. 2020 May 7;21:344. doi: 10.1186/s12864-020-6742-6

Table 3.

Significant SNPs associated with teat number in Canadian Duroc pigs

SSC^a	SNP ID	Position (bp)^b	MAF	Single-locus GWAS			Multi-locus GWAS			Nearest gene^e	Distance/bp^f
SSC^a	SNP ID	Position (bp)^b	MAF	P-value	R²(%)^c	Model^d	LOD	R²(%)^c	Model^d	Nearest gene^e	Distance/bp^f
1	rs333890665	271,354,424	0.31	1.28E-05	0.8	I	4.86	1.42	V	PRRC2B	within
1	rs321500205	271,382,273	0.45	1.40E-05	0.94	I	4.43–6.09	0.79–1.47	II,III,IV,V	ENSSSCG00000022130	36,815
2	rs81363870	121,140,488	0.49				4.02–6.41	4.77–7.26	II,III,IV,V	SEMA6A	453,157
3	rs344649466	5,715,228	0.35				3.15–3.51	0.78–1.42	II,III	NPTX2	− 5452
5	rs81384813	66,721,316	0.06				3.52	2.54	II	PRMT8	within
5	rs81384838	66,734,388	0.1				3.92	1.52	V	PRMT8	within
6	rs324552394	164,807,745	0.24				3.58	0.77	V	EFCAB14	within
7	rs80864749	7,655,911	0.36				3.24	0.79	III	ELOVL2	within
7	rs330783620	9,154,293	0.15				3.18	0.37	IV	PHACTR1	−191,156
7	rs80888936	96,128,654	0.35	2.67E-07	3.78	I				ENSSSCG00000033840	122,929
7	rs324614194	96,278,617	0.47	1.11E-14	6.07	I				ENSSSCG00000028159	−10,186
7	rs331807204	96,632,217	0.36	1.46E-07	3.9	I				NUMB	within
7	rs81265875	96,660,861	0.36	1.38E-07	3.92	I				NUMB	within
7	rs329434246	96,694,364	0.36	9.91E-08	3.97	I				NUMB	within
7	rs81396029	96,727,497	0.36	1.46E-07	3.9	I				NUMB	within
7	rs81295281	96,731,838	0.35	2.25E-07	3.79	I				NUMB	within
7	rs81396040	96,743,525	0.36	1.50E-07	3.9	I				NUMB	within
7	rs81227580	96,786,714	0.35	2.47E-07	3.79	I				NUMB	within
7	rs81396043	96,806,775	0.35	2.49E-07	3.77	I				NUMB	6800
7	rs342685919	97,048,514	0.44	1.93E-13	5.84	I				ENSSSCG00000035322	−708
7	rs80843834	97,109,772	0.35	1.63E-07	3.76	I				ELMSAN1	32,738
7	rs80805264	97,126,583	0.35	1.63E-07	3.76	I				ENSSSCG00000002351	−47,593
7	rs327357811	97,347,282	0.33	4.97E-14	5.61	I				BBOF1	within
7	rs319296259	97,394,296	0.33	1.76E-13	5.5	I				LIN52	within
7	rs346287309	97,427,849	0.33	1.99E-13	5.48	I				LIN52	within
7	rs692640845	97,568,284	0.48	7.51E-21	8.68	I	36.46	9.31	V	ABCD4	within
7	rs1113960993	97,575,068	0.48	7.54E-21	8.68	I				ABCD4	within
7	rs330032123	97,584,287	0.48	7.54E-21	8.68	I				ABCD4	within
7	VRTN_mutation	97,615,880	0.49	6.81E-20	7.8	I				VRTN	within
7	rs343248943	97,617,907	0.48	7.54E-21	8.68	I				VRTN	within
7	rs80894106	97,652,632	0.48	8.65E-20	8.34	I				SYNDIG1L	− 4101
7	rs81238639	97,946,666	0.46	2.28E-09	5.23	I				FCF1	within
7	rs80864705	97,954,258	0.46	2.29E-09	5.23	I				FCF1	within
7	rs80929215	97,973,860	0.46	2.29E-09	5.23	I				YLPM1	− 2277
7	rs80813473	98,066,911	0.47	4.67E-16	7.73	I				PROX2	within
7	rs80836267	98,089,286	0.47	5.07E-16	7.71	I				DLST	− 1527
7	rs80865802	102,479,725	0.33	5.99E-05	2.98	I				ENSSSCG00000021315	within
7	rs338075156	102,513,443	0.33	3.84E-05	3.01	I				ENSSSCG00000021315	within
7	rs80975884	102,552,105	0.33	3.84E-05	3.01	I				ENSSSCG00000021315	within
7	rs80822795	102,658,822	0.30	3.96E-05	3.02	I				ENSSSCG00000021315	within
7	rs80795811	103,109,678	0.19	5.27E-05	2.82	I				DIO2	within
7	NA	103,132,435	0.19	5.27E-05	2.82	I				DIO2	within
7	rs80847916	103,151,323	0.19	5.27E-05	2.82	I				DIO2	within
7	NA	103,164,950	0.19	5.27E-05	2.82	I				DIO2	within
8	rs81401285	72,626,638	0.33				5.75	0.9	IV	SEPT11	within
8	rs343488415	73,599,016	0.36				6.52	2.5	II	FRAS1	within
8	rs81335362	136,866,026	0.16				3.28	1.1	V	BMP3	−12,934
10	rs334392548	16,387,485	0.47				4.03	0.97	II	SDCCAG8	within
11	rs80803790	6,291,044	0.26	4.86E-06	1.11	I	3.12–5.39	0.51–2.39	II,III,IV,V	MTUS2	within
11	rs80914601	6,324,834	0.27	6.52E-06	0.93	I				MTUS2	within
11	rs343377111	15,473,025	0.36				3.29	1	II	MRPS31	801
11	rs80930723	70,370,312	0.29				3.81–4.21	0.62–1.33	III,IV,V	FGF14	within
12	rs81440983	17,695,233	0.33				3.96–4.53	0.84–1.59	II,III	WNT3	within
13	rs335055280	244,235	0.11				3.97–5.35	1.60–3.59	II,III	CPNE4	−123,572
13	rs345752157	198,613,309	0.2				3.42–3.66	0.86–1.58	II,V	RUNX1	within
14	rs345307243	24,753,992	0.39				4.07	0.91	V	PIWIL1	within
14	rs81450840	57,407,462	0.24				4.56–6.50	0.77–2.68	II,III,IV,V	ENSSSCG00000010164	−17,318
14	rs80823799	136,408,216	0.18				3.31	0.78	III	DOCK1	within
16	rs322985099	6,124,952	0.31	2.53E-05	0.59	I	3.34–4.09	0.48–1.37	II,III,IV,V	MYO10	within
17	rs80843610	8,468,654	0.44				3.00–5.39	0.36–1.25	II,III,IV,V	FAT1	within
18	rs321942793	6,398,431	0.26				3.94–4.24	1.38–1.99	II,III	GIMAP2	within
18	rs81471144	51,455,200	0.41				5.17	1.1	II	HECW1	within

^aSus scrofa chromosome ^b SNP position in Ensembl ^c Proportion of total phenotypic variation explained by each SNP. Bold text indicates the maximum phenotypic variance explained by the multi-locus model ^d MLM, mrMLM, FASTmrMLM, FASTmrEMMA and ISIS EM-BLASSO were indicated by I-V, respectively. The bold data represent the model that explained largest phenotypic variance ^e Underline indicates that the gene was newly identified as a candidate for teat number ^f The SNP located upstream/downstream of the nearest gene