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Genes obtained after transcriptome-wide association study mapped to QTL regions related to percentage of fiber types I, IIA, and IIB I fiber type SSC QTL ID SCRN2 12 2819 2821 UTP18 2819 2821 TOM1L1 2819 2821 WRAP53 2819 2821 FASTKD1 15 2832 HNRNPA3 2832 IIA fiber type SSC QTL ID SLF1 2 2797 CAST 2797 ANAPC7 14 7018 PPTC7 7018 AP1B1 7018 MTR 7018 ARV1 7018 RAB4A 7018 SUPV3L1 7018 FAM45A 2827 TACC2 2827 PAF1 2827 IIB fiber type SSC QTL ID RGP1 1 2795 IKBKAP 2795 TTL 3 7037 UXS1 7037 IL1R1 7037 MAP4K4 7037 NAGK 7037 PCYOX1 7037 EFEMP1 7037 MTIF2 7037 FEZ2 7037 CRIM1 7037 HDGF 4 2807 2810 PAQR6 2807 2810 RFX5 2807 2810 ANAPC7 14 7038 PPTC7 7038 AP1B1 7038 MTR 7038 ARV1 7038 RAB4A 7038 SUPV3L1 7038 FAM45A 2828 TACC2 2828 PAF1 2828 QTL, quantitative trait loci; SSC, chromosome 2.
Genes included are: trafficking protein particle complex 8 (TRAPPC8) for HMC and apolipoprotein B antigen (APOB), ataxia telangiectasia mutated (ATM), coiled-coil domain containing 88A (CCDC88A; transcript variant 1), complement factor H (CFH), collagen, type XXVIII, alpha 1 (COL28A1), glycoprotein IX (GP9 [platelet]), ligase IV (LIG4, DNA, ATP-dependent), melanoma inhibitory activity family, member 3 (MIA3), microtubule associated monooxygenase, calponin and LIM domain containing 2 (MICAL2), RE1silencing transcription factor (REST), small nuclear RNA activating complex, polypeptide 1 (SNAPC1, 43 kDa; transcript variant 1), TNF receptor-associated factor 1 (TRAF1), UTP18 small subunit processome component homolog (UTP18 [yeast]), and LOC428119 (uncharacterized protein) for LMC.
Molecules, such as APOB, ATM, MIA3, MICAL2, REST, TRAF1, UTP18, TRAPPC8, CCDC88A, and SNAPC1 in the network were shown to bind directly to UBC (ubiquitin C) by proteomic analyses of ubiquitylated proteomes [12-15], suggesting that the various cellular functions including protein degradation by ubiquitylation may play a role for the expression of muscle color in chickens though the specific roles of each factor in regulating muscle color development need further investigations.