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. 2020 Jan 13;21:38. doi: 10.1186/s12864-019-6273-1

Table 5.

Five topmost significantly enriched biological functions for carcass merit traits, and genes involved in the specific function

Traita Biological Function Genes Involved in the biological function
HCW Gene expression (23) BMP7, BTRC, CTCFL, DTX1, HIF3A, IRF9, KAT7, KDM8, LGALS1, MAPK1, MRAS, MS4A15, NFIA, NR5A1, PARD3, PCTP, PEG10, PPARGC1A, RNF4, RXRB, SIAH1, TADA3, TFCP2L1
Carbohydrate metabolism (26) AGMO, ALPI, BID, BMP7, CMAS, CYP2J2, FCGR2B, GRPR, KDM8, LGALS1, MAPK1, MRAS, NGFR, PARD3, PCTP, PDK2, PIGP, PIK3CB, PLA2G2A, PLEKHA3, PPARGC1A, PRKCB, PTHLH, ST8SIA1, UGT2B17, VDAC1
Nucleic acid metabolism (18) ADCY4, ATP5PF, BMP7, CFTR, CMAS, GART, GNAI1, GRPR, MAPK1, NUDT9, OLA1, PDK2, PPARGC1A, PRKCB, PTHLH, SLC25A5, ST8SIA1, VDAC1
Small molecule biochemistry (54)

ACSL6, AGMO, AKR1C3, AKR1C4, ALPI, ANGPTL4, ATP5PF, BID, BMP7, CFTR, CLEC11A, CMAS, CNTFR, CYP2J2, DHRS4, ELOVL4, ERLIN1, FCGR2B, GBA3, GNAI1, GRPR, INHA, KCNE2, KCNE1B, LGALS1, MAPK1, MOGAT2, MRAS, NGFR, NR5A1, P2RY13, PARD3, PCCB, PCSK2, PCTP, PDK2, PIGP, PIK3CB, PLA2G2A, PLEKHA3, PPARGC1A, PPARGC1B, PRKCB, PTHLH, RXRB, SLC22A6, ST8SIA1

