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 3 Top floating SNPs^a 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

SNP ID	SSC^b	SNP Position (bp)	MAF^c	Trait^d	Blood^e	FDR	GVar (%)^f	1-Mb window start SNP^g position (bp)	Dominance effect ± standard error	Additive effectⁱ ± standard error
SNP10^h: rs319452131	1	18,792,764	0.37	MCV	Blood 1	0.003	0.18	18,536,535	−0.16 ± 0.18	0.52 ± 0.14^j
					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
SNP11^h: 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
SNP12^h: 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
SNP14^h: 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

^aThe most significant SNP without a group of supportive SNPs
^bSus scrofa chromosome
^cMinor allele frequency
^dMCV mean corpuscular volume, PLT platelet concentration, MCH mean corpuscular hemoglobin, MCHC mean corpuscular hemoglobin concentration
^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
^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
^hSNPs identified and results estimated by multivariate SSGWAS
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
^jSignificant estimates of additive and dominance effects are highlighted in bold (p < 0.05)

ISSN: 1471-2164