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 1 The number of preselected SNPs and INDELs from common variants dataset that were present on the WGS and imputed-based WGS and estimated heritability

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

Traits^a	Variants' number and heritability^b	Variants type^c	Marker density
Traits^a	Variants' number and heritability^b	Variants type^c	1K	3K	10K	30K	100K	500K	1,000K	5,000K	10,000k
	Number of preselection variants	SNP	1,017	2,968	10,009	29,931	100,070	500,006	1,000,006	4,999,686	10,001,734
	Number of preselection variants	INDEL	1,018	3,063	9,973	30,122	100,130	500,971	1,000,565
IMF	Estimated heritability (Mean ± SE)	SNP	0.13 ± 0.03	0.18 ± 0.04	0.23 ± 0.04	0.14 ± 0.05	0.25 ± 0.05	0.26 ± 0.05	0.26 ± 0.05	0.26 ± 0.05	0.26 ± 0.05
		INDEL	0.13 ± 0.03	0.18 ± 0.03	0.24 ± 0.04	0.25 ± 0.05	0.25 ± 0.05	0.26 ± 0.05	0.27 ± 0.05
		SNP+INDEL	0.16 ± 0.05	0.20 ± 0.04	0.25 ± 0.05	0.25 ± 0.05	0.26 ± 0.05	0.26 ± 0.05	0.27 ± 0.05
MC		SNP	0.15 ± 0.03	0.20 ± 0.04	0.29 ± 0.05	0.28 ± 0.05	0.28 ± 0.05	0.30 ± 0.05	0.30 ± 0.05	0.30 ± 0.05	0.30 ± 0.05
		INDEL	0.12 ± 0.03	0.21 ± 0.04	0.24 ± 0.04	0.29 ± 0.05	0.29 ± 0.05	0.30 ± 0.05	0.30 ± 0.05
		SNP+INDEL	0.17 ± 0.03	0.24 ± 0.04	0.28 ± 0.05	0.29 ± 0.05	0.29 ± 0.05	0.30 ± 0.05	0.30 ± 0.05
L*		SNP	0.07 ± 0.03	0.12 ± 0.03	0.15 ± 0.04	0.14 ± 0.04	0.14 ± 0.04	0.15 ± 0.04	0.15 ± 0.04	0.15 ± 0.04	0.15 ± 0.04
		INDEL	0.07 ± 0.02	0.12 ± 0.03	0.13 ± 0.04	0.14 ± 0.04	0.15 ± 0.04	0.15 ± 0.04	0.15 ± 0.04
		SNP+INDEL	0.08 ± 0.03	0.14 ± 0.04	0.15 ± 0.04	0.15 ± 0.04	0.15 ± 0.04	0.15 ± 0.04	0.15 ± 0.04
a*		SNP	0.28 ± 0.03	0.34 ± 0.04	0.51 ± 0.05	0.56 ± 0.05	0.59 ± 0.05	0.61 ± 0.05	0.61 ± 0.05	0.61 ± 0.05	0.61 ± 0.05
		INDEL	0.27 ± 0.03	0.39 ± 0.04	0.47 ± 0.05	0.54 ± 0.05	0.60 ± 0.05	0.62 ± 0.05	0.62 ± 0.05
		SNP+INDEL	0.36 ± 0.04	0.44 ± 0.04	0.55 ± 0.05	0.58 ± 0.05	0.60 ± 0.05	0.62 ± 0.05	0.62 ± 0.05
b*		SNP	0.04 ± 0.02	0.08 ± 0.03	0.11 ± 0.04	0.11 ± 0.04	0.11 ± 0.04	0.11 ± 0.04	0.11 ± 0.04	0.11 ± 0.04	0.11 ± 0.04
		INDEL	0.05 ± 0.02	0.09 ± 0.03	0.09 ± 0.04	0.11 ± 0.04	0.12 ± 0.04	0.11 ± 0.04	0.12 ± 0.04
		SNP+INDEL	0.06 ± 0.03	0.10 ± 0.04	0.11 ± 0.04	0.11 ± 0.04	0.12 ± 0.04	0.12 ± 0.04	0.12 ± 0.04

^aIMF Intramuscular fat content (also refers to marbling score in this study), MC Meat color, L* Lightness, a* Redness, b* Yellowness
^bSE Standard error
^cSNP+INDEL: variants used in MultiBLUP

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ISSN: 2049-1891

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