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Table 3 Top floating 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
SNP10h: rs319452131 1 18,792,764 0.37 MCV Blood 1 0.003 0.18 18,536,535 −0.16 ± 0.18 0.52 ± 0.14j
     Blood 3 0.004 0.21 18,546,024 0.03 ± 0.13 0.52 ± 0.10
     Blood 4 0.02 0.15 18,536,535 −0.02 ± 0.14 0.37 ± 0.11
SNP11h: rs1109789977 5 64,520,638 0.31 PLT Blood 1 0.001 0.09 63,861,170 −3.80 ± 6.83 26.78 ± 5.18
     Blood 3 0.001 0.09 63,861,170 −9.28 ± 7.44 23.92 ± 5.39
     Blood 4 0.03 0.05 63,861,170 −10.57 ± 7.40 18.33 ± 5.46
SNP12h: rs320615395 9 40,919,049 0.45 MCH Blood 1 0.03 0.05 39,919,771 0.07 ± 0.08 0.21 ± 0.07
     Blood 3 0.04 0.07 40,490,005 −0.04 ± 0.05 0.19 ± 0.05
     Blood 4 0.04 0.06 40,490,005 0.03 ± 0.05 0.21 ± 0.05
SNP13: rs80784550 11 13,749,336 0.12 MCHC Δ14 0.02 0.07 13,011,748 1.89 ± 2.42 2.38 ± 2.33
SNP14h: rs323585109 12 22,234,265 0.3 MCV Blood 3 0.04 0.08 21,749,390 −0.06 ± 0.14 −0.40 ± 0.10
  1. aThe most significant SNP without a group of supportive SNPs
  2. bSus scrofa chromosome
  3. cMinor allele frequency
  4. dMCV mean corpuscular volume, PLT platelet concentration, MCH mean corpuscular hemoglobin, MCHC mean corpuscular hemoglobin concentration
  5. eBlood 1, Blood 3, and Blood4: CBC measured in blood samples collected at 2-weeks before, and 2- and 6-weeks after a polymicrobial infectious challenge; Δ14: the change of CBC measures from Blood 1 collected at 2-weeks before the challenge to Blood 4 collected at 6-weeks after the challenge
  6. fThe largest percentage of additive genetic variance explained by the top significant 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)
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BMC Genomics

ISSN: 1471-2164

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