Transcriptomics in Portuguese local pig breeds: an approach to explore the molecular mechanisms underlying lipid metabolism and muscle growth

Abstract

This study aimed to characterize the genetic component of economically relevant production traits by exploring the transcriptomics of the dorsal subcutaneous fat (DSF) and Longissimus lumborum (LL) muscle tissues from the local Alentejano (AL) and Bísaro (BI) pig breeds using RNA-seq technology and qPCR for validation. DSF yielded 458 differently expressed genes (DEGs), with an overrepresentation of genes associated with de novo lipogenesis in AL, agreeing with its fatter profile. Meanwhile, a higher lipolytic activity in BI pigs may be mediated by the growth hormone and AMPK signalling pathways. Lower CD40 signalling in AL suggests lower insulin sensitivity due to the pro-inflammatory effect of the excessive amount of lipids. Higher levels of leptin in AL suggests that this breed has developed leptin-resistance, as previously proposed for the genetically similar Iberian pig. Furthermore, several genes that play important roles in growth were found overexpressed in BI, supporting the idea that development stimuli can occur and be regulated at a multiple tissue level. LL yielded 49 DEGs, with different signalling mechanisms for slow type myosins identified for AL (MYH7) and BI (MYH3), while no markers for fast fibre types were found differently expressed between breeds. On the other hand, the higher expression of TNNT1 in AL pigs agrees with their lower values of shear force, suggesting the rigor mortis process to occur to a less extent in this breed, causing less shortening of the myofibers, lowering the hardiness of its meat. Overexpression of MAP3K14 in AL pigs may be associated with their lower loin proportion, induced insulin resistance, and increased inflammatory response via NFkB. Finally, overexpression of RUFY1 in AL may explain their higher IMF content via higher GLUT4 recruitment and consequently higher glucose uptake that can be stored as fat.