Validating porcine SCD haplotype effects on fatty acid desaturation and fat deposition in different genetic backgrounds

Fatty acid composition and fat desaturation+ have profound effects on meat quality. One of the major enzymes participating in fatty acid metabolism is the stearoyl-CoA desaturase (SCD), which is the key enzyme involved in the fatty acid desaturation, in particular in the synthesis of C18:1 from C18:0 and C16:1 from C16:0. Previous studies have reported a likely causal SCD haplotype (g.2108C>T, g.2228T>C, g.2281A>G) determining desaturation potential in Duroc-based populations. In the current study we have evaluated the effects of SCD polymorphisms on fatty acid desaturation and SCD gene expression in muscle and subcutaneous fat in three experimental backcrosses and validated these effects in a Chinese-European hybrid pigs. In addition, we have evaluated the joint effects of SCD polymorphisms and major mutations (LEPR c.1987C>T, RYR1c.1843C>T, MC4Rc.1426A>G) previously reported to be involved in porcine fat deposition and fatty acids metabolism, in order to clarify SCD polymorphisms' actual effects. The obtained results from association and gene expression analyses support the SCD haplotype effects on fatty acid desaturation, and moreover on fat atherogenic and thrombogenic indexes. It also reveals potential effects on intramuscular fat content, not previously reported, likely conditional on breed fatness status. Moreover, a new polymorphism, g.2520G>A, that could impact splicing and SCD translation and which appears in complete linkage disequilibrium with the causal SCD haplotype, has been here identified. In addition, the conducted joint analyses of SCD with LEPR, RYR1 and MC4R genetic variants show complex gene relations that could hamper the discrimination of specific gene effects and the success of selection strategies.