TABLE 3.
Effect1 of selected SNPs2 associated with sample-to-positive (S/P) ratio on reproductive traits3 across PRRS phases.
| SNP | Genotypes | TNB | NBA | NBD | NSB | NBM | NW |
| Pre-PRRS | |||||||
|
| |||||||
| Duroc | |||||||
| ASGA0031860 | AA | 9.74 (0.68) | 8.45 (0.67) | 0.78 (0.12) | 0.54 (0.11) | 0.28 (0.09) | 7.29 (0.48) |
| AB | 9.22 (0.34) | 8.25 (0.34) | 0.64 (0.06) | 0.46 (0.06) | 0.18 (0.04) | 7.21 (0.25) | |
| BB | 9.26 (0.27) | 8.13 (0.27) | 0.74 (0.05) | 0.50 (0.04) | 0.23 (0.04) | 7.11 (0.21) | |
| p-value | 0.698 | 0.822 | 0.301 | 0.713 | 0.310 | 0.816 | |
| MARC0089437 | AA | 9.40 (0.64) | 8.31B (0.63) | 0.68 (0.12) | 0.42 (0.11) | 0.27 (0.08) | 7.56 (0.46) |
| AB | 9.92 (0.47) | 8.79A (0.46) | 0.72 (0.08) | 0.52 (0.08) | 0.20 (0.06) | 7.34 (0.34) | |
| BB | 8.90 (0.61) | 7.73B (0.60) | 0.75 (0.11) | 0.57 (0.10) | 0.21 (0.08) | 6.71 (0.43) | |
| p-value | 0.107 | 0.089 | 0.967 | 0.803 | 0.866 | 0.195 | |
| ASGA0032063 | AA | 9.45 (0.31) | 8.26 (0.30) | 0.77 (0.06) | 0.52 (0.05) | 0.25 (0.04) | 7.13 (0.23) |
| AB | 9.37 (0.47) | 8.29 (0.46) | 0.67 (0.08) | 0.48 (0.08) | 0.20 (0.06) | 7.28 (0.34) | |
| p-value | 0.823 | 0.931 | 0.344 | 0.687 | 0.349 | 0.544 | |
| MARC0058875 | AA | 9.83 (0.55) | 8.75 (0.55) | 0.68 (0.10) | 0.50 (0.09) | 0.19 (0.07) | 7.57 (0.40) |
| AB | 9.27 (0.47) | 8.20 (0.46) | 0.69 (0.09) | 0.46 (0.08) | 0.24 (0.06) | 7.25 (0.34) | |
| BB | 9.11 (0.70) | 7.88 (0.69) | 0.79 (0.12) | 0.55 (0.11) | 0.26 (0.09) | 6.80 (0.50) | |
| p-value | 0.523 | 0.514 | 0.931 | 0.842 | 0.750 | 0.491 | |
| ASGA0032151 | AA | 9.51 (0.53) | 8.61 (0.52) | 0.57 (0.09) | 0.45 (0.08) | 0.14 (0.07) | 7.35 (0.38) |
| AB | 9.27 (0.39) | 8.02 (0.38) | 0.81 (0.07) | 0.57 (0.06) | 0.25 (0.05) | 7.09 (0.28) | |
| BB | 9.44 (0.37) | 8.20 (0.36) | 0.79 (0.07) | 0.49 (0.06) | 0.29 (0.05) | 7.17 (0.27) | |
| p-value | 0.736 | 0.302 | 0.132 | 0.313 | 0.152 | 0.624 | |
| Landrace | |||||||
| ASGA0031860 | AA | 13.35 (0.62) | 11.91 (0.54) | 1.03 (0.09) | 0.68 (0.08) | 0.28 (0.06) | 9.00 (0.39) |
| AB | 13.78 (0.39) | 12.18 (0.34) | 1.09 (0.05) | 0.69 (0.05) | 0.34 (0.04) | 9.54 (0.25) | |
| BB | 13.31 (0.34) | 11.91 (0.30) | 0.99 (0.05) | 0.65 (0.04) | 0.29 (0.03) | 9.54 (0.23) | |
| p-value | 0.332 | 0.604 | 0.623 | 0.877 | 0.438 | 0.305 | |
| MARC0089437 | AB | 13.33 (0.53) | 11.76 (0.46) | 1.12 (0.08) | 0.70 (0.07) | 0.35 (0.05) | 9.08B (0.34) |
