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

Hess, Melanie K.; Zetouni, Larissa; Hess, Andrew S.; Budel, Juliana; Dodds, Ken G.; Henry, Hannah M.; Brauning, Rudiger; McCulloch, Alan F.; Hickey, Sharon M.; Johnson, Patricia L.; Elmes, Sara; Wing, Janine; Bryson, Brooke; Knowler, Kevin; Hyndman, Dianne; Baird, Hayley; McRae, Kathryn M.; Jonker, Arjan; Janssen, Peter H.; McEwan, John C.; Rowe, Suzanne J.

doi:10.1186/s12711-023-00822-1

Genetics Selection Evolution

Table 5 Variance components and prediction accuracies for methane-related traits from metagenome profiles at different ages

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

Phenotype	Metagenome profile	Model^a	Component^b	Proportion of variance^c	Accuracy^d	Regression coefficient^e
Grass adult CH4	Grass lamb	G	G_G	0.32 ± 0.07	0.16 ± 0.12	0.76 ± 0.57
		M	M_M	0.52 ± 0.17	0.22 ± 0.09	1.00 ± 0.37
		G + M	G_G+M	0.31 ± 0.07	0.16 ± 0.11	0.75 ± 0.56
			M_G+M	0.47 ± 0.16	0.22 ± 0.08	1.09 ± 0.37
			G + M_G+M	0.78 ± 0.17	0.28 ± 0.12	1.01 ± 0.41
Grass lamb CH4	Grass adult	G	G_G	0.30 ± 0.08	0.13 ± 0.10	0.78 ± 0.61
		M	M_M	0.52 ± 0.21	0.16 ± 0.10	1.03 ± 0.69
		G + M	G_G+M	0.27 ± 0.08	0.12 ± 0.12	0.78 ± 0.80
			M_G+M	0.45 ± 0.20	0.15 ± 0.09	1.14 ± 0.72
			G + M_G+M	0.71 ± 0.21	0.18 ± 0.09	0.86 ± 0.28
Grass adult CH4Ratio	Grass lamb	G	G_G	0.35 ± 0.08	0.16 ± 0.17	0.82 ± 0.82
		M	M_M	0.31 ± 0.15	0.14 ± 0.10	0.91 ± 0.62
		G + M	G_G+M	0.34 ± 0.08	0.17 ± 0.16	0.90 ± 0.84
			M_G+M	0.21 ± 0.12	0.14 ± 0.09	1.21 ± 0.78
			G + M_G+M	0.55 ± 0.14	0.20 ± 0.13	0.86 ± 0.50
Grass lamb CH4Ratio	Grass adult	G	G_G	0.28 ± 0.07	0.14 ± 0.07	0.92 ± 0.58
		M	M_M	0.37 ± 0.18	0.13 ± 0.11	1.30 ± 1.48
		G + M	G_G+M	0.26 ± 0.07	0.13 ± 0.07	0.92 ± 0.59
			M_G+M	0.18 ± 0.15	0.11 ± 0.11	2.89 ± 3.98
			G + M_G+M	0.43 ± 0.16	0.15 ± 0.09	0.97 ± 0.72
Grass adult LW	Grass lamb	G	G_G	0.41 ± 0.08	0.20 ± 0.08	0.84 ± 0.42
		M	M_M	0.34 ± 0.15	0.17 ± 0.11	1.32 ± 1.00
		G + M	G_G+M	0.39 ± 0.08	0.20 ± 0.09	0.84 ± 0.45
			M_G+M	0.28 ± 0.14	0.16 ± 0.09	1.35 ± 0.95
			G + M_G+M	0.67 ± 0.15	0.25 ± 0.07	0.91 ± 0.36
Grass lamb LW	Grass adult	G	G_G	0.37 ± 0.08	0.17 ± 0.07	0.71 ± 0.36
		M	M_M	0.79 ± 0.24	0.20 ± 0.06	1.21 ± 0.67
		G + M	G_G+M	0.34 ± 0.07	0.16 ± 0.08	0.71 ± 0.38
			M_G+M	0.56 ± 0.22	0.19 ± 0.06	1.49 ± 0.79
			G + M_G+M	0.90 ± 0.21	0.23 ± 0.07	0.85 ± 0.36

CH4 = scaled methane emissions; CH4Ratio = scaled methane ratio (CH₄/(CH₄ + CO₂)); CO2 = scaled carbon dioxide emissions; LW = liveweight at time of rumen sampling
^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 the component
^dCorrelation between phenotype adjusted for fixed effects and the component 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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