Host and rumen microbiome contributions to feed efficiency traits in Holstein cows

Area of Science:

• Animal Genetics and Genomics
• Microbiome Research
• Ruminant Nutrition

Background:

• Dairy cow performance is a complex trait influenced by host genome and rumen microbiome.
• Heritability (h²), microbiability (m²), direct heritability (h²d), and holobiability (ho²) quantify genetic and microbial contributions.
• Understanding these interactions is crucial for improving feed efficiency.

Purpose of the Study:

• Estimate h², h²d, m², and ho² for dry matter intake, milk energy, and residual feed intake.
• Evaluate predictive ability of models incorporating genome, microbiome, and their interaction.
• Investigate the role of the rumen microbiome in mediating host genetic effects on feed efficiency.

Main Methods:

• Utilized feed efficiency records, SNP genotype data, and 16S rRNA rumen microbial abundances from 448 Holstein cows.
• Fitted three kernel models: genomic (G), genomic-microbiome (GM), and genomic-microbiome-interaction (GMO).
• Assessed model goodness-of-fit and predictive ability using correlation and bias metrics.

Main Results:

• The holobiont model (GMO) demonstrated the best goodness-of-fit.
• Direct heritability (h²d) was 10-15% lower than heritability (h²), indicating genetic effects mediated by the microbiome.
• Microbiome contribution (m²) was moderate, up to 26% for milk energy; holobiability (ho²) exceeded the sum of h²d and m², highlighting genome-by-microbiome interactions.

Conclusions:

• The rumen microbiome has a moderate but significant contribution to feed efficiency in lactating Holstein cows.
• Genome-by-microbiome interactions play a substantial role in feed efficiency.
• Incorporating microbiome data improves predictive models for dairy cow performance, suggesting microbiome-mediated genetic effects.