Host genetics and the gut microbiota jointly shape apparent fiber digestibility in pigs

Host genes regulate gut microbial composition, but the mechanisms by which they influence porcine fiber-degrading bacteria remain poorly understood. Additionally, the potential for integrating host genetics and microbiota data into genomic selection (GS) models for fiber digestibility in pigs has yet to be explored.

This study aimed to identify host genes and gut microbes that impact fiber digestibility and to enhance the predictive accuracy of GS models for this trait.

This study sacrificed 360 pigs to measure fiber digestibility and collected genomic and colonic microbiota data via sequencing. Genome-wide association studies (GWAS), microbiota-wide association studies (MWAS), and microbial abundance GWAS (mGWAS) were performed to identify host genes and key microbes involved in fiber digestion, along with genes influencing the abundance of these microbes. The results were then integrated to optimize the GS model.

Fiber apparent digestibility exhibited higher microbiability (0.31-0.33) than heritability (0.03-0.05). GWAS identified 50 SNPs associated with fiber digestibility, with the most significant loci on SSC17 explaining 0.96% and 0.97% of variance. Six novel QTLs and five candidate genes for fiber digestion were discovered. Combined MWAS and linear discriminant analysis effect size revealed 89 key microbes influencing fiber digestibility. Heritability of Christensenellaceae_R-7_group and UCG-002 was 0.312 and 0.104, respectively. mGWAS identified 201 SNPs, with the most significant loci each explaining 0.96% of the phenotypic variance. Four novel QTLs and six candidate genes for microbial abundance were identified. The GS model, integrating genomic and key microbial information data, achieved the highest genomic prediction accuracy (0.421 ± 0.002).

The Christensenellaceae_R-7_group and UCG-002, key players in host fiber digestion, are regulated by host genes, including GALNT7. The integration of host genetics and microbiota holds significant potential for GS in pigs for improved fiber digestibility.