Prediction of genomic breeding values for growth, carcass and meat quality traits in a multi-breed sheep population using a HD SNP chip

Brito, Luiz F.; Clarke, Shannon M.; McEwan, John C.; Miller, Stephen P.; Pickering, Natalie K.; Bain, Wendy E.; Dodds, Ken G.; Sargolzaei, Mehdi; Schenkel, Flávio S.

doi:10.1186/s12863-017-0476-8

Table 4 Heritability estimates, expected accuracy, theoretical accuracy, effective number of progeny and observed accuracies of molecular breeding values in different scenarios for meat quality traits

From: Prediction of genomic breeding values for growth, carcass and meat quality traits in a multi-breed sheep population using a HD SNP chip

Trait¹	h² ± SE	AccE	AccT	ENP	GB0	GB2PC	GB4PC	GB6PC	GB10	GB20	GBRCV	GBKCV	GBC
A24	0.17 ± 0.02	0.36	0.39	3	0.31	0.31	0.30	0.30	0.31	0.30	0.37 ± 0.07	0.24 ± 0.04	0.20 ± 0.07
A24ad	0.16 ± 0.02	0.35	0.38	4	0.35	0.34	0.35	0.35	0.34	0.33	0.37 ± 0.06	0.22 ± 0.08	0.26 ± 0.08
A48	0.17 ± 0.02	0.36	0.35	2	0.23	0.22	0.22	0.21	0.22	0.21	0.38 ± 0.02	0.27 ± 0.05	0.14 ± 0.10
A48ad	0.17 ± 0.02	0.36	0.37	2	0.26	0.25	0.25	0.25	0.26	0.25	0.40 ± 0.02	0.30 ± 0.06	0.16 ± 0.10
A96	0.19 ± 0.02	0.38	0.36	2	0.23	0.22	0.21	0.19	0.24	0.24	0.35 ± 0.03	0.19 ± 0.06	0.11 ± 0.10
A96ad	0.18 ± 0.02	0.37	0.38	2	0.26	0.25	0.25	0.24	0.26	0.26	0.37 ± 0.03	0.23 ± 0.05	0.16 ± 0.11
A168	0.06 ± 0.02	0.22	0.20	1	0.02	−0.04	0.06	−0.06	0.02	0.03	0.19 ± 0.05	0.07 ± 0.07	0.21 ± 0.14
A168ad	0.06 ± 0.02	0.22	0.15	1	0.08	−0.02	0.03	−0.03	0.08	0.09	0.25 ± 0.04	0.12 ± 0.10	0.19 ± 0.11
B24	0.14 ± 0.02	0.33	0.28	3	0.29	0.28	0.28	0.28	0.29	0.29	0.33 ± 0.04	0.18 ± 0.05	0.22 ± 0.13
B48	0.13 ± 0.02	0.33	0.34	2	0.24	0.23	0.23	0.23	0.24	0.24	0.29 ± 0.03	0.16 ± 0.05	0.19 ± 0.11
B96	0.13 ± 0.02	0.32	0.35	3	0.29	0.29	0.29	0.28	0.28	0.28	0.34 ± 0.04	0.24 ± 0.08	0.23 ± 0.07
B168	0.14 ± 0.02	0.32	0.28	4	0.32	0.30	0.31	0.30	0.32	0.31	0.35 ± 0.05	0.24 ± 0.06	0.23 ± 0.06
L24	0.18 ± 0.02	0.37	0.38	3	0.32	0.31	0.31	0.31	0.32	0.32	0.42 ± 0.03	0.22 ± 0.04	0.28 ± 0.07
L48	0.20 ± 0.02	0.39	0.39	2	0.31	0.31	0.32	0.32	0.31	0.31	0.39 ± 0.03	0.24 ± 0.06	0.26 ± 0.10
L96	0.21 ± 0.02	0.40	0.39	3	0.33	0.31	0.32	0.32	0.33	0.33	0.41 ± 0.04	0.23 ± 0.06	0.25 ± 0.11
L168	0.20 ± 0.02	0.38	0.38	3	0.33	0.32	0.32	0.32	0.34	0.34	0.43 ± 0.05	0.22 ± 0.05	0.26 ± 0.14
SHF	0.26 ± 0.03	0.43	0.41	2	0.28	0.28	0.27	0.27	0.28	0.28	0.41 ± 0.03	0.27 ± 0.05	0.19 ± 0.09
SHFad	0.27 ± 0.03	0.44	0.44	2	0.30	0.29	0.29	0.28	0.30	0.30	0.41 ± 0.03	0.27 ± 0.05	0.18 ± 0.11
MARB	0.31 ± 0.03	0.47	0.44	5	0.52	0.43	0.43	0.43	0.52	0.52	0.50 ± 0.03	0.35 ± 0.03	0.33 ± 0.14
MARBad	0.31 ± 0.03	0.47	0.45	5	0.52	0.46	0.46	0.45	0.52	0.53	0.52 ± 0.03	0.36 ± 0.03	0.36 ± 0.13
LPH	0.14 ± 0.02	0.33	0.32	4	0.33	0.32	0.31	0.29	0.33	0.33	0.27 ± 0.03	0.15 ± 0.07	0.20 ± 0.07
LPHad	0.13 ± 0.02	0.32	0.31	4	0.34	0.32	0.32	0.29	0.34	0.34	0.27 ± 0.03	0.15 ± 0.08	0.20 ± 0.06
Average	0.16 ± 0.07	0.34 ± 0.07	0.35	2.83 ± 1.11	0.29 ± 0.10	0.27 ± 0.11	0.28 ± 0.10	0.26 ± 0.11	0.29 ± 0.11	0.28 ± 0.11	0.36 ± 0.08	0.21 ± 0.07	0.23 ± 0.06

¹Abbreviations are presented in Table 1; “ad”: traits that were adjusted for correlated variables; h²: heritability estimate; AccE: Expected accuracy; AccT: Theoretical accuracy from the MME; ENP: effective number of progeny calculated using the accuracies from GB0; GB0: GBLUP accuracies fitting only G matrix; GB10 and GB20: accuracies of GBLUP fitting G matrix and 10 or 20% of A matrix, respectively; GB2PC, GB4PC and GB6PC: GBLUP accuracies fitting for 2, 4 or 6 principal components, respectively; GBRCV: GBLUP accuracies for random cross-validation; GBKCV: GBLUP accuracies for k-means clustering; GBC: GBLUP accuracies for predictions performed within each cluster

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