Table 2.

Summary of significant KEGG pathways and combined pathways

		Number of pathways to pass			Combined pathways		Number of pathways to pass
		$H_{95}^2$	L R 95	Both	Number of SNPs	$H_{\mathit{\text{set}}}^2$		χ 2	FDR
Health traits
	Mastitis 1.1	20	20	18	8590	12.9		13	3
	Mastitis 1.2	10	18	9	7959	11.1		12	0
	Somatic Cell Score	11	8	8	2757	3.6		3	0
	Udder-health	17	22	16	11514	13.7		14	1
Production traits
	Fat yield	14	16	14	7639	19.7		11	8
	Milk yield	15	19	14	10695	11.2		10	8
	Protein yield	14	23	13	12076	9.8		19	5

The ‘Combined pathways’ combine all markers associated with pathways found significant for each trait into a single pathway. All seven ‘Combined pathways’ were found significant by both L R ₉₅ and $H_{95}^2$. $H_{\mathit{\text{set}}}^2$: Proportion of explained genomic variance. $H_{95}^2$ and L R ₉₅: Empirical cut-offs for $H_{\mathit{\text{set}}}^2$ and LR. FDR: Benjamini and Hochberg p-value adjustment