Primer design of DNA suckermouth catfish (Pterygoplichthys sp.) and their aplication in pempek using real Time PCR (RT – PCR): Primer design of  suckermouth catfish (Pterygoplichthys sp.) DNA and their aplication in pempek using real Time PCR (RT – PCR)

Dedy Suseno; Intan Razari

doi:10.17844/nrth5y06

Authors

Dedy Suseno Halal Research Center Universitas YARSI
Intan Razari Genomic Research Center, Universitas YARSI https://orcid.org/0000-0003-1430-2643

DOI:

https://doi.org/10.17844/nrth5y06

Keywords:

D-Loop, EvaGreen, Pterygoplichthys pardalis, Ciliwung River

Abstract

Pempek is a traditional food from South Sumatra that uses fish as the main ingredient. In addition to mackerel, several other types of fish are used as raw materials for making pempek, such as snakehead fish, tilapia, and catfish. Suckermouth catfish can also be used as an ingredient for making pempek; however, several studies have reported that suckermouth catfish from the Ciliwung River are contaminated with heavy metals and microplastics. The presence of heavy metals and microplastics in suckermouth catfish makes it dangerous to use as a food ingredient, especially in pempek. This study aimed to design specific DNA primers for suckermouth catfish and analyze the presence or absence of suckermouth catfish DNA in pempek using RT-PCR with a dye-based marker (EvaGreen). Suckermouth catfish DNA was analyzed using specific primers and amplified using RT-PCR. The results showed that the primers used were specific only to suckermouth catfish compared to DNA samples from nine other fish species. A suckermouth catfish DNA concentration of 0.00064 ng/µL still showed amplification, with a Cq value of 38.98. A comparison between raw pempek ingredients and suckermouth catfish meat (w/w) at a ratio of 20:1 still showed an amplification curve with a Cq value of 23.55. None of the 16 pempek samples tested contained suckermouth catfish DNA, as no amplification curves were observed on the RT-PCR device.

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