Muscle glycogen level and occurrence of acid meat in commercial hybrid pigs are regulated by two low-frequency causal variants with large effects and multiple common variants with small effects

Table 6 Multiple SNPs associated with RG level at a significance threshold of P < 1e−4, detected by the GWAS conditioning on both PRKAG3 R200Q and PHKG1g.8283C>A variants

Top SNP	Chr	Pos (bp)	Nearest or candidate genes^a	MAF^b	Effects^c	P-value	Var (%)^d
rs81347579	Unknown^e	2,127,646^e	CKB	0.14	3.79	3.58E−05	2.37
rs324148419	9	35,634,517	GRIA4	0.21	2.84	4.76E−05	2.84
rs81270133	18	45,962,926	ENSSCG0000003394 ^f	0.34	1.74	6.90E−05	1.09
rs81475445	4	124,944,340	BTBD8	0.28	2.03	7.35E−05	1.58
rs81240897	3	123,200,355	LRATD1	0.38	3.03	8.01E−05	2.23
rs80965652	4	96,151,597	S100A6	0.45	1.99	9.62E−05	2.39
rs81379369	3	27,217,537	XYLT1	0.37	1.27	9.99E−05	0.91

^aAnnotated genes that located nearest to the most significant SNP or involved in energy homeostasis (candidate gene shown in bold); gene names starting with ENSSSCG follow the Ensembl nomenclature while other gene symbols follow the HUGO nomenclature
^bMinor allele frequency
^cAdditive effects
^dPhenotypic variance explained by the top SNPs
^ePosition of SNP rs81347579 on the AEMK02000452 scaffold, which is not assigned to any chromosome, a human-pig comparative map and linkage disequilibrium mapping (data not shown) indicate that it is likely located at ~ 120 Mb (near the telomere) on SSC7
^fEncodes a lincRNA

ISSN: 1297-9686