Combining host and rumen metagenome profiling for selection in sheep: prediction of methane, feed efficiency, production, and health traits

Table 7 Variance components and prediction accuracies for liveweight at eight months using genotypes and metagenomes

Metagenome profile	Model^a	Component^b	Proportion of variance^c	Accuracy^d	Regression coefficient^e
Grass lamb	G	G_G	0.35 ± 0.07	0.16 ± 0.11	0.67 ± 0.48
	M	M_M	0.31 ± 0.13	0.16 ± 0.11	1.09 ± 0.76
	G + M	G_G+M	0.35 ± 0.07	0.16 ± 0.11	0.68 ± 0.47
		M_G+M	0.28 ± 0.12	0.16 ± 0.11	1.12 ± 0.80
		G + M_G+M	0.63 ± 0.13	0.22 ± 0.11	0.81 ± 0.45
Grass adult	G	G_G	0.36 ± 0.07	0.16 ± 0.13	0.66 ± 0.49
	M	M_M	0.39 ± 0.18	0.16 ± 0.07	1.32 ± 0.76
	G + M	G_G+M	0.34 ± 0.07	0.16 ± 0.12	0.67 ± 0.49
		M_G+M	0.24 ± 0.15	0.15 ± 0.07	1.83 ± 1.10
		G + M_G+M	0.58 ± 0.15	0.20 ± 0.11	0.78 ± 0.45
Lucerne lamb	G	G_G	0.42 ± 0.08	0.18 ± 0.10	0.66 ± 0.36
	M	M_M	0.43 ± 0.16	0.12 ± 0.02	0.78 ± 0.18
	G + M	G_G+M	0.42 ± 0.08	0.36 ± 0.31	1.08 ± 0.57
		M_G+M	0.45 ± 0.16	0.29 ± 0.37	1.17 ± 0.69
		G + M_G+M	0.86 ± 0.17	0.41 ± 0.33	0.95 ± 0.23

^aModel fitting the random effects of animal genetics (G), metagenome profile (M) or both (G + M)
^bLarge letter(s) represent the component (genomics = G; metagenome = M; or sum of the two = G + M), and the subscript represents the model used
^cProportion of the phenotypic variance (adjusted for fixed effects) explained by animal genetics (G, heritability), the metagenome profile (M, microbiability) or both (G + M)
^dCorrelation between phenotype adjusted for fixed effects and either breeding value (G), metagenome value (M) or the sum of both (G + M) when using cross-fold validation
^eRegression coefficient of phenotype adjusted for fixed effects on either breeding value (G), metagenome value (M) or the sum of both (G + M) when using cross-fold validation with each Cohort a different fold

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