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

Table 2 Summary of the genomic regions associated with each trait at a genome-wide significance threshold

Trait	SSC	Position (Mb)	Line	Number of significant SNPs	Most significant SNP
					Position (bp)	− log₁₀(P-value)	MAF
LDP	1	158.36–158.36	A	1	158,355,905	6.9	0.32
LDP	1	159.7–161.33	B	3	160,347,188	8.36	0.24
LDP	1	270.35–270.35	D	1	270,354,493	6.66	0.31
LDP	2	0.12–0.69	B	5	404,057	18.83	0.06
LDX	2	2.05–2.05	D	2	2,051,230	7.57	0.23
LDP	2	2.05–3.99	B	13	2,215,904	14.1	0.18
LDP	5	66.1–66.22	D	3	66,103,958	27.4	0.43
LDX	5	66.1–66.22	D	3	66,103,958	23.47	0.43
LDP	6	45.74–47.55	A	7	45,744,000	11.14	0.29
LDX	7	20.59–20.59	D	1	20,586,603	7.26	0.26
LDP	7	30.1–30.23	D	2	30,095,798	6.71	0.03
LDX	7	30.1–30.23	D	2	30,095,798	6.28	0.03
LDP	7	30.32–31.64	A	6	30,317,219	8.94	0.31
LDP	7	30.32–31.96	B	6	30,317,219	9.74	0.26
LDP	9	47.65–47.65	A	1	47,650,875	9.59	0.36
LDX	9	47.28–47.65	D	2	47,650,875	6.81	0.36
LDP	12	25.48–25.53	A	2	25,532,133	6.03	0.28
LDP	16	33.18–33.49	B	5	33,283,559	8.25	0.44
LDP	16	31.83–36.49	C	54	34,100,484	21.55	0.17
LDX	16	32.39–36.86	C	61	34,893,593	21.56	0.18
LDP	16	48.16–48.62	C	3	48,157,349	6.41	0.28
LDP	17	5.31–5.31	C	1	5,307,502	6.64	0.18
LDX	17	5.31–5.31	C	1	5,307,502	6.3	0.2
LDP	18	2.36–2.38	A	2	2,380,106	8.43	0.03
PHLOIN	15	119.93–121.09	D	8	120,437,865	6.42	0.23

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, MAF minor allele frequency

ISSN: 1297-9686