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Table 5 Five topmost significantly enriched biological functions for RFI and its component traits, and genes involved in the specific function

From: Genetic architecture of quantitative traits in beef cattle revealed by genome wide association studies of imputed whole genome sequence variants: I: feed efficiency and component traits

Traita

Biological Function

Genes Involved in the biological function

RFI

1-Cell Morphology

AMPH, ARHGAP32, ATL1, BID, C3AR1, CAMP, CCND1, CD4, CFTR, CHL1, CLEC11A, CLIC4, CNTFR, CSTB, CTHRC1, CUL3, DVL1, EPO, FGL1, GDF3, GSDMD, HAND1, HAUS4, HELLS, IFNA2, INHA, INTU, KCNE2, KCNK2, KIF11, KIF13B, KIFC1, LGALS1, LIF, LIMK2, MAPK1, MAPT, MMP20,NDUFAB1,NEFHNFIA, NGFR, NMNAT3, NTRK2, OSMR, P2RY12, PALLD, PARD3, PARD6B, PCTP, PEG10, PKP1, PLXNB2, POLG, PPARGC1A, PPARGC1B, PTHLH, PTPN1, RIPK1, RNF4, RXRB, SCYL1, SERPINA3, SERPINE2, SGCE, TRAK2, UCP1UPK2, VDAC1

2-Cellular Assembly and Organization

ADNP, ATG4B, ATG4C, BID, CAMP, CBLB, CCND1, CD4, CHL1, CLEC11A, CLIC4, CTHRC1, ENC1, EXO5, FSCN1, HAND1, IDE, KCNK2, KIF11, KIFC1, KLHDC8B, LANCL1, LGALS1, MAPT, NDUFAB1, NDUFS2, NEFH, NGFR, NLGN1, NR5A1, NTRK2, OLA1, P2RY12, PARD3, POLG, PPARGC1A, PPARGC1B, SERPINA3, SLC25A5, SRCIN1, SS18, SSNA1, TP53INP1, TTR, UCP1, VDAC1

3-Cellurar Function and Maintenance

LANCL1, ST8SIA1, PARD3, ATL1, PPARGC1A, CCDC103, PARD6B, CD4, SS18, RIPK1, CELSR2, CLEC11A, UCP1, COQ7, CTHRC1, LIF, SERPINA3, NFIA, NDUFAB1, CCDC39, EPO, CHL1, CCND1, BID, KCNK2, VDAC1, LGALS1, TP53INP1, TCF7L1, CAMP, KIF11, KIF13B, P2RY12, NLGN1, PPARGC1B, POLG, PLXNB2, ARMC4, CLIC4, MAPT, NTRK2, IFNA2, FSCN1, TRAK2, DVL1, NMNAT3, HAND1, NEFH, NDUFS2, IDE, FCGR2B, NGFR, ARHGAP32, KIFC1, TFCP2L1

4-Lipid Metabolism

ABHD3, ACSL6, AGMO, AKR1C3, AKR1C4, AKR1C1/AKR1C2, ALPI, ANGPTL4, ANGPTL6, ATP5PF, BID, BMP7, CAMP, CD4, CERS5, CFTR, CLDN16, CLEC11A, CNTFR, CTDNEP1, CYP2C18, CYP2J2, CYP7B1, DEGS2, DHRS4, ELOVL4, ERLIN1, FCGR2B, FGL1, GNAI1, GPC3, IL1RN, INHA, KCNE1B, KIF13B, LGALS1, LIF, MAPK1, MOGAT2, MRAS, NGFR, NR5A1, NTRK2, P2RY12, P2RY13, PARD3, PCTP, PDK2, PIGP, PIK3CB, PLA2G2A, PLEKHA3, PLVAP, POLG, PPARGC1A, PPARGC1B, PRKCB, PTHLH, PTPN1, RGS2, SERPINE2, ST8SIA1, TFCP2L1, TRHR, TTR, UCP1, UGT2B4, UGT2B11, UGT2B17

