High‐throughput identification of tuna (Thunnus spp.) larvae in the Gulf of Mexico using unlabelled‐probe high‐resolution melting analysis

The genus Thunnus (family Scombridae) comprises eight species of tunas of which all but one are targeted by industrialized fisheries. Although intact individuals of these species can be distinguished by morphological characteristics, researchers and managers often rely on dressed, frozen, juvenile o...

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Bibliographic Details
Published in:Journal of fish biology 2023-06, Vol.102 (6), p.1425-1433
Main Authors: Smith, Brad L., Lu, Ching‐Ping, Cornic, Maëlle, Alvarado Bremer, Jaime R.
Format: Article
Language:English
Subjects:
Animals
Assaying
Cost analysis
DNA, Mitochondrial - genetics
Fish
Fisheries
Fisheries surveys
Genetic analysis
genetic species identification
Genomes
Genotype
Genotypes
Genotyping
Gulf of Mexico
Gulf of Mexico tunas
high‐resolution melting analysis
Identification
Juveniles
Larva
Larvae
Marine fishes
Masking
Melt temperature
Melting
Mitochondrial DNA
Morphology
NADH dehydrogenase
Nicotinamide adenine dinucleotide
Physical characteristics
Species
Species identification
Thunnus
Thunnus albacares
Thunnus atlanticus
Thunnus obesus
Thunnus spp
Thunnus thynnus
Tuna
Tuna - genetics
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Summary:The genus Thunnus (family Scombridae) comprises eight species of tunas of which all but one are targeted by industrialized fisheries. Although intact individuals of these species can be distinguished by morphological characteristics, researchers and managers often rely on dressed, frozen, juvenile or larval fish samples, which often necessitates the identification of molecular species. Here the authors investigate short amplicon (SA) and unlabelled probe high‐resolution melting analysis (UP‐HRMA) as a low‐cost, high‐throughput molecular genotyping assay capable of distinguishing between albacore tuna (Thunnus alalunga), blackfin tuna (Thunnus atlanticus), bigeye tuna (Thunnus obesus), Atlantic bluefin tuna (Thunnus thynnus) and yellowfin tuna (Thunnus albacares) in the Gulf of Mexico. Although SA‐HRMA of variable regions in the NADH dehydrogenase subunit 4 (ND4) and subunit 5 (ND5), and subunit 6 (ND6) of the mtDNA genome did yield some species‐specific diagnostic melting curves (e.g., ND4 assay can reliably distinguish Atlantic bluefin tuna), genotype masking produced excessive variation in melting curves for reliable multi‐species identification. To minimize the genotyping masking of SA‐HRMA a 26 base pair long UP containing four SNPs was developed within a 133 bp segment of ND4. The UP‐HRMA is able to reliably distinguish Gulf of Mexico species T. thynnus, T. obesus, T. albacares and T. atlanticus by UP melting temperature at 67, 62, 59 and 57°C, respectively. The developed UP‐HRMA assay is a lower‐cost, higher‐throughput, alternative to previously published molecular assays for tuna identification that can be easily automated for large data sets, including ichthyological larval surveys, fisheries specimens lacking distinguishing morphological characteristics or detection of fraudulent trading of tuna species.
ISSN:0022-1112
1095-8649
DOI:10.1111/jfb.15391