Data Ecosystem (Purdue)
Milkability and behavior traits in automated milking systems (Purdue)
Udder conformation traits based on XYZ coordinates from AMS (Purdue)
Modelling overall resilience in lactating cows (Purdue)
Meta-analysis of genetic parameters of resilience and efficiency traits (Purdue)
Novel traits from automatic milk feeders: calf feeding behavior and resilience (Purdue)
Feed efficiency in dairy cows (UW)
Investigating resilience indicators in U.S. dairy cattle (UW)
Feasibility study of genetic evaluation for Johne’s disease on US Holstein cows (UW)
Probability of survival in Jersey cattle (UW)
Genomic prediction of bull fertility in Italian Brown Swiss cattle (UW)
Genetic analysis of estrus expression in dairy cows (UW)

Objective 3: Collaborate with the National Animal Germplasm Program (NAGP) Dairy Committee, Animal Genomics and Improvement Laboratory (AGIL), and the Council on Dairy Cattle Breeding (CDCB) to improve genetic variation of dairy and optimize economic merit indices.

Genomic comparison between Jersey bulls in the National Animal Germplasm Program (NAGP) and Jersey bulls in the population (Cornell)
Progress in genetic evaluation for CDCB (UGA)
Why spurious signals in GWAS measures? (UGA)
Why do we look at 1 M windows? (UGA)
Are p-values worth anything? (UGA)
Negative effects of genomic selection (UGA)
Embryo Transfer & fertility evaluation (USDA)
Milking Speed Research Project (USDA)
Increasing the Accuracy of Genomic Prediction, Developing Algorithms, Selecting Markers, and Evaluating New Traits to Improve Dairy Cattle (USDA, UGA, NCSU)

Objective 4: Develop variant discovery strategies to incorporate functional –omics data into breeding schemes for economically important traits

Inheritance of a mutation causing Jersey neuropathy with splayed forelimbs (USDA)

Objective 5: Carry out interdisciplinary collaborations to improve dairy cow and calf health through increased partnerships with researchers, industry, and stakeholders

Precision crossbreeding for African Dairy Production Systems (UMN)
REML for Scalable Genome-Partitioning of Quantitative Genetic Variation (NCSU)

Objective 6: Create a pipeline of diverse graduate students in the fields of quantitative and functional genetics and bioinformatics via outreach and educational opportunities

Graduate research opportunities (Cornell, UMN, UW, PSU, MSU, NCSU, UFL, Purdue)
Undergraduate research opportunities (Cornell, UMN)

Impacts

(i) Development and implementation of national genetic evaluations for new traits
(ii) Development of crossbreeding rotations for dairy farm profitability and feed efficiency
(iii) Better understanding of the genetic control of health traits for calves and cows
(iv) Improvement in genomic evaluation for future traits
(v) Training of graduate student in dairy cattle genetics
(vi) Collaboration with the National Animal Germplasm Program (NAGP) Dairy Committee, Animal Genomics and Improvement Laboratory (AGIL), and the Council on Dairy Cattle Breeding (CDCB) to improve genetic variation of dairy and optimize economic merit indices

Publications

Basiel, B.L., L.C. Hardie, B.J. Heins+, C.D. Dechow. 2021. Genetic parameters and genomic regions associated with horn fly resistance in organic Holstein cattle. J. Dairy Sci. 104:12724-12740. https://doi.org/10.3168/jds.2021-20366

Haagen, I.W. L.C. Hardie, B.J. Heins, C.D. Dechow. 2021. Genetic parameters of calf morbidity and stayability for US organic Holstein calves J. Dairy Sci. 104: 11770-11778. https://doi.org/10.3168/jds.2021-20432

Hardie, L. C., I. W. Haagen, B. J. Heins, and C. D. Dechow. 2022. Genetic parameters and association of national evaluations with breeding values for health traits in US organic Holstein cows J. Dairy Sci. 105:495-508. https://doi.org/10.3168/jds.2021-20588

Wu, X.-L., Gaddis, K. L. P., Burchard, J., Norman, H. D., Nicolazz, E. Connor, E. E., Cole, J. B., Durr, J. (2021) An alternative interpretation of residual feed intake by phenotypic recursive relationships in dairy cattle. JDS Communications. 2(6):371-375.

Wu XL, Wiggans GR, Norman HD, Miles AM, Van Tassell CP, Baldwin RL, Burchard J, Dürr J. (2022) Statistical Methods Revisited for Estimating Daily Milk Yields: How Well do They Work? Front Genet. 13:943705.

Sigdel A, Wu XL, Parker Gaddis KL, Norman HD, Carrillo JA, Burchard J, Peñagaricano F, Dürr J. (2022) Genetic Evaluations of Stillbirth for Five United States Dairy Breeds: A Data-Resource Feasibility Study. Front Genet. 13:819678.

