Meta-analysis across Nellore cattle populations identifies common metabolic mechanisms that regulate feed efficiency-related traits

Mota, Lucio F. M.; Santos, Samuel W. B.; Júnior, Gerardo A. Fernandes; Bresolin, Tiago; Mercadante, Maria E. Z.; Silva, Josineudson A. V.; Cyrillo, Joslaine N. S. G.; Monteiro, Fábio M.; Carvalheiro, Roberto; Albuquerque, Lucia G.

doi:10.1186/s12864-022-08671-w

Table 2 Genes surrounding the significant genomic regions (-log₁₀(p -value) > 5) identified using the multi-trait meta-analysis statistical test of genome-wide association (GWAS) results for Feed efficiency-related traits (FE, FCR, RFI, and its components ADG, DMI), in IZ and Qualitas populations

From: Meta-analysis across Nellore cattle populations identifies common metabolic mechanisms that regulate feed efficiency-related traits

BTA	Windows (Mb)^a	IZ population Traits^b	Qualitas population Traits^b	Genes
1	94.55—95.90	ADG, DMI, FE, RFI	ADG, DMI, FCR, RFI	ECT2, NCEH1, TNFSF10, GHSR, FNDC3B, TMEM212, PLD1, STXBP5L, POLQ, SPATA16
2	104.14—105.06	ADG, DMI, FCR, FE, RFI	ADG, DMI, FCR, FE, RFI	XRCC5, MARCH4, SMARCAL1, RPL37A, IGFBP2, IGFBP5, TRNAS-GGA, TNP1
3	78.99—80.84	DMI, FE	ADG, DMI	PDE4B, MGC137454, LEPR, LEPROT, DNAJC6, AK4, JAK1, bta-mir-101–1, RAVER2, CACHD1
4	70.88—71.85	ADG, DMI, FCR, FE, RFI	FCR, FE	OSBPL3, GSDME, MPP6, NPY
5	65.95—67.03	FCR, RFI	FE	NUP37, PARPBP, PMCH, IGF1, PAH, ASCL1, U1
7	15.60—16.54	ADG, DMI, FCR, FE, RFI	ADG, FCR, FE	KANK2, ACP5, ANGPTL8, ARHGEF18, CAMSAP3, CCDC151, CCDC159, CNN1, DOCK6, ECSIT, ELAVL3, ELOF1, EPOR, FCER2, INSR, MBD3L3, MCOLN1, PCP2, PET100, PEX11G, PLPPR2, PNPLA6, PRKCSH, RAB3D, RETN, RGL3, STXBP2, SWSAP1, TEX45, TMEM205, TRAPPC5, TSPAN16, U4, VN2R404P, XAB2, ZNF358, ZNF557, ZNF653
8	66.71—67.82	ADG	DMI, RFI	LPL, SLC18A1, ATP6V1B2, LZTS1
11	73.89—74.76	ADG, DMI, FCR, FE, RFI	DMI, FCR, RFI	DTNB, DNMT3A, bta-mir-1301, POMC, EFR3B, DNAJC27, ADCY3, CENPO, PTRHD1, NCOA1
14	22.62—24.71	ADG, DMI, FCR, FE, RFI	ADG, DMI, FCR, FE, RFI	FAM110B, LYN, XKR4, TMEM68, RPS20, TMEM68, TGS1, TRNAT-AGU, U1, LYN, MOS, PLAG1, CHCHD7, SDR16C5, SDR16C6, PENK, U6, IMPAD1, FAM110B, UBXN2B, CYP7A1
15	56.22—56.63	ADG	ADG	ACER3, B3GNT6, CAPN5, OMP, MYO7A
18	35.00—35.79	FE	DMI, RFI	CTCF, CARMIL2, ACD, PARD6A, ENKD1, GFOD2, RANBP10, TSNAXIP1, CENPT, THAP11, NUTF2, EDC4, NRN1L, PSKH1, PSMB10, LCAT, SLC12A4, DPEP3, DPEP2, DDX28, DUS2, NFATC3, ESRP2, PLA2G15, SLC7A6, SLC7A6OS, PRMT7, SMPD3, TPPP3, ZDHHC1, HSD11B2, ATP6V0D1, AGRP, RIPOR1, CTCF, C18H16orf86
18	49.66—50.93	DMI, RFI	ADG, FCR, FE, RFI	ITPKC, SNRPA, MIA, RAB4B, bta-mir-12057, EGLN2, CYP2F1, CYP2B6, CYP2S1, AXL, HNRNPUL1, TGFB1, B9D2, TMEM91, EXOSC5, BCKDHA, B3GNT8, DMAC2, ERICH4, CEACAM1, LIPE, PLD3, HIPK4, PRX, SERTAD1, SERTAD3, BLVRB, SPTBN4, SHKBP1, LTBP4, NUMBL, COQ8B, CCDC97, C18H19orf47, C18H19orf54
21	7.62—8.15	ADG, DMI, FE, RFI	DMI, RFI	IGF1R, PGPEP1L
29	48.75—50.42	FCR, RFI	ADG, FCR, FE	KCNQ1, TRPM5, TSSC4, CD81, TSPAN32, ASCL2, TH, INS, IGF2, MRPL23, TNNT3, LSP1, TNNI2, SYT8, CTSD, IFITM10, DUSP8, MOB2, TOLLIP, AP2A2

^a The windows region represents the lower and maximum position for SNP markers deemed significantly (\(-{log}_{10}(p-value)\) > 5) from the multi-trait statistic test combination
^b Trait in which the genomic regions was significant using a multi-trait weighted genome-wide association studies (GWAS)

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