The heritable landscape of near-infrared and Raman spectroscopic measurements to improve lipid content in Atlantic salmon fillets

Abstract

Background Product quality and production efficiency of Atlantic salmon are, to a large extent, influenced by the deposition and depletion of lipid reserves. Fillet lipid content is a heritable trait and is unfavourably correlated with growth, thus genetic management of fillet lipid content is needed for sustained genetic progress in these two traits. The laboratory-based reference method for recording fillet lipid content is highly accurate and precise but, at the same time, expensive, time-consuming, and destructive. Here, we test the use of rapid and cheaper vibrational spectroscopy methods, namely near-infrared (NIR) and Raman spectroscopy both as individual phenotypes and phenotypic predictors of lipid content in Atlantic salmon. Results Remarkably, 827 of the 1500 individual Raman variables (i.e. Raman shifts) of the Raman spectrum were significantly heritable (heritability (h2) ranging from 0.15 to 0.65). Similarly, 407 of the 2696 NIR spectral landscape variables (i.e. wavelengths) were significantly heritable (h2 = 0.27–0.40). Both Raman and NIR spectral landscapes had significantly heritable regions, which are also informative in spectroscopic predictions of lipid content. Partial least square predicted lipid content using Raman and NIR spectra were highly concordant and highly genetically correlated with the lipid content values ($${r}_{\text{g}}$$ r g = 0.91–0.98) obtained with the reference method using Lin’s concordance correlation coefficient (CCC = 0.63–0.90), and were significantly heritable ($${h}^{2}$$ h 2 = 0.52–0.67). Conclusions Both NIR and Raman spectral landscapes show substantial additive genetic variation and are highly genetically correlated with the reference method. These findings lay down the foundation for rapid spectroscopic measurement of lipid content in salmonid breeding programmes.

Genomic and Phenotypic Agreement Defines the Use of Microwave Dielectric Spectroscopy for Recording Muscle Lipid Content in European Seabass (Dicentrarchus labrax)

“…However, we were able to calculate the CCC between magnetic resonance imaging and dielectric spectrometry in Rainbow trout (Oncorhynchus mykiss) from Blay et al (2021), which was 0.59. Furthermore, the CCC values herein are lower or comparable to that obtained for fillet lipid content in Atlantic salmon (Salmo salar) using a commercial near infrared (NIR) scanner on whole fillet and the reference method (CCC = 0.63) or a laboratory based NIR system on ground samples (CCC = 0.68) with the reference method (Difford et al, 2021). However, they are substantially less than that reported for Raman spectroscopy predicted lipid content compared to the reference method in Atlantic salmon CCC = 0.92 (Difford et al, 2021).…”

“…Furthermore, the CCC values herein are lower or comparable to that obtained for fillet lipid content in Atlantic salmon (Salmo salar) using a commercial near infrared (NIR) scanner on whole fillet and the reference method (CCC = 0.63) or a laboratory based NIR system on ground samples (CCC = 0.68) with the reference method (Difford et al, 2021). However, they are substantially less than that reported for Raman spectroscopy predicted lipid content compared to the reference method in Atlantic salmon CCC = 0.92 (Difford et al, 2021). Whilst the agreement between dielectric spectroscopy and the reference method appears to be lower than the majority of aforementioned studies, it is the only method which does not require sacrificing the fish.…”

“…To the best of our knowledge this is the first non-salmonid species to have genetic correlations estimated between the reference method and an alternative method for muscle lipid content. The genetic correlations herein are in the range of other spectroscopic measurements compared to the reference method in Atlantic salmon, for example a non-invasive field NIR system (r g = 0.91), a laboratory NIR system (r g = 0.93) and a laboratory Raman system (r g = 0.98; Difford et al, 2021). These findings demonstrate that almost all the genetic variation in Lipid True is captured by the handheld dielectric spectrometer, validating its use in selection programs for fillet lipid percentage.…”

“…These findings suggest that dielectric spectroscopy for fillet lipid percentage can be improved by using an in-sample calibration with the reference method to quantify and correct for the inaccuracy. The use of in-sample calibration equations with the reference method is widespread in vibrational spectroscopy, for example for lipids in the milk of dairy cows (Rutten et al, 2010) and lipid in the fillets of Atlantic salmon (Difford et al, 2021).…”

Genetic architecture and genomic selection of fatty acid composition predicted by Raman spectroscopy in rainbow trout

“…Specifically, this method enables the qualitative and quantitative characterisation of molecules through analyses of spectral bands with respect to the fundamental vibrational modes of their chemical bonds. This technology has already been used to determine total lipid concentration in minced salmon flesh [ 47 ] and FA composition in pork adipose tissue [ 48 ], as well as in fish oils [ 49 , 50 ] and in Atlantic salmon flesh [ 51 ].…”