Improving the accuracy of genomic prediction for meat quality traits using whole genome sequence data in pigs

Zhuang, Zhanwei; Wu, Jie; Qiu, Yibin; Ruan, Donglin; Ding, Rongrong; Xu, Cineng; Zhou, Shenping; Zhang, Yuling; Liu, Yiyi; Ma, Fucai; Yang, Jifei; Sun, Ying; Zheng, Enqin; Yang, Ming; Cai, Gengyuan; Yang, Jie; Wu, Zhenfang

doi:10.1186/s40104-023-00863-y

Journal of Animal Science and Biotechnology

Table 2 The mean accuracy and bias values of genomic prediction using preselected SNPs and INDELs from common variants dataset that were present on the WGS and imputed-based WGS

From: Improving the accuracy of genomic prediction for meat quality traits using whole genome sequence data in pigs

Traits^a	Model^b	Variants type	Marker density
Traits^a	Model^b	Variants type	1K	3K	10K	30K	100K	500K	1,000K	5,000K	10,000K
IMF	GBLUP	SNP	0.23 ± 1.04	0.25 ± 1.05	0.26 ± 1.01	0.26 ± 1.00	0.27 ± 1.02	0.27 ± 1.02	0.27 ± 1.02	0.27 ± 1.02	0.27 ± 1.01
	GBLUP	INDEL	0.23 ± 1.05	0.25 ± 1.06	0.26 ± 1.02	0.27 ± 1.02	0.27 ± 1.03	0.27 ± 1.02	0.27 ± 1.02
	MultiBLUP	SNP+INDEL	0.24 ± 1.03	0.26 ± 1.06	0.27 ± 1.02	0.27 ± 1.01	0.27 ± 1.02	0.27 ± 1.02	0.27 ± 1.02
MC	GBLUP	SNP	0.22 ± 1.03	0.25 ± 1.05	0.29 ± 1.05	0.27 ± 1.05	0.28 ± 1.05	0.29 ± 1.04	0.29 ± 1.04	0.29 ± 1.04	0.29 ± 1.04
	GBLUP	INDEL	0.21 ± 1.11	0.26 ± 1.04	0.26 ± 1.05	0.28 ± 1.04	0.28 ± 1.06	0.28 ± 1.05	0.28 ± 1.05
	MultiBLUP	SNP+INDEL	0.24 ± 1.06	0.27 ± 1.05	0.28 ± 1.05	0.28 ± 1.04	0.28 ± 1.05	0.29 ± 1.05	0.29 ± 1.05
L*	GBLUP	SNP	0.12 ± 1.16	0.15 ± 1.04	0.16 ± 1.04	0.16 ± 1.07	0.16 ± 1.06	0.16 ± 1.05	0.16 ± 1.05	0.16 ± 1.05	0.16 ± 1.05
	GBLUP	INDEL	0.13 ± 1.15	0.16 ± 1.08	0.15 ± 1.09	0.16 ± 1.05	0.16 ± 1.05	0.16 ± 1.06	0.16 ± 1.06
	MultiBLUP	SNP+INDEL	0.13 ± 1.13	0.16 ± 1.05	0.16 ± 1.06	0.16 ± 1.06	0.16 ± 1.05	0.16 ± 1.05	0.16 ± 1.05
a*	GBLUP	SNP	0.38 ± 1.03	0.40 ± 1.00	0.46 ± 1.01	0.46 ± 1.00	0.46 ± 1.00	0.47 ± 1.00	0.47 ± 1.00	0.47 ± 1.00	0.47 ± 1.00
	GBLUP	INDEL	0.36 ± 0.99	0.42 ± 1.00	0.43 ± 1.00	0.44 ± 1.00	0.46 ± 1.01	0.47 ± 1.01	0.47 ± 1.01
	MultiBLUP	SNP+INDEL	0.40 ± 1.00	0.43 ± 1.00	0.46 ± 1.01	0.46 ± 1.00	0.46 ± 1.01	0.47 ± 1.01	0.47 ± 1.01
b*	GBLUP	SNP	0.08 ± 1.34	0.12 ± 1.14	0.14 ± 1.16	0.14 ± 1.15	0.13 ± 1.18	0.13 ± 1.16	0.13 ± 1.16	0.13 ± 1.15	0.13 ± 1.15
	GBLUP	INDEL	0.10 ± 1.35	0.11 ± 1.22	0.13 ± 1.13	0.13 ± 1.18	0.14 ± 1.15	0.13 ± 1.17	0.14 ± 1.16
	MultiBLUP	SNP+INDEL	0.10 ± 1.31	0.12 ± 1.14	0.14 ± 1.15	0.14 ± 1.15	0.14 ± 1.14	0.13 ± 1.14	0.13 ± 1.14

^aIMF Intramuscular fat content (also refers to marbling score in this study), MC Meat color, L* Lightness, a* Redness, b* Yellowness
^bGBLUP Genomic best linear unbiased prediction, MultiBLUP An extended BLUP model that included multiple random effects

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ISSN: 2049-1891

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