Bioinformatics and genetic variants analysis of FGF10 gene promoter with their association at carcass quality and body measurement traits in Qinchuan beef cattle.

The fibroblast growth factor 10 (FGF10) gene regulates adipogenesis and myogensis. In this study, sequencing of FGF10 prompter region identified three SNPs at loci g.78G > A, g.116C > T and g.201A > T. Each SNP yields three genotypes as GG, GA and AA at loci g.78G > A, CC, CT and TT at loci g.116C > T and AA, AT and TT at loci g.201A > T. Allelic and genotypic frequencies of all three SNPs deviated from the Hardy-Weinberg equilibrium (HWE) (P < 0.05) and were found highly polymorphic as PIC (0.25 < PIC < 0.50). Moreover, we found highest LD (D'/γ2) between SNP2 and SNP3 (0.989/0.909), followed by SNP1 and SNP3 (0.944/0.796). Moreover, three variants of FGF10 gene promoter exhibited significant (P < 0.05) association with body measurement and carcass quality traits in Qinchuan beef cattle. At loci g.78G > A, the genotype GG showed significantly (P < 0.01) larger body length (BL), rump length (RL), chest depth (CD), chest circumference (CC) and ultrasound loin area (ULA). The genotype TC at loci g.116C > T showed significantly (P < 0.01 and 0.05) larger body measurement and intramuscular fat, and ultrasound loin area (ULA). In addition to that, at loci g.201A > T, genotype TT showed significantly (P < 0.01 and P < 0.05) larger body length (BL), rump length (RL), hip width (HW), chest circumference (CC) and ultrasound loin area (ULA). Additionally, screening of promoter sequence of FGF10 gene explored loss of four TFs binding sites (KLF3, ZNF37α, GLIS2 and BCL11A) at g.116C > T because of SNP2. However, a single TF binding site was lost at g.202A > T due to SNP3. Interestingly, none of TF binding site was lost at g.78G > A in SNP1; however, one new TF binding site was gained at this location due to SNP1. These findings conclude that genotype GG, TC and TT could be used as genetic markers of FGF10 gene for body measurement and carcass quality traits in Qinchuan beef cattle.

Bioinformatics analysis and transcriptional regulation of TORC1 gene through transcription factors NRF1 and Smad3 in bovine preadipocytes.

Intramuscular fat is the an important factor that defines meat quality; however, enhancing its deposition without increasing the other three adipose depots (subcutaneous, visceral, and intermuscular fat) is a challenge for animal science and the meat industry. The TORC1 is a key regulator of adipogenesis and its regulation in bovine intramuscular preadipocytes has not been studied. The TORC1 is a member of the gene family that codes for a binding proteins which regulate transcription of cAMP which, is a key regulator of adipogenesis. In the present study, expression and sub-cellular localization of the TORC1 gene was analyzed in bovine preadipocytes. Bioinformatics tools were applied to characterize TORC1. To investigate the molecular mechanism of bovine TORC1 gene regulation, we cloned a 1008 bp of the 5'UTR regulatory region into a luciferase reporter vector. Different fragments were amplified using 5'UTR unidirectional deletion of the TORC1 promoter. Site directed mutation, dual luciferase reporter assay, RNAi interference and DNA-protein interaction (EMSA) were used to validate the regulatory roles of Smad3 and NRF1 in the regulation of TORC1 gene in bovine preadipocytes. The core promoter region of the TORC1 gene was identified at a location -410 to -155 bp upstream of transcription start site. Different vectors were constructed through serial deletion of the 5'UTR flanking region and in combination with site directed mutations and transcription interference through siRNA or shRNA, two transcription factors of NRF1 and Smad3 were found to be repressors in the promoter of the TORC1 gene. These findings were further confirmed through Electrophoretic Mobility Shift Assay (EMSA) within nuclear extracts of bovine adipocytes. The core promoter region of the TORC1 gene, spanning from -410 to -155 bp upstream of the transcription start site was specified in this study and this information will provide opportunity for the improvement of intramuscular fat in cattle.