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

Table 1 Top significant SNPs identified by univariate SSGWAS for significant associations with white blood cell traits at a genome-wise false discovery rate (FDR) of 0.05

Trait^a	Blood^b	SNP ID	SNP status^c	SSC^d	SNP position (bp)	MAF^e	FDR	GVar (%)^f	1-Mb window start SNP position^g (bp)	Dominance effect ± standard error	Additive effect^h ± standard error
EOS	Blood 3	SNP1: rs336560074	Top lead	4	93,647,202	0.31	0.006	0.46	93,331,316	0.001 ± 0.01	−0.05 ± 0.01ⁱ
EOS	Blood 3	SNP2: rs346258273	Top lead	10	8,186,695	0.08	0.03	0.35	7,396,201	−0.09 ± 0.04	0.14 ± 0.04
EOS	Blood 3	SNP3: rs339860061	Top lead	12	36,308,994	0.13	0.003	0.53	35,450,868	0.002 ± 0.02	−0.06 ± 0.01
MONO	Δ13	SNP4: rs321357560	Top floating	2	120,341,201	0.47	0.049	0.12	120,219,793	−0.03 ± 0.02	0.08 ± 0.02
MONO	Δ13	SNP5: rs327963623	Top lead	9	105,461,701	0.43	0.049	1.23	105,461,701	−0.02 ± 0.02	−0.08 ± 0.02

^aEOS eosinophil concentration, MONO monocyte concentration
^bBlood 3: the CBC measures in Blood 3 collected at 2-weeks after the challenge; Δ13: the change of CBC measures from Blood 1 collected at 2-weeks before the challenge to Blood 3 collected at 2-weeks after a polymicrobial infectious challenge
^cTop lead: the most significant SNP with a group of supportive SNPs; Top floating: the most significant SNP without a group of supportive SNPs
^dSus scrofa chromosome
^eMinor allele frequency
^fThe largest percentage of additive genetic variance explained by the top significant SNP and its adjacent SNPs in a 1 Mb window
^gPositions of the start SNP for the 1 Mb window segment with the largest amount of additive genetic variance
^hEstimates 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
ⁱSignificant estimates of additive and dominance effects are highlighted in bold (p < 0.05)

ISSN: 1471-2164