A gene co-association network regulating gut microbial communities in a Duroc pig population

Analyses of gut microbiome composition in livestock species have shown its potential to contribute to the regulation of complex phenotypes. However, little is known about the host genetic control over the gut microbial communities. In pigs, previous studies are based on classical "single-gene-s...

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Bibliographic Details
Published in:Microbiome 2021-02, Vol.9 (1), p.52-52, Article 52
Main Authors: Reverter, Antonio, Ballester, Maria, Alexandre, Pamela A, Mármol-Sánchez, Emilio, Dalmau, Antoni, Quintanilla, Raquel, Ramayo-Caldas, Yuliaxis
Format: Article
Language:English
Subjects:
Abundance
Algorithms
Animal diseases
Animals
Bacteria
Bacteria - classification
Bacteria - genetics
Bacteria - isolation & purification
Cbfa-1 protein
Disabled-1 protein
Female
Gastrointestinal Microbiome - genetics
Gene network
Gene Regulatory Networks
Genes
Genetic control
Genetic diversity
Genetic markers
Genome-Wide Association Study
Genomes
Genotype & phenotype
Hogs
Immune response
Impact factors
Information theory
Interleukin 1
Intestinal microflora
Livestock
Lymphocytes T
Male
MAP kinase
Microbiomes
Microbiota
MicroRNAs
Nitric-oxide synthase
Phenotypes
Pig
Pleiotropy
Polygenic inheritance
Protist
Regulators
Single-nucleotide polymorphism
Sox9 protein
Stat1 protein
Swine - classification
Swine - genetics
Swine - microbiology
Symbiosis - genetics
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Summary:Analyses of gut microbiome composition in livestock species have shown its potential to contribute to the regulation of complex phenotypes. However, little is known about the host genetic control over the gut microbial communities. In pigs, previous studies are based on classical "single-gene-single-trait" approaches and have evaluated the role of host genome controlling gut prokaryote and eukaryote communities separately. In order to determine the ability of the host genome to control the diversity and composition of microbial communities in healthy pigs, we undertook genome-wide association studies (GWAS) for 39 microbial phenotypes that included 2 diversity indexes, and the relative abundance of 31 bacterial and six commensal protist genera in 390 pigs genotyped for 70 K SNPs. The GWAS results were processed through a 3-step analytical pipeline comprised of (1) association weight matrix; (2) regulatory impact factor; and (3) partial correlation and information theory. The inferred gene regulatory network comprised 3561 genes (within a 5 kb distance from a relevant SNP-P 
ISSN:2049-2618
2049-2618
DOI:10.1186/s40168-020-00994-8