MINING AND MAPPING OF SNP IN GROWTH HORMONE RECEPTOR OF Clarias magur
Aquaculture is one of the fastest growing food production sectors with an average annual rate of more than 8 per cent. Among different fishes, catfishes (Order: Siluriformes) have got special attention due to their hardiness and are being cultured in different agro-climatic zones. However, culture of Clarias magur could not expanded due to poor growth rate and lack of standardized breeding technology. This fish grows up to 200 to 250g in 6 - 8 month culture period which is very less as compared to other catfishes and carps. In order to improve the growth rate, selective breeding programme has been initiated by ICAR-CIFE, Mumbai. Single nucleotide polymorphisms (SNPs) are the most abundant genetic markers and can be very useful in association studies. Frequently, SNPs could be present in protein coding regions of the gene. Modelling three dimensional structure of the protein can give valuable information related to role of SNPs in protein function. The growth hormone receptor (GHR) is a member of the class I cytokine receptor family and is known for regulating growth, metabolism and controlling physiological processes. The aim of the present study is to identify single nucleotide polymorphisms (SNPs) in GHR gene and to identify the substituted amino acid in 3D structure of the protein to understand its function. The division of Fish Genetics and Biotechnology, ICAR-CIFE has developed transcriptome database of C. magur using Illumina NGS platform. SNPs were mined using CLC genomics work bench with variant calling feature. Full ORF of GHR gene was extracted from the assembled reads and a complete ORF of GHR gene coding for 445 amino acid residues was confirmed using BLASTp search. The BLASTp result shows highest similarity (84.38%) with growth hormone receptor of Pangasianodon hypophthalmus. A SNP was found at position 66 leading to change of asparagine to glutamine (fig.1). Protein 3D structure was generated by SWISS-MODEL by taking the human growth hormone as a template with its soluble binding protein (Chain B; PDB ID: 1hwh.1.B). The target sequence similarity was 43% with a coverage of 25%. Out of 445 amino acids, the region containing residue 2 to 116 was modelled and 3D structure was generated. The model was validated using QMEAN Z score (fig.2) and Ramachandran plot analysis. UCSF Chimera software was used to map the SNP in protein 3D structure. The location of SNP (substituted amino acid) was identified to be at extracellular region of fibronectin type 3 (FN3) domain. This is one of the three types of internal repeats of the plasma protein fibronectin (growth hormone receptor) and act as an important site for growth hormone binding. The SNP at this location might be influencing the growth hormone binding kinetics which could affect the growth performance of catfish.
IGF-1R plays a critical role in many physiological activities, such as development, growth,
metabolism, and reproduction. Identication of genetic markers in the IGF-1R gene signicantly asso-
ciated with important growth traits of Odontobutis potamophila may accelerate genetic improvement.
