Evidence map›Paper›PMID 40999243›Full record

ArticleMammalian genome : official journal of the International Mammalian Genome Society2025

Exploring genome, transcriptome, and microbiome interactions related to feed efficiency and methane emissions in Bos indicus through multi-omics network analysis.

Tainã Figueiredo Cardoso, Jennifer Jessica Bruscadin, Juliana Afonso, Liliane Costa Conteville, Bruno Gabriel Nascimento Andrade, Jessica Moraes Malheiros, Anna Carolina Fernandes, Wellison J S Diniz, Priyanka Banerjee, Priscila S N de Oliveira and 4 more

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Article in Mammalian genome : official journal of the International Mammalian Genome Society, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

14 authors.

Tainã Figueiredo CardosoEmbrapa Southeast Livestock, São Carlos, São Paulo, Brazil. taina.cardoso@colaborador.embrapa.br.
Jennifer Jessica BruscadinEmbrapa Southeast Livestock, São Carlos, São Paulo, Brazil.
Juliana AfonsoEmbrapa Southeast Livestock, São Carlos, São Paulo, Brazil.
Liliane Costa ContevilleEmbrapa Southeast Livestock, São Carlos, São Paulo, Brazil.
Bruno Gabriel Nascimento AndradeDepartment of Computer Sciences, Munster Technological University, Cork, Ireland.
Jessica Moraes MalheirosEmbrapa Southeast Livestock, São Carlos, São Paulo, Brazil.
Anna Carolina FernandesDepartment of Animal Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo/ESALQ, Piracicaba, São Paulo, Brazil.
Wellison J S DinizDepartment of Animal Sciences, Auburn University, Auburn, AL, USA.
Priyanka BanerjeeDepartment of Animal Sciences, Auburn University, Auburn, AL, USA.
Priscila S N de OliveiraEmbrapa Southeast Livestock, São Carlos, São Paulo, Brazil.
Adhemar ZerlotiniEmbrapa Agricultural Informatics, Campinas, São Paulo, Brazil.
Gerson Barreto MourãoDepartment of Animal Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo/ESALQ, Piracicaba, São Paulo, Brazil.
Luiz Lehmann CoutinhoDepartment of Animal Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo/ESALQ, Piracicaba, São Paulo, Brazil.
Luciana Correia de Almeida RegitanoEmbrapa Southeast Livestock, São Carlos, São Paulo, Brazil. luciana.regitano@embrapa.br.

Funding

ADAPT Centre for Digital Content Technology Resource Centre 13/RC/2106_P2Agricultural Research Service, U.S. Department of Agriculture 58-6010-1-005Conselho Nacional de Desenvolvimento Científico e Tecnológico 456191/2014-3FAPESP 2018/11953-2FAPESP 2023/10717-1Foundation to Support the Research of São Paulo State, FAPESP 2019/04089-2Fundação de Amparo à Pesquisa do Estado de São Paulo 2012/23638-8Fundação de Amparo à Pesquisa do Estado de São Paulo 2022/06281-0
6 · The paper itself

Abstract

The minor effects of many SNP interactions often determine complex traits. This interaction, known as epistasis, represents a non-additive genetic effect in which the influence of one variant depends on the presence of others. In this study, we tested for epistatic effects on the residual feed intake (RFI) and residual methane emission (RME) traits of Nelore cattle. Additionally, we evaluated the impact of these interactions in other omics layers (i.e., microorganism profiles in the rumen content and feces and mRNA and miRNA expression in the rumen wall). The genomic interaction modules identified 14 and 10 significant SNP-SNP modules associated with RME and RFI traits, respectively. The majority of these SNPs were located in intronic and intergenic regions. The top pathways and processes associated with the SNP-SNP modules were identified, with several pathways related to the immune system and actin cytoskeleton organization. Furthermore, many other omics data were correlated with these SNP-SNP modules. Our findings suggest that the immune response and cilium organization may play important roles in feed efficiency. These insights not only provide novel candidates for enhancing these traits through microbiota composition and transcriptional regulation but also underscore the power of network analysis in uncovering new functional interactions. This research provides new insights and highlights candidate features for improving cattle feed efficiency and methane emissions.

Indexed as

Gastrointestinal MicrobiomeGenomeMethaneMicrobiotaTranscriptomeAnimal FeedAnimalsCattleEpistasis, GeneticGene Regulatory NetworksMultiomicsPolymorphism, Single NucleotideRumenMethane

Identifiers

PMID40999243

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.