RNA-seq of muscle from pigs divergent in feed efficiency and product quality identifies differences in immune response, growth, and macronutrient and connective tissue metabolism

Horodyska, Justyna; Wimmers, Klaus; Reyer, Henry; Trakooljul, Nares; Mullen, Anne Maria; Lawlor, Peadar G.; Hamill, Ruth M.

doi:10.1186/s12864-018-5175-y

Table 5 Correlations between product quality traits and selected differentially expressed genes, out of the 272, in pigs divergent for feed efficiency.

From: RNA-seq of muscle from pigs divergent in feed efficiency and product quality identifies differences in immune response, growth, and macronutrient and connective tissue metabolism

Gene	pH 45m	pH 24h	DL	WBSF D1	WBSF D7	CL D1	CL D7	Fat depth	Muscle depth	Lean	IMF	SFA	MUFA	PUFA
CCR2	0	-0.51	0.44	0.01	0.16	0.2	0.06	0.01	-0.08	0.01	-0.38	-0.26	-0.22	-0.37
CCR2	0.99	0.04	0.09	0.98	0.56	0.45	0.83	0.96	0.77	0.97	0.15	0.34	0.41	0.16
COL11A1	0.44	-0.45	-0.13	0.04	-0.46	0.25	0.24	-0.32	-0.42	0.14	-0.03	0	-0.02	0.14
COL11A1	0.09	0.08	0.64	0.88	0.07	0.36	0.38	0.23	0.11	0.6	0.92	1	0.93	0.59
COL6A5	0.34	-0.46	0.27	0.24	0.31	0.42	0.21	-0.11	0.12	0.29	-0.22	-0.41	-0.43	-0.18
COL6A5	0.2	0.07	0.31	0.37	0.24	0.11	0.44	0.69	0.67	0.28	0.42	0.12	0.1	0.51
CXCL10	0.31	-0.25	0.22	-0.07	-0.13	0.37	-0.29	-0.34	0.04	0.36	-0.63	-0.61	-0.65	-0.46
CXCL10	0.24	0.35	0.41	0.8	0.64	0.16	0.27	0.19	0.88	0.16	0.01	0.01	0.01	0.07
CYBB	0.28	-0.4	0.3	-0.04	0.21	0.11	-0.04	-0.44	0.06	0.5	-0.59	-0.53	-0.54	-0.36
CYBB	0.29	0.13	0.26	0.89	0.44	0.7	0.89	0.09	0.82	0.04	0.02	0.04	0.03	0.16
FOXO1	-0.43	0.52	-0.2	0.02	0.08	-0.63	-0.35	0.54	0.16	-0.53	0.26	0.5	0.62	0.09
FOXO1	0.1	0.04	0.46	0.93	0.77	0.01	0.19	0.03	0.55	0.04	0.32	0.04	0.01	0.74
GM2A	0.39	-0.57	0.28	-0.14	-0.09	0.4	0.33	-0.41	-0.28	0.39	-0.33	-0.37	-0.43	-0.1
GM2A	0.14	0.02	0.29	0.61	0.73	0.12	0.22	0.12	0.29	0.14	0.22	0.16	0.1	0.71
HK3	0.09	-0.35	0.08	-0.23	-0.05	0.35	-0.31	-0.7	0.07	0.68	-0.54	-0.63	-0.74	-0.37
HK3	0.75	0.19	0.76	0.4	0.85	0.19	0.24	<0.01	0.81	<0.01	0.03	0.01	<0.01	0.16
LPCAT2	0.35	-0.34	-0.11	-0.01	-0.25	0.48	0.29	-0.35	-0.16	0.27	-0.22	-0.20	-0.27	0.09
LPCAT2	0.18	0.20	0.68	0.98	0.35	0.06	0.27	0.18	0.55	0.32	0.41	0.46	0.31	0.73
ETV1	0.31	-0.37	0.09	0.30	0.11	0.38	0.23	-0.33	-0.04	0.33	-0.36	-0.34	-0.38	-0.13
ETV1	0.25	0.16	0.75	0.26	0.68	0.14	0.40	0.21	0.90	0.22	0.16	0.19	0.15	0.63
NAAA	-0.11	-0.33	0.47	-0.05	0.36	0.05	-0.09	-0.14	0.03	0.18	-0.44	-0.38	-0.38	-0.33
NAAA	0.69	0.22	0.07	0.86	0.18	0.86	0.74	0.61	0.93	0.51	0.08	0.15	0.14	0.21
RAPGEF3	-0.33	0.24	-0.08	0.18	0.47	-0.49	-0.06	0.40	0.12	-0.40	0.42	0.57	0.60	0.15
RAPGEF3	0.21	0.36	0.76	0.50	0.07	0.05	0.83	0.13	0.66	0.12	0.10	0.02	0.01	0.59
