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 4 Variance components and prediction accuracies for methane-related traits

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

Phenotype	Model^a	Component^b	Lucerne lamb		Grass lamb		Grass adult
Phenotype	Model^a	Component^b	PropVar^c	Accuracy^d	PropVar^c	Accuracy^d	PropVar^c	Accuracy^d
CH4	G	G_G	0.35 ± 0.08	0.11 ± 0.05	0.25 ± 0.07	0.13 ± 0.10	0.33 ± 0.07	0.18 ± 0.08
	M	M_M	0.86 ± 0.10	0.38 ± 0.03	0.78 ± 0.15	0.32 ± 0.10	0.95 ± 0.20	0.31 ± 0.14
	G + M	G_G+M	0.22 ± 0.06	0.08 ± 0.06	0.18 ± 0.06	0.13 ± 0.14^f	0.25 ± 0.11^f	0.17 ± 0.08^f
		M_G+M	0.78 ± 0.06	0.38 ± 0.03	0.71 ± 0.15	0.32 ± 0.10^f	0.75 ± 0.11^f	0.31 ± 0.14^f
		G + M_G+M	1.00 ± 0.00	0.38 ± 0.03	0.89 ± 0.15	0.34 ± 0.09^f	1.00 ± 0.00^f	0.35 ± 0.12^f
CH4Ratio	G	G_G	0.35 ± 0.07	0.18 ± 0.04	0.24 ± 0.07	0.10 ± 0.06	0.33 ± 0.07	0.17 ± 0.18
	M	M_M	0.60 ± 0.10	0.36 ± 0.10	0.76 ± 0.16	0.30 ± 0.06	0.83 ± 0.22	0.23 ± 0.10
	G + M	G_G+M	0.25 ± 0.07	0.15 ± 0.03	0.21 ± 0.06	0.09 ± 0.05^f	0.28 ± 0.07	0.17 ± 0.17
		M_G+M	0.53 ± 0.10	0.36 ± 0.10	0.67 ± 0.15	0.30 ± 0.07^f	0.59 ± 0.21	0.22 ± 0.10
		G + M_G+M	0.78 ± 0.11	0.37 ± 0.07	0.88 ± 0.16	0.30 ± 0.05^f	0.86 ± 0.20	0.24 ± 0.14
CO2	G	G_G	0.27 ± 0.07	0.14 ± 0.08	0.19 ± 0.06	0.18 ± 0.13	0.38 ± 0.07	0.24 ± 0.12
	M	M_M	0.46 ± 0.12	0.24 ± 0.11	0.00 ± 0.00	− 0.05 ± 0.09	0.14 ± 0.13	0.05 ± 0.09
	G + M	G_G+M	0.27 ± 0.08	0.13 ± 0.08	0.19 ± 0.06	0.18 ± 0.13	0.37 ± 0.07	0.24 ± 0.12
		M_G+M	0.42 ± 0.11	0.24 ± 0.11	0.00 ± 0.00	− 0.05 ± 0.10	0.05 ± 0.08	0.04 ± 0.10
		G + M_G+M	0.69 ± 0.13	0.27 ± 0.09	0.19 ± 0.06	0.15 ± 0.10	0.42 ± 0.11	0.24 ± 0.13
LW	G	G_G	0.45 ± 0.08	0.19 ± 0.06	0.33 ± 0.07	0.14 ± 0.06	0.44 ± 0.07	0.22 ± 0.09
	M	M_M	0.33 ± 0.09	0.26 ± 0.04	0.45 ± 0.14	0.22 ± 0.10	0.88 ± 0.21	0.26 ± 0.11
	G + M	G_G+M	0.42 ± 0.08	0.19 ± 0.06	0.33 ± 0.07	0.16 ± 0.06	0.41 ± 0.11^e,f	0.23 ± 0.09^f
		M_G+M	0.26 ± 0.08	0.25 ± 0.05	0.42 ± 0.13	0.22 ± 0.10	0.59 ± 0.11^e,f	0.25 ± 0.11^f
		G + M_G+M	0.68 ± 0.10	0.28 ± 0.06	0.76 ± 0.13	0.28 ± 0.07	1.00 ± 0.00^e,f	0.32 ± 0.06^f

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
^cPropVar = Proportion of the phenotypic variance (adjusted for fixed effects) explained by the component
^dAccuracy = Correlation between phenotype adjusted for fixed effects and the component when using cross-fold validation with each Cohort a different fold
^eRun in ASReml 4.2 because ASReml 4.1 had major convergence issues
^fAt least one of the models contributing to this value had convergence or singularity issues

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ISSN: 1297-9686

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