Table 1.

Significant genomic regions in the pig genome associated with the relative composition of genera and the candidate genes found within.

Region	Genus	Chr.a	Position in Mb Start - End	No. SNPsb	Most significant SNP	Effect (%)	p-value	FDR	Candidate genes
A1	Akkermansia	3	0.89–3.04	3	rs81335357; rs81246645	7.72	4.04 × 10−6	4.58 × 10−2	CARD11; CHST12
A2	Akkermansia	6	101.46–103.46	1	rs81390429	25.85	6.06 × 10−6	4.58 × 10−2	TGIF1
A3	Akkermansia	7	112.61–114.61	1	rs325604118	6.56	1.33 × 10−5	7.55 × 10−2	LGMN; CHGA
A4	Akkermansia	9	47.53–49.57	2	rs81410866; rs81410881	8.78	5.25 × 10−6	4.58 × 10−2	ssc-mir-125b-1; ssc-mir-100; SORL1
A5	Akkermansia	15	99.10–101.10	1	rs80982646	7.94	3.04 × 10−6	4.58 × 10−2	SLC39A10
B1	CF231	4	119.91–121.91	1	rs319005051	7.07	5.72 × 10−6	6.48 × 10−2
B2	CF231	X	112.48–114.50	3	rs329229283	6.34	4.10 × 10−6	6.48 × 10−2	FGF13; ATP11C
C1	Phascolarctobacterium	9	65.33–67.33	1	rs81223434	7.73	1.25 × 10−6	5.68 × 10−2	SLC45A3; RAB7B; RAB29; NUCKS1; IKBKE; MAPKAPK2
D1	Prevotella	8	3.81–5.81	1	rs326174858	10.88	7.79 × 10−7	3.53 × 10−2	CYTL1; WFS1; MAN2B2
E1	SMB53	10	18.51–22.05	5	rs344136854	14.25	4.92 × 10−9	1.68 × 10−4	CAPN8; CAPN2; SUSD4; DENND1B; PTPRC; ssc-mir-181b-1; ssc-mir-181a-1
E2	SMB53	10	53.89–55.89	1	rs341165563	8.87	3.15 × 10−5	7.14 × 10−2	MALRD1
E3	SMB53	11	28.22–33.50	14	rs80835110	10.42	1.37 × 10−6	1.47 × 10−2	PCDH17
F1	Streptococcus	9	23.45–25.66	3	rs319168851	6.15	3.11 × 10−5	9.41 × 10−2	FAT3
F2	Streptococcus	13	2.97–5.15	4	rs81310237	11.88	1.20 × 10−5	9.41 × 10−2	PLCL2; GALNT15; RFTN1
F3	Streptococcus	14	133.80–135.80	1	rs337448241	10.51	3.46 × 10−6	9.41 × 10−2	CTBP2; UROS
F4	Streptococcus	15	25.15–27.87	9	rs331341379	8.72	1.12 × 10−5	9.41 × 10−2	ERCC3; BIN1; MAP3K2
F5	Streptococcus	18	44.25–46.25	1	rs334064749	7.7	2.26 × 10−5	9.41 × 10−2	ssc-mir-196b-1

^aChromosome.

^bNumber of significant SNPs found in the region (FDR ≤ 0.1).