About the existence of common determinants of gene expression in the porcine liver and skeletal muscle

González-Prendes, Rayner; Mármol-Sánchez, Emilio; Quintanilla, Raquel; Castelló, Anna; Zidi, Ali; Ramayo-Caldas, Yuliaxis; Cardoso, Tainã Figueiredo; Manunza, Arianna; Cánovas, Ángela; Amills, Marcel

doi:10.1186/s12864-019-5889-5

BMC Genomics

Table 1 List of the genome-wide significant cis-eQTLs detected in the gluteus medius (GM) muscle (those that have been consistently detected in the liver are shown in bold)¹

From: About the existence of common determinants of gene expression in the porcine liver and skeletal muscle

Muscle cis-eQTL										Gene
SSC	N	SNP	Region (Mb)	P-value	q-value	B	δ ± SE	A₁	MAF	Acronym	Region (Mb)
1	51	ASGA0000817	0.2–9.9	6.69E-08	2.12E-04	1.91E-03	−0.37 ± 0.06	A	0.388	ARID1B	9.7–10.2
1	15	ALGA0002427	32.2–36.6	2.74E-11	5.90E-07	7.80E-07	0.58 ± 0.06	A	0.365	AKAP7	32.2–32.3
1	10	INRA0003613	101.9–108.9	3.29E-12	2.00E-08	9.00E-08	−0.29 ± 0.03	C	0.433	WDR7	106.0–106.4
1	2	MARC0039560	125.9–128.7	5.67E-06	3.24E-02	1.62E-01	−0.16 ± 0.03	G	0.481	HYPK	127.7–127.7
1	5	DIAS0000210	183.3–183.9	5.36E-07	7.63E-03	1.53E-02	0.28 ± 0.05	C	0.466	CNIH1	183.8–183.8
1	9	ASGA0006202	231.0–239.7	3.49E-11	8.10E-07	9.90E-07	0.50 ± 0.07	A	0.115	GRHPR	238.1–238.1
1	18	M1GA0001375	240.2–249.6	1.92E-13	1.00E-08	1.00E-08	0.27 ± 0.03	A	0.399	ALG2	240.9–240.9
1	1	H3GA0004649	260.9–260.9	2.36E-06	3.24E-02	6.73E-02	−0.36 ± 0.07	A	0.17	PSMD5	260.8–260.8
2	1	ALGA0011482	5.8–5.8	1.47E-06	4.20E-02	4.20E-02	0.28 ± 0.06	A	0.144	*CTSF*	5.8–5.8
2	22	MARC0095742	32.5–39.3	4.52E-10	4.30E-06	1.29E-05	−0.53 ± 0.08	A	0.354	HTATIP2	39.0–39.0
2	24	ALGA0013197	33.0–39.3	1.24E-14	0.00E+ 00	0.00E+ 00	−0.52 ± 0.06	A	0.25	PRMT3	38.8–39.0
2	4	ALGA0115180	115.1–116.1	9.98E-09	2.36E-04	2.84E-04	0.37 ± 0.06	A	0.141	WDR36	115.8–115.9
2	8	DIAS0000550	140.2–145.0	1.54E-06	1.97E-02	4.40E-02	−0.31 ± 0.05	G	0.466	ETF1	140.4–140.5
2	15	H3GA0055810	147.1–148.7	2.30E-08	6.56E-04	6.56E-04	−0.30 ± 0.05	G	0.16	LARS	147.4–147.5
3	1	MARC0045458	3.6–3.6	3.41E-08	9.72E-04	9.72E-04	0.26 ± 0.04	G	0.223	AP5Z1	3.6–3.6
3	2	MARC0020406	4.1–4.2	4.17E-08	7.28E-04	1.19E-03	−0.68 ± 0.12	A	0.121	ZNF12	4.4–4.4
3	14	ALGA0017913	18.6–19.8	1.33E-09	1.78E-05	3.78E-05	0.30 ± 0.05	G	0.125	NSMCE1	19.6–19.6
3	2	DRGA0003838	29.6–29.6	5.05E-07	7.81E-03	1.44E-02	−0.37 ± 0.06	A	0.37	MKL2	28.9–29.2
3	26	MARC0101576	30.0–34.4	5.74E-09	1.64E-04	1.64E-04	−0.22 ± 0.04	G	0.345	RSL1D1	31.2–31.2
3	17	MARC0000159	48.6–54.6	2.77E-06	9.87E-03	7.89E-02	−0.27 ± 0.06	G	0.194	MRPS9	49.6–49.6
3	18	MARC0049447	93.7–97.2	3.90E-07	2.78E-03	1.11E-02	0.29 ± 0.05	A	0.272	THADA	96.8–97.1
3	7	M1GA0026608	126.9–127.8	4.55E-09	6.48E-05	1.30E-04	0.58 ± 0.10	A	0.178	CYS1	126.3–126.4
