The Resilient Dairy Genome Project-A general overview of methods and objectives related to feed efficiency and methane emissions

Nienke van Staaveren¹, Hinayah Rojas de Oliveira², Kerry Houlahan¹, Tatiane C S Chud¹, Gerson A Oliveira Jr¹, Dagnachew Hailemariam³, Gerrit Kistemaker⁴, Filippo Miglior², Graham Plastow³, Flavio S Schenkel¹, Ronaldo Cerri⁵, Marc Andre Sirard⁶, Paul Stothard³, Jennie Pryce⁷, Adrien Butty⁸, Patrick Stratz⁸, Emhimad A E Abdalla⁹, Dierck Segelke¹⁰, Eckhard Stamer¹¹, Georg Thaller¹², Jan Lassen¹³, Coralia Ines V Manzanilla-Pech¹⁴, Rasmus B Stephansen¹⁴, Noureddine Charfeddine¹⁵, Aser García-Rodríguez¹⁶, Oscar González-Recio¹⁷, Javier López-Paredes¹⁸, Ransom Baldwin¹⁹, Javier Burchard²⁰, Kristen L Parker Gaddis²⁰, James E Koltes²¹, Francisco Peñagaricano²², José Eduardo P Santos²³, Robert J Tempelman²⁴, Michael VandeHaar²⁴, Kent Weigel²², Heather White²², Christine F Baes²⁵

Affiliations

¹ Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada.
² Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada; Lactanet Canada, Guelph, ON N1K 1E5, Canada.
³ Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2R3, Canada.
⁴ Lactanet Canada, Guelph, ON N1K 1E5, Canada.
⁵ Applied Animal Biology, Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC, Canada V6T 1Z4.
⁶ Department of Animal Sciences, Laval University, Qubec G1V 0A6, QC, Canada.
⁷ School of Applied Systems Biology, La Trobe University, Bundoora, Victoria 3083, Australia; Agriculture Victoria Research, LaTrobe University, Bundoora, Victoria 3083, Australia.
⁸ Qualitas AG, 6300 Zug, Switzerland.
⁹ Vereinigte Informationssysteme Tierhaltung w.V. (vit), Heinrich-Schröder-Weg 1, 27283, Verden, Germany.
¹⁰ Vereinigte Informationssysteme Tierhaltung w.V. (vit), Heinrich-Schröder-Weg 1, 27283, Verden, Germany; Institute of Animal Breeding and Husbandry, Christian-Albrechts-University, 24098, Kiel, Germany.
¹¹ TiDa Tier und Daten GmbH, 24259 Westensee/Brux, Germany.
¹² Institute of Animal Breeding and Husbandry, Christian-Albrechts-University, 24098, Kiel, Germany.
¹³ Viking Genetics, Ebeltoftvej 16, 8960 Assentoft, Denmark.
¹⁴ Center for Quantitative Genetics and Genomics, Aarhus University, DK-8830 Tjele, Denmark.
¹⁵ Spanish Holstein Association (CONAFE), Ctra. Andalucía km 23600 Valdemoro, 28340 Madrid, Spain.
¹⁶ Department of Animal Production, NEIKER-Basque Institute for Agricultural Research and Development, 01192 Arkaute, Spain.
¹⁷ Department of Animal Breeding, Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA-CSIC), 28040 Madrid, Spain.
¹⁸ Federación Española de Criadores de Limusín, C/Infanta Mercedes, 31, 28020 Madrid, Spain.
¹⁹ Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705.
²⁰ Council on Dairy Cattle Breeding, Bowie, MD 20716.
²¹ Department of Animal Science, Iowa State University, Ames, IA 50011.
²² Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI 53706.
²³ Department of Animal Sciences, University of Florida, Gainesville, FL 32611.
²⁴ Department of Animal Science, Michigan State University, East Lansing, MI 48824.
²⁵ Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada; Vetsuisse Faculty, Institute of Genetics, University of Bern, 3012 Bern, Switzerland. Electronic address: cbaes@uoguelph.ca.

PMID: 37690718
DOI: 10.3168/jds.2022-22951

Free article

The Resilient Dairy Genome Project-A general overview of methods and objectives related to feed efficiency and methane emissions

Nienke van Staaveren et al. J Dairy Sci. 2024 Mar.

Free article

. 2024 Mar;107(3):1510-1522.

doi: 10.3168/jds.2022-22951. Epub 2023 Sep 9.

Authors

Affiliations

¹ Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada.
² Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada; Lactanet Canada, Guelph, ON N1K 1E5, Canada.
³ Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2R3, Canada.
⁴ Lactanet Canada, Guelph, ON N1K 1E5, Canada.
⁵ Applied Animal Biology, Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC, Canada V6T 1Z4.
⁶ Department of Animal Sciences, Laval University, Qubec G1V 0A6, QC, Canada.
⁷ School of Applied Systems Biology, La Trobe University, Bundoora, Victoria 3083, Australia; Agriculture Victoria Research, LaTrobe University, Bundoora, Victoria 3083, Australia.
⁸ Qualitas AG, 6300 Zug, Switzerland.
⁹ Vereinigte Informationssysteme Tierhaltung w.V. (vit), Heinrich-Schröder-Weg 1, 27283, Verden, Germany.
¹⁰ Vereinigte Informationssysteme Tierhaltung w.V. (vit), Heinrich-Schröder-Weg 1, 27283, Verden, Germany; Institute of Animal Breeding and Husbandry, Christian-Albrechts-University, 24098, Kiel, Germany.
¹¹ TiDa Tier und Daten GmbH, 24259 Westensee/Brux, Germany.
¹² Institute of Animal Breeding and Husbandry, Christian-Albrechts-University, 24098, Kiel, Germany.
¹³ Viking Genetics, Ebeltoftvej 16, 8960 Assentoft, Denmark.
¹⁴ Center for Quantitative Genetics and Genomics, Aarhus University, DK-8830 Tjele, Denmark.
¹⁵ Spanish Holstein Association (CONAFE), Ctra. Andalucía km 23600 Valdemoro, 28340 Madrid, Spain.
¹⁶ Department of Animal Production, NEIKER-Basque Institute for Agricultural Research and Development, 01192 Arkaute, Spain.
¹⁷ Department of Animal Breeding, Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA-CSIC), 28040 Madrid, Spain.
¹⁸ Federación Española de Criadores de Limusín, C/Infanta Mercedes, 31, 28020 Madrid, Spain.
¹⁹ Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705.
²⁰ Council on Dairy Cattle Breeding, Bowie, MD 20716.
²¹ Department of Animal Science, Iowa State University, Ames, IA 50011.
²² Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI 53706.
²³ Department of Animal Sciences, University of Florida, Gainesville, FL 32611.
²⁴ Department of Animal Science, Michigan State University, East Lansing, MI 48824.
²⁵ Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada; Vetsuisse Faculty, Institute of Genetics, University of Bern, 3012 Bern, Switzerland. Electronic address: cbaes@uoguelph.ca.

PMID: 37690718
DOI: 10.3168/jds.2022-22951

Abstract

The Resilient Dairy Genome Project (RDGP) is an international large-scale applied research project that aims to generate genomic tools to breed more resilient dairy cows. In this context, improving feed efficiency and reducing greenhouse gases from dairy is a high priority. The inclusion of traits related to feed efficiency (e.g., dry matter intake [DMI]) or greenhouse gases (e.g., methane emissions [CH₄]) relies on available genotypes as well as high quality phenotypes. Currently, 7 countries (i.e., Australia, Canada, Denmark, Germany, Spain, Switzerland, and United States) contribute with genotypes and phenotypes including DMI and CH₄. However, combining data are challenging due to differences in recording protocols, measurement technology, genotyping, and animal management across sources. In this study, we provide an overview of how the RDGP partners address these issues to advance international collaboration to generate genomic tools for resilient dairy. Specifically, we describe the current state of the RDGP database, data collection protocols in each country, and the strategies used for managing the shared data. As of February 2022, the database contains 1,289,593 DMI records from 12,687 cows and 17,403 CH₄ records from 3,093 cows and continues to grow as countries upload new data over the coming years. No strong genomic differentiation between the populations was identified in this study, which may be beneficial for eventual across-country genomic predictions. Moreover, our results reinforce the need to account for the heterogeneity in the DMI and CH₄ phenotypes in genomic analysis.

Keywords: dairy cattle breeding; dry matter intake; feed efficiency; methane; resilience.

The Authors. Published by Elsevier Inc. and Fass Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

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The Resilient Dairy Genome Project-A general overview of methods and objectives related to feed efficiency and methane emissions

Affiliations

The Resilient Dairy Genome Project-A general overview of methods and objectives related to feed efficiency and methane emissions

Authors

Affiliations

Abstract

MeSH terms

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LinkOut - more resources

Full Text Sources

Research Materials