Genome-wide association analyses for boar taint components and testicular traits revealed regions having pleiotropic effects

Table 3 Chromosome wide significant associations identified in subset B1 for boar taint and testes size parameters

Trait ¹	SNP	SSC ²	Pos ³	Mut ⁴	MAF ⁵	eEff (se) ⁶	Chi2	Emp. P-value ⁷	Var ⁸
lnAND	ALGA0039432	7	23184219	G/A	0.48	0.13 (0.03)	14.73	1.27E-05*	5.80%
lnAND	MARC0059955	7	24223914	G/A	0.37	0.13 (0.03)	14.40	1.59E-05*	5.68%
lnAND	MARC0097446	18	3346636	C/A	0.03	0.36 (0.10)	13.55	2.83E-05*	5.36%
lnAND	ASGA0104833	NA	NA	G/A	0.23	0.15 (0.04)	15.61	7.01E-06#	6.13%
lnAND	ASGA0094873	NA	NA	A/G	0.48	−0.12 (0.03)	15.29	8.64E-06#	6.02%
lnSKA	H3GA0000454	1	6764028	A/C	0.45	−0.20 (0.05)	18.66	1.45E-06**	7.24%
lnSKA	ASGA0048539	10	63586433	G/A	0.13	0.24 (0.06)	14.05	2.91E-05*	5.55%
lnSKA	ASGA0077381	17	54986042	G/A	0.06	0.37 (0.09)	16.10	7.61E-06**	6.31%
lnIND	H3GA0000454	1	6764028	A/C	0.45	−0.22 (0.05)	17.27	5.55E-06*	6.74%
lnIND	H3GA0012922	4	77217709	G/A	0.36	−0.20 (0.05)	16.44	9.30E-06*	6.44%
lnIND	ALGA0025735	4	77249057	G/C	0.36	−0.20 (0.05)	16.44	9.30E-06*	6.44%
width	ASGA0098931	18	56634280	A/G	0.02	−12.76 (2.95)	18.74	7.88E-06**	7.75%
GSI	ALGA0108818	12	49085493	G/A	0.13	0.0003 (0.0001)	15.83	2.04E-05*	7.54%

¹: androstenone, log-transformed (lnAND); skatole, log-transformed (lnSKA); indole, log-transformed (lnIND); testis length, width and weight (length, width and weight); gonadosomatic index (GSI); ²: sus scrofa chromosome (SSC); ³: position in Mb; ⁴: mutation (Mut); ⁵: minor allele frequency (MAF); ⁶: substitution effect and standard error (se), ⁷: empirical p-value and significant thresholds, Bonferroni corrected **p<0.01 chromosome-wide and *p<0.05 chromosome-wide significance level, #p<0.05 significance level of not annotated SNPs; ⁸: proportion of the explained variation (Var, %).

ISSN: 2730-6844