Genome-wide association study and accuracy of genomic prediction for teat number in Duroc pigs using genotyping-by-sequencing

Table 3 Chromosome regions with significant SNP effects on teat number

Chr	Region (Mb)	Size (Mb)	Most significant SNP				Contribution	Gene region
Chr	Region (Mb)	Size (Mb)	Name	MAF	p value	% of \({\text{h}}_{\upalpha}^{2}\)	% of \(\widehat{\text{R}}_{0}\)	Gene region
1	29.63–30.18	0.55	S1_29635241	0.499	2.68 (10⁻⁰⁷)	2.25	1.51	TNFAIP3, OLIG3
7	102.91–103.80	0.89	S7_102911357	0.438	2.49 (10⁻¹⁶)	7.35	6.98	PTGR2 (U), FAM161B, LIN52, VRTN (U, D), FCF1, AREL1 (16 genes)
7	116.07–117.43	1.36	S7_116899295	0.342	2.97 (10⁻⁰⁸)	3.07	2.13	GALC, KCNK10, SPATA7, PTPN21, ZC3H14, EML5, TTC8
11	56.56–58.58*	2.21	S11_58558301	0.422	7.14 (10⁻⁷)	1.64	2.27	SPRY2, SNORA70
11	77.75–79.69	1.94	S11_79009219	0.226	9.16 (10⁻¹⁰)	5.07	5.23	FGF14, BIVM (U, D), LOC102167592, LOC102167785 (U)
12	4.53–6.26*	1.73	S12_5615207	0.335	3.16 (10⁻⁰⁷)	2.59	2.63	MFSD11-KCTD2 (49 genes)
12	50.54–51.74	1.20	S12_51574540	0.138	1.06 (10⁻⁰⁷)	0.64	1.16	OR3A2, ASPA, TRPV3, TRPV1, CTNS, TAX1BP3, EMC6, CAMKK1

Chr = chromosome; MAF = minor allele frequency. \({\text{h}}_{\upalpha}^{2}\) is the additive heritability. \(\widehat{\text{R}}_{0}\) is the observed accuracy of prediction. U indicate the significant SNP is located upstream of the gene. D indicates the significant SNP is located downstream of the gene. Contribution was calculated for the six most significant SNPs in each region. * This region has three significant SNPs

ISSN: 1297-9686