5-Molecular Transport

GPC3, ST8SIA1, KLF15, MRAS, INHA, PIK3CB, ANGPTL4, CLDN16, PPARGC1A, IL1RN, PDK2, P2RY13, PRKCB, FGL1, CD4, CA4, CTDNEP1, PCSK2, CLEC11A, UCP1, MOGAT2, DIO3, LIF, DUOXA2, SLC37A2, ANGPTL6, PTPN1, HBA1/HBA2, CFTR, BID, PLA2G2A, TTR, GNAI1, KCNE2, VDAC1, ALPI, LGALS1, PKN1, TRHR, CAMP, TP53INP1, KIF13B, PPARGC1B, POLG, CLIC4, NTRK2, NR5A1, BMP7, GCNT4, SLC22A6, PTGER1, KCNE1B, SLC20A2, PCTP, FCGR2B, AGMO, PLVAP, NGFR, IP6K1, MAPK1, AOC3, GRPR, PTHLH

DMI

1-Cabohydrate Metabolism

GNAI1, ST8SIA1, VDAC1, ALPI, PARD3, LGALS1, MRAS, KDM8, PIK3CB, PIGP, PPARGC1A, PLEKHA3, PPARGC1B, PDK2, PRKCB, BMP7, UGT2B17, CYP2J2, PCTP, CMAS, NGFR, AGMO, MAPK1, GRPR, BID, PTHLH, PLA2G2A

2-Nucleoc Acid Metabolism

GNAI1, ST8SIA1, VDAC1, NUDT9, ATP5PF, PPARGC1A, GART, CMAS, PDK2, PRKCB, MAPK1, CBLB, GRPR, CFTR, BID, OLA1, PTHLH, BMP7

3- Small molecule Biochemistry

ST8SIA1, PARD3, MRAS, INHA, PIK3CB, DHRS4, PIGP, C3AR1, ACSL6, PPARGC1A, PDK2, P2RY13, PRKCB, CBLB, PCSK2, CLEC11A, MOGAT2, TGM1,CYP2J2, AKR1C4, AKR1C3, CFTR, BID, PLA2G2A, GNAI1, KCNE2, VDAC1, ALPI, LGALS1, NUDT9, ERLIN1, ATP5PF, CNTFR, STC2, PLEKHA3, PPARGC1B, NR5A1, BMP7, GBA3, UPK2, UGT2B17, SLC22A6, KCNE1B, ATP6V1G1, PCTP, CMAS, AGMO, NGFR, MAPK1, GRPR, PTHLH, TFCP2L1

4-Cellular Development

KCNK2, ITIH4, LGALS1, NASP, UGT2B17, ITGA11, KCNE1B, INHA, NFIA, PIK3CB, C3AR1, KR1C3, PPARGC1A, NGFR, MAPK1, CLIC4, BID, PTHLH, NR5A1, TFCP2L1, BMP7, FSCN1

5-Lipid metabolism

GNAI1, ST8SIA1, ALPI, PARD3, LGALS1, MRAS, ERLIN1, ATP5PF, INHA, CNTFR, PIK3CB, DHRS4, PIGP, C3AR1, ACSL6, PPARGC1A, PLEKHA3, PPARGC1B, PDK2, P2RY13, PRKCB, NR5A1, BMP7, GBA3, CLEC11A, MOGAT2, UGT2B17, CYP2J2, KCNE1B, AKR1C4, PCTP, AKR1C3, AGMO, NGFR, MAPK1, CFTR, BID, PTHLH, TFCP2L1, PLA2G2A

ADG

1-Cabohydrate Metabolism

ST8SIA1, PARD3, LGALS1, UGT2B17, MRAS, KDM8, PIK3CB, PIGP, PPARGC1A, CMAS, PLEKHA3, NGFR, PPARGC1B, PDK2, MAPK1, GRPR, BID, PTHLH, BMP7, PLA2G2A

2-Nucleoc Acid Metabolism

ST8SIA1, CMAS, UGT2B17, PDK2, MAPK1, GRPR, CFTR, BID, BMP7

3-Small molecule Biochemistry

ST8SIA1, PARD3, LGALS1, MRAS, ERLIN1, CNTFR, KDM8, PIK3CB, DHRS4, PIGP, ACSL6, PPARGC1A, PLEKHA3, PPARGC1B, PDK2, P2RY13, NR5A1, BMP7, GBA3, CLEC11A, MOGAT2, TGM1, UGT2B17, SLC22A6, CMAS, NGFR, MAPK1, GRPR, CFTR, BID, PTHLH, PLA2G2A, TFCP2L1

4-Lipid Metabolism

ST8SIA1, PARD3, LGALS1, MRAS, ERLIN1, CNTFR, PIK3CB, DHRS4, PIGP, ACSL6, PPARGC1A, PLEKHA3, PPARGC1B, PDK2, P2RY13, NR5A1, BMP7, GBA3, CLEC11A, MOGAT2, UGT2B17, TGM1, NGFR, MAPK1, CFTR, BID, PTHLH, TFCP2L1, PLA2G2A

