Table 6.
Most significant (in italics) and suggestive SNPs in identified vQTL for litter size variabilitya
| SSC | Name | Position (Mb) | MAF | SNP effect (with SE) | Genetic variance explained | Phenotypic variance explained | − log(p-value) | SNP location | Candidate genes | Previously detected QTL |
|---|---|---|---|---|---|---|---|---|---|---|
| 7 | AX-116317026 | 36.25 | 0.016 | 0.055 (0.013) | 0.007 | 0.002 | 4.59 | Non-coding | Nonea | Birthweight variability [66]; number mummified piglets [67]; age at puberty [68] |
| AX-116317099 | 36.59 | 0.470 | 0.022 (0.004) | 0.016 | 0.004 | 5.93 | Non-coding | NCR2 | ||
| AX-116317136 | 36.72 | 0.480 | − 0.020 (0.004) | 0.014 | 0.004 | 5.36 | Non-coding | FOXP4 | ||
| AX-116317145 | 36.74 | 0.310 | − 0.025 (0.005) | 0.019 | 0.005 | 5.60 | Non-coding | FOXP4 | ||
| AX-116317156 | 36.79 | 0.310 | − 0.026 (0.005) | 0.019 | 0.005 | 5.76 | Exon | FOXP4 | ||
| AX-116317159 | 36.80 | 0.490 | 0.017 (0.004) | 0.011 | 0.003 | 4.88 | Non-coding | MDFI; FOXP4 | ||
| AX-116317341 | 37.52 | 0.332 | 0.017 (0.004) | 0.008 | 0.002 | 4.06 | Intron | TRERF1 | ||
| AX-116317343 | 37.53 | 0.332 | 0.017 (0.004) | 0.008 | 0.002 | 4.06 | Intron | TRERF1 | ||
| AX-116317552 | 38.26 | 0.361 | 0.017 (0.004) | 0.009 | 0.002 | 4.04 | Intron | CUL9 | ||
| AX-116317553 | 38.26 | 0.361 | 0.017 (0.004) | 0.009 | 0.002 | 4.05 | Intron | CUL9 | ||
| AX-116689108 | 41.80 | 0.010 | 0.110 (0.016) | 0.018 | 0.005 | 11.57 | Non-coding | ADGRF1; ADGRF5 | ||
| 7 | AX-116320104 | 50.68 | 0.312 | 0.020 (0.004) | 0.012 | 0.003 | 5.15 | Non-coding | Nonea | Teat number [71]; number mummified piglets [67] |
| AX-116320268 | 51.43 | 0.248 | 0.019 (0.005) | 0.009 | 0.002 | 4.41 | Intron | SH3GL3 | ||
| AX-116320489 | 52.20 | 0.345 | 0.017 (0.004) | 0.009 | 0.002 | 4.25 | Non-coding | FSD2; AP3B2 | ||
| AX-116320491 | 52.20 | 0.332 | 0.02 (0.004) | 0.012 | 0.003 | 5.10 | Non-coding | FSD2; AP3B2 | ||
| AX-116320493 | 52.21 | 0.330 | 0.021 (0.004) | 0.013 | 0.003 | 5.43 | Intron | AP3B2 | ||
| AX-116689308 | 52.22 | 0.332 | 0.019 (0.004) | 0.011 | 0.003 | 4.71 | Intron | AP3B2 | ||
| AX-116320498 | 52.22 | 0.332 | 0.019 (0.004) | 0.011 | 0.003 | 4.53 | Intron | AP3B2 | ||
| AX-116320499 | 52.23 | 0.339 | 0.020 (0.004) | 0.012 | 0.003 | 5.30 | Intron | AP3B2 | ||
| AX-116320501 | 52.23 | 0.331 | 0.019 (0.004) | 0.011 | 0.003 | 4.53 | Intron | AP3B2 | ||
| AX-116320502 | 52.23 | 0.242 | 0.019 (0.005) | 0.009 | 0.002 | 4.52 | Intron | AP3B2 | ||
| AX-116321160 | 57.08 | 0.069 | − 0.028 (0.007) | 0.007 | 0.002 | 4.00 | Non-coding | PSTPIP1; RCN2 | ||
| AX-116321525 | 58.97 | 0.057 | − 0.035 (0.008) | 0.009 | 0.002 | 4.35 | Intron | ARID3B | ||
| 11 | AX-116416565 | 5.71 | 0.018 | − 0.048 (0.012) | 0.006 | 0.002 | 4.30 | Intron | FLT1 | Teat number [72]; number mummified piglets [67]; uterine horn length [73] |
| AX-116416787 | 6.87 | 0.036 | 0.041 (0.010) | 0.008 | 0.002 | 4.43 | Non-coding | None4 | ||
| AX-116416839 | 7.04 | 0.05 | 0.038 (0.008) | 0.009 | 0.002 | 5.50 | Intron | KATNAL1 | ||
| AX-116416845 | 7.08 | 0.036 | 0.041 (0.010) | 0.008 | 0.002 | 4.49 | Intron | KATNAL1 | ||
| AX-116779844 | 7.30 | 0.036 | 0.041 (0.010) | 0.008 | 0.002 | 4.53 | Non-coding | USPL1 | ||
| AX-116416878 | 7.32 | 0.038 | 0.038 (0.010) | 0.007 | 0.002 | 4.14 | Non-coding | USPL1 | ||
| AX-116779846 | 7.37 | 0.039 | 0.037 (0.009) | 0.007 | 0.002 | 4.28 | Non-coding | USPL1; ALOX5AP | ||
| AX-116851433 | 7.39 | 0.039 | 0.037 (0.009) | 0.007 | 0.002 | 4.28 | Non-coding | USPL1; ALOX5AP | ||
| AX-116650934 | 8.77 | 0.231 | 0.020 (0.005) | 0.01 | 0.003 | 4.16 | Non-coding | FRY; ZAR1L |
SSC Sus Scrofa chromosomes; two clusters of SNPs on SSC7 and one on SSC11 present confirmed candidate QTL regions
MAF minor allele frequency
aObtained with Double Hierarchical GLM
bWithin ± 50 kb