Data representing applicability of developed growth hormone 1 (GH1) gene detection method for detecting Atlantic salmon (Salmo salar) at high specificity to processed salmon commodities

This article is referred to the research article entitled “Development of a novel method for specific detection of genetically modified Atlantic salmon, AquAdvantage, using real-time polymerase chain reaction” by Soga et al. (2020). Applicability of the developed growth hormone 1 (GH1) and 18S ribosomal DNA (18S rDNA) detection methods using real-time polymerase chain reaction (PCR) for detecting Atlantic salmon (Salmo salar) to processed food commodities was examined. DNAs extracted and purified from 24 commodities labelled to include salmon as an ingredient were used as template. Yield and purity of DNAs obtained and Cq values from real-time PCR analyses were provided.


a b s t r a c t
This article is referred to the research article entitled "Development of a novel method for specific detection of genetically modified Atlantic salmon, AquAdvantage, using real-time polymerase chain reaction" by Soga et al. (2020). Applicability of the developed growth hormone 1 (GH1) and 18S ribosomal DNA (18S rDNA) detection methods using real-time polymerase chain reaction (PCR) for detecting Atlantic salmon (Salmo salar) to processed food commodities was examined. DNAs extracted and purified from 24 commodities labelled to include salmon as an ingredient were used as template. Yield and purity of Real Value of the Data These data provide information concerning applicability of GH1 and 18S rDNA detection methods to various processed salmon commodities to detect Salmo salar (Atlantic salmon) ingredient. The data are beneficial for researchers who are trying to detect or confirm the presence of Atlantic salmon derived ingredient in foods. These data show potential of developed real-time PCR detection method to monitor Atlantic salmon in various processed salmon commodities at high sensitivity and specificity. The data provide information concerning DNA yield and purification efficiency from various processed salmon commodities that were produced worldwide and applicability of developed GH1 detection method [1] that was more sensitive than the original method described [2] to the commodities. Table 1 summarizes the information on processed salmon commodities, including food processing type, production country, food ingredient labelled in Japan and recommended preservation state. Table  2 is the list of information on sequences of real-time PCR primer pairs and probes used in this dataset. Table 3 presents the specificity test data using developed 18S rDNA detection method. Table 4 shows the data of DNA yields and purity obtained from 24 kinds of processed salmon commodities, and of real-time PCR tests using 18S rDNA and GH1 detection methods.

Experimental design, materials, and methods
Twenty-four processed salmon commodities including six types (smoked, sliced, canned, dried, roe and pickled) were purchased through the Internet in Japan. Details of food ingredients labelled, production country and recommended preservation state were described in Table 1. The commodities were selected taking into account that a wide range of salmonids species is covered in the test, based on the phylogeny identified in salmonid species [3].
Sampling weight was 1 g for smoked, sliced, canned, roe and pickled commodities, and 0.5 g for dried commodities. DNA extraction and purification were done using GM quicker 3 kit (Nippon gene, Toyama, Japan) for smoked, sliced, canned and dried commodities. Genomic-tip 20/G (Qiagen, Hilden, Germany) was used for salmon roe and pickled commodities. The quantity and the quality of DNA obtained were estimated from the ultraviolet (UV) absorption at 260 nm and its ratios at 260 and 280 nm (A260/A280) and 260 and 230 nm (A260/A230), respectively, using ND-1000 spectrophotometer (Thermo Fisher Scientific). The primer pair and probe targeting GH1 were used as described previously [1,2]. The primer pair and probe targeting 18S rDNA were designed using Primer Express Software (Thermo Fisher Scientific, Version 3.0.1), based on the sequence given by NCBI (Salmo salar 18S ribosomal RNA gene, partial sequence, GenBank accession no. FJ710886) ( Table 2). The probes were labelled with 6carboxyfluorescein (FAM) at 5 0 terminus and with 6-carboxytetramethylrhodamine (TAMRA) at 3' Table 2 List of oligonucleotide primers and probes used.

Detection method
Target region (GenBank accession no.)

Name
Nucleotide sequences (5 0 /3 0 ) a Amplicon (bp) Reference  terminus. Oligonucleotide sequences of primer pairs and probes used in this dataset are shown in Table 2. Fifty nanograms of extracted and purified DNA were used as template for real-time PCR analysis in duplicate tests per a sample. The fluorescence intensity when amplifying targeted DNA sequences was monitored by ABI PRISM 7900 Sequence Detection System (Thermo Fisher Scientific). Thermal cycling conditions were 95 C for 10 min, followed by 50 cycles of 15 sec at 95 C and 1 min at 57 C.The baseline was set to cycles 3 through 15. The DRn threshold for plotting the cycle threshold (Cq) values was set to 0.2 during exponential amplification.
For tests, reactions with the Cq value of less than 48 and exponential amplification plots were scored as positive. If the Cq value was more than 48 or could not be obtained, the reaction was scored as negative. Reactions with the Cq value of less than 48, but without exponential amplification as judged by visual inspection of the respective DRn plots and multi-component plots were scored as negative.
Specificity test of 18S rDNA method was performed using 17 kinds of plants, 2 kinds of animals and 8 kinds of fishes (Table 3).

Acknowledgments
This project was conducted under the support of the Ministry of Health, Labour and Welfare of Japan.