Polymorphism, sequencing and phylogenetic characterization of growth differentiation factor 9 (GDF9) gene in Assam Hill goat

Abstract

Assam hill goat (Capra hircus) is a prolific local goat in India. Growth differentiation factor (GDF9) gene was studied as a candidate gene for the prolificacy of goats. The objective of the present study was to detect the incidence of mutation in the exonic region of GDF9 gene of Assam hill goat. Total number of 90 blood samples were collected randomly from different parts of Assam and genomic DNA were extracted using modified phenol-chloroform method. The quantity and quality of extracted DNA was examined using spectrophotometry and gel electrophoresis, respectively. A 294 bp fragment of GDF9 gene was amplified using polymerase chain reaction (PCR). The purified product was digested with DdeI, HhaI and AluI restriction enzymes which produced single type of banding pattern 242 and 52 bp, 140 and 154 bp, 134 and 160bp, respectively. The present study revealed wild type alleles and all the samples showed AA genotype. Nucleotide sequencing revealed two new mutations 495 (C ® A) and 387 (G ® A). Phylogenetic analysis showed that the sequences of Assam Hill goat belong to a common cluster which differs from that of the other goat breeds. The analysis of polymorphism for GDF9 in Assam Hill goat indicates that the genetic factor responsible for prolificacy or multiple kidding rate is not related to the reported mutated alleles of GDF9 gene. Therefore, attempts to be made to detect other single nucleotide polymorphism (SNPs) for GDF9 gene or otherwise effort should be made towards other fecundity gene which might be responsible for the prolificacy of Assam Hill goat.

Keywords: Assam Hill goat, GDF9, polymorphism, polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP).

Afr. J. Biotechnol Vol. 12 No. 50