TABLE 3.

Description of SNPs significantly associated with CL, BL, and BH in DLY pigs.

Traits	SSC a	SNP ID	Position (bp) b	MAF	p -value (MLM)	p -value (FarmCPU)	r 2/% c	Distance (bp)	Nearest gene
CL	3	MARC0004652	6,498,219	0.16		1.00E–05	4.09	Within	FAM200A
	4	WU_10.2_4_3046732	3,559,394	0.14		3.34E–05	2.96	494,158	TRAPPC9
	4	WU_10.2_4_136884741	125,301,443	0.42		1.07E–06	3.31	within	TGFBR3
	7	WU_10.2_7_49907567	43,478,519	0.28		1.71E–08	6.31	118,773	MMUT
	7	ASGA0034652	81,310,017	0.09		2.46E–07	3.51	101,683	RYR3
	8	WU_10.2_8_25141199	24,043,163	0.14	9.03E–05		5.55	––	––
	12	ALGA0122685	43,952,687	0.42		1.23E–05	3.48	33,053	KSR1
	13	ALGA0067792	8,080,882	0.43		4.95E–05	2.12	155,446	ZNF385D
	13	WU_10.2_13_134401849	124,927,734	0.11	6.76E–05		4.79	8,421	RTP1
	14	14_12,070,780	10,892,893	0.12		7.03E–07	4.54	94,443	STMN4
	17	WU_10.2_17_17479009	15,827,454	0.37	2.28E–05		6.39	66,239	BMP2
	17	WU_10.2_17_17981232	16,253,154	0.33	1.60E–07	2.94E–06	9.74	491,286	HA O 1
	17	WU_10.2_17_18300615	1,6401737	0.39	6.63E–05		6.72	342,703	HA O 1
	17	MARC0028591	16,634,316	0.21	5.04E–05		5.37	110,124	HA O 1
	17	DBMA0000205	18,319,097	0.24	6.39E–05		6.37	83,449	PLCB4
BL	1	WU_10.2_1_168,922259	152,527,914	0.29		1.16E–04	1.06	65,735	SOCS6
	2	M1GA0024370	41,570,652	0.36		1.73E–05	6.91	Within	OTOG
	5	H3GA0015868	17,192,568	0.42		1.65E–05	0.95	23,004	SCN8A
	5	ALGA0031952	50,860,053	0.36		4.43E–06	4.7	54,759	ETNK1
	7	SIRI0000046	29,878,705	0.12		5.18E–05	5.6	Within	ITPR3
	7	ALGA0042427	65,595,703	0.36		9.20E–05	2.97	209,797	EGLN3
	7	ASGA0034393	65,625,414	0.36		9.20E–05	2.96	180,086	EGLN4
	8	ALGA0124320	96,665,022	0.09		5.22E–06	4.04	Within	JADE1
	10	ASGA0045707	740,406	0.22		3.89E–05	0.93	Within	UCHL5
	10	ALGA0056836	7,925,254	0.33		1.07E–08	4.94	Within	SPATA17
	12	WU_10.2_12_57752831	55,009,055	0.41		7.76E–07	1.86	37,840	MYH13
	13	WU_10.2_13_138014916	1,28,619,134	0.35	5.26E–05	1.20E–08	7.85	238	CCDC50
	14	ASGA0060896	7,192,572	0.26		9.86E–05	2.08	19,369	PEBP4
	14	ASGA0062769	37,378,781	0.42		2.94E–06	0.21	204,041	TBX3
	14	ALGA0077889	57,422,121	0.18		4.10E–06	7.16	2,783	MAP3K21
	14	ALGA0080935	108,956,441	0.17	1.15E–04	1.04E–04	8.94	2,435	C10orf62
	15	ALGA0085736	63,541,092	0.23	3.19E–05	1.15E–05	7.51	35,848	NR4A2
	17	ALGA0123867	13,717,308	0.26	7.91E–08	6.96E–08	13.04	11,990	PRNP
	17	WU_10.2_17_14580447	13,779,206	0.36	3.30E–06		8.3	5,914	RASSF2
	17	WU_10.2_17_15712448	14,734,253	0.17	5.59E–07		12.13	26,347	SHLD1
	17	ASGA0075536	15,196,027	0.35	7.42E–05		3.32	58,274	FERMT1
	17	WU_10.2_17_17075196	15,689,085	0.36	1.05E–05		9.56	60,750	BMP2
	17	WU_10.2_17_17013787	15,710,331	0.35	4.87E–05		7.11	39,504	BMP2
	17	WU_10.2_17_17479009	15827454	0.37	9.70E–07		8.41	66,239	BMP2
	17	DBMA0000205	18,319,097	0.24	1.24E–05		8.44	83,449	PLCB4
	17	DRGA0016692	29,138,019	0.24	6.14E–05		5.97	30,351	XRN2
BH	2	WU_10.2_2_9315312	9,766,370	0.44		2.72E–05	4.74	35,642	DAGLA
	4	MARC0012235	107,879,743	0.24	4.30E–06		6.36	23,759	WNT2B
	6	WU_10.2_6_13750573	13,837,643	0.33		3.80E–05	6.42	46,402	VAC14
	7	SIRI0000046	29,878,705	0.12		4.91E–05	4.87	Within	ITPR3
	7	ALGA0044383	105,954,725	0.17		2.67E–06	4.64	—	—
	9	ALGA0112140	21,921,748	0.36	7.13E–05		6.78	4,933	GRM5
	9	H3GA0027617	59,226,678	0.46	2.31E–05		5.95	188,970	OPCML
	13	WU_10.2_13_27755688	25,296,621	0.23		6.25E–06	3.39	Within	ULK4
	13	ALGA0073322	185,848,189	0.10	3.61E–05		5.7	168,304	NCAM2
	17	ALGA0123867	13,717,308	0.26	2.71E–05		7.08	12,423	PRND
	17	WU_10.2_17_15792357	14,642,640	0.26	9.69E–06		8.49	41,447	SHLD1
	17	WU_10.2_17_15712448	14,734,253	0.17	3.90E–05		7.24	26,347	SHLD1
	17	WU_10.2_17_17479009	15827454	0.37	9.23E–08	3.71E–08	9.5	66,239	BMP2
	17	DRGA0016582	15,949,323	0.36	1.12E–04		5	188,108	BMP2

The italic values were genes nearest the significant SNPs.

^a Sus scrofa chromosome.

^bThe positions of the associated SNPs on the Sus scrofa Build 11.1 assembly.

^cProportion of total phenotypic variation explained by each SNP.