5-Cell to cell Signal and interaction

PARD3, LGALS1, MAPK1, CLIC4, GRPR, CNTFR, CFTR, PTHLH, BMP7

MWT

1-Cellular Compromise

LANCL1, HPSE, SERPINE2, LIF, CAMP, SIAH1, SCYL1, EPO, NEFH, GCH1, PPARGC1A, PPARGC1B, MAPT, NTRK2, CFTR, PSMC6, BID, PTHLH

2-Lipid Metabolism

GPC3, UGT2B11, ST8SIA1, CYP7B1, PARD3, INHA, PIK3CB, DHRS4, PIGP, ACSL6, PPARGC1A, IL1RN, P2RY13, PRKCB, RGS2, CTDNEP1, DEGS2, CLEC11A, MOGAT2, UCP1, CYP2J2, LIF, AKR1C4, ELOVL4, AKR1C3, CFTR, BID, PLA2G2A, TTR, GNAI1, ALPI, LGALS1, TRHR, SERPINE2, ERLIN1, ATP5PF, CAMP, CNTFR, P2RY12, CYP2C18, PLEKHA3, PPARGC1B, POLG, NR5A1, BMP7, GBA3, UGT2B4, CERS5, UGT2B17, HAND1, PCTP, FCGR2B, AGMO, NGFR, MAPK1, ABHD3, TFCP2L1

3-Molecular Transport

GPC3, HCRTR1, INHA, PIK3CB, ACSL6, PPARGC1A, IL1RN, PDK2, PRKCB, CA4, PCSK2, CLEC11A, UCP1, COQ7, MOGAT2, DIO3, LIF, DUOXA2, SLC37A2, EPO, HBA1/HBA2, CFTR, PLA2G2A, TTR, GNAI1, KCNE2, VDAC1, LGALS1, PKN1, TRHR, CAMP, TP53INP1, P2RY12, PPARGC1B, POLG, OSCP1, CLIC4, NTRK2, NR5A1, BMP7, GCNT4, UPK2, SLC22A6, PTGER1, SLC20A2, SIAH1, NGFR, MAPK1, AOC3, GRPR, PTHLH

4-Small Molecule Biochemistry

GPC3, HCRTR1, UGT2B11, ST8SIA1, CYP7B1, PARD3, INHA, PIK3CB, DHRS4, PIGP, ACSL6, PPARGC1A, IL1RN, PDK2, P2RY13, ADPRHL2, PRKCB, RGS2, CTDNEP1, PCSK2, DEGS2, CLEC11A, MOGAT2, UCP1, DIO3, CYP2J2, LIF, DUOXA2, AKR1C4, ELOVL4, AKR1C3, EPO, CFTR, BID, PLA2G2A, TTR, GNAI1, KCNE2, ALPI, LGALS1, NUDT9, TRHR, SERPINE2, ERLIN1, ATP5PF, CAMP, CNTFR, TP53INP1, P2RY12, CYP2C18, PLEKHA3, PPARGC1B, POLG, OSCP1, NTRK2, NR5A1, BMP7, GBA3, GCNT4, UGT2B4, CERS5, RENBP, UGT2B17, PTGER1, SIAH1, HAND1, PCTP, FCGR2B, CMAS, AGMO, NGFR, DPYD, MAPK1, ABHD3, GRPR, PTHLH, TFCP2L1

5-Cell Morphology

PARD3, GDF3, AMPH, INHA, C3AR1, SCYL1, PALLD, PPARGC1A, CLEC11A, PEG10, UCP1, CSTB, LIF, SERPINA3, NFIA, NDUFAB1, OSMR, EPO, CHL1, CFTR, BID, KCNE2, KCNK2, INTU, VDAC1, LGALS1, SERPINE2, CNTFR, CAMP, P2RY12, PPARGC1B, POLG, PLXNB2, CLIC4, NTRK2, MAPT, CUL3, IFNA2, GSDMD, CERS5, UPK2, PKP1, RXRB, SGCE, NMNAT3, HAND1, PCTP, NEFH, NGFR, MMP20, MAPK1, PTHLH

  1. a RFI residual feed intake in kg of DMI per day, DMI daily dry matter intake in kg per day, ADG average daily gain in kg, MWT metabolic body weight in kg