TFCP2L1, TGM1, TTR, UGT2B11, UGT2B17, UPK2, VDAC1
Molecular transport (45) ACSL6, AGMO, ALPI, ANGPTL4, ATP10A, ATP6V1E1, ATP6V1G1, BID, BMP7, CA4, CCS, CFTR, CLEC11A, CLIC4, CNTFR, COQ7, FCGR2B, GNAI1, GRPR, HBA1/HBA2, INHA, KCNE2, KCNE1B, KCNK2, LGALS1, MAPK1, MOGAT2, MRAS, NGFR, NR5A1, P2RY13, PCTP, PDK2, PIK3CB, PLA2G2A, PPARGC1A, PPARGC1B, PRKCB, PTHLH, SLC20A2, SLC22A6, ST8SIA1, TTR, UPK2, VDAC1
AFAT Carbohydrate metabolism (22) AGMO, BID, BMP7, CMAS, GRPR, KDM8, LGALS1, MAPK1, MRAS, NGFR, PARD3, PDK2, PIK3CB, PLA2G2A, PPARGC1A, PPARGC1B, PTHLH, ST8SIA1, UGT2B17
Nucleic acid metabolism (10) BID, BMP7, CMAS, GART, GNAI1, GRPR, MAPK1, PDK2, ST8SIA1, UGT2B17
Small molecule biochemistry (36) ACSL6, AGMO, BID, BMP7, CFTR, CLEC11A, CMAS, CNTFR, DHRS4, ERLIN1, GART, GBA3, GNAI1, GRPR, KDM8, LGALS1, MAPK1, MOGAT2, MRAS, NGFR, NR5A1, P2RY13, PARD3, PDK2, PIGP, PIK3CB, PLA2G2A, PLEKHA3, PPARGC1A, PPARGC1B, PTHLH, SLC22A6, ST8SIA1, TFCP2L1, TGM1, UGT2B17
Lipid metabolism (31) ACSL6, AGMO, BID, BMP7, CFTR, CLEC11A, CNTFR, DHRS4, ERLIN1, GBA3, GNAI1, LGALS1, MAPK1, MOGAT2, MRAS, NGFR, NR5A1, P2RY13, PARD3, PDK2, PIGP, PIK3CB, PLA2G2A, PLEKHA3, PPARGC1A, PPARGC1B, PTHLH, ST8SIA1, TFCP2L1, TGM1, UGT2B17
Cell morphology (25) BID, BMP7, BTRC, CFTR, CLEC11A, CLIC4, CNTFR, FSCN1, GDF3, KCNK2, LGALS1, MAPK1, MRAS, NDUFAB1, NGFR, NR5A1, PCSK2, PLA2G2A, PLXNB2, PPARGC1A, PPARGC1B, PTHLH, SERPINA3, ST8SIA1, UPK2
REA Cell morphology (71) BID, CAMP, CCND1, CD4, CERS5, CFTR, CHL1, CLEC11A, CLIC4, CNTFR, CSTB, CUL3, DVL1, EPO, FGL1, GDF3, GSDMD, HAND1, HAUS4, HELLS, INHA, INTU, KCNK2, KIF11, KIFC1, LGALS1, LIF, LIMK2, MAPK1, MAPT, NDUFAB1, NEFH, NFIA, NGFR, NTRK2, OSMR, P2RY12, PALLD, PCTP, PEG10, PLXNB2, PPARGC1A, PPARGC1B, PTHLH, PTPN1, RNF4, SCYL1, SERPINA3, UCP1, UPK2
Cellular assembly and organization (58) AMPH, ARHGAP32, ARPC4, ATG4B, ATG4C, ATL1, BID, CAMP, CBLB, CCND1, CD4, CFTR, CLEC11A, CLIC4, CLTB, CSTB, CTDNEP1, DRP2, DVL1, EPO, EXO5, HAND1, IDE, KCNK2, KIF11, KIF13B, KIFC1, KLHDC8B, LANCL1, LGALS1, LIF, MAPT, NDUFAB1, NDUFS2, NEFH, NFIA, NGFR, NLGN1, NR5A1, NTRK2, OLA1, P2RY12, PALLD, PARD3, PLXNB2, POLG, PPARGC1A, PPARGC1B, REPS2, SERPINA3, SLC25A5, SNX9, SRCIN1, TP53INP1, TRAK2, TTR, UCP1, VDAC1
Cellular function and maintenance (51) ARHGAP32, ARMC4, ATL1, BID, CAMP, CCDC103, CCDC39, CCND1, CD4, CELSR2, CLEC11A, CLIC4, COQ7, CSTB, DVL1, EPO, FCGR2B, HAND1, IDE, IFNA2, KCNK2, KIF11, KIF13B, KIFC1, LANCL1, LGALS1, LIF, MAPT, NDUFAB1, NDUFS2, NEFH, NFIA, NGFR, NLGN1, NMNAT3, NTRK2, PARD3, PLXNB2, POLG, PPARGC1A, PPARGC1B, SCYL1, SERPINA3, SS18, ST8SIA1, TCF7L1, TFCP2L1, TP53INP1, TRAK2, UCP1, VDAC1
Lipid metabolism (77) ABHD3, ACSL6, AGMO, AKR1C3, AKR1C4, AKR1C1/AKR1C2, ALPI, ANGPTL4, ANGPTL6, ATP5PF, BID, BMP7, C3AR1, CAMP, CD4, CERS5, CFTR, CLDN16, CLEC11A, CNTFR, CTDNEP1, CYP2C18, CYP2J2, CYP7B1, DEGS2, DHRS4, ELOVL4, EPO, ERLIN1, FCGR2B, FGL1, GBA3, GNAI1, GPC3, IL1RN, INHA, KCNE1B, KIF13B, KLF15, LGALS1, LIF, MAPK1, MAPT, MOGAT2, MRAS, NGFR, NONO, NR5A1, NTRK2, OSMR, P2RY12, P2RY13, PARD3, PCTP, PDK2, PIGP, PIK3CB, PLA2G2A, PLEKHA3, POLG, PPARGC1A, PPARGC1B, PRKCB, PTHLH, PTPN1, RENBP, RGS2, RXRB, SERPINE2, ST8SIA1, TFCP2L1, TRHR, TTR, UCP1, UGT2B4, UGT2B11, UGT2B17
