Genome-wide mapping of Quantitative Trait Loci for fatness, fat cell characteristics and fat metabolism in three porcine F2 crosses

Geldermann, Hermann; Čepica, Stanislav; Stratil, Antonin; Bartenschlager, Heinz; Preuss, Siegfried

doi:10.1186/1297-9686-42-31

Genetics Selection Evolution

Table 4 Genome-wide significant QTL for fat related traits identified in the three Hohenheim crosses

From: Genome-wide mapping of Quantitative Trait Loci for fatness, fat cell characteristics and fat metabolism in three porcine F₂ crosses

SSC	Trait^a	Cross^b	Position^c		Flanking markers^d	F ratio^e		VF₂^f	a ± SE^g	d ± SE^g
			USDA	Hoh.	proximal/distal
1	CW	W × M	54.1	69.0	SW2130/IGFR	10.0	*	5.3	-4.44 ± 1.00	1.35 ± 1.64
	CW	W × P	77.4	115.7	SW307/S0082	15.9	**	8.9	-6.12 ± 1.09	0.65 ± 1.55
	CW	W × P	44.8	62.7	S0008/SW2130	14.5	**	8.2	-5.73 ± 1.07	-0.36 ± 1.68
	CW	W × P	59.1	87.9	SW2130/SW307	13.1	**	7.4	-6.15 ± 1.21	0.08 ± 2.05
	AFW	M × P	142.7	207.2	EAA	8.5	*	4.6	0.20 ± 0.05	-0.27 ± 0.11
	AFW	W × M	107.6	131.1	TGFBR1/SW705	10.3	*	5.4	-0.13 ± 0.03	0.13 ± 0.06
	AFW	W × P	76.3	112.7	SW307/S0082	9.2	*	5.1	-0.09 ± 0.02	0.06 ± 0.03
	HEFW	W × M	57.2	73.0	SW2130/IGFR	13.6	**	7.2	-0.30 ± 0.06	0.03 ± 0.10
	HEFW	W × M	91.5	114.7	TPM2	10.7	**	5.6	-0.17 ± 0.05	0.21 ± 0.07
	HEFW	W × P	77.8	116.7	SW307/S0082	20.7	**	11.5	-0.26 ± 0.04	0.04 ± 0.06
	HEFW	W × P	45.4	64.7	S0008/SW2130	10.6	**	5.9	-0.19 ± 0.04	-0.03 ± 0.07
	HEFW	W × P	64.4	93.9	SW2130/SW307	12.9	**	7.2	-0.23 ± 0.05	-0.01 ± 0.07
	SEFW	W × M	113.4	137.1	TGFBR1/SW705	11.0	**	5.8	-0.12 ± 0.03	0.01 ± 0.04
	SEFW	W × P	86.9	136.3	SW780/SW803	11.1	**	6.2	-0.10 ± 0.02	0.00 ± 0.04
	SEFW	W × P	76.7	113.7	SW307/S0082	11.0	**	6.2	-0.10 ± 0.02	0.00 ± 0.03
	BFW	W × M	107.6	131.1	TGFBR1/SW705	15.5	**	8.2	-0.33 ± 0.07	0.29 ± 0.11
	BFW	W × P	77.1	114.7	SW307/S0082	19.6	**	10.9	-0.33 ± 0.05	0.08 ± 0.08
	BFW	W × P	63.5	92.9	SW2130/SW307	14.0	**	7.9	-0.31 ± 0.06	0.04 ± 0.10
	BFW	W × P	100.8	161.2	SW803/SW705	11.3	**	6.4	-0.28 ± 0.06	-0.05 ± 0.12
	FCP	M × P	139.3	201.3	SW705/EAA	9.3	*	5.1	1.92 ± 0.44	-0.77 ± 0.93
	FCP	W × M	104.7	128.1	TGFBR1/SW705	14.9	**	7.9	-1.41 ± 0.28	1.12 ± 0.46
	FCP	W × P	86.9	136.3	SW780/SW803	9.4	*	5.2	-1.14 ± 0.26	0.21 ± 0.45
	BFML	W × P	89.0	140.3	SW780/SW803	15.3	**	8.6	-2.58 ± 0.47	-0.26 ± 0.82
	BFML	W × P	76.3	112.7	SW307/S0082	14.8	**	8.3	-2.53 ± 0.47	0.29 ± 0.69
	FD10	W × M	89.5	112.9	TPM2/SW803	12.7	**	6.7	-2.20 ± 0.49	1.76 ± 0.73
	FD10	W × P	77.8	116.7	SW307/S0082	14.1	**	7.9	-2.11 ± 0.40	0.56 ± 0.56
	ABFD	W × M	91.4	114.6	SW780/TPM2	11.6	**	6.2	-1.90 ± 0.47	1.89 ± 0.68
	ABFD	W × P	78.4	118.2	S0082/SW780	12.5	**	7.0	-2.01 ± 0.40	0.44 ± 0.57
	FAML	W × P	76.7	113.7	SW307/S0082	15.6	**	8.8	-2.53 ± 0.46	0.25 ± 0.67
	FAML	W × P	87.4	137.3	SW780/SW803	15.0	**	8.5	-2.61 ± 0.48	0.27 ± 0.82
	FMR	M × P	113.8	166.3	TGFBR1/SW705	13.4	**	7.5	0.09 ± 0.02	0.04 ± 0.03
	FMR	M × P	135.8	196.3	SW705/EAA	12.1	**	6.8	0.11 ± 0.02	0.01 ± 0.05
	FMR	W × M	111.4	135.1	TGFBR1/SW705	8.8	*	4.6	-0.12 ± 0.03	0.01 ± 0.05
	FMR	W × P	90.6	143.3	SW780/SW803	12.8	**	7.3	-0.06 ± 0.01	-0.01 ± 0.02
	FMR	W × P	76.0	111.7	SW307/S0082	10.6	**	6.0	-0.06 ± 0.01	0.01 ± 0.02
	MDHO	W × P	94.3	150.2	SW803	9.1	*	5.1	-0.03 ± 0.01	-0.05 ± 0.02
	FV114	W × P	103.8	166.2	SW803/SW705	8.8	*	5.2	-4.93 ± 1.21	4.26 ± 2.65
	FVCM	W × M	91.5	114.7	TPM2	9.9	*	16.8	8.97 ± 2.50	-9.29 ± 3.85
	FVCM	W × M	111.4	135.1	TGFBR1/SW705	8.5	*	14.5	12.33 ± 3.00	0.88 ± 5.35
	FVCL	W × M	114.3	138.1	TGFBR1/SW705	9.2	*	15.7	-13.53 ± 3.16	-0.07 ± 5.44
	FVCL	W × M	91.5	114.7	TPM2	8.9	*	15.3	-9.19 ± 2.70	9.56 ± 4.15
2	CW	W × P	74.4	94.3	SW395/S0010	8.7	*	4.8	-3.80 ± 1.01	-3.41 ± 1.61
	HEFW	W × P	57.4	69.3	MYOD1	10.9	**	6.1	-0.19 ± 0.04	-0.14 ± 0.08
	SEFW	W × P	71.4	90.3	SW395/S0010	8.6	*	4.8	-0.06 ± 0.02	-0.08 ± 0.03
	BFW	W × P	72.9	92.3	SW395/S0010	11.0	**	6.2	-0.20 ± 0.05	-0.24 ± 0.08
	FCP	M × P	48.0	61.4	SW240/MLP	8.6	*	4.7	1.14 ± 0.28	0.29 ± 0.46
	FMR	M × P	49.7	63.4	SW240/MLP	9.8	*	5.4	0.07 ± 0.02	0.04 ± 0.03
4	CW	M × P	71.2	65.0	SW1089/V-ATPase	10.0	*	5.5	-4.84 ± 1.10	1.27 ± 1.59
	SEFW	M × P	77.6	79.4	ATP1A2	9.5	*	5.2	-0.11 ± 0.03	0.04 ± 0.04
	BFW	M × P	37.0	37.9	SW835/SWR73	11.4	**	6.3	-0.30 ± 0.07	-0.19 ± 0.10
	RFNCLO	W × P	54.7	59.2	SW2128/SW1073	9.9	*	5.9	-15.18 ± 3.52	-4.26 ± 5.59
	FV73	W × P	74.4	76.8	S0073	9.7	*	5.7	-2.67 ± 0.61	0.28 ± 0.95
	FV146	W × P	74.4	76.8	S0073	10.6	**	6.3	4.31 ± 0.99	-2.10 ± 1.53
	FVCL	W × P	73.9	75.9	V-ATPase/S0073	8.6	*	5.1	4.15 ± 1.11	-3.00 ± 1.74
	RFVCSL	W × P	53.0	58.2	SW2128/SW1073	9.7	*	5.8	-0.15 ± 0.04	-0.05 ± 0.05
5	CW	W × M	94.4	81.5	S0005/SW152	8.7	*	4.6	3.76 ± 0.94	1.80 ± 1.42
	SEFW	W × M	85.7	73.0	SW2/S0005	10.1	*	5.3	0.10 ± 0.02	0.05 ± 0.04
6	AFW	M × P	75.6	97.8	TGFB1	13.5	**	7.5	0.15 ± 0.03	0.11 ± 0.04
	HEFW	M × P	75.6	97.8	TGFB1	12.2	**	6.8	0.29 ± 0.06	0.15 ± 0.09
	SEFW	M × P	75.6	97.8	TGFB1	11.8	**	6.6	0.12 ± 0.03	0.07 ± 0.04
	BFW	M × P	75.6	97.8	TGFB1	9.4	*	5.2	0.26 ± 0.07	0.17 ± 0.09
	FCP	M × P	75.6	96.9	LIPE	28.1	**	15.0	1.87 ± 0.27	0.91 ± 0.36
	FCP	W × P	76.5	81.4	A1BG	11.4	**	6.4	0.77 ± 0.21	1.00 ± 0.31
	BFML	M × P	75.6	97.8	TGFB1	14.5	**	8.1	2.52 ± 0.50	1.20 ± 0.67
	BFML	W × P	76.5	81.4	A1BG	9.1	*	5.0	1.11 ± 0.40	1.94 ± 0.57
	FD10	M × P	75.6	97.8	TGFB1	9.1	*	5.0	1.51 ± 0.48	1.75 ± 0.64
	ABFD	M × P	75.6	97.8	TGFB1	11.8	**	6.6	1.80 ± 0.50	2.12 ± 0.67
	FMR	M × P	75.6	96.9	LIPE	17.8	**	9.9	0.10 ± 0.02	-0.01 ± 0.02
	FMR	W × P	78.5	88.2	EAH/NPPB	10.8	**	6.1	0.04 ± 0.01	0.05 ± 0.02
7	CW	W × M	67.2	87.9	TNFB/S0102	9.5	*	5.0	-3.74 ± 0.91	1.59 ± 1.34
	AFW	M × P	72.6	88.1	S0102/PSMA4	17.4	**	9.7	-0.19 ± 0.04	-0.08 ± 0.05
	SEFW	W × M	64.9	85.9	TNFB/S0102	9.9	*	5.2	-0.10 ± 0.02	0.05 ± 0.03
	BFML	M × P	63.9	78.8	TNFB/S0102	11.0	**	6.1	-2.17 ± 0.54	-1.99 ± 0.79
	FD10	M × P	63.9	78.8	TNFB/S0102	23.8	**	12.9	-3.27 ± 0.49	-1.31 ± 0.71
	FD10	W × M	57.7	78.8	TNFA	16.9	**	8.9	2.73 ± 0.47	0.10 ± 0.67
	ABFD	M × P	60.4	75.8	TNFB/S0102	18.6	**	10.3	-2.99 ± 0.51	-1.41 ± 0.73
	ABFD	W × M	57.7	78.8	TNFA	8.5	*	4.4	1.94 ± 0.48	0.48 ± 0.68
	MDHO	M × P	53.8	67.3	S0064/KE6	15.2	**	8.5	-0.12 ± 0.02	-0.03 ± 0.03
	MDHO	W × M	50.1	71.8	SWR1078/TNFA	9.4	*	5.0	0.06 ± 0.01	0.02 ± 0.02
	PCO	M × P	51.1	63.1	S0064/KE6	10.5	*	5.8	0.57 ± 0.13	0.14 ± 0.19
	LGSEO	M × P	53.1	66.2	S0064/KE6	10.8	**	6.0	-0.07 ± 0.02	-0.01 ± 0.02
	LGSEO	W × M	55.5	76.8	SWR1078/TNFA	10.8	**	5.9	0.04 ± 0.01	0.02 ± 0.01
	MDHI	M × P	63.9	78.8	TNFB/S0102	12.0	**	6.7	-0.13 ± 0.03	-0.03 ± 0.04
	MDHI	M × P	47.8	58.1	S0064/KE6	10.0	*	5.5	-0.13 ± 0.03	-0.01 ± 0.05
	MDHOI	M × P	62.8	77.8	TNFB/S0102	15.4	**	8.6	-0.12 ± 0.02	-0.03 ± 0.03
	MDHOI	W × M	50.1	71.8	SWR1078/TNFA	10.1	*	5.5	0.07 ± 0.02	-0.00 ± 0.02
	LGSEOI	M × P	63.9	78.8	TNFB/S0102	11.3	**	6.3	-0.07 ± 0.01	0.00 ± 0.02
	LGSEOI	W × M	56.6	77.8	SWR1078/TNFA	8.6	*	4.6	0.03 ± 0.01	0.01 ± 0.01
	FN73	M × P	59.3	74.8	TNFB/S0102	9.7	*	5.5	2.43 ± 0.55	0.42 ± 0.77
	FN92	M × P	54.5	68.3	S0064/KE6	13.4	**	7.7	4.28 ± 0.83	1.00 ± 1.16
	FN92	M × P	82.2	103.3	PSMA4/S0066	8.7	*	4.9	3.32 ± 0.80	-0.33 ± 1.08
	FN92	W × M	32.9	55.9	SWR1078	8.6	*	14.8	-1.82 ± 1.03	-5.78 ± 1.49
	FN146	M × P	58.1	73.8	TNFB	9.8	*	5.6	-3.55 ± 0.89	-2.53 ± 1.22
	FN183	M × P	62.8	77.8	TNFB/S0102	10.2	*	5.8	-1.49 ± 0.38	-1.31 ± 0.55
	FNCM	M × P	60.4	75.8	TNFB/S0102	12.0	**	6.9	8.22 ± 1.68	1.69 ± 2.38
	FNCM	M × P	80.9	101.3	PSMA4/S0066	9.7	*	5.5	7.19 ± 1.64	-1.32 ± 2.25
	FNCM	W × M	32.9	55.9	SWR1078	10.3	*	17.5	-3.07 ± 2.40	-15.39 ± 3.47
	FNCL	M × P	59.3	74.8	TNFB/S0102	12.0	**	6.9	-5.11 ± 1.16	-3.88 ± 1.63
	FV73	W × M	82.8	118.5	S0066	9.0	*	15.4	-2.31 ± 0.63	-1.68 ± 0.84
	FV92	M × P	58.1	73.8	TFNB	15.0	**	8.6	4.49 ± 0.85	1.84 ± 1.16
	FV92	W × P	74.6	79.8	S0102/PSMA4	9.9	*	5.9	3.33 ± 0.86	-2.91 ± 1.34
	FV92	W × P	90.7	106.4	S0066/S0115	9.3	*	5.5	3.59 ± 1.00	-5.31 ± 1.98
	FV114	M × P	60.4	75.8	TNFB/S0102	12.0	**	6.8	4.41 ± 0.98	3.01 ± 1.39
	FV114	M × P	80.9	101.3	PSMA4/S0066	8.8	*	5.0	4.01 ± 0.96	-0.93 ± 1.32
	FV146	M × P	58.1	73.8	TNFB	9.9	*	5.6	-5.64 ± 1.30	-2.11 ± 1.79
	FV146	W × P	90.1	105.4	S0066/S0115	9.0	*	5.3	-3.95 ± 1.17	6.35 ± 2.27
	FV146	W × P	75.7	81.8	S0102/PSMA4	8.8	*	5.2	-3.37 ± 1.00	3.77 ± 1.54
	FV183	M × P	62.8	77.8	TNFB/S0102	15.9	**	9.1	-4.83 ± 0.94	-3.50 ± 1.36
	FVCM	M × P	59.3	74.8	TNFB/S0102	21.2	**	12.0	10.48 ± 1.69	5.21 ± 2.35
	FVCM	M × P	88.4	112.2	S0066/S0115	9.6	*	5.4	8.26 ± 1.89	-1.96 ± 2.99
	FVCM	W × P	91.4	107.4	S0066/S0115	9.8	*	5.8	3.67 ± 1.24	-8.87 ± 2.49
	FVCL	M × P	59.3	74.8	TNFB/S0102	19.1	**	10.8	-10.78 ± 1.83	-5.37 ± 2.56
	FVCL	W × P	90.7	106.4	S0066/S0115	10.1	*	6.0	-4.17 ± 1.30	8.75 ± 2.57
	FVCL	W × P	75.2	80.8	S0102/PSMA4	9.2	*	5.4	-3.75 ± 1.12	4.56 ± 1.74
	RFVCML	M × P	58.1	73.8	TNFB	11.3	**	6.5	0.66 ± 0.14	0.14 ± 0.19
	RFVCLO	M × P	58.1	73.8	TNFB	9.5	*	5.4	0.70 ± 0.16	0.11 ± 0.22
	RFVCLO	W × M	82.8	118.5	S0066	8.9	*	15.2	-1.00 ± 0.28	-0.75 ± 0.37
8	FN73	W × M	108.2	116.4	SW16/SW61	9.6	*	16.4	-1.29 ± 0.85	-5.33 ± 1.31
	FN92	W × M	107.5	114.4	SW16/SW61	17.1	**	26.8	-0.33 ± 1.17	-9.87 ± 1.70
	FNCM	W × M	107.8	115.4	SW16/SW61	17.1	**	26.8	0.13 ± 2.80	-24.41 ± 4.17
9	CW	W × P	142.5	193.2	SW1349	8.9	*	4.9	-3.00 ± 0.96	3.66 ± 1.42
12	PCO	M × P	113.1	109.3	SWR1021	8.7	*	4.8	-0.32 ± 0.12	-0.51 ± 0.17
	FV146	W × M	106.6	135.4	S0106/SWR1021	9.3	*	15.9	2.14 ± 2.69	16.69 ± 4.06
13	FN185	M × P	98.2	129.8	SW520/SW38	9.3	*	5.3	0.99 ± 0.37	-2.08 ± 0.55
	FV185	M × P	95.5	126.8	SW520/SW38	8.9	*	5.1	2.03 ± 1.00	-6.21 ± 1.56
14	RFNCSL	W × P	48.0	52.8	SW210/SW2488	9.7	*	5.8	10.19 ± 2.46	-4.25 ± 3.97
	RFNCML	W × P	56.2	62.8	SW210/SW2488	9.9	*	5.9	6.63 ± 1.71	-6.02 ± 3.06
	RFNCLO	W × P	51.3	56.8	SW210/SW2488	11.5	**	6.8	17.23 ± 3.83	-8.45 ± 6.57
16	FN73	M × P	34.1	43.0	S0077/S0026	8.5	*	4.8	-1.82 ± 0.54	-1.93 ± 0.76
18	PCO	M × P	19.0	25.6	EAI/LEP	9.6	*	5.3	-0.35 ± 0.13	0.64 ± 0.19
X	CW	W × M	80.0	90.0	ACSL4/CAPN6	10.0	*	10.3	-11.72 ± 2.89	7.36 ± 3.22
	HEFW	W × M	80.0	90.0	ACSL4/CAPN6	9.6	*	10.0	-0.58 ± 0.16	0.30 ± 0.18
	SEFW	W × P	80.6	105.5	SW259/SW1943	9.7	*	10.2	0.27 ± 0.08	-0.15 ± 0.09
	PCO	M × P	28.4	29.1	SW980/SW2126	9.4	*	10.8	3.22 ± 0.74	-3.25 ± 0.81
	PCO	M × P	122.2	139.3	FMR1	8.9	*	10.3	3.11 ± 0.74	-3.13 ± 0.78
	PCO	W × M	81.0	95.5	CAPN6	11.2	**	11.8	0.77 ± 0.26	-0.12 ± 0.28
	LGSEO	M × P	56.9	55.7	SW2456/AR	8.5	*	9.8	-0.38 ± 0.10	0.33 ± 0.10
	LGSEI	M × P	29.3	30.1	SW980/SW2126	11.4	**	13.1	-0.36 ± 0.08	0.38 ± 0.08
	LGSEI	M × P	113.8	128.2	SW2453/FMR1	11.3	**	13.1	-0.45 ± 0.09	0.43 ± 0.10
	PCI	W × M	80.4	92.0	ACSL4/CAPN6	11.0	*	11.7	0.83 ± 0.32	0.05 ± 0.36
	PCOI	W × M	80.7	94.0	ACSL4/CAPN6	12.5	**	13.1	0.80 ± 0.27	-0.04 ± 0.30
	LGSEOI	M × P	111.5	125.2	SW2453/FMR1	11.2	**	13.0	-0.46 ± 0.10	0.44 ± 0.11
	LGSEOI	M × P	29.3	30.1	SW980/SW2126	11.0	*	12.8	-0.34 ± 0.07	0.36 ± 0.08
	LGSEOI	M × P	56.9	55.7	SW2456/AR	11.2	**	12.9	-0.40 ± 0.09	0.37 ± 0.09
	FV73	M × P	55.4	53.7	SW2456	9.2	*	10.7	10.51 ± 2.75	-8.17 ± 2.84
	RFVCSL	M × P	55.4	53.7	SW2456	12.2	**	14.1	0.68 ± 0.15	-0.55 ± 0.15
	RFVCSL	M × P	126.0	144.2	FMR1/SW2588	10.9	*	12.7	0.67 ± 0.15	-0.57 ± 0.16

^a trait: acronym, for definition see Table 2; ^b cross: Hohenheim F₂ crosses (M: Meishan, P: Pietrain, W: European wild boar); ^c position: USDA, position in USDA MARC map; Hoh.: position in Hohenheim map; ^d flanking markers: nearest proximal/distal locus in the Hohenheim map; if the QTL position coincides with that of the marker, only one locus is indicated; ^e F ratio: mean square estimates of the additive and dominant components in relation to the error variance of the model; significance for the genome wide 5% (*) and 1% (**) level calculated by permutation test [19]; for SSCX, only the results for female animals are listed; for threshold values see Table 5; ^f VF₂: proportion of error variance reduction by inclusion of additive and dominant components in the initial model; ^g a: additive effect (positive/negative signs indicate the superior/inferior trait values inherited from the paternal resource group); d:dominant effect (positive for higher values of heterozygous individuals than the mean of homozygotes, negative for lower values); SE: standard error of estimates

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