Table 2 Haplotypes affecting TNB. The genomic location and haplotype frequency is provided in columns 1–5. The “homozygotes” section shows expected and observed homozygotes including statistical test. Information on carrier x carrier (C x C) matings and progeny is provided in the “matings” section. Effect on the phenotype is provided in the “reduction in TNB” section
From: A systematic survey to identify lethal recessive variation in highly managed pig populations
Abbreviation | Chr | Start | End | Hap. Freq | Homozygotes | Matings | Reduction in TNB | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
Expected | Observed | Exact binomial test | C x C matings | Genotyped progeny | Het. carrier progeny | Percent | P | |||||
BR1 | SSC2 | 156 | 159 | 3.8 | 8 | 0 | 0.000138 | 42 | 32 | 13 | 8.192 | 0.054 |
BR2 | SSC2 | 158.5 | 159.5 | 4.8 | 18.75 | 0 | 5.70E-10 | 69 | 75 | 38 | 9.220 | 0.008 |
BR3 | SSC16 | 85.5 | 86.5 | 5.4 | 17.25 | 1 | 8.22E-08 | 53 | 69 | 23 | 7.037 | 0.046 |
LR1 | SSC1 | 295 | 296 | 11.4 | 30.25 | 0 | 1.71E-15 | 370 | 121 | 97 | 3.243 | 0.012 |
LR2 | SSC2 | 10.5 | 13.5 | 6 | 6.75 | 0 | 0.000585 | 148 | 27 | 18 | 4.35 | 0.026 |
LR3 | SSC8 | 78 | 79 | 2.6 | 8.25 | 0 | 0.000144 | 30 | 33 | 17 | 8.505 | 0.017 |
LR4 | SSC13 | 28.75 | 29.25 | 3.6 | 5.75 | 0 | 0.002581 | 44 | 23 | 16 | 17.130 | 2.16E-06 |
LW1 | SSC1 | 294.5 | 295.5 | 2 | 7.5 | 0 | 0.000138 | 44 | 30 | 20 | 9.552 | 0.010 |
LW2 | SSC1 | 294.75 | 295.25 | 11.5 | 132.75 | 1 | 1.87E-72 | 619 | 531 | 418 | 2.843 | 0.007 |
LW3 | SSC1 | 295 | 295.5 | 5.9 | 30.25 | 0 | 5.67E-17 | 259 | 121 | 94 | 4.522 | 0.003 |
LW4 | SSC1 | 295 | 295.5 | 5.1 | 37.5 | 2 | 1.16E-19 | 206 | 150 | 116 | 4.213 | 0.008 |
LW5 | SSC1 | 313.75 | 314.25 | 7.4 | 126.75 | 3 | 3.00E-60 | 483 | 507 | 146 | 3.875 | 0.000121 |
LW6 | SSC3 | 142.75 | 143.25 | 5.8 | 24.25 | 0 | 4.27E-14 | 207 | 97 | 31 | 4.275 | 0.012 |
LW7 | SSC4 | 4 | 8 | 2.6 | 26.25 | 5 | 7.04E-10 | 111 | 105 | 45 | 5.311 | 0.013 |
LW8 | SSC4 | 6.5 | 7.5 | 4.5 | 14.25 | 1 | 4.16E-08 | 50 | 57 | 32 | 9.854 | 0.009 |
LW9 | SSC7 | 40 | 44 | 2.6 | 6.75 | 0 | 0.000138 | 30 | 27 | 12 | 15.612 | 0.001 |
LW10 | SSC8 | 78 | 80 | 3.3 | 19.5 | 5 | 5.44E-09 | 173 | 78 | 60 | 4.200 | 0.023 |
LW11 | SSC9 | 46.75 | 47.25 | 4 | 6 | 0 | 0.00036 | 56 | 24 | 16 | 7.622 | 0.012 |
LW12 | SSC10 | 5.5 | 6.5 | 6.5 | 50.25 | 5 | 9.23E-23 | 296 | 201 | 123 | 4.169 | 0.003 |
LW13 | SSC12 | 26.5 | 27.5 | 5.2 | 20 | 0 | 9.31E-11 | 102 | 80 | 52 | 7.383 | 0.004 |
LW14 | SSC14 | 146 | 150 | 1.6 | 8 | 0 | 0.000144 | 28 | 32 | 15 | 11.252 | 0.004 |
LW15 | SSC17 | 10.5 | 11 | 3.1 | 16 | 0 | 3.80E-09 | 42 | 64 | 29 | 9.920 | 0.012 |
LW16 | SSC18 | 34.5 | 37.5 | 2.8 | 6 | 0 | 0.000954 | 30 | 24 | 14 | 11.621 | 0.027 |
LW17 | SSC18 | 36 | 40 | 4.3 | 15.25 | 2 | 5.22E-07 | 74 | 61 | 28 | 7.517 | 0.017 |
LW18 | SSC18 | 42.75 | 43.25 | 5.5 | 15.75 | 3 | 1.32E-07 | 127 | 63 | 43 | 15.438 | 1.27E-12 |
LW19 | SSC18 | 43 | 44 | 4.3 | 11.75 | 0 | 1.29E-06 | 88 | 47 | 32 | 18.715 | 4.91E-12 |