A genome-wide association study for loin depth and muscle pH in pigs from intensely selected purebred lines

Desire, Suzanne; Johnsson, Martin; Ros-Freixedes, Roger; Chen, Ching-Yi; Holl, Justin W.; Herring, William O.; Gorjanc, Gregor; Mellanby, Richard J.; Hickey, John M.; Jungnickel, Melissa K.

doi:10.1186/s12711-023-00815-0

Genetics Selection Evolution

Table 4 Candidate variants identified for the genome-wide significant lead GWAS SNPs based on pCADD scores

From: A genome-wide association study for loin depth and muscle pH in pigs from intensely selected purebred lines

Trait	SSC	Lead GWAS SNP		seqSNP
Trait	SSC	Position (bp)	Line	r²	Dist (Mb)	pCADD score	VEP	Position (bp)	Open chromatin	Gene	Supporting evidence
LDP	1	158,355,905	A	0.84	− 3.51	24.86	missense	161,864,397	No	ENSSSCG00000004911	-
LDP	1	160,347,188	B	0.97	− 0.43	34.19	missense	160,773,437	No	MC4R	Associated with growth and fatness [2]
LDP	1	270,354,493	D	0.96	− 0.05	30.69	missense	270,408,730	Yes	HMCN2	Differential methylation between Chinese and YP [27]
LDP	2	404,057	B	0.95	− 0.03	22.4	missense	432,824	Yes	TMEM80	–
LDX	2	2,051,230	D	0.81	0	20.4	missense	2,048,612	Yes	SLC22A18	Hypermethylated in Duroc (fat), compared to Pietrain (lean) pigs [28]
LDP	2	2,215,904	B	0.91	0	11.74	intron	2,213,982	No	OSBPL5	Candidate gene for ADG [29]
LDP	5	66,103,958	D	0.98	− 0.01	13.49	intron	66,109,890	Yes	CCND2	Overexpressed in SM muscle [30]
LDX	5	66,103,958	D	0.98	− 0.01	13.49	intron	66,109,890	Yes	CCND2	Overexpressed in SM muscle [30]
LDP	6	45,744,000	A	0.86	− 6.29	34.95	missense	52,032,079	Yes	GIPR	–
LDX	7	20,586,603	D	0.91	0.28	9.91	intron	20,305,193	No	CARMIL1	Suggested gene for backfat GWAS [31]
LDP	7	30,095,798	D	0.94	− 0.08	14.82	missense	30,179,826	Yes	GRM4	eQTL for fatty acid composition [32]
LDX	7	30,095,798	D	0.94	− 0.08	14.82	missense	30,179,826	Yes	GRM4	eQTL for fatty acid composition [32]
LDP	7	30,317,219	A	0.88	− 2.11	28.78	synonymous	32,427,677	No	CPNE5	Candidate gene for muscle lightness [33]
LDP	7	30,317,219	B	0.87	− 0.03	17.58	3 prime UTR	30,350,337	Yes	NUDT3	Associated with loin muscle area [34, 35]
LDP	9	47,650,875	A	0.96	0.18	11.79	intron	47,475,749	Yes	ARHGEF12
LDX	9	47,650,875	D	0.92	0.24	7.22	intron	47,406,822	No	POU2F3	–
LDP	12	25,532,133	A	0.93	0.23	34.62	missense	25,299,992	No	ENSSSCG00000030269	–
LDP	16	33,283,559	B	0.92	0.09	17.4	intron	33,194,036	No	ARL15	Candidate gene for growth [36]
LDP	16	34,100,484	C	0.96	0.05	43.19	missense	34,048,944	No	ENSSSCG00000016898	–
LDX	16	34,893,593	C	0.9	0.84	43.19	missense	34,048,944	No	ENSSSCG00000016898	–
LDP	16	48,157,349	C	0.84	− 3.7	21.66	synonymous	51,852,935	Yes	SH3PXD2B	Implicated in growth rate of pigs [37]
LDP	17	5,307,502	C	0.91	0.06	34.21	synonymous	5,246,513	Yes	SLC7A2	–
LDX	17	5,307,502	C	0.91	0.06	34.21	synonymous	5,246,513	Yes	SLC7A2	–
LDP	18	2,380,106	A	0.91	− 0.04	23.47	intergenic	2,422,486	No	ENSSSCG00000042976	–
PHLOIN	15	120,437,865	D	0.97	− 0.28	41.82	synonymous	120,713,562	Yes	RNF25	Suggested role in muscle development in cattle [38]

seqSNP the SNP with a top ranking pCADD score from sequence data, LDP loin depth (purebreds), LDX loin depth (crossbreds), PHHAM pH of semimembranosus muscle measured 22 h post-slaughter, PHLOIN pH of longissimus muscle measured 22 h post-slaughter, seqSNP SNP with the highest pCADD score in high LD (r² > 0.07) with the lead GWAS SNP. r²: linkage disequilibrium between lead GWAS SNP and seqSNP; Distance: distance in Mbp between lead GWAS SNP and seqSNP; VEP = Ensembl variant effect prediction of the seqSNP; Position of the seqSNP; Gene refers to the gene each seqSNP was located within, or the closest gene if the seqSNP was intergenic

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ISSN: 1297-9686

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