| BB | 13.61 (0.29) | 12.24 (0.26) | 0.96 (0.04) | 0.65 (0.04) | 0.26 (0.03) | 9.65A (0.20) | |
| p-value | 0.587 | 0.256 | 0.291 | 0.699 | 0.200 | 0.063 | |
| ASGA0032063 | AA | 13.65 (0.77) | 12.63 (0.67) | 0.66B (0.11) | 0.39B (0.10) | 0.20 (0.08) | 9.54 (0.49) |
| AB | 13.49 (0.45) | 11.79 (0.39) | 1.25A (0.06) | 0.84A (0.06) | 0.34 (0.04) | 9.34 (0.29) | |
| BB | 13.30 (0.54) | 11.58 (0.47) | 1.26A (0.08) | 0.85A (0.07) | 0.38 (0.05) | 9.20 (0.34) | |
| p-value | 0.925 | 0.512 | 0.067 | 0.061 | 0.386 | 0.865 | |
| MARC0058875 | AA | 13.24 (0.51) | 11.49 (0.44) | 1.28 (0.07) | 0.84 (0.07) | 0.38 (0.05) | 9.34 (0.33) |
| AB | 13.50 (0.43) | 12.25 (0.38) | 0.88 (0.06) | 0.57 (0.06) | 0.27 (0.04) | 9.50 (0.28) | |
| BB | 13.70 (0.58) | 12.26 (0.51) | 0.97 (0.09) | 0.63 (0.08) | 0.27 (0.06) | 9.25 (0.37) | |
| p-value | 0.843 | 0.383 | 0.110 | 0.138 | 0.416 | 0.648 | |
| ASGA0032151 | AA | 13.30 (0.50) | 11.87 (0.44) | 0.97 (0.07) | 0.64 (0.07) | 0.29 (0.05) | 9.47 (0.32) |
| AB | 13.69 (0.41) | 12.22 (0.36) | 1.01 (0.06) | 0.70 (0.05) | 0.26 (0.04) | 9.29 (0.27) | |
| BB | 13.45 (0.45) | 11.91 (0.40) | 1.13 (0.06) | 0.69 (0.06) | 0.37 (0.04) | 9.32 (0.29) | |
| p-value | 0.586 | 0.504 | 0.693 | 0.767 | 0.191 | 0.782 | |
|
| |||||||
| PRRS | |||||||
|
| |||||||
| Duroc | |||||||
| ASGA0031860 | AA | 7.91 (0.85) | 5.27 (0.86) | 1.62B (0.19) | 0.41 (0.15) | 1.19 (0.18) | 2.97 (0.83) |
| AB | 8.86 (0.43) | 5.91 (0.43) | 1.75B (0.10) | 0.70 (0.07) | 0.93 (0.09) | 3.81 (0.44) | |
| BB | 8.90 (0.35) | 5.43 (0.36) | 2.26A (0.08) | 0.80 (0.06) | 1.24 (0.08) | 3.41 (0.37) | |
| p-value | 0.458 | 0.300 | 0.058 | 0.175 | 0.120 | 0.317 | |
| MARC0089437 | AA | 8.35 (0.84) | 5.36 (0.85) | 1.92 (0.19) | 0.40 (0.14) | 1.42 (0.18) | 3.70 (0.83) |
| AB | 8.19 (0.59) | 5.36 (0.59) | 1.62 (0.14) | 0.69 (0.10) | 0.83 (0.13) | 3.52 (0.59) | |
| BB | 9.12 (0.81) | 5.89 (0.82) | 2.07 (0.18) | 0.84 (0.14) | 1.14 (0.18) | 2.97 (0.81) | |
| p-value | 0.505 | 0.805 | 0.625 | 0.471 | 0.312 | 0.778 | |
| ASGA0032063 | AA | 8.34 (0.38) | 5.44 (0.38) | 1.74 (0.09) | 0.62 (0.07) | 1.09 (0.08) | 3.61 (0.40) |
| AB | 8.77 (0.60) | 5.63 (0.61) | 2.00 (0.13) | 0.64 (0.10) | 1.14 (0.13) | 3.18 (0.60) | |
| p-value | 0.389 | 0.704 | 0.418 | 0.851 | 0.829 | 0.377 | |
