Analysis of consequences of non-synonymous SNP in feed conversion ratio associated TGF-β receptor type 3 gene in chicken

• Investigated functional nsSNP p.Val451Leu (rs312979494) in feed conversion ratio (FCR) associated TGFBR3 of chicken
• Computational tools (SIFT and I-Mutant 2.0) predicted that this nsSNP was deleterious.
• Mutant structure of TGFBR3 showed high energies and RMS deviations compared to native using MD simulation.
• Molecular docking of TGFBR3 with interacting protein TGFBR2 showed an increase in global energy of mutant compared to native.
• We have predicted that functional SNP has an impact on TGFBR3 of chicken and thus can be treated as candidate SNP in screening.

The recent advances in high throughput sequencing technology accelerate possible ways for the study of genome wide variation in several organisms and associated consequences. In the present study, mutations in TGFBR3 showing significant association with FCR trait in chicken during exome sequencing were further analyzed. Out of four SNPs, one nsSNP p.Val451Leu was found in the coding region of TGFBR3. In silico tools such as SnpSift and PANTHER predicted it as deleterious (0.04) and to be tolerated, respectively, while I-Mutant revealed that protein stability decreased. The TGFBR3 I-TASSER model has a C-score of 0.85, which was validated using PROCHECK. Based on MD simulation, mutant protein structure deviated from native with RMSD 0.08 Å due to change in the H-bonding distances of mutant residue. The docking of TGFBR3 with interacting TGFBR2 inferred that mutant required more global energy. Therefore, the present study will provide useful information about functional SNPs that have an impact on FCR traits.