4	6	ASGA0018519	14.3–15.8	3.76E-06	3.03E-02	1.07E-01	−0.21 ± 0.04	C	0.393	NDUFB9	15.1–15.1
4	2	ASGA0018539	14.6–14.6	9.98E-09	2.84E-04	2.84E-04	0.19 ± 0.03	G	0.322	WASHC5	14.5–14.6
4	6	ALGA0024302	30.2–31.5	2.51E-06	9.62E-03	7.15E-02	−0.40 ± 0.07	G	0.433	OXR1	30.7–31.2
4	11	DIAS0000176	95.2–99.8	2.07E-07	1.97E-03	5.91E-03	0.33 ± 0.06	A	0.252	*APH1A*	98.8–98.8
4	4	M1GA0006152	95.3–96.1	3.55E-07	1.01E-02	1.01E-02	−0.23 ± 0.04	G	0.341	S100A13	96.0–96.0
5	4	ASGA0104541	20.3–23.5	1.61E-06	1.57E-02	4.59E-02	0.17 ± 0.03	A	0.325	TSPAN31	23.0–23.0
5	12	SIRI0000318	25.6–29.4	2.96E-07	2.11E-03	8.43E-03	−0.53 ± 0.10	A	0.306	TMEM5	28.2–28.2
5	24	MARC0113779	80.3–84.7	2.66E-10	7.10E-07	7.58E-06	−0.39 ± 0.06	A	0.136	C12orf73	80.5–80.5
6	25	ASGA0098408	17.0–21.7	1.11E-08	1.40E-04	3.16E-04	0.49 ± 0.08	G	0.24	*ARL2BP*	19.2–19.2
6	28	DIAS0004785	45.5–55.4	4.23E-06	1.72E-02	1.21E-01	−0.15 ± 0.03	A	0.471	RABAC1	49.9–49.9
6	13	ASGA0094600	70.1–71.6	8.61E-07	7.64E-03	2.45E-02	−0.33 ± 0.06	G	0.296	*LZIC*	70.2–70.2
6	17	MARC0031169	70.1–71.6	3.65E-06	1.16E-02	1.04E-01	−0.19 ± 0.03	G	0.279	DFFA	70.7–70.7
6	36	ASGA0028827	81.9–89.9	5.30E-12	1.00E-08	1.50E-07	−0.39 ± 0.05	G	0.238	*BSDC1*	88.8–88.8
6	52	MARC0015713	90.6–99.9	2.96E-08	4.21E-04	8.43E-04	−0.20 ± 0.03	A	0.379	AFG3L2	97.2–97.2
6	2	ALGA0122704	95.9–99.4	3.18E-06	6.66E-03	9.05E-02	0.37 ± 0.08	A	0.327	RAB12	99.2–99.2
6	6	ALGA0037549	157.5–158.8	2.07E-08	5.89E-04	5.89E-04	0.29 ± 0.05	A	0.262	MRPL37	158.0–158.1
6	1	ASGA0030033	158.6–158.6	5.27E-06	2.15E-02	1.50E-01	−0.22 ± 0.05	G	0.359	*YIPF1*	158.4–158.4
7	19	ASGA0035147	86.3–89.1	1.55E-12	4.00E-08	4.00E-08	0.41 ± 0.05	A	0.5	MTHFD1	88.4–88.5
7	21	ALGA0043682	92.1–99.8	7.12E-09	2.03E-04	2.03E-04	−0.26 ± 0.04	G	0.333	DCAF5	92.7–92.8
8	11	ALGA0112294	10.6–17.6	1.63E-09	6.63E-06	4.64E-05	−0.25 ± 0.04	C	0.399	*TAPT1*	11.3–11.4
8	6	ALGA0049334	117.4–118.2	9.95E-09	8.85E-05	2.84E-04	−0.29 ± 0.05	A	0.335	BDH2	117.9–117.9
9	37	ASGA0042057	20.2–24.2	2.61E-10	7.44E-06	7.44E-06	0.56 ± 0.08	G	0.49	CTSC	21.7–21.7
9	9	ASGA0043022	40.3–47.6	8.95E-11	2.55E-06	2.55E-06	−0.28 ± 0.03	A	0.165	ARHGEF12	47.4–47.6
10	4	ASGA0046443	10.0–14.1	1.10E-16	0.00E+ 00	0.00E+ 00	−0.92 ± 0.09	G	0.228	*MARC2*	10.1–10.1
10	11	ASGA0048312	51.7–58.7	5.83E-08	1.66E-03	1.66E-03	−0.33 ± 0.04	A	0.409	COMMD3	52.5–52.6
10	2	ALGA0059373	54.1–54.4	4.39E-08	6.26E-04	1.25E-03	0.33 ± 0.06	G	0.298	PLXDC2	54.2–54.6
11	3	DIAS0002284	20.7–21.0	3.50E-08	9.98E-04	9.98E-04	−0.21 ± 0.04	A	0.296	ESD	20.6–20.6
12	4	ALGA0115312	4.2–4.8	4.24E-07	1.21E-02	1.21E-02	−0.20 ± 0.04	G	0.296	ST6GALNAC2	4.9–4.9
12	3	DRGA0011563	4.2–4.8	3.95E-06	3.75E-02	1.13E-01	−0.42 ± 0.07	A	0.17	EXOC7	5.3–5.3
12	3	ALGA0064915	10.9–11.6	1.19E-06	1.70E-02	3.39E-02	−0.40 ± 0.08	G	0.291	ABCA5	11.0–11.1
