Use of bioinformatics tools to study exon 2 of GDF9 gene in Tali and Beetal goats

Using molecular technology has resulted in discovering mutations with major effect on reproduction efficiency in sheep and goat. Most of these mutations have been found in BMP15, GDF9 and Booroola genes, for example, in GDF9, FecGH and FecTT have this effect. Due to the importance of prolificacy in goat, existence of mentioned and new mutations in GDF9 were investigated in both Beetal and Tali goats. A total of 50 and 60 blood samples were collected from Beetal and Tali goats, respectively. After DNA extraction, PCR reactions started for five PCR products (from individuals with different kidding records) from both Beetal and Tali goats were sequenced. Results from sequencing and phylogenic tree were analyzed by Vector NTI and MEGA4 software’s. 3-dimensional structures of GDF9 protein was evaluated by professional web site such as ps2. In Tali goats no nucleotide change has been found, but in Beetal goats with high kidding records a heterozygote mutation (C to T), substitution of an alanine with a valine was found Individuals with high kidding records were heterozygote but the others were wild type. Analyzing of special amino acid residues frequency in second structure shows that alanine has an intrinsic tendency to take part in α helix but valine has an intrinsic tendency to take part in β sheet. So, the mutation found in this research causes a change in third structure and probably function of the protein. In prediction of 3-dimension structure of protein, a difference was found between mutant and non-mutant sequence. Analyzing of special amino acid residues frequency in second structure shows that alanine has an intrinsic tendency to take part in α helix but valine has an intrinsic tendency to take part in β sheet that causes a change in third structure and probably function of the protein. Investigation of phylogenetic tree between some different types of animals showed that BMP15 protein sequence of goat is similar to sheep.