| MARC0058875 | AA | 8.71 (0.77) | 5.70 (0.77) | 1.72 (0.17) | 0.40 (0.13) | 1.20 (0.16) | 3.75 (0.77) |
| AB | 9.09 (0.62) | 5.92 (0.63) | 2.18 (0.14) | 0.53 (0.11) | 1.56 (0.14) | 3.47 (0.62) | |
| BB | 7.87 (0.85) | 5.00 (0.86) | 1.72 (0.19) | 1.02 (0.15) | 0.69 (0.19) | 2.96 (0.84) | |
| p-value | 0.425 | 0.638 | 0.558 | 0.239 | 0.131 | 0.825 | |
| ASGA0032151 | AA | 9.36 (0.72) | 6.26 (0.73) | 1.73 (0.16) | 0.51 (0.12) | 1.13 (0.15) | 3.74 (0.71) |
| AB | 8.43 (0.50) | 5.50 (0.51) | 1.76 (0.11) | 0.60 (0.09) | 1.07 (0.11) | 3.18 (0.52) | |
| BB | 7.88 (0.51) | 4.85 (0.51) | 2.12 (0.12) | 0.79 (0.09) | 1.15 (0.11) | 3.27 (0.52) | |
| p-value | 0.209 | 0.232 | 0.567 | 0.387 | 0.924 | 0.675 | |
| Landrace | |||||||
| ASGA0031860 | AA | 13.54 (0.77) | 7.69 (0.89) | 3.86 (0.16) | 1.07 (0.12) | 2.64 (0.17) | 4.68 (0.72) |
| AB | 13.18 (0.49) | 7.79 (0.56) | 3.68 (0.10) | 1.19 (0.08) | 2.09 (0.11) | 5.06 (0.46) | |
| BB | 13.31 (0.47) | 7.22 (0.54) | 4.01 (0.10) | 1.16 (0.08) | 2.31 (0.10) | 4.98 (0.45) | |
| p-value | 0.853 | 0.622 | 0.793 | 0.860 | 0.457 | 0.834 | |
| MARC0089437 | AB | 13.69 (0.75) | 7.78 (0.86) | 3.74 (0.16) | 1.18 (0.12) | 2.20 (0.16) | 5.16 (0.70) |
| BB | 13.00 (0.33) | 7.35 (0.38) | 3.96 (0.07) | 1.10 (0.05) | 2.48 (0.07) | 4.65 (0.33) | |
| p-value | 0.370 | 0.625 | 0.777 | 0.759 | 0.624 | 0.465 | |
| ASGA0032063 | AA | 14.30 (0.94) | 8.09 (1.09) | 4.74 (0.20) | 1.18 (0.15) | 2.86 (0.21) | 4.88 (0.87) |
| AB | 12.98 (0.56) | 7.26 (0.63) | 3.73 (0.11) | 1.16 (0.09) | 2.41 (0.12) | 4.86 (0.53) | |
| BB | 12.76 (0.71) | 7.35 (0.82) | 3.20 (0.15) | 1.09 (0.11) | 1.82 (0.15) | 4.98 (0.67) | |
| p-value | 0.465 | 0.790 | 0.523 | 0.959 | 0.410 | 0.979 | |
| MARC0058875 | AA | 12.62 (0.63) | 7.07 (0.73) | 3.79 (0.13) | 1.22 (0.10) | 2.17 (0.14) | 4.76 (0.60) |
| AB | 13.59 (0.52) | 7.60 (0.60) | 4.03 (0.11) | 1.07 (0.08) | 2.48 (0.11) | 4.99 (0.49) | |
| BB | 13.83 (0.73) | 8.04 (0.85) | 3.72 (0.15) | 1.14 (0.12) | 2.37 (0.16) | 4.97 (0.69) | |
| p-value | 0.402 | 0.700 | 0.838 | 0.793 | 0.816 | 0.943 | |
| ASGA0032151 | AA | 13.02 (0.63) | 7.90 (0.73) | 3.55 (0.13) | 1.12 (0.10) | 2.23 (0.14) | 4.79 (0.59) |
| AB | 13.40 (0.53) | 7.72 (0.61) | 3.82 (0.11) | 1.11 (0.08) | 2.26 (0.12) | 4.97 (0.51) | |
| BB | 13.62 (0.62) | 7.08 (0.72) | 4.19 (0.13) | 1.20 (0.10) | 2.53 (0.14) | 4.95 (0.59) | |
