Table 5.

The averaged correlation coefficient (r) among 15 amino acids between the observed values (each amino acid content) and the GEBVs predicted from (1) all 23,279 SNPs, (2) the 231 SNP markers, and (3) only the associated SNP markers with the specific amino acid content using RR-BLUP in rrBLUP software, and from (4) the 231 SNP markers in reference set (training set) and inference set (validation set) using CBLUPin Gapit.

	RR-BLUP in rrBLUP			CBLUP in Gapit
	23279 SNPs in 249 accessions	231 SNPs associated with amino acids	Associated SNPs*	231 SNPs in training set	231 SNPs in validation set
Ala	0.30	0.45	0.33	0.76	0.52
Arg	0.61	0.68	0.61	0.80	0.59
Asp	0.22	0.53	0.41	0.77	0.57
Glu	0.31	0.48	0.48	0.74	0.52
Gly	0.23	0.56	0.35	0.79	0.60
His	0.46	0.57	0.46	0.76	0.55
Ile	0.25	0.61	0.53	0.80	0.61
Leu	0.30	0.53	0.49	0.77	0.53
Lys	0.42	0.61	0.54	0.82	0.59
Phe	0.50	0.68	0.35	0.84	0.68
Pro	0.26	0.49	0.34	0.76	0.46
Ser	0.18	0.47	0.42	0.73	0.51
Thr	0.39	0.63	0.50	0.85	0.63
Tyr	0.36	0.54	0.44	0.81	0.57
Val	0.25	0.52	0.53	0.75	0.54
Average	0.34	0.56	0.45	0.78	0.56

*Associated SNPs signifies that the average correlation coefficient (r) for each amino acid in column-4 was calculated with the SNP markers only associated with the individual amino acid to predict the GEBV for each amino acid, such as for r = 0.33 for Ala, which was calculated from 11 associated SNPs.