Copy Number Variation on ABCC2-DNMBP Loci Affects the Diversity and Composition of the Fecal Microbiota in Pigs
Ramayo-Caldas, Yuliaxis (Institut de Recerca i Tecnologia Agroalimentàries)
Crespo-Piazuelo, Daniel (Institut de Recerca i Tecnologia Agroalimentàries)
Morata, Jordi (Centre de Recerca en Agrigenòmica)
González-Rodríguez, Olga (Institut de Recerca i Tecnologia Agroalimentàries)
Sebastià, Cristina (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments)
Castelló Farré, Anna (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments)
Dalmau Bueno, Antoni (Institut de Recerca i Tecnologia Agroalimentàries)
Ramos Onsins, Sebastián Ernesto (Centre de Recerca en Agrigenòmica)
Alexiou, Konstantinos G. (Centre de Recerca en Agrigenòmica)
Folch, Josep M. (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments)
Quintanilla, Raquel (Institut de Recerca i Tecnologia Agroalimentàries)
Ballester Devis, Maria (Institut de Recerca i Tecnologia Agroalimentàries)

Data:	2023
Resum:	Genetic variation in the pig genome partially modulates the composition of porcine gut microbial communities. Previous studies have been focused on the association between single nucleotide polymorphisms (SNPs) and the gut microbiota, but little is known about the relationship between structural variants and fecal microbial traits. The main goal of this study was to explore the association between porcine genome copy number variants (CNVs) and the diversity and composition of pig fecal microbiota. For this purpose, we used whole-genome sequencing data to undertake a comprehensive identification of CNVs followed by a genome-wide association analysis between the estimated CNV status and the fecal bacterial diversity in a commercial Duroc pig population. A CNV predicted as gain (DUP) partially harboring ABCC2-DNMBP loci was associated with richness (P = 5. 41 × 10 -5, false discovery rate [FDR] = 0. 022) and Shannon α-diversity (P = 1. 42 × 10 -4, FDR = 0. 057). The in silico predicted gain of copies was validated by real-time quantitative PCR (qPCR), and its segregation, and positive association with the richness and Shannon α-diversity of the porcine fecal bacterial ecosystem was confirmed in an unrelated F1 (Duroc × Iberian) cross. Our results advise the relevance of considering the role of host-genome structural variants as potential modulators of microbial ecosystems and suggest the ABCC2-DNMBP CNV as a host-genetic factor for the modulation of the diversity and composition of the fecal microbiota in pigs. IMPORTANCE A better understanding of the environmental and host factors modulating gut microbiomes is a topic of greatest interest. Recent evidence suggests that genetic variation in the pig genome partially controls the composition of porcine gut microbiota. However, since previous studies have been focused on the association between single nucleotide polymorphisms and the fecal microbiota, little is known about the relationship between other sources of genetic variation, like the structural variants and microbial traits. Here, we identified, experimentally validated, and replicated in an independent population a positive link between the gain of copies of ABCC2-DNMBP loci and the diversity and composition of pig fecal microbiota. Our results advise the relevance of considering the role of host-genome structural variants as putative modulators of microbial ecosystems and open the possibility of implementing novel holobiont-based management strategies in breeding programs for the simultaneous improvement of microbial traits and host performance.
Drets:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Llengua:	Anglès
Document:	Article ; recerca ; Versió publicada
Matèria:	Diversity ; Microbiota ; Modulators ; Porcine ; Structural variants
Publicat a:	Microbiology Spectrum, Vol. 11 (may 2023) , ISSN 2165-0497

DOI: 10.1128/spectrum.05271-22
PMID: 37255458

12 p, 1.3 MB

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