Genome-wide association and transcriptome studies identify candidate genes and pathways for feed conversion ratio in pigs

Table 2 Summary of identified pathways, DEGs and genes with significant SNPs

SNP ID	Candidate Gene	Pathway			Differentially expressed genes
SNP ID	Candidate Gene	Pathway name	P-Value	FDR	Differentially expressed genes
rs80811321	GRIP1	GABAergic synapse	1.1E-6	2.4E-5	GNG13,ADCY1,GABRB2, ADCY8, ADCY7,GABRD,GABRE,GABRQ,GABBR2,GAD2,HAP1,PRKCG
rs80811321	GRIP1	Glutamatergic synapse	4.0E-7	1.3E-5	GNG13,DLGAP1,SHANK3, ADCY1,ADCY8,ADCY7,GRM4, HOMER2,KCNJ3,PRKCG,SLC17A6,SLC17A7
rs339913443	TPH2	Serotonergic synapse	1.6E-3	1.2E-2	ALOX5,GABRB2,KCNN2,KCND2,KCNJ3,PTGS1,PRKCG
rs339913443	TPH2	Oxytocin signaling pathway	1.2E-4	1.6E-3	ADCY1,ADCY8,ADCY7,CACNG5,CAMK4,CAMKK2,CDKN1A,NPR1,OXT,KCNJ3,PRKCG,CACNB4,
rs80811321 rs332237334 rs81344478 rs323754097	GRIP1 FRS2 FRS2 TRHDE CNOT2	Thyroid hormone synthesis	1.8E-2	8.0E-2	ADCY1,ADCY8,ADCY7,GPX3,PRKCG,TSHR,
		Thyroid hormone signaling pathway	3.4E-1	6.7E-1	TRH,PIK3CG,PLCD4,PRKCG,
		Autoimmune thyroid disease	8.1E-1	8.2E-1	SLA-DMB,SLA-DMA

*CNOT2: There were no significant SNP located within the gene, but there were significant SNPs located in the upstream and downstream of the gene

ISSN: 1471-2164