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Table 5 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
1 AX-116127462 129.07 0.01 − 0.083 (0.020) 0.013 0.002 4.57 Intron GANC None
AX-116127463 129.08 0.01 − 0.100 (0.021) 0.017 0.003 5.53 Intron GANC
AX-116127466 129.09 0.01 − 0.097 (0.020) 0.018 0.003 6.02 Intron GANC
AX-116702728 129.17 0.01 − 0.083 (0.018) 0.015 0.003 5.30 Intron VPS39
AX-116127269 127.69 0.03 − 0.047 (0.012) 0.012 0.002 4.23 Non-coding Nonea
7 AX-116317099 36.59 0.47 0.020 (0.005) 0.016 0.003 4.35 Non-coding NCR2 Birthweight variability [66]; number mummified piglets [67]; age at puberty [68]
AX-116317159 36.80 0.49 0.019 (0.004) 0.015 0.003 4.78 Non-coding NRN1
AX-116317552 38.26 0.36 0.018 (0.005) 0.013 0.002 4.03 Intron CUL9
AX-116317553 38.26 0.36 0.018 (0.005) 0.013 0.002 4.07 Intron CUL9
AX-116317740 38.97 0.36 − 0.019 (0.005) 0.015 0.003 4.43 Non-coding Nonea
AX-116689108 41.80 0.01 0.106 (0.018) 0.020 0.003 8.50 Non-coding ADGRF1; ADGRF5
18 AX-116596013 18.07 0.05 − 0.039 (0.009) 0.012 0.002 4.60 Intron LMBR1 Litter weight [69]; litter size [69]; litter weight of piglets born alive [69]; birthweight [70]
AX-116596024 18.19 0.09 − 0.030 (0.007) 0.013 0.002 4.83 Non-coding KLF14; TSGA13; COPG2
AX-116596140 18.88 0.04 0.045 (0.011) 0.01 0.002 4.08 Intron UBE2H
AX-116596204 19.30 0.07 − 0.034 (0.008) 0.012 0.002 4.53 Intron AHCYL2
AX-116596216 19.37 0.09 − 0.029 (0.007) 0.011 0.002 5.01 Intron AHCYL2
AX-116596225 19.40 0.06 − 0.041 (0.009) 0.015 0.003 5.56 Intron AHCYL2
AX-116596239 19.45 0.05 − 0.039 (0.009) 0.013 0.002 4.82 Intron SMO
  1. SSC Sus scrofa chromosomes; SNPs on each SSC present confirmed candidate QTL region
  2. MAF minor allele frequency
  3. aObtained with a log-transformed variance of residuals
  4. bWithin ± 50 kb