Gorr, A., V. E. Cabrera, J. Meronek, and K. A. Weigel. 2022. Decision-support tool for global allocation of dairy sire semen based on regional demand, supply constraints, and genetic profiles. Journal of Dairy Science (in press)

Liang, Z., D. Prakapenka, K. L. Parker Gaddis, M. J. VandeHaar, K. A. Weigel, R. J. Tempelman, J. E. Koltes, J. E. P. Santos, H. M. White, F. Peñagaricano, R. L. Baldwin, and Y. Da. 2022. Impact of epistasis effects on the accuracy of predicting phenotypic values of residual feed intake in U.S. Holstein cows. Frontiers in Genetics (in press)

Sigdel, A., R. S. Bisinotto, and F. Peñagaricano (2022) Genetic analysis of fetal loss in Holstein cattle. Journal of Dairy Science 105: 9012-9020 (https://doi.org/10.3168/jds.2022-22000)

Brown, W., M. J. Martin, C. Siberski, J. E. Koltes, F. Peñagaricano, K. A. Weigel, and H. M. White. 2022. Predicting dry matter intake in mid-lactation Holstein cows using point-in-time data streams available on dairy farms. Journal of Dairy Science 105: 8130-8142 (https://doi.org/10.3168/jds.2022-22093)

Pacheco, H. A., 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. (https://doi.org/10.1038/s41598-022-14889-1)

Cavani, L., W. E. Brown, K. L. Parker Gaddis, R. J. Tempelman, M. J. VandeHaar, H. M. White, F. Peñagaricano, and K. A. 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 (https://doi.org/10.3168/jds.2022-22066)

Zhang, F., K. A. Weigel, and V. E. Cabrera. 2022. Predicting daily milk yield for primiparous cows using data of within herd relatives to capture genotype-by-environment interactions. Journal of Dairy Science 105: 6739-6748 (https://doi.org/10.3168/jds.2021-21559)

Sigdel, A., X. L. Wu, K. L. Parker Gaddis, H. D. Norman, J. A. Carrillo, J. F. Burchard, F. Peñagaricano, and J. W. Dürr (2022) Genetic evaluations of stillbirth for five US dairy breeds: a data-resource feasibility study. Frontiers in Genetics 13: 819678 (https://doi.org/10.3389/fgene.2022.819678)

Khanal, P., K. L, Parker Gaddis, M. J. VandeHaar, K. A. Weigel, H. White, F. Peñagaricano, J. E. Koltes, J. E. P. Santos, R. L. Baldwin, J. F. Burchard, J. W. Dürr, and R. J. Tempelman. 2022. Multiple trait random regression modeling of feed efficiency in US Holsteins. Journal of Dairy Science 105: 5954-5971 (https://doi.org/10.3168/jds.2021-21739)

Williams, K., K. A. Weigel, W. Coblentz, N. M. Esser, H. Schlesser, P. C. Hoffman, R. Ogden, H. Su, and M. S. Akins. 2022. Effect of diet energy level and genomic residual feed intake on bred Holstein dairy heifer growth and feed efficiency. Journal of Dairy Science 105: 2201-2214 (https://doi.org/10.3168/jds.2020-19982)

Novo, L. C., L. Cavani, P. Pinedo, P. Melendez, and F. Peñagaricano (2022) Genomic analysis of visceral fat accumulation in Holstein cows. Frontiers in Genetics 12: 803216. (https://doi.org/10.3389/fgene.2021.803216)

Cavani, L., M. B. Poindexter, C. D. Nelson, J. E. P. 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 (https://doi.org/10.3168/jds.2021-20872)

Martin, M. J., R. S. Pralle, I. R. Bernstein, M. J. VandeHaar, K. A. Weigel, Z. Zhou, and H. M. White. 2021. Circulating metabolites indicate differences in high and low residual feed intake Holstein dairy cows. Metabolites 11, 868 (https://doi.org/10.3390/metabo11120868)

Martin, M. J., J. R. R. Dorea, M. R. Borchers, R. L. Wallace, S. J. Bertics, S. K. DeNise, K. A. Weigel, and H. M. White. 2021. Comparison of methods to predict feed intake and residual feed intake using behavioral and metabolite data in addition to classical performance variables. Journal of Dairy Science 104: 8765-8782 (https://doi.org/10.3168/jds.2020-20051)

Quick, A. E., J. Meronek, K. Amburn, K. Rozeboom, and K. A. Weigel. 2021. Predicting sperm production of young dairy bulls using collection history and management factors. Journal of Dairy Science 104: 5817-5826 (https://doi.org/10.3168/jds.2020-19617)

Martin, M. J., K. A. Weigel, and H. M. White. 2021. Assessment of the relationship between postpartum health and mid-lactation performance, behavior, and feed efficiency in Holstein dairy cows. Animals 11, 1385. (https://doi.org/10.3390/ani11051385)

Harbowy, R, Niles D, Bartlett P, Taxis TM. (2022) Controlling Bovine Leukemia Virus in a Large Dairy Herd by Selective Culling Based on Diagnostic Testing. Applied Animal Science, Under Review September 2022.

LaHuis, C, Benitez O, Droscha C, Singh S, Borgman A, Lohr C, Bartlett P, Taxis TM. (2022) Identification of BoLA Alleles Associated with BLV Disease Progression in US Beef Cows. Pathogens, 11(10), 1093. https://doi.org/10.3390/pathogens11101093.

Lohr CE, Sporer KRB, Brigham KA, Pavliscak LA, Mason MM, Borgman A, Ruggiero VJ, Taxis TM, Bartlett PC, Droscha CJ. (2022) Phenotypic Selection of Dairy Cattle Infected with Bovine Leukemia Virus Demonstrates Immunogenetic Resilience Through NGS-based Genotyping of BoLA MHC Class II genes. Pathogens 11(1), 104. https://doi.org/10.3390/pathogens11010104.

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