Molecular transport (105) ACSL6, AGMO, AKR1C4, AKR1C1/AKR1C2, ALPI, ANGPTL4, ANGPTL6, AOC3, APPBP2, ATP10A, ATP6V1E1, ATP6V1G1, BID, BMP7, C3AR1, CA4, CAMP, CBLB, CCS, CD4, CERS5, CFTR, CLDN16, CLEC11A, CLIC4, CNTFR, COQ7, CTDNEP1, DIO3, DUOXA2, DVL1, ELOVL4, EPO, FCGR2B, FGL1, GCNT4, GNAI1, GPC3, GRPR, HBA1/HBA2, IL1RN, INHA, IP6K1, KCNAB1, KCNE2, KCNE1B, KCNK2, KDM8, KIF13A, KIF13B, KLF15, LGALS1, LIF, MAPK1, MAPT, MOGAT2, MRAS, NDC1, NGFR, NONO, NR5A1, NTRK2, OGG1, OSMR, P2RY12, P2RY13, PCSK2, PCTP, PDK2, PIK3CB, PKN1, PLA2G2A, POLG, PPARGC1A, PPARGC1B, PRKCB, PTGER1, PTHLH, PTPN1, RENBP, RXRB, SCN9A, SLC16A4, SLC20A2, SLC22A6, SLC37A2, SLC39A7, SLC6A7, SLC8B1, SMG6, SNX9, SRCIN1, ST8SIA1, STRADA, STRADB, SVBP, SYNDIG1, TMED2, TP53INP1, TRAK2, TRHR, TTR, UCP1, VDAC1, ZFP36L1
LMY Gene expression (23) BMP7, BTRC, CTCFL, DTX1, HIF3A, IRF9, KAT7, KDM8, LGALS1, MAPK1, MRAS, MS4A15, NFIA, NR5A1, PARD3, PCTP, PEG10, PPARGC1A, RNF4, RXRB, SIAH1, TADA3, TFCP2L1
Lipid metabolism (47) ACSL6, AGMO, AKR1C3, AKR1C4, ALPI, ANGPTL4, ATP5PF, BID, BMP7, CFTR, CLEC11A, CNTFR, CYP2J2, DHRS4, ELOVL4, ERLIN1, FCGR2B, GBA3, GNAI1, INHA, KCNE1B, LGALS1, LIF, MAPK1, MOGAT2, MRAS, NGFR, NR5A1, P2RY13, PARD3, PCCB, PCTP, PDK2, PIGP, PIK3CB, PLA2G2A, PLEKHA3, PPARGC1A, PPARGC1B, PRKCB, PTHLH, RXRB, ST8SIA1, TFCP2L1, TTR, UGT2B11, UGT2B17
Small molecule biochemistry (55) ACSL6, AGMO, AKR1C3, AKR1C4, ALPI, ANGPTL4, ATP5PF, BID, BMP7, CFTR, CLEC11A, CMAS, CNTFR, CYP2J2, DHRS4, ELOVL4, ERLIN1, FCGR2B, GBA3, GNAI1, GRPR, INHA, KCNE1B, KCNE2, LGALS1, LIF, MAPK1, MOGAT2, MRAS, NGFR, NR5A1, P2RY13, PARD3, PCCB, PCSK2, PCTP, PDK2, PIGP, PIK3CB, PLA2G2A, PLEKHA3, PPARGC1A, PPARGC1B, PRKCB, PTHLH, RXRB, SLC22A6, ST8SIA1, TFCP2L1, TGM1, TTR, UGT2B11, UGT2B17, UPK2, VDAC1
Vitamin and mineral metabolism (17) AKR1C3, AKR1C4, BMP7, CFTR, CYP2J2, DHRS4, INHA, LIF, NR5A1, P2RY13, PCTP, PPARGC1A, ST8SIA1, TTR, UGT2B11, UGT2B17, VDAC1
Carbohydrate metabolism (26) AGMO, ALPI, BID, BMP7, CMAS, CYP2J2, FCGR2B, GRPR, KDM8, LGALS1, MAPK1, MRAS, NGFR, PARD3, PCTP, PDK2, PIGP, PIK3CB, PLA2G2A, PLEKHA3, PPARGC1A, PRKCB, PTHLH, ST8SIA1, UGT2B17, VDAC1
CMAR Carbohydrate Metabolism (23) AGMO, BID, BMP7, CMAS, GNAI1, GRPR, KDM8, LGALS1, MAPK1, MRAS, NGFR, PARD3, PCTP, PDK2, PIGP, PIK3CB, PLA2G2A, PLEKHA3, PPARGC1A, PPARGC1B, PTHLH, ST8SIA1, UGT2B17
Nucleic acid metabolism (10) BID, BMP7, CMAS, GART, GNAI1, GRPR, MAPK1, PDK2, ST8SIA1, UGT2B17
Small molecule biochemistry (40) ACSL6, AGMO, AKR1C3, AKR1C4, BID, BMP7, CFTR, CLEC11A, CMAS, CNTFR, DHRS4, ERLIN1, GART, GBA3, GNAI1, GRPR, KDM8, LGALS1, MAPK1, MOGAT2, MRAS, NGFR, NR5A1, P2RY13, PARD3, PCSK2, PCTP, PDK2, PIGP, PIK3CB, PLA2G2A, PLEKHA3, PPARGC1A, PPARGC1B, PTHLH, SLC22A6, ST8SIA1, TFCP2L1, TGM1, UGT2B17
Cellular development (24) AKR1C3, B9D1, BID, BMP7, CBLB, CLEC11A, CLIC4, FSCN1, ITGA11, ITIH4, KCNK2, LGALS1, MAPK1, MRAS, NASP, NGFR, NR5A1, PIK3CB, PPARGC1A, PTHLH, TGM1, UGT2B17, UPK2, ZFP36L1
Lipid metabolism (33) ACSL6, AGMO, AKR1C3, AKR1C4, BID, BMP7, CFTR, CLEC11A, CNTFR, DHRS4, ERLIN1, GBA3, GNAI1, LGALS1, MAPK1, MOGAT2, MRAS, NGFR, NR5A1, P2RY13, PARD3, PCTP, PDK2, PIGP, PIK3CB, PLA2G2A, PLEKHA3, PPARGC1A, PPARGC1B, PTHLH, ST8SIA1, TFCP2L1, UGT2B17

aHCW hot carcass weight in kg, AFAT average backfat thickness in mm, REA rib eye area in cm2, LMY lean meat yield in %, CMAR carcass marbling score from 100 (trace marbling) to 499 (more marbling)