Skip to main content

Table 2 Top lead SNPsa identified by univariate and multivariate SSGWAS for significant associations with red blood cell and platelet traits at a genome-wise false discovery rate (FDR) of 0.05

From: Investigating the genetic architecture of disease resilience in pigs by genome-wide association studies of complete blood count traits collected from a natural disease challenge model

SNP ID SSCb SNP position (bp) MAFc Traitd Bloode FDR GVar (%)f 1-Mb window start SNPg position (bp) Dominance effect
± standard error
Additive effecti ± standard error
SNP6: rs336055186 4 91,591,493 0.38 MCHC Blood 3 0.04 1.15 91,291,800 1.08 ± 0.02j −2.13 ± 0.02
SNP7h: rs325274805 6 28,511,423 0.41 MCH Blood 1 0.04 0.29 28,110,554 0.10 ± 0.07 −0.25 ± 0.06
    MCV Blood 1 0.001 0.57 28,110,554 0.29 ± 0.07 −0.73 ± 0.06
     Blood 3 0.002 0.49 28,096,004 0.05 ± 0.04 −0.45 ± 0.04
     Blood 4 0.002 0.48 28,096,004 −0.12 ± 0.04 −0.53 ± 0.04
    RBC Blood 1 0.01 0.44 28,110,554 −0.02 ± 0.07 0.08 ± 0.06
     Blood 3 0.01 0.44 28,110,554 0.001 ± 0.04 0.08 ± 0.04
     Blood 4 0.03 0.40 28,110,554 −0.04 ± 0.05 0.06 ± 0.04
SNP8h: rs344612650 8 41,156,538 0.45 MCH Blood 1 0.01 0.36 40,257,441 0.15 ± 0.06 0.20 ± 0.05
     Blood 3 0.04 0.36 40,257,441 0.11 ± 0.04 0.16 ± 0.04
     Blood 4 0.04 0.35 40,257,441 −0.006 ± 0.04 0.18 ± 0.04
    MCV Blood 1 0.03 0.33 40,219,864 0.35 ± 0.06 0.59 ± 0.05
     Blood 3 0.006 0.27 40,219,864 0.19 ± 0.04 0.38 ± 0.04
     Blood 4 0.002 0.33 40,219,864 0.04 ± 0.04 0.51 ± 0.04
    RBC Blood 1 0.007 0.31 40,219,864 0.01 ± 0.06 −0.08 ± 0.05
     Blood 3 0.02 0.31 40,219,864 −0.02 ± 0.04 −0.06 ± 0.04
     Blood 4 0.03 0.30 40,219,864 0.01 ± 0.04 −0.06 ± 0.04
SNP9h: rs323125939 17 59,739,745 0.34 MPV Blood 1 0.02 0.49 59,053,639 0.002 ± 0.10 0.28 ± 0.08
     Blood 4 0.04 0.40 59,053,639 −0.09 ± 0.07 0.25 ± 0.05
  1. aThe most significant SNP with a group of supportive SNPs
  2. bSus scrofa chromosome
  3. cMinor allele frequency
  4. dMCHC mean corpuscular hemoglobin concentration, MCH mean corpuscular hemoglobin, MCV mean corpuscular volume, RBC red blood cell concentration, MPV mean platelet volume
  5. eBlood 1, Blood 3, and Blood 4: CBC measures in blood samples collected at 2-weeks before, and 2- and 6-weeks after a polymicrobial infectious challenge
  6. fThe largest percentage of additive genetic variance explained by the top lead SNP and its adjacent SNPs in a 1 Mb window
  7. gPositions of the start SNP for the 1 Mb window segment with the largest amount of additive genetic variance
  8. hSNPs identified and results estimated by multivariate SSGWAS
  9. iEstimates of additive effects per additional copy of the “B” allele. When the dominance effect was not significant (p > 0.05) the estimate of the additive effect was based on a model without the dominance effect
  10. jSignificant estimates of additive and dominance effects are highlighted in bold (p < 0.05)