| p-value | 0.736 | 0.691 | 0.766 | 0.928 | 0.866 | 0.944 | |
|
| |||||||
| Post-PRRS | |||||||
|
| |||||||
| Duroc | |||||||
| ASGA0031860 | AA | 9.36 (0.64) | 8.26 (0.59) | 0.73 (0.11) | 0.59 (0.09) | 0.16 (0.07) | 7.87A (0.60) |
| AB | 8.91 (0.30) | 7.88 (0.28) | 0.72 (0.05) | 0.49 (0.04) | 0.20 (0.03) | 6.89B (0.31) | |
| BB | 8.94 (0.23) | 7.89 (0.22) | 0.68 (0.04) | 0.44 (0.03) | 0.23 (0.02) | 6.67B (0.25) | |
| p-value | 0.741 | 0.777 | 0.822 | 0.378 | 0.599 | 0.090 | |
| MARC0089437 | AA | 10.03a (0.62) | 8.43A (0.57) | 1.02 (0.10) | 0.58 (0.09) | 0.44a (0.07) | 7.80A (0.58) |
| AB | 9.32a (0.43) | 8.43A (0.40) | 0.60 (0.07) | 0.46 (0.06) | 0.12b (0.05) | 7.46A (0.42) | |
| BB | 7.85b (0.57) | 7.17B (0.51) | 0.55 (0.09) | 0.48 (0.08) | 0.05b (0.06) | 6.17B (0.53) | |
| p-value | 0.041 | 0.068 | 0.126 | 0.675 | 0.004 | 0.063 | |
| ASGA0032063 | AA | 8.77 (0.26) | 7.78 (0.24) | 0.68 (0.04) | 0.51 (0.04) | 0.16 (0.03) | 6.88 (0.27) |
| AB | 9.36 (0.44) | 8.23 (0.41) | 0.74 (0.07) | 0.49 (0.06) | 0.23 (0.05) | 7.40 (0.43) | |
| p-value | 0.109 | 0.179 | 0.585 | 0.783 | 0.115 | 0.124 | |
| MARC0058875 | AA | 10.29a (0.62) | 8.82 (0.56) | 0.89 (0.10) | 0.56 (0.08) | 0.33a (0.07) | 8.14A (0.57) |
| AB | 8.89ab (0.41) | 7.81 (0.38) | 0.72 (0.07) | 0.46 (0.06) | 0.26a (0.04) | 7.01AB (0.40) | |
| BB | 8.02b (0.57) | 7.40 (0.52) | 0.54 (0.09) | 0.49 (0.08) | 0.02b (0.06) | 6.28B (0.53) | |
| p-value | 0.037 | 0.149 | 0.452 | 0.720 | 0.013 | 0.069 | |
| ASGA0032151 | AA | 8.92 (0.53) | 7.95 (0.49) | 0.69 (0.09) | 0.49 (0.07) | 0.19 (0.06) | 7.22 (0.50) |
| AB | 9.14 (0.36) | 7.98 (0.34) | 0.76 (0.06) | 0.55 (0.05) | 0.18 (0.04) | 7.09 (0.36) | |
| BB | 9.15 (0.35) | 8.10 (0.32) | 0.69 (0.06) | 0.47 (0.05) | 0.22 (0.04) | 7.12 (0.35) | |
| p-value | 0.904 | 0.934 | 0.713 | 0.423 | 0.623 | 0.950 | |
| Landrace | |||||||
| ASGA0031860 | AA | 14.61 (0.53) | 13.16 (0.49) | 0.97 (0.08) | 0.53 (0.07) | 0.39 (0.06) | 10.48a (0.45) |
| AB | 14.02 (0.35) | 12.71 (0.33) | 0.84 (0.05) | 0.55 (0.05) | 0.26 (0.04) | 10.14a (0.32) | |
| BB | 13.58 (0.37) | 12.35 (0.34) | 0.84 (0.06) | 0.49 (0.05) | 0.32 (0.04) | 9.45b (0.33) | |
| p-value | 0.221 | 0.320 | 0.676 | 0.657 | 0.133 | 0.050 | |
| MARC0089437 | AB | 14.54A (0.53) | 13.12 (0.49) | 0.96 (0.08) | 0.54 (0.07) | 0.35 (0.06) | 10.36 (0.46) |
| BB | 13.60B (0.24) | 12.35 (0.23) | 0.82 (0.04) | 0.50 (0.03) | 0.30 (0.03) | 9.69 (0.23) | |