12	16	MARC0016809	20.3–24.8	3.26E-12	9.00E-08	9.00E-08	0.49 ± 0.06	G	0.272	*PNPO*	24.1–24.2
12	2	DIAS0000973	23.5–23.6	1.52E-06	2.34E-02	4.33E-02	0.24 ± 0.04	C	0.257	MRPL10	24.0–24.0
12	8	DIAS0000242	40.0–48.8	3.14E-06	2.01E-02	8.96E-02	0.25 ± 0.05	G	0.433	TMEM98	42.0–42.1
12	6	ASGA0054801	44.3–46.5	1.28E-06	2.18E-02	3.66E-02	0.20 ± 0.04	G	0.481	*TMEM97*	44.6–44.6
12	7	ALGA0066917	50.5–59.3	4.57E-11	4.50E-07	1.30E-06	0.37 ± 0.05	G	0.335	*RABEP1*	51.6–51.8
12	1	ALGA0120796	51.9–51.9	2.27E-07	6.46E-03	6.46E-03	−0.13 ± 0.02	C	0.412	PSMB6	52.0–52.0
12	7	MARC0002558	59.0–59.9	3.63E-10	1.03E-05	1.03E-05	0.41 ± 0.05	A	0.35	ALDH3A2	59.9–59.9
13	2	ALGA0067450	2.5–2.7	7.69E-07	2.19E-02	2.19E-02	0.34 ± 0.06	A	0.306	SH3BP5	2.5–2.5
13	9	ASGA0086643	12.4–14.4	1.64E-12	1.00E-08	5.00E-08	0.52 ± 0.06	A	0.422	NGLY1	12.6–12.6
13	5	ALGA0068741	19.4–23.1	1.67E-06	2.38E-02	4.77E-02	−0.16 ± 0.03	G	0.269	PDCD6IP	19.5–19.6
13	5	MARC0000523	31.1–32.5	3.32E-11	9.50E-07	9.50E-07	−0.35 ± 0.05	A	0.155	MAPKAPK3	33.0–33.1
14	12	H3GA0038597	6.1–7.2	6.65E-13	2.00E-08	2.00E-08	−0.23 ± 0.03	A	0.383	*POLR3D*	6.5–6.5
14	1	SIRI0001291	22.7–22.7	4.88E-08	1.39E-03	1.39E-03	−0.20 ± 0.03	G	0.291	PGAM5	22.7–22.7
14	8	MARC0094155	40.6–43.2	4.74E-10	5.71E-06	1.35E-05	−0.44 ± 0.06	G	0.212	ACADS	40.6–40.6
14	5	ASGA0065742	102.7–106.9	3.84E-08	5.48E-04	1.10E-03	−0.34 ± 0.06	A	0.147	IDE	103.9–104.1
14	4	MARC0043866	110.5–111.0	2.01E-06	2.86E-02	5.72E-02	0.30 ± 0.05	A	0.49	COX15	110.8–110.8
14	11	ALGA0081813	124.1–125.1	1.19E-08	1.70E-04	3.39E-04	0.44 ± 0.07	G	0.277	CASP7	124.0–124.0
15	11	ASGA0069526	42.2–49.0	7.12E-13	0.00E+ 00	2.00E-08	1.33 ± 0.16	G	0.067	SORBS2	46.5–46.9
15	54	ALGA0085678	54.5–69.7	4.49E-08	1.28E-03	1.28E-03	−0.36 ± 0.06	G	0.112	UGGT1	59.1–59.2
15	9	ASGA0070490	116.4–118.5	1.07E-10	3.05E-06	3.05E-06	0.35 ± 0.05	A	0.471	XRCC5	118.3–118.4
16	1	ALGA0090252	34.2–34.2	1.21E-06	3.45E-02	3.45E-02	−0.24 ± 0.04	C	0.485	SLC38A9	34.7–34.8
16	6	MARC0049616	72.0–73.1	7.13E-08	1.46E-03	2.03E-03	−0.32 ± 0.05	A	0.288	CCT5	72.2–72.2
17	2	ALGA0096195	57.0–57.1	9.93E-08	1.42E-03	2.83E-03	−0.36 ± 0.05	A	0.223	FAM210B	56.9–56.9
18	5	ALGA0097540	24.4–25.8	1.38E-07	3.94E-03	3.94E-03	0.44 ± 0.08	A	0.142	FAM3C	25.5–25.6

¹SSC: porcine chromosome, N: Number of SNPs significantly associated with the trait under study, SNP: SNP displaying the most significant association with the trait under study, Region (Mb): region containing SNPs significantly associated with the trait under study, P-value: nominal P-value, q-value: q-value calculated with a false discovery rate approach, B: Bonferroni corrected P-values, δ: allelic effect and its standard error (SE), A₁: minority allele, MAF: frequency of the minority allele

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