Table 1.

Prediction accuracy and regression coefficients of 21 traits in chicken using genomic best linear unbiased prediction (GBLUP) with different genotype data.

Traits1	600K array2		WGS (internal)3		WGS (external)4		WGS (combined)5
	${\text{r}}_{(\widehat{\text{g}},\text{p})}^6$	${\text{b}}_{(\widehat{\text{g}},\text{p})}^7$	${\text{r}}_{(\widehat{\text{g}},\text{p})}$	${\text{b}}_{(\widehat{\text{g}},\text{p})}$	${\text{r}}_{(\widehat{\text{g}},\text{p})}$	${\text{b}}_{(\widehat{\text{g}},\text{p})}$	${\text{r}}_{(\widehat{\text{g}},\text{p})}$	${\text{b}}_{(\widehat{\text{g}},\text{p})}$
ADG	0.34 (0.01)	0.98 (0.05)	0.33 (0.01)	0.99 (0.06)	0.33 (0.01)	1.0 2(0.06)	0.33 (0.01)	0.99 (0.06)
ADFI	0.40 (0.01)	1.01 (0.04)	0.43 (0.01)	1.00 (0.04)	0.42 (0.01)	1.02 (0.04)	0.42 (0.01)	1.0 0(0.04)
RFI	0.45 (0.01)	1.03 (0.04)	0.47 (0.01)	1.03 (0.04)	0.46 (0.01)	1.03 (0.04)	0.47 (0.01)	1.03 (0.04)
FCR	0.26 (0.01)	0.92 (0.06)	0.26 (0.01)	0.95 (0.06)	0.27 (0.01)	0.98 (0.06)	0.26 (0.01)	0.94 (0.06)
CW	0.30 (0.01)	1.01 (0.06)	0.31 (0.01)	0.99 (0.06)	0.29 (0.01)	1.01 (0.06)	0.30 (0.01)	0.99 (0.06)
EWG	0.28 (0.01)	0.97 (0.07)	0.29 (0.01)	0.99 (0.07)	0.27 (0.01)	1.00 (0.08)	0.28 (0.01)	0.99 (0.07)
EW	0.26 (0.01)	0.96 (0.07)	0.27 (0.02)	1.00 (0.08)	0.26 (0.02)	1.00 (0.08)	0.27 (0.02)	1.00 (0.08)
BMW	0.26 (0.02)	1.04 (0.09)	0.27 (0.01)	1.04 (0.08)	0.25 (0.01)	1.04 (0.08)	0.27 (0.01)	1.04 (0.08)
DW	0.20 (0.01)	1.10 (0.14)	0.22 (0.01)	1.11 (0.14)	0.20 (0.01)	1.12 (0.14)	0.21 (0.01)	1.10 (0.12)
AFW	0.36 (0.01)	1.04 (0.05)	0.36 (0.01)	1.02 (0.04)	0.36 (0.01)	1.04 (0.05)	0.36 (0.01)	1.02 (0.04)
AFP	0.32 (0.01)	1.00 (0.04)	0.33 (0.01)	1.00 (0.04)	0.32 (0.01)	0.98 (0.04)	0.33 (0.01)	1.00 (0.04)
GW	0.23 (0.01)	1.15 (0.10)	0.23 (0.01)	1.18 (0.10)	0.23 (0.01)	1.17 (0.10)	0.24 (0.01)	1.16 (0.10)
IL	0.24 (0.01)	1.09 (0.07)	0.25 (0.01)	1.07 (0.07)	0.24 (0.01)	1.08 (0.07)	0.25 (0.01)	1.07 (0.07)
BW45	0.28 (0.01)	1.06 (0.07)	0.27 (0.01)	1.06 (0.07)	0.25 (0.01)	1.09 (0.08)	0.27 (0.01)	1.05 (0.07)
BW49	0.27 (0.01)	1.07 (0.06)	0.29 (0.01)	1.06 (0.05)	0.26 (0.01)	1.08 (0.06)	0.28 (0.01)	1.05 (0.05)
BW56	0.29 (0.01)	1.19 (0.09)	0.30 (0.01)	1.18 (0.08)	0.27 (0.01)	1.19 (0.09)	0.30 (0.01)	1.18 (0.08)
BW63	0.26 (0.01)	1.22 (0.10)	0.26 (0.02)	1.23 (0.11)	0.24 (0.02)	1.28 (0.12)	0.26 (0.02)	1.25 (0.11)
BW70	0.26 (0.01)	1.06 (0.07)	0.25 (0.01)	1.06 (0.07)	0.24 (0.01)	1.08 (0.07)	0.25 (0.01)	1.04 (0.07)
BW77	0.29 (0.01)	0.99 (0.06)	0.30 (0.01)	1.03 (0.07)	0.29 (0.01)	1.06 (0.07)	0.29 (0.01)	1.02 (0.07)
BW84	0.32 (0.01)	1.05 (0.05)	0.33 (0.01)	1.05 (0.05)	0.31 (0.01)	1.07 (0.06)	0.32 (0.01)	1.06 (0.05)
BW91	0.30 (0.01)	1.01 (0.05)	0.31 (0.01)	0.98 (0.04)	0.30 (0.01)	1.00 (0.05)	0.31 (0.01)	0.98 (0.04)

¹These traits were average daily gain (ADG), average daily feed intake (ADFI), residual feed intake (RFI), feed conversion ratio (FCR), carcass weight (CW), breast muscle weight (BMW), eviscerated weight with giblets (EWG), eviscerated weight (EW), drumstick weight (DW), abdominal fat weight (AFW), abdominal fat percentage (AFP), gizzard weight (GW), intestine length (IL), body weight in 45 days (BW45), body weight in 49 days (BW49), body weight in 56 days (BW56), body weight in 63 days (BW63), body weight in 70 days (BW70), body weight in 77 days (BW77), body weight in 84 days (BW84), and body weight in 91 days (BW91).

²600K array: the 600K Affymetrix^® Axiom^® HD genotyping array.

³WGS (internal): the imputed whole-genome sequencing data obtained from internal reference panel.

⁴WGS (external): the imputed whole-genome sequencing data obtained from external reference panel.

⁵WGS (combined): the imputed whole-genome sequencing data obtained from combined reference panel.

⁶${\text{r}}_{(\widehat{\text{g}},\text{p})}$: the Pearson correlation between the predicted genetic values (ĝ) and the observed phenotypes (p) corrected for fixed effect. Means and standard errors (in parentheses) of ${\text{r}}_{(\widehat{\text{g}},\text{p})}$ are shown in the table. Bold font was used to represent values that were higher than others.

⁷${\text{b}}_{(\widehat{\text{g}},\text{p})}$: regression of the predicted genetic values (ĝ) and the observed phenotypes (p) corrected for fixed effect. Means and standard errors (in parentheses) of regression coefficients are shown in the table.