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Table 6 Most significant (in italics) and suggestive SNPs in identified vQTL for litter size variabilitya

From: Evaluation of the phenotypic and genomic background of variability based on litter size of Large White pigs

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
  1. SSC Sus Scrofa chromosomes; two clusters of SNPs on SSC7 and one on SSC11 present confirmed candidate QTL regions
  2. MAF minor allele frequency
  3. aObtained with Double Hierarchical GLM
  4. bWithin ± 50 kb