Genetic markers for flesh quality in farmed fish

The objective of the follow-on funding was to provide commercial scale validation of genetic markers for increased fillet yield and superior texture in Atlantic salmon to strengthen a filed patent application. Other aims were 1) to establish the relationship between texture measurements and process yield losses during secondary processing in order to quantify the value of texture markers to salmon farmers 2) to carry out proof of concept studies with a salmon breeder and farmer for the commercial use of genetic markers for flesh quality traits and 3) to complete laboratory scale validation of fillet yield markers in Nile Tilapia.

Populations of farmed animals, including Atlantic salmon, show natural variations in gene sequence. Some of this variation is associated with characteristics which make the animals more valuable for farming. Genetic markers for the valuable sequence variation can be used to select broodstock for breeding. In this project we validated genetic markers for increased fillet yield and texture in salmon and increased fillet yield in Nile Tilapia. Using the salmon yield markers to select broodstock could result in an average 3% increase in meat yield across all populations tested resulting in an economic gain of £300 per metric tonne. In 2012 the UK produced 158,000 metric tonnes of salmon.

Genetic markers were identified that can distinguish Atlantic salmon (Salmo salar) with significantly improved fillet yield and flesh firmness. Single nucleotide polymorphisms (SNPs) were discovered by screening sequence variation in 37 candidate genes associated with muscle accretion and maintenance and by bulk segregant analysis of trait-selected restriction-site associated (RAD) libraries. Individual fillet yield (n=522) and mechanical texture data (n=254) were analysed in 8 batches of Scottish farmed salmon obtained from a commercial processor. Unique dam and sire identities and sex were determined using microsatellite and male-specific DNA markers respectively. Parent identity and sex were fitted as factors in generalized linear models and used to associate genotypes with fillet traits. Non-synonymous SNPs in calpastatin (Cast2) (4.7%, 1.8%), myoblast determination factor 1b (MyoD1b) (1.0%, 35.4%), and calpain 3 (Capn3) (0.8%, 48.2%) showed significant associations with fillet yield (% gain selected relative to batch average, % fish with favourable genotype) (P<0.015). Fish with a combination of the favourable Cast2 and Myod1b genotypes exhibited a 6.0% improvement in fillet yield relative to average (P=0.001). Other SNPs were significantly associated with flesh texture, with the favourable genotypes resulting in increased flesh firmness (Capn3, RADtag49325) or greater tensile strength (Capn1, RADtag4083 and 49325), a parameter that is inversely correlated with gaping severity. The identified SNPs could be used to increase fillet yield and quality in farmed salmon using marker assisted selection. Next Generation Sequencing of pools of high and low meat yield Nile Tilapia revealed 5 SNPs significantly associated with a 3% increase in fillet yield.