Genomic and functional genomic analysis of fatty acid composition in swine /

Resumen

Pork is one of the main sources of human-consumed meat and consumer’s preference towards high quality meat is increasing. Hence, understanding the molecular mechanisms affecting meat production and quality would help in the selection of these traits. Meat quality is determined largely by its fatty acid (FA) composition and understanding the underlying molecular processes of FA composition is the general objective of this thesis. We analyzed quantitative trait loci (QTL) on porcine chromosome 8 (SCC8) for FA composition in backfat, identifying two trait-associated SNP regions at 93 Mb and 119 Mb. The strongest statistical signals for both regions were observed for palmitoleic acid and, C18:0/C16:0 and C18:1(n-7)/C16:1(n-7) elongation ratios. MAML3 and SETD7 genes were analyzed as positional candidate genes in the 93 Mb region. The two novel microsatellites analyzed in the MAML3 gene, and the SETD7:c.700G>T SNP in the SETD7 gene did not show the strongest signal in this region, discarding these polymorphisms as the causal mutations. Furthermore, in the 119 Mb region, the ELOVL6:c.-533C>T SