A dimensional reduction approach to modulate the core ruminal microbiome associated with methane emissions via selective breeding

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dc.creatorSaborío Montero, Alejandro
dc.creatorLópez García, Adrián
dc.creatorGutiérrez Rivas, Mónica
dc.creatorAtxaerandio Galdos, Raquel
dc.creatorGoiri Zamora, Idoia
dc.creatorGarcía Rodríguez, Aser
dc.creatorJiménez Montero, José Antonio
dc.creatorGonzález Verdejo, Carmen
dc.creatorTamames, Javier
dc.creatorPuente Sánchez, Fernando
dc.creatorVarona Aguado, Luis
dc.creatorSerrano Noreña, Magdalena
dc.creatorOvilo Martin, Cristina
dc.creatorGonzález Recio, Oscar
dc.date.accessioned2023-02-21T21:24:04Z
dc.date.available2023-02-21T21:24:04Z
dc.date.issued2021-03-15
dc.description.abstractThe rumen is a complex microbial system of substantial importance in terms of greenhouse gas emissions and feed efficiency. This study proposes combining metagenomic and host genomic data for selective breeding of the cow hologenome toward reduced methane emissions. We analyzed nanopore long reads from the rumen metagenome of 437 Holstein cows from 14 commercial herds in 4 northern regions in Spain. After filtering, data were treated as compositional. The large complexity of the rumen microbiota was aggregated, through principal component analysis (PCA), into few principal components (PC) that were used as proxies of the core metagenome. The PCA allowed us to condense the huge and fuzzy taxonomical and functional information from the metagenome into a few PC. Bivariate animal models were applied using these PC and methane production as phenotypes. The variability condensed in these PC is controlled by the cow genome, with heritability estimates for the first PC of ~0.30 at all taxonomic levels, with a large probability (>83%) of the posterior distribution being >0.20 and with the 95% highest posterior density interval (95%HPD) not containing zero. Most genetic correlation estimates between PC1 and methane were large (≥0.70), with most of the posterior distribution (>82%) being >0.50 and with its 95%HPD not containing zero. Enteric methane production was positively associated with relative abundance of eukaryotes (protozoa and fungi) through the first component of the PCA at phylum, class, order, family, and genus. Nanopore long reads allowed the characterization of the core rumen metagenome using whole-metagenome sequencing, and the purposed aggregated variables could be used in animal breeding programs to reduce methane emissions in future generations.es_ES
dc.description.procedenceUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Agroalimentarias::Centro de Investigación en Nutrición Animal (CINA)es_ES
dc.description.procedenceUCR::Vicerrectoría de Docencia::Ciencias Agroalimentarias::Facultad de Ciencias Agroalimentarias::Escuela de Zootecniaes_ES
dc.description.sponsorshipThis research was financed by the METALGEN project (RTA2015-00022-C03) from the national plan for research, development, and innovation 2013–2020 and the Department of Economic Development and Competitiveness (Madrid, Spain).es_ES
dc.identifier.citationhttps://www.journalofdairyscience.org/article/S0022-0302(21)00550-6/fulltextes_ES
dc.identifier.doihttps://doi.org/10.3168/jds.2020-20005
dc.identifier.issn1525-3198
dc.identifier.urihttps://hdl.handle.net/10669/88220
dc.language.isoenges_ES
dc.rightsacceso abierto
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/*
dc.sourceJournal of Dairy Science 104:8135–8151 2021es_ES
dc.subjectGenetic correlationes_ES
dc.subjectHeritabilityes_ES
dc.subjectGREENHOUSE GAS EMISSIONSes_ES
dc.subjectMicrobiomees_ES
dc.subjectPRINCIPAL COMPONENT ANALYSISes_ES
dc.subjectGANADOes_ES
dc.titleA dimensional reduction approach to modulate the core ruminal microbiome associated with methane emissions via selective breedinges_ES
dc.typeartículo originales_ES

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