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

Kiran D Rasal; Tejas M Shah; Megha Vaidya; Subhash J Jakhesara; Chaitanya G Joshi

doi:10.1016/j.mgene.2015.03.006

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

Meta Gene. 2015 Apr 25:4:107-17. doi: 10.1016/j.mgene.2015.03.006. eCollection 2015 Jun.

Authors

Kiran D Rasal¹, Tejas M Shah², Megha Vaidya², Subhash J Jakhesara², Chaitanya G Joshi²

Affiliations

¹ Department of Fish Genetics Biotechnology, Central Institute of Freshwater Aquaculture, ICAR, Bhubaneswar, Odisha 751002, India.
² Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand 388 001, Gujarat, India.

Abstract

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.

Keywords: AASs, amino acid substitutions; Chicken; FCR, feed conversion ratio; Feed conversion ratio (FCR); I-TASSER, iterative threading assembly refinement; MD, molecular dynamics; Modeling; Non-synonymous SNP; PANTHER, protein analysis through evolutionary relationships; RMSD, root mean square deviation; RMSF, root mean square fluctuation; SIFT, sorting intolerant from tolerant; SNP, single nucleotide polymorphism; TGFB, transforming growth factor beta; TGFBR3; UTR, un-translated region; nsSNPs, non-synonymous single nucleotide polymorphisms.