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 2 Top lead 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
SNP6: rs336055186	4	91,591,493	0.38	MCHC	Blood 3	0.04	1.15	91,291,800	1.08 ± 0.02^j	−2.13 ± 0.02
SNP7^h: 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
SNP8^h: 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
SNP9^h: 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
SNP9^h: rs323125939					Blood 4	0.04	0.40	59,053,639	−0.09 ± 0.07	0.25 ± 0.05

^aThe most significant SNP with a group of supportive SNPs
^bSus scrofa chromosome
^cMinor allele frequency
^dMCHC mean corpuscular hemoglobin concentration, MCH mean corpuscular hemoglobin, MCV mean corpuscular volume, RBC red blood cell concentration, MPV mean platelet volume
^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
^fThe largest percentage of additive genetic variance explained by the top lead 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