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

Nurgulsim K. Khan R. Raza S.H.A. Ayari-Akkari A. Jeridi M. Ahmad I. Arain U.M. Abd El-Aziz A.H. Khan H. Zan L.
2023 Taylor and Francis Ltd.

Animal Biotechnology
2023 #34 Issue 6 1950 - 1959 pp.

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.

FGF10 gene , meat quality , promoter region , SNPs , transcription factors

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College of Animal Science and Technology, Northwest A&F University, Yangling, China
Faculty of Veterinary and Livestock Technology, S. Seifullin Kazakh Agro technical University, Nur-Sultan, Kazakhstan
Department of Livestock Management, Breeding and Genetic, The University of Agriculture, Peshawar, Pakistan
Biology Department, College of Sciences in Abha, King Khalid University, Abha, Saudi Arabia
Department of Poultry Husbandry, Sindh Agriculture University, Tandojam, Pakistan
Department of Animal Breeding and Production, Faculty of Veterinary Medicine, Damanhour University, Damanhur, Egypt
College of Veterinary Sciences, The University of Agriculture Peshawar, Peshawar, Pakistan

College of Animal Science and Technology
Faculty of Veterinary and Livestock Technology
Department of Livestock Management
Biology Department
Department of Poultry Husbandry
Department of Animal Breeding and Production
College of Veterinary Sciences

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