Genome-wide detection of genetic markers associated with growth and fatness in four pig populations using four approaches

Guo, Yuanmei; Huang, Yixuan; Hou, Lijuan; Ma, Junwu; Chen, Congying; Ai, Huashui; Huang, Lusheng; Ren, Jun

doi:10.1186/s12711-017-0295-4

Genetics Selection Evolution

Table 1 Genome-wide significant loci for nine fatness and growth traits identified by four GWAS approaches in this study

From: Genome-wide detection of genetic markers associated with growth and fatness in four pig populations using four approaches

QTL^a	Chr^b	Trait^c	Population	Method	Top SNP	Pos Mb^d	Effect ± SE^e	P value^f	N ^g_SNP	Boundary SNPs
1	2	HBF	Meta	SM	ss131211507	3.61	0.127 ± 0.026	1.28E−06*	1	–	–
2	4	Multi-trait	Meta	MM	ss131269439	81.71	–	7.88E−10**	8	ss131269439	ss478935222
2	4	FBF	Meta	SM	ss131269439	81.71	0.168 ± 0.032	1.20E−07**	1	–	–
2	4	HBF	Meta	SM	ss131269678	82.25	0.156 ± 0.032	1.08E−06*	1	–	–
2	4	SBF	Meta	SM	ss478935222	85.09	0.166 ± 0.035	1.53E−06**	1	–	–
3	6	ADG_210–240	Meta	SM	ss131029816	71.60	0.040 ± 0.008	1.38E−06*	1	–	–
4	7	ADG₂₁₀	F₂	SS	ss131342496	32.96	-0.026 ± 0.005	5.95E−07*	1	–	–
4	7	Multi-trait	Meta	MM	ss131343534	34.56	–	2.65E−18**	27	ss120018804	ss131348342
4	7	SBF	Meta	SM	ss131343534	34.56	0.255 ± 0.042	1.11E−09**	6	ss131341589	ss107890951
4	7	FBF	Meta	SM	ss131343534	34.56	0.315 ± 0.040	4.88E−15**	17	ss131341589	ss131348342
4	7	HBF	Meta	SM	ss131343534	34.56	0.379 ± 0.045	3.16E−17**	25	ss120018804	ss131348342
4	7	Multi-trait	F₂	MS	ss107837325	34.80	–	3.97E−33**	107	ss23131766	ss478941636
4	7	AFW	F₂	SS	ss107837325	34.80	0.163 ± 0.022	8.99E−11**	34	ss131066868	ss131345041
4	7	FBF	F₂	SS	ss107837325	34.80	0.691 ± 0.060	3.10E−17**	69	ss131341676	ss131348342
4	7	HBF	F₂	SS	ss107837325	34.80	0.773 ± 0.072	1.97E−14**	64	ss131341676	ss131347489
4	7	LBF	F₂	SS	ss107837325	34.80	0.571 ± 0.057	1.77E−14**	60	ss131341676	ss131348342
4	7	LFW	F₂	SS	ss107837325	34.80	0.650 ± 0.058	1.75E−18**	63	ss131341766	ss131347489
4	7	SBF	F₂	SS	ss107837325	34.80	0.487 ± 0.057	1.94E−12**	45	ss131341766	ss131346335
4	7	Multi-trait	Erhualian	MS	ss131343870	34.84	–	1.29E−15**	6	ss131342502	ss131347459
4	7	FBF	Erhualian	SS	ss131343870	34.84	0.585 ± 0.073	2.13E−13**	8	ss131336720	ss131347459
4	7	HBF	Erhualian	SS	ss131343870	34.84	0.502 ± 0.075	1.49E−10**	5	ss131343870	ss131347459
4	7	LBF	Erhualian	SS	ss131343870	34.84	0.523 ± 0.064	6.96E−14**	5	ss131343870	ss131347459
4	7	LFW	Erhualian	SS	ss131343870	34.84	0.453 ± 0.067	2.39E−10**	5	ss131343870	ss131347459
4	7	SBF	Erhualian	SS	ss131343870	34.84	0.453 ± 0.079	4.08E−08**	2	ss131343870	ss478941599
4	7	LFW	Meta	SM	ss131344553	36.20	0.140 ± 0.028	7.18E−07*	2	ss131344553	ss131347175
4	7	LBF	Meta	SM	ss131347175	40.85	0.155 ± 0.024	1.27E−10**	13	ss131337529	ss131348342
5	X	SBF	Meta	SM	ss131570179	46.75	0.124 ± 0.020	5.42E−10**	5	ss131036304	ss131562987
5	X	VFW	F₂	SS	ss107834496	51.70	0.091 ± 0.013	5.39E−10**	21	ss478944418	ss478935791
5	X	Multi-trait	F₂	MS	ss23131102	63.65	–	5.78E−35**	79	ss131067158	ss131563360
5	X	FBF	F₂	SS	ss23131102	63.65	0.164 ± 0.023	2.94E−07*	2	ss478943984	ss23131102
5	X	HBF	F₂	SS	ss23131102	63.65	0.278 ± 0.029	6.81E−12**	24	ss478936157	ss131562911
5	X	Multi-trait	Sutai	MS	ss478934917	78.58	–	3.19E−10**	38	ss478944000	ss131570171
5	X	Multi-trait	Meta	MM	ss131070541	106.48	–	1.61E−15**	14	ss478936157	ss131562987
5	X	FBF	Meta	SM	ss131070541	106.48	0.110 ± 0.018	1.33E−09**	10	ss131036304	ss131562987
5	X	HBF	Meta	SM	ss131070541	106.48	0.187 ± 0.021	9.06E−19**	18	ss131067158	ss131563051
5	X	LBF	Meta	SM	ss131070541	106.48	0.108 ± 0.018	1.46E−09**	1	–	–

^aWe operationally define two loci with the distance between their lead SNPs less than 5 Mb as the same QTL except the loci on chromosome X. All loci close to the recombination cold spot (more than 30 Mb, with an extremely low rate of recombination) in the middle of X chromosome was considered the same QTL because of too few SNPs in this region
^bChromosome
^cAbbreviations of trait names are in Additional file 1: Table S1
^dThe position of the unmapped SNP (ss131029816) is deduced by its tightly linked SNP (ss131566312)
^eThe direction of SNP effect estimated by the meta-GWAS was not shown because the linkage phase may be inconsistent among the four populations, and the SNP effect cannot be estimated by the multi-trait GWAS
^f** 1% genome-wide significant; * 5% genome-wide significant
^gNumber of SNPs that surpass the significance level

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ISSN: 1297-9686

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