With consumers demanding higher quality in fish products, ecologically farmed fish are increasingly favored due to their quality being close to that of wild fish. However, the differences between the ecologically farmed and wild fish remain largely unclear. In the present study, the wild and ecologically farmed large yellow croakers of the same size were captured simultaneously from the same marine area around Nanji islands (27.479°E, 121.052°N). Then, synchronous tests were conducted to evaluate quality to clarify the key quality parameters that differentiate between the wild and farmed fish. We obtained 49 quality parameters after orthogonal partial least squares discriminant analysis (OPLS-DA) with variable importance in projection (VIP) scores >1 and p < 0.05 using 307 indicators related to 121 length ratios, 4 body color indicators, 5 muscle fiber characteristic indicators, 87 nutrition quality parameters, 40 taste parameters, and 50 volatile compounds. Compared to the farmed fish, the wild fish exhibited a more yellow skin color, higher levels of carotenoids, and a more streamlined conical shape. Changes in histology and ultrastructure of muscle fibers were noted, including increased muscle fiber density and the ratio of fiber area to gap, as well as reduced I band width, observed in the wild fish. The wild fish had high nutritional value of fatty acids and minerals and low nutritional value of amino acids, as reflected by higher levels of C22: 6n3 (DHA), Σn-3 PUFA (polyunsaturated fatty acids), Σn-3/Σn-6 PUFA, Na (sodium), K (potassium), Fe (iron), and Se (selenium), and lower values of ΣMUFA (monosaturated fatty acids), Σn-6 PUFA, TI (thrombogenic index), amino acid and chemistry scores of isoleucine, ΣEAA/ΣTAA (essential amino acid/ total amino acid), and ΣTAA/ΣNEAA (total amino acid/non-essential amino acid) in the muscles of the wild fish. The wild fish muscle showed high levels of hydrolyzed glycine and proline and free methionine, and low levels of free glycine and proline, indicating a propensity for collagen synthesis. Despite significant differences in the contents of fourteen flavor substances of free amino acids, 5′-nucleotides, and volatile compounds, their concentrations were notably below the corresponding threshold and contributed minimally to flavor, suggesting that the wild and farmed fish shared similar flavor characteristics. In summary, this study reveals the quality differences between ecologically farmed and wild large yellow croaker based on on-site synchronous sampling, providing a theoretical foundation for further enhancing the quality of this species.
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