Microbiome

Estimation of microbiability of production traits in Duroc pigs under different gut microbial classification and heritabilities

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Abstract

Pig phenotypes are influenced by host genetics and the gut microbiota. The proportion of host phenotypic variance explained by the gut microbiota is referred to as microbiability. To apply gut microbial information to pig breeding, it is necessary to determine which gut microbial information is important. The objective of this study is to evaluate the impacts of gut microbiota with different classifications and heritabilities on the microbiability estimation of production traits in Duroc pigs. A total of 961 Duroc pigs with both phenotypic and pedigree data were used in this study. Fecal samples were collected through rectal swabs from individual pigs at the end of the testing period. Genomic DNA from fecal samples was extracted, and the bacterial 16S rRNA V3-V4 region were sequenced. The relative abundances of the amplicon sequence variants (ASVs) were calculated, and a total of 2715 ASVs were used for subsequent analyses. The heritability and microbiability for production traits were estimated based on a single-trait animal model by ASReml software. The model included breeding value based on an additive relationship matrix and microbial effects based on a microbial relationship matrix as random effects simultaneously. First, the effective microbial classification was evaluated by estimating microbiability in production traits under five different microbial classifications (i.e., sequence-level features, taxonomly-level features, and three microbial functions). Microbiability for all traits was higher when estimated using ASVs than when using other microbial classifications. Therefore, the ASV classification was used in subsequent analyses. In addition, the microbiability estimates of daily gain (DG) and backfat thickness (BF) (0.21 and 0.15, respectively) were higher than those of other traits such as body measurement traits (range of 0.00-0.06). Second, the heritability for the relative abundance of ASVs with high prevalence was estimated. In total, 154 of 368 ASVs with high prevalence were significantly heritable in this population. Third, microbiability was estimated for production traits using models including ASVs with differences in prevalence (low or high prevalence) and heritable (heritable and non-heritable with high prevalence) classifications. A difference in microbiability estimates between ASV effects with high and low prevalence (0.10 and 0.09, respectively) was not observed in DG, but ASV effects with low prevalence were not detected in BF. In addition, the microbiability estimates using heritable ASVs (0.08) was higher than that using non-heritable ASVs (0.02) in DG. Our results indicate that the gut microbiota explains a substantial portion of phenotypic variance, in DG and BF. In addition, it is important to differentiate between heritable and non-heritable ASVs when evaluating the impact of host genetics and the gut microbiota on host phenotypes in pigs.

Keywords: 2026

How to Cite:

Hirose, K., Ito, T., Iwata, S., Kamikawa, M., Kitazawa, H., Maruyama, T., Nagai, R., Ogawa, M., Tanaka, G. & Uemoto, Y., (2026) “Estimation of microbiability of production traits in Duroc pigs under different gut microbial classification and heritabilities”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2283804. doi: https://doi.org/10.31274/wcgalp.23514

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