Table 3.

QTL regions for conformation traits and the most significant SNP within each region in three pig breeds

Trait	n	Chr	QTL region		Most significant SNP			Candidate genesb
			Right position (bp)	Left position (bp)	SNPa	P value	Effect size (%)
Landrace
BACK	41	1	63,345,571	68,207,754	rs80850790	3.53 × 10−8	0.12	SRSF12, PNRC1
		1	81,835,391	105,362,894	rs81287678	1.48 × 10−8	0.13	SLC14A2
		3	117,911,196	118,765,898	rs81258584	1.64 × 10−7	0.11	PPM1G
		5	67,981,416	68,326,348	rs80985094	9.93 × 10−8	0.14	CCND2
		7	36,202,231	37,157,566	rs80828473	7.41 × 10−12	0.19	PPARD
HIND	25	1	216,980,027	242,984,908	rs80946156	5.21 × 10−8	0.13	RCL1
CONF	104	3	97,726,517	97,741,803	rs81303888	2.72 × 10−7	0.11	LRPPRC
		3	117,911,196	117,911,196		2.42 × 10−7	0.11	BRE, ENSSSCG00000026465
		5	67,518,456	69,897,370	rs81384722	2.29 × 10−8	0.15	ENSSSCT00000000782
		6	74,354,607	84,927,021	rs81389032	1.84 × 10−10	0.17	ENSSSCT00000032147, ENSSSCT00000003913
		7	21,053,530	37,812,119	rs80828473	6.28 × 10−11	0.18	PPARD
		7	131,126,819	131,126,819	rs81397155	6.20 × 10−8	0.15	TDRD9, CEP170B
		12	24,812,751	26,022,727	rs81312521	3.16 × 10−8	0.13	NGFR
		12	46,857,615	47,352,945	rs81435770	2.09 × 10−7	0.11	PIPOX
Yorkshire
FRONT	2	7	52,843,780	52,860,434	rs80995679	1.27 × 10−6	0.09	CHRNB4, PSMA4
BACK	2	6	142,725,268	142,803,333	rs81305243	1.08 × 10−6	0.10	DAB1
HIND	57	1	92,766,049	101,369,745		5.66 × 10−8	0.12	RIPPLY2, SNAP91
		1	198,725,106	205,843,789	rs80999532	1.41 × 10−9	0.15	TMX1, FRMD6
		7	103,101,452	121,513,304	rs80894106	3.36 × 10−8	0.12	VRTN, SYNDIG1L
CONF	222	1	92,766,049	92,766,049		4.99 × 10−12	0.20	RIPPLY2, SNAP91
		1	198,725,106	208,707,283	rs80783847	2.42 × 10−13	0.22	ENSSSCT00000005518
		6	41,235,400	43,110,092	rs81395827	3.82 × 10−9	0.15	ZNF382
		7	102,881,143	103,495,170	rs80894106	3.86 × 10−11	0.18	VRTN, SYNDIG1L
		10	18,665,600	18,920,852	rs81309142	8.35 × 10−8	0.12	ENSSCG00000030502, ZBTB18
		12	14,208,800	15,365,718	rs81440562	5.63 × 10−12	0.20	CD79B, GH1
		18	10,626,879	14,885,152	rs81469271	4.39 × 10−9	0.15	ENSSCG000000288580
Duroc
FRONT	12	3	97,469,056	99,288,792	rs323557679	3.28 × 10−7	0.16	MSH2
		6	47,212,157	57,685,509	rs81226413	4.22 × 10−8	0.18	ENSSCT00000003685
BACK	128	3	100,232,086	100,448,894	rs81373717	6.41 × 10−31	0.85	EPAS1, PRKCE
		6	47,212,157	53,526,888	rs338147539	2.59 × 10−8	0.19	CCDC61
HIND	31	6	54,949,995	60,446,765	rs81327648	9.17 × 10−11	0.25	WRAP73
CONF	235	2	36,580,946	46,128,234		6.01 × 10−8	0.16	ANO3
		3	97,469,056	100,477,666	rs81373756	6.44 × 10−20	0.54	PRKCE
		4	99,503,615	111,556,304	rs81382406	3.88 × 10−8	0.17	CHRNB2
		6	47,573,330	57,685,509	rs81333163	5.30 × 10−20	0.52	A1BG, RPS5
		7	34,755,602	36,697,937	rs80852624	9.4 × 10−8	0.18	HMGA1, RPS10
		7	103,495,170	103,495,170	rs80894106	8.60 × 10−11	0.25	VRTN, SYNDIG1L
		12	25,298,982	25,580,071	rs327303574	3.80 × 10−11	0.26	ENSSCT00000022825, B4GALNT2
		13	132,640,404	133,032,413		1.21 × 10−6	0.14	IGF2BP2

FRONT front leg quality, BACK back quality, HIND hind leg quality, CONF overall conformation, n number of significant SNPs, Chr Sus scrofa chromosome, Effect size percentage of phenotypic variance explained by the most significant SNP

^a SNP rsID

^b Candidate genes in which the most significant SNPs located are in italic