Whole-genome SNP association analysis of reproduction traits in the Finnish Landrace pig breed

Table 2 Allele effects and P-values of significant (in bold face) and suggestive SNP

Trait¹	Marker	CHR²	Position (bp)	CR²	MAF1²	MAF2²	MAF3²	N	b³	S.E.	P-value
TNB1	ALGA0054078	9	79167181	0.99	0.10	0.13	0.19	316	0.55	0.11	4.24E-07
TNB1	H3GA0027863	9	79597323	1.00	0.10	0.13	0.19	319	0.52	0.10	8.21E-07
TNB1	MARC0003458	9	79667545	1.00	0.10	0.13	0.19	319	0.52	0.10	8.21E-07
TNB1	MARC0027588	9	79869109	1.00	0.10	0.13	0.19	319	0.52	0.10	8.21E-07
TNB1	DRGA0009645	9	95379632	1.00	0.14	0.13	0.22	319	0.51	0.10	3.21E-07
TNB2	ALGA0054078	9	79167181	0.99	0.10	0.13	0.19	312	0.55	0.11	5.62E-07
TNB2	H3GA0027863	9	79597323	1.00	0.10	0.13	0.19	315	0.53	0.11	1.03E-06
TNB2	MARC0003458	9	79667545	1.00	0.10	0.13	0.19	315	0.53	0.11	1.03E-06
TNB2	MARC0027588	9	79869109	1.00	0.10	0.13	0.19	315	0.53	0.11	1.03E-06
TNB2	DRGA0009645	9	95379632	1.00	0.14	0.13	0.22	315	0.55	0.10	8.45E-08
NSB2	ALGA0009013	1	261069838	1.00	0.36	0.40	0.54	310	-0.15	0.03	3.97E-06
NSB2	ASGA0006533	1	261117360	1.00	0.36	0.40	0.54	310	-0.15	0.03	3.97E-06
PM1	ASGA0043706	9	65533618	0.94	0.34	0.39	0.39	295	-0.18	0.04	2.92E-06
PM1	MARC0027886	9	65764105	1.00	0.37	0.40	0.40	313	-0.18	0.04	2.50E-06
PM2	MARC0016206	7	89927000	1.00	0.21	0.22	0.15	306	-0.21	0.04	2.89E-06
PM2	ALGA0042932	7	90018155	1.00	0.20	0.21	0.15	306	-0.22	0.04	2.51E-06
PM2	ASGA0043706	9	65533618	0.94	0.34	0.39	0.39	288	-0.22	0.04	6.94E-08
PM2	MARC0027886	9	65764105	1.00	0.37	0.40	0.40	306	-0.21	0.04	7.98E-08
PM2	ALGA0053783	9	66630460	0.99	0.33	0.36	0.38	303	-0.20	0.04	8.85E-07
PM2	MARC0023136	9	95402048	0.99	0.35	0.47	0.52	304	-0.18	0.04	3.30E-06
FFI	H3GA0014078	4	112914704	1.00	0.57	0.37	0.23	300	2.40	0.49	2.01E-06
SFI	ALGA0000673	1	8282135	1.00	0.24	0.20	0.23	288	2.38	0.50	3.83E-06

¹TNB1 = total number of piglets born in first parity; TNB2 = total number of piglets born in later parities; NSB2 = number of stillborn piglets in later parities; PM1 = piglet mortality between birth and weaning in first parity; PM2 = piglet mortality between birth and weaning in later parities; FFI = first farrowing interval; SFI = second farrowing interval
²CHR = chromosome; CR = call rate; MAF1 = minor allele frequency of animals born in 1996 - 1999; MAF2 = minor allele frequency of animals born in 2000 - 2004; MAF3 = minor allele frequency of animals born after 2004
³the regression coefficient is expressed as a dose effect of the minor allele

ISSN: 1297-9686