| p-value | 0.081 | 0.117 | 0.380 | 0.668 | 0.487 | 0.138 | |
| ASGA0032063 | AA | 14.13 (0.73) | 13.14 (0.67) | 0.65 (0.12) | 0.34 (0.11) | 0.29 (0.08) | 10.21 (0.62) |
| AB | 14.06 (0.41) | 12.53 (0.38) | 0.98 (0.06) | 0.60 (0.06) | 0.32 (0.04) | 9.78 (0.37) | |
| BB | 14.03 (0.47) | 12.55 (0.43) | 1.05 (0.07) | 0.63 (0.07) | 0.36 (0.05) | 10.09 (0.41) | |
| p-value | 0.995 | 0.714 | 0.311 | 0.254 | 0.865 | 0.626 | |
| MARC0058875 | AA | 13.78 (0.47) | 12.46 (0.44) | 0.90 (0.07) | 0.52 (0.07) | 0.35 (0.05) | 9.86 (0.41) |
| AB | 14.28 (0.37) | 13.03 (0.35) | 0.85 (0.06) | 0.51 (0.06) | 0.31 (0.04) | 10.33 (0.33) | |
| BB | 14.15 (0.54) | 12.73 (0.49) | 0.94 (0.08) | 0.53 (0.08) | 0.32 (0.06) | 9.88 (0.46) | |
| p-value | 0.626 | 0.398 | 0.840 | 0.974 | 0.883 | 0.269 | |
| ASGA0032151 | AA | 14.39 (0.47) | 13.09 (0.44) | 0.86 (0.07) | 0.49AB (0.07) | 0.32 (0.05) | 10.67A (0.41) |
| AB | 14.07 (0.38) | 12.82 (0.35) | 0.85 (0.06) | 0.43B (0.06) | 0.40 (0.04) | 9.88B (0.34) | |
| BB | 13.74 (0.49) | 12.30 (0.45) | 0.94 (0.08) | 0.65A (0.07) | 0.26 (0.05) | 9.53B (0.42) | |
| p-value | 0.623 | 0.448 | 0.852 | 0.089 | 0.129 | 0.057 | |
TNB, total number of piglets born; NBA, number of piglets born alive; NBD, number of piglets born dead; NSB, number of stillborn piglets; NBM, number of mummified piglets; NW, number of piglets weaned; PRRS, porcine reproductive and respiratory syndrome.
1Results for each genotype expressed as number of piglets (standard errors within parenthesis).
2SNPs are located on Sus scrofa chromosome 7 as follow according to the Sscrofa11.1 (GCA_000003025.6) assembly: ASGA0031860/rs80959936 (7:22,075,114), MARC0089437/rs80900036 (7:24,217,931), ASGA0032063/rs80940999 (7:24,247,099), MARC0058875/rs80986722 (7:24,865,378), and ASGA0032151/rs80947467 (7:25,967,157). SNP markers MARC0089437 and ASGA0032063 were associated with S/P ratio in this study, in Duroc and Landrace populations, respectively. The other markers were associated with S/P ratio in Landrace sows in Serão et al. (2014).
3Results for NBD, NSB, and NBM were back-transformed from ln(phenotype+1).
a–bExpected values within row lacking the same superscript indicate differences at p-value <0.05.
A–BExpected values within row lacking the same superscript indicate differences at p-value <0.10.