ITGB2	0.36	-0.52	0.35	-0.09	0.1	0.41	0.06	-0.49	-0.14	0.53	-0.5	-0.54	-0.6	-0.37
ITGB2	0.17	0.04	0.18	0.75	0.71	0.12	0.84	0.04	0.6	0.04	0.04	0.03	0.01	0.15
LIPC	-0.04	-0.08	0.24	0	0.27	0.15	-0.05	-0.06	0.41	0.17	-0.24	-0.36	-0.44	-0.28
LIPC	0.87	0.78	0.38	0.99	0.32	0.59	0.85	0.82	0.12	0.52	0.37	0.16	0.09	0.29
MYC	0.01	0.46	-0.21	-0.23	0.09	-0.72	-0.14	0.1	0.25	-0.03	0.24	0.28	0.26	0.2
MYC	0.97	0.07	0.44	0.39	0.73	<0.01	0.6	0.7	0.36	0.92	0.38	0.29	0.32	0.47
NEU3	-0.24	-0.24	0.54	0.23	0.62	0.12	0.06	0.14	-0.11	-0.14	-0.06	-0.07	-0.06	-0.06
NEU3	0.38	0.38	0.03	0.39	0.01	0.65	0.84	0.62	0.69	0.61	0.84	0.8	0.81	0.82
NFATC1	-0.23	0.12	0.21	0.28	0.7	-0.49	-0.32	0.34	0.36	-0.24	0.14	0.21	0.25	-0.13
NFATC1	0.39	0.65	0.42	0.29	<0.01	0.06	0.23	0.19	0.17	0.36	0.61	0.43	0.36	0.63
NFATC2	-0.29	0.38	0.07	-0.12	0.35	-0.81	-0.27	0.57	0.35	-0.44	0.28	0.38	0.46	-0.08
NFATC2	0.28	0.15	0.8	0.66	0.18	<0.01	0.31	0.02	0.18	0.09	0.3	0.15	0.07	0.76
PDK4	-0.41	0.46	-0.59	0.14	-0.1	-0.27	-0.25	0.18	0.08	-0.25	0.33	0.48	0.51	0.26
PDK4	0.11	0.08	0.02	0.62	0.72	0.32	0.35	0.5	0.77	0.35	0.21	0.06	0.05	0.32
PIK3C2B	-0.02	-0.22	0.51	-0.09	0.16	0.13	0.27	0.22	-0.5	-0.4	0.06	0.19	0.21	0.18
PIK3C2B	0.95	0.42	0.04	0.73	0.55	0.63	0.31	0.41	0.05	0.13	0.84	0.47	0.44	0.5
PLIN1	0.18	0.3	-0.49	-0.26	-0.32	-0.22	0.34	-0.02	-0.17	-0.11	0.51	0.61	0.61	0.59
PLIN1	0.51	0.27	0.05	0.33	0.23	0.41	0.2	0.95	0.52	0.69	0.04	0.01	0.01	0.02
PON3	0.32	-0.3	-0.04	0.25	-0.14	0.56	0.62	-0.13	-0.31	0.07	-0.01	-0.06	-0.05	0.28
PON3	0.23	0.26	0.88	0.34	0.62	0.02	0.01	0.63	0.24	0.8	0.98	0.82	0.86	0.3
SDC4	-0.32	0.54	-0.19	-0.04	0.21	-0.5	-0.58	0.14	0.41	0	-0.05	0.02	0.07	-0.22
SDC4	0.23	0.03	0.49	0.87	0.44	0.05	0.02	0.59	0.11	1	0.85	0.93	0.8	0.41
SLC1A2	0.09	-0.53	0.29	0.35	0.2	0.51	-0.24	-0.52	-0.23	0.44	-0.61	-0.47	-0.53	-0.29
SLC1A2	0.76	0.04	0.29	0.21	0.48	0.05	0.38	0.05	0.41	0.1	0.02	0.08	0.04	0.29
TREH	0.23	-0.27	0.45	-0.28	0.15	0.05	0.33	-0.06	-0.23	0.01	-0.16	-0.18	-0.19	0.02
TREH	0.41	0.33	0.09	0.31	0.59	0.85	0.23	0.83	0.42	0.97	0.58	0.52	0.49	0.95

Correlation coefficient is presented in the upper row and a P-value is shown in the bottom row. Significant correlations are highlighted in bold. DL drip loss (%), WBSF D1 Warner Bratzler shear force day 1 pm (N), WBSF D7 Warner Bratzler shear force day 7 pm (N), CL D1 cook loss day 1 pm (%), CL D7 cook loss day 7 pm (%), Fat depth (mm), Muscle depth (mm), Lean (%), IMF intramuscular fat content (%), SFA saturated fatty acid (mg), MUFA monounsaturated fatty acid (mg), PUFA polyunsaturated fatty acid (mg)

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