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

Table 2.

Significant SNPs associated with teat number in American 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	rs81296766	26,423,644	0.41				3.23–4.11	0.22–0.36	II,III,V	TNFAIP3	−50,291
1	rs81353367	32,198,014	0.02	4.83E-05	1.94	I				AKAP7	−23,051
1	rs81354014	49,632,560	0.41				4.66	0.51	IV	ADGRB3	12,781
1	rs80808645	50,037,586	0.3				4.1	1.01	V	LMBRD1	59,597
1	rs80855587	166,253,306	0.32				3.18	0.53	V	ITGA11	within
1	rs80805477	248,169,556	0.46				3.12–5.68	0.41–0.68	IV,V	ZNF462	within
1	rs81315010	251,816,790	0.14				4	1.39	III	ENSSSCG00000005457	within
2	rs81356579	27,110,325	0.5				4.54–5.08	0.56–0.57	II,III,V	FBXO3	−35,449
2	rs330333016	77,481,598	0.11				4.15	0.48	IV	R3HDM4	within
2	rs338630193	127,747,767	0.19				3.6	0.73	III	ZNF608	−300,480
3	rs81314408	20,394,893	0.11				3.28–4.12	0.80–1.32	II,III,V	ENSSSCG00000039406	−150,340
3	rs81338014	32,426,287	0.05				4.82	2.78	II	EMP2	−24,223
4	rs318980859	117,518,657	0.42				3.47	0.32	IV	VCAM1	7446
5	rs341491167	10,879,898	0.35				4.38–4.77	0.36–0.55	II,III,V	NCF4	within
5	rs328599079	75,707,707	0.05				3.86	1.36	V	NELL2	within
6	rs81395407	35,040,992	0.27				3.12–3.43	0.55–0.80	II,III,V	ZNF423	within
6	rs333592328	49,265,869	0.27				3.14	0.48	III	AXL	within
6	rs81389632	89,786,916	0.05				3.19	2.55	V	CSMD2	within
6	rs81391820	134,798,234	0.19	1.87E-05	1.28	I	5.19–7.16	0.62–3.03	II,III,IV,V	PTGFR	21,471
6	rs705289935	168,268,278	0.43	1.74E-05	0.38	I	3.01	0.29	V	ENSSSCG00000039458	−13,851
7	rs80964371	92,809,231	0.49				4.08	0.49	V	DCAF5	within
9	rs81420227	14,459,452	0.44				3.09	0.17	V	ENSSSCG00000014896	−370,357
11	rs81305437	25,782,658	0.15				3.43–4.82	0.94–1.45	II,III,V	ENSSSCG00000036698	within
11	rs80809451	34,924,123	0.04				4.29–5.25	4.23–4.69	II,III	ENSSSCG00000040542	− 248,706
14	rs345307243	24,753,992	0.47				4.57	0.5	IV	PIWIL1	within
14	rs80848162	26,467,369	0.49				3.21	0.27	V	TMEM132C	within
14	rs80890762	69,437,518	0.21				3.03	0.29	IV	CTNNA3	within
14	rs321772507	115,176,455	0.01	8.3E-05	1.11	I				CFAP43	2412
14	rs327004523	133,536,115	0.38				3.64	1.07	II	CHST15	within
14	rs80794466	137,506,343	0.28				4	0.73	V	ENSSSCG00000026302	210,031
15	rs80957887	111,327,896	0.5				3.72	0.41	V	ENSSSCG00000023264	within
15	rs333698977	129,904,530	0.27				3.58–4.00	0.33–0.96	IV,V	PID1	− 174,602
16	rs81316660	27,084,056	0.38				3.77–6.24	0.38–1.90	II,III,IV,V	GHR	−42,296
16	rs81461904	69,106,054	0.48				3.22	0.39	V	MFAP3	within
17	rs319134655	44,791,974	0.31				3.49	0.44	V	ENSSSCG00000038990	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