Integration of epigenomic and genomic data to predict residual feed intake and the feed conversion ratio in dairy sheep via machine learning algorithms

Table 3 Mean (± standard deviation) for the root mean squared error (RMSE) and mean squared pearson correlation (rho²) obtained in the 100 rounds of random assignment of Ewes in the training and test datasets for each machine learning model to predict residual feed intake (RFI) and the feed conversion ratio (FCR)

Prediction	Deepleaning		RF		xgboost
	Mean RMSE	Mean rho²	Mean RMSE	Mean rho²	Mean RMSE	Mean rho²
mRFI_RFI	0.20 ± 0.05	0.18 ± 0.22	0.17 ± 0.03	0.14 ± 0.16	0.18 ± 0.03	0.16 ± 0.20
mFCR_FCR	0.35 ± 0.10	0.14 ± 0.18	0.31 ± 0.07	0.15 ± 0.17	0.35 ± 0.07	0.14 ± 0.17
mCons_RFI	0.19 ± 0.08	0.16 ± 0.19	0.17 ± 0.03	0.17 ± 0.21	0.18 ± 0.02	0.16 ± 0.16
mCons_FCR	0.35 ± 0.11	0.18 ± 0.20	0.31 ± 0.08	0.14 ± 0.17	0.34 ± 0.08	0.17 ± 0.21
mRFI_RFI + VARs	0.25 ± 0.15	0.18 ± 0.22	0.17 ± 0.03	0.15 ± 0.16	0.17 ± 0.03	0.11 ± 0.15
mFCR_FCR + VARs	0.59 ± 0.41	0.19 ± 0.20	0.31 ± 0.09	0.14 ± 0.14	0.35 ± 0.07	0.18 ± 0.20
mCons_RFI + VARs	0.24 ± 0.08	0.20 ± 0.23	0.18 ± 0.04	0.17 ± 0.19	0.18 ± 0.03	0.18 ± 0.20
mCons_FCR + VARs	0.44 ± 0.13	0.20 ± 0.22	0.30 ± 0.08	0.13 ± 0.15	0.33 ± 0.08	0.15 ± 0.20

mRFI_RFI: Mean methylation within DRMs identified comparing RFI groups used to predict RFI; mFCR_FCR: Mean methylation within DRMs identified comparing FCR groups used to predict FCR; mCons_RFI: Mean methylation within DRMs identified comparing Consensus groups used to predict RFI; mCons_FCR: Mean methylation within DRMs identified comparing Consensus groups used to predict FCR; mRFI_RFI + SNPs: Mean methylation within DRMs identified comparing RFI groups plus SNPs within the same DMRs used to predict RFI; mFCR_FCR + SNPs: Mean methylation within DRMs identified comparing FCR groups plus SNPs within the same DMRs used to predict FCR; mCons_RFI + SNPs: Mean methylation within DRMs identified comparing Consensus groups plus SNPs within the same DMRs used to predict RFI; mCons_FCR + SNPs: Mean methylation within DRMs identified comparing Consensus groups plus SNPs within the same DMRs used to predict FCR

ISSN: 1471-2164