Homology modeling of single nuleotide polymorphisms in candidate genes controlling embryonic growth of buffalo

Pregnancy involves interactions of numerous growth factors, proteins and hormones exerting their biological functions in cellular growth, migration, differentiation and signal transduction. FGF2, STAT5A and UTMP are important mediators of intra-cellular signals transduction and transcription functions during pregnancy. Mutations in these genes will eventually disrupt their biological functions leading to embryonic death. The present study was designed to analyze in silico the SNPs in buffalo FGF2, STAT5A and UTMP genes by homology modeling. In the present study genomic DNA was isolated from the blood of 75 adult female buffaloes which was subsequently used for the amplification of FGF2, STAT5A and UTMP gene specific regions. PCR products of 167 bp, 429 bp and 279 bp were obtained for specific FGF2, STAT5A and UTMP gene regions, respectively. Sequenced PCR products showed 96–97% similarity with bovine sequences on BLAST analysis for all the 3 gene segments. Sequence analysis showed 9, 3 and 9 distinct nucleotide differences in the regions of FGF2, STAT5A, UTMP genes, respectively. Furthermore, based on the nucleotide difference 3 variants for FGF2 and UTMP genes were deduced in comparison with the bovine sequence. Promotor region analysis of FGF2 and homology modeling of STAT5A and UTMP gene revealed modification in the protein structure arising due to the presence of nucleotide changes. In the present study single nucleotide polymorphism were deduced in FGF2, STAT5A and UTMP gene region of buffalo and homology modeling of the studied gene portions were carried out.