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