Rumen metagenome as a genomic selection target to reduce enteric methane emissions

Ruminant digestion emits methane, a potent greenhouse gas contributing to global warming and reducing feed efficiency. Reducing enteric methane emissions (EME) through breeding decisions is theoretically possible, yet measuring these emissions on commercial farms is currently challenging and costly....

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Autores: Sepúlveda, Boris, González Recio, Oscar, Chamberlain, Amanda, Khansefid, Majid, Cocks, B. G., Wang, J., Prowse-Wilkins, Claire, Marett, Leah, Williams, Richard, Jacobs, Joe, García-Rodríguez, Aser, Jiménez-Montero, J. A., Pryce, J. E.
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2025
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/399289
Acceso en línea:http://hdl.handle.net/10261/399289
https://api.elsevier.com/content/abstract/scopus_id/105011274769
Access Level:acceso abierto
Palabra clave:Genomic selection
Metagenomics
Methane production
Rumen microorganisms
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spelling Rumen metagenome as a genomic selection target to reduce enteric methane emissionsSepúlveda, BorisGonzález Recio, OscarChamberlain, AmandaKhansefid, MajidCocks, B. G.Wang, J.Prowse-Wilkins, ClaireMarett, LeahWilliams, RichardJacobs, JoeGarcía-Rodríguez, AserJiménez-Montero, J. A.Pryce, J. E.Genomic selectionMetagenomicsMethane productionRumen microorganismsRuminant digestion emits methane, a potent greenhouse gas contributing to global warming and reducing feed efficiency. Reducing enteric methane emissions (EME) through breeding decisions is theoretically possible, yet measuring these emissions on commercial farms is currently challenging and costly. It is common for EME to be measured using different technologies, which may show weak correlations between them, complicating the combination of reference populations, especially between countries. Here, using the same sequencing strategy, we identified a group of ruminant metagenomic features (a core) present in at least 90% of 410 dairy cows in Australia and 434 in Spain. With subsets of this core (the breeding core subsets) we estimated larger reductions on EME than using direct selection on EME. A combination of direct selection on EME and indirect selection on the breeding core subsets was estimated to produce even larger reductions. Combining the principal components of the core with some genera, Kyoto Encyclopedia of Genes and Genomes ontology and Clusters of Orthologous Groups could enhance EME reductions in breeding programs. We estimated an EME reduction of 0.41 phenotypic standard deviations per generation by selecting the top 30% of individuals with desirable ruminal microbiota profiles. An R Shiny application to estimate those reductions is provided. Additionally, the breeding core subsets could predict EME irrespective of each population's EME trait (sulfur hexafluoride in Australia and sniffers in Spain). These results suggest that rumen metagenome features could be used as selection criteria for genomic selection programs to reduce EME, as many of these features are heritable and correlated with EME. Features in the core could connect EME from different cattle populations, irrespective of the methane phenotype used in those populations. We propose that our methodology should be applied to much larger datasets to improve the accuracy of identifying a breeding core. Therefore, we propose a global effort to validate a common core of EME-associated ruminal features.Peer reviewedElsevier BVAmerican Dairy Science AssociationSepúlveda, Boris [0000-0002-6946-7376]González Recio, Oscar [0000-0002-9106-4063]Chamberlain, Amanda 0000-0002-9395-1299]Khansefid, Majid [0000-0002-5091-7293]Cocks, B. G. [0000-0001-9776-1508]Prowse-Wilkins, Claire [0000-0002-7506-862X]Marett, Leah [0000-0001-9698-8401]Williams, Richard [0000-0003-1321-6487]Jacobs, Joe [0000-0003-2104-4320]García-Rodríguez, Aser [0000-0001-5519-6766]Jiménez-Montero, J. A. [0000-0002-8121-1509]Pryce, J. E. [0000-0002-1397-1282]Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202520252025info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionapplication/pdfhttp://hdl.handle.net/10261/399289https://api.elsevier.com/content/abstract/scopus_id/105011274769reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)InglésThe underlying dataset has been published as supplementary material of the article in the publisher platform at DOI https://doi.org/10.1007/s10479-024-06295-9https://doi.org/10.3168/jds.2024-25436Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/3992892026-05-22T06:33:51Z
dc.title.none.fl_str_mv Rumen metagenome as a genomic selection target to reduce enteric methane emissions
title Rumen metagenome as a genomic selection target to reduce enteric methane emissions
spellingShingle Rumen metagenome as a genomic selection target to reduce enteric methane emissions
Sepúlveda, Boris
Genomic selection
Metagenomics
Methane production
Rumen microorganisms
title_short Rumen metagenome as a genomic selection target to reduce enteric methane emissions
title_full Rumen metagenome as a genomic selection target to reduce enteric methane emissions
title_fullStr Rumen metagenome as a genomic selection target to reduce enteric methane emissions
title_full_unstemmed Rumen metagenome as a genomic selection target to reduce enteric methane emissions
title_sort Rumen metagenome as a genomic selection target to reduce enteric methane emissions
dc.creator.none.fl_str_mv Sepúlveda, Boris
González Recio, Oscar
Chamberlain, Amanda
Khansefid, Majid
Cocks, B. G.
Wang, J.
Prowse-Wilkins, Claire
Marett, Leah
Williams, Richard
Jacobs, Joe
García-Rodríguez, Aser
Jiménez-Montero, J. A.
Pryce, J. E.
author Sepúlveda, Boris
author_facet Sepúlveda, Boris
González Recio, Oscar
Chamberlain, Amanda
Khansefid, Majid
Cocks, B. G.
Wang, J.
Prowse-Wilkins, Claire
Marett, Leah
Williams, Richard
Jacobs, Joe
García-Rodríguez, Aser
Jiménez-Montero, J. A.
Pryce, J. E.
author_role author
author2 González Recio, Oscar
Chamberlain, Amanda
Khansefid, Majid
Cocks, B. G.
Wang, J.
Prowse-Wilkins, Claire
Marett, Leah
Williams, Richard
Jacobs, Joe
García-Rodríguez, Aser
Jiménez-Montero, J. A.
Pryce, J. E.
author2_role author
author
author
author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Sepúlveda, Boris [0000-0002-6946-7376]
González Recio, Oscar [0000-0002-9106-4063]
Chamberlain, Amanda 0000-0002-9395-1299]
Khansefid, Majid [0000-0002-5091-7293]
Cocks, B. G. [0000-0001-9776-1508]
Prowse-Wilkins, Claire [0000-0002-7506-862X]
Marett, Leah [0000-0001-9698-8401]
Williams, Richard [0000-0003-1321-6487]
Jacobs, Joe [0000-0003-2104-4320]
García-Rodríguez, Aser [0000-0001-5519-6766]
Jiménez-Montero, J. A. [0000-0002-8121-1509]
Pryce, J. E. [0000-0002-1397-1282]
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Genomic selection
Metagenomics
Methane production
Rumen microorganisms
topic Genomic selection
Metagenomics
Methane production
Rumen microorganisms
description Ruminant digestion emits methane, a potent greenhouse gas contributing to global warming and reducing feed efficiency. Reducing enteric methane emissions (EME) through breeding decisions is theoretically possible, yet measuring these emissions on commercial farms is currently challenging and costly. It is common for EME to be measured using different technologies, which may show weak correlations between them, complicating the combination of reference populations, especially between countries. Here, using the same sequencing strategy, we identified a group of ruminant metagenomic features (a core) present in at least 90% of 410 dairy cows in Australia and 434 in Spain. With subsets of this core (the breeding core subsets) we estimated larger reductions on EME than using direct selection on EME. A combination of direct selection on EME and indirect selection on the breeding core subsets was estimated to produce even larger reductions. Combining the principal components of the core with some genera, Kyoto Encyclopedia of Genes and Genomes ontology and Clusters of Orthologous Groups could enhance EME reductions in breeding programs. We estimated an EME reduction of 0.41 phenotypic standard deviations per generation by selecting the top 30% of individuals with desirable ruminal microbiota profiles. An R Shiny application to estimate those reductions is provided. Additionally, the breeding core subsets could predict EME irrespective of each population's EME trait (sulfur hexafluoride in Australia and sniffers in Spain). These results suggest that rumen metagenome features could be used as selection criteria for genomic selection programs to reduce EME, as many of these features are heritable and correlated with EME. Features in the core could connect EME from different cattle populations, irrespective of the methane phenotype used in those populations. We propose that our methodology should be applied to much larger datasets to improve the accuracy of identifying a breeding core. Therefore, we propose a global effort to validate a common core of EME-associated ruminal features.
publishDate 2025
dc.date.none.fl_str_mv 2025
2025
2025
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/399289
https://api.elsevier.com/content/abstract/scopus_id/105011274769
url http://hdl.handle.net/10261/399289
https://api.elsevier.com/content/abstract/scopus_id/105011274769
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv The underlying dataset has been published as supplementary material of the article in the publisher platform at DOI https://doi.org/10.1007/s10479-024-06295-9
https://doi.org/10.3168/jds.2024-25436
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Elsevier BV
American Dairy Science Association
publisher.none.fl_str_mv Elsevier BV
American Dairy Science Association
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15.812455

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