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Table 4 Top genome-wide significant SNPs associated with growth, body measurements, carcass measurements and fat area

From: SNP- and haplotype-based genome-wide association studies for growth, carcass, and meat quality traits in a Duroc multigenerational population

   Most significant SNP Haplotype-based Nearby genesg
Traita SSCb Positionc (bp) refSNP variation ID EAd EAFd β (SE) Proportione P-value P-valuef  
Growth
  DG 1 304,667,314 rs81352956 A 0.454 −34.75 (6.035) 0.06 1.22 × 10−8 6.71 × 10−6 h PRDM12_EXOSC2
  BF 1 304,694,455 rs81352969 A 0.495 0.18 (0.029) 0.07 6.30 × 10−10 2.26 × 10−5 h ABL1
   10 27,636,391 rs81422289 G 0.227 0.17 (0.034) 0.04 7.04 × 10−7 3.63 × 10−2 KIF14
Body measurements
  CW 1 304,694,455 rs81352969 A 0.495 0.45 (0.084) 0.05 1.17 × 10−7 1.45 × 10−4 ABL1
  CC 1 304,694,455 rs81352969 A 0.495 0.87 (0.148) 0.06 6.82 × 10−9 3.36 × 10−5 h ABL1
  CCB at F105 7 39,512,713 rs80892802 G 0.171 0.29 (0.045) 0.07 3.14 × 10−10 1.75 × 10−3 DNAH8
  CCB at R105 7 39,089,506 rs196955082 G 0.249 0.21 (0.039) 0.05 4.38 × 10−8 1.19 × 10−3 BTBD9
Carcass measurements
  CL 7 103,457,401 VRTN C 0.368 1.13 (0.187) 0.14 3.64 × 10−9 3.36 × 10−6 h VRTN
  CL1 7 103,457,401 VRTN C 0.368 1.13 (0.162) 0.18 1.56 × 10−11 4.87 × 10−8 H VRTN
  CL2 7 103,457,401 VRTN C 0.368 1.37 (0.172) 0.22 2.96 × 10−14 2.22 × 10−9 H VRTN
   7 107,279,922 rs80977788 G 0.267 −0.97 (0.196) 0.09 1.20 × 10−6 1.25 × 10−5 h NRXN3
  CL3 7 103,457,401 VRTN C 0.368 1.48 (0.159) 0.27 3.10 × 10−18 1.94 × 10−11 H VRTN
   7 106,308,596 rs80813652 G 0.311 1.02 (0.177) 0.12 2.14 × 10−8 1.55 × 10−5 h LOC102158165
   11 53,204,914 rs330963199 G 0.253 −1.00 (0.191) 0.10 3.32 × 10−7 1.31 × 10−2 LOC102167198
  TVN 7 101,863,838 rs80966250 G 0.349 −0.35 (0.059) 0.13 9.93 × 10−9 4.44 × 10−16 H LOC102164420_LOC102164550
   7 103,457,401 VRTN C 0.368 0.67 (0.046) 0.50 9.42 × 10−37 4.44 × 10−16 H VRTN
   7 106,308,596 rs80813652 G 0.311 0.44 (0.056) 0.20 5.17 × 10−14 2.67 × 10−9 H LOC102158165
  BSFT 18 7,107,781 rs81345146 A 0.361 −0.19 (0.037) 0.10 4.37 × 10−7 7.80 × 10−4 ZYX
  LSFT 9 46,466,374 rs81257576 A 0.017 0.65 (0.129) 0.07 7.36 × 10−7 4.41 × 10−1 ZBTB16_NNMT
  LEA at 45r 9 124,098,143 rs81415869 G 0.023 3.98 (0.746) 0.10 1.94 × 10−7 8.35 × 10−1 LOC102162561_LOC100524389
Fat area of carcass cross section at 4–5 rib
  IFAat 45r 8 25,653,506 rs81398418 A 0.279 7.15 (1.380) 0.09 4.18 × 10−7 1.14 × 10−4 LOC100624133_LOC102162593
Fat area of carcass cross section at the middle
  SFA at HBL 7 41,720,015 rs80928067 G 0.030 −16.52 (3.219) 0.11 5.35 × 10−7 5.11 × 10−1 LOC100737927
  ALLFA at HBL 7 41,720,015 rs80928067 G 0.030 −30.43 (5.433) 0.13 5.09 × 10−8 5.41 × 10−1 LOC100737927
  1. aAbbreviations of trait are shown in Table 2
  2. b SSC Sus Scrofa chromosome
  3. cPosition for genome build 10.2
  4. d EA effect allele, EAF effect allele frequency
  5. eThe proportion of phenotypic variance explained by the SNP effects
  6. fThe results of haplotype-based association study are indicated by h = suggestive, H = significant difference
  7. gNearby genes are bolded if SNP is within the reference gene