Single Nucleotide Polymorphisms (SNPs) in the immunoglobulin M heavy chain gene of five African catfish (Clarias gariepinus) strains in Indonesia
Huria Marnis*, Khairul Syahputra, Bambang Iswanto

*Research institute for fish breeding, Subang

Abstract

A single nucleotide polymorphism (SNP) represents the most abundant genetic variants among individuals. While most of the SNPs do not show functional impact, some are functional and cause important phenotypic effects. This study was aimed to evaluate SNPs in immunoglobulin M (IgM) heavy chain assumed to affect the immune system in five African catfish strains, namely Dumbo, Sangkuriang, Paiton, Masamo and Egypt. Genomic DNA was extracted from caudal fins and IgM heavy chain gene was partially amplified in a PCR system, cloned using pJET1.2, and sequenced. Strains were characterized based on morphological analysis. The resulting data were aligned to the NCBI database. Three hundred and five nucleotide sequences were successfully sequenced from Sangkuriang, Paiton, Egypt, and Masamo that encode 101 amino acid residues, while Dumbo strain had 229 nucleotide sequences encoding 99 amino acid residues. Blastn analysis showed that IgM heavy chain sequences of Paiton, Sangkuriang, Masamo, and Egypt had similarity (85%) to channel catfish (Ictalurus punctatus), and 82% identity was found between Dumbo IgM heavy chain and channel catfish. A total of 54, 53, 53, 53, and 52 SNPs were observed in Dumbo, Paiton, Sangkuriang, Egypt, and Masamo strains, respectively, and all existed in coding region (exon). Analysis of the alignment of IgM heavy chain sequences among strains revealed that Dumbo had a greater number of SNPs (10 sequences) than other strains. Nonsynonymous nucleotide substitutions existed in the exon, thereby altering the amino acid product. Dumbo, Paiton, Masamo, and Sangkuriang strains had similar morphologies, except for Egypt. The Egypt strain had unique morphology. This study indicated that the structure of the IgM heavy chain gene might be associate with differences in immune performance among the five African catfish strains.

Keywords: Single nucleotide polymorphism- Immunoglobulin heavy chain gene- Clarias gariepinus- Cloning

Topic: Aquatic Biodiversity (International)