Application of alternative models to identify QTL for growth traits in an F2 Duroc x Pietrain pig resource population

Choi, Igseo; Steibel, Juan P; Bates, Ronald O; Raney, Nancy E; Rumph, Janice M; Ernst, Catherine W

doi:10.1186/1471-2156-11-97

Table 1 Position and significance level of growth trait QTL.

From: Application of alternative models to identify QTL for growth traits in an F₂ Duroc x Pietrain pig resource population

Chr¹	Position²	Trait	Type³	-log₁₀P⁴	FDR⁵	Flanking Markers	Additive⁶	Dominance⁷
4	25	22-wk total body fat tissue, kg	HS	3.17	0.0484	SW2509 - S0301
	42	22-wk 10th-rib backfat, mm	HS	3.65	0.0209	S0301 - SW871
	57	22-wk LM area, cm²	LC	3.29	0.0351	S0301 - SW871	-1.10 (0.29)	-0.66 (0.51)
	65	16-wk last-rib backfat, mm	HS	3.97	0.0120	S0301 - SW871
6	25	22-wk empty body lipid, kg	HS	3.76	0.0179	S0099 - SW2406
	26	22-wk total body fat tissue, kg	HS	3.29	0.0398	S0099 - SW2406
	129	22-wk fat-free total lean, kg	LC	5.30	0.0006	S0220 - SW122	-0.35 (0.09)	0.44 (0.14)
	129	22-wk empty body protein, kg	LC	4.85	0.0016	S0220 - SW122	-0.13 (0.03)	0.14 (0.05)
	164	13-wk 10th-rib backfat, mm	LC	21.81	0.0000	SW1647 - SW1881	0.98 (0.10)	-0.74 (0.15)
	164	22-wk 10th-rib backfat, mm	LC	18.49	0.0000	SW1647 - SW1881	2.17 (0.25)	-1.37 (0.36)
	164	22-wk last-rib backfat, mm	LC	22.25	0.0000	SW1647 - SW1881	1.55 (0.17)	-1.24 (0.24)
	165	10-wk 10th-rib backfat, mm	LC	22.90	0.0000	SW1647 - SW1881	0.70 (0.07)	-0.57 (0.11)
	165	13-wk last-rib backfat, mm	LC	21.85	0.0000	SW1647 - SW1881	0.58 (0.06)	-0.39 (0.09)
	165	16-wk last-rib backfat, mm	LC	22.26	0.0000	SW1647 - SW1881	0.86 (0.10)	-0.81 (0.14)
	166	10-wk last-rib backfat, mm	LC	20.30	0.0000	SW1647 - SW1881	0.43 (0.05)	-0.30 (0.07)
	166	19-wk last-rib backfat, mm	LC	27.25	0.0000	SW1647 - SW1881	1.32 (0.13)	-1.03 (0.18)
	168	22-wk total body fat tissue, kg	LC	4.69	0.0023	SW1881 - SW322	0.57 (0.13)	-0.38 (0.19)
	169	19-wk 10th-rib backfat, mm	LC	25.29	0.0000	SW1881 - SW322	1.78 (0.18)	-1.61 (0.27)
	172	16-wk 10th-rib backfat, mm	LC	23.45	0.0000	SW1881 - SW322	1.38 (0.14)	-0.97 (0.22)
	174	22-wk empty body lipid, kg	LC	8.61	0.0000	SW1881 - SW322	0.46 (0.09)	-0.50 (0.14)
	229	22-wk fat-free total lean, kg	HS	3.38	0.0343	SW607 - SW2419
7	44	10-wk LM area, cm²	HS	3.41	0.0325	S0064 - SW1369
	48	19-wk LM area, cm²	HS	4.78	0.0024	S0064 - SW1369
	138	19-wk LM area, cm^2†	LC	5.02	0.0011	SW859 - SW2040	-1.38 (0.29)	-0.55 (0.62)
	169	10-wk LM area, cm^2†	LC	3.51	0.0236	SW2040 - S0115	-0.43 (0.11)	0.05 (0.16)
	185	13-wk LM area, cm^2†	LC	3.22	0.0391	S0115 - SW632	-0.49 (0.13)	0.26 (0.20)
8	137	22-wk empty body lipid, kg	HS	3.30	0.0397	S0017 - SW2160
9	7	22-wk body weight, kg^†	LC	3.10	0.0485	SW21 - SW983	-0.52 (0.71)	4.12 (1.10)
	9	22-wk empty body lipid, kg	CB	3.55	0.0433	SW21 - SW983
	12	19-wk body weight, kg	CB	3.78	0.0297	SW21 - SW983
11	91	19-wk last-rib backfat, mm	LC	3.98	0.0093	S0230 - SW66	0.20 (0.19)	-1.11 (0.27)
	93	19-wk 10th-rib backfat, mm	LC	3.37	0.0307	S0230 - SW66	-0.63 (0.28)	-1.28 (0.41)
	106	22-wk empty body lipid, kg	LC	3.28	0.0356	S0230 - SW66	-0.22 (0.15)	-1.03 (0.29)
15	39	16-wk LM area, cm^2†	LC	3.19	0.0413	S0148 - SW1989	-0.75 (0.19)	0.05 (0.30)
	69	19-wk LM area, cm^2†	LC	3.28	0.0356	S0088 - SW1683	-0.86 (0.22)	-0.01 (0.35)
	74	22-wk 10th-rib backfat, mm	HS	4.43	0.0048	SW1683 - SW906
	96	19-wk 10th-rib backfat, mm	HS	4.38	0.0053	SW1983 - SW1119
16	93	22-wk total body fat tissue, kg	LC	3.64	0.0186	SW2517	-0.47 (0.18)	-0.89 (0.31)
	93	19-wk 10th-rib backfat, mm	HS	3.36	0.0355	SW2517
	93	22-wk body weight, kg	CB	3.57	0.0424	SW2517
18	4	16-wk 10th-rib backfat, mm^†	LC	3.54	0.0222	SW2540 - SW1023	0.55 (0.14)	0.23 (0.20)

¹Chr = chromosome
²Position in Haldane cM
³LC = QTL declared as line-cross type; HS = half-sib type; CB = combined type.
⁴Negative logarithm of the comparison-wise p value of the test statistic against the null hypothesis of no QTL at the most likely position for the inferred QTL model.
⁵FDR = false discovery rate
⁶Estimates of additive effects with standard errors for LC QTL. The effects are expressed as (DD-PP)/2, where D = Duroc allele and P = Pietrain allele.
⁷Estimates of dominance effects with standard errors for LC QTL. The effects are expressed as DP-PD, where D = Duroc allele and P = Pietrain allele.
^†New QTL detected with the line-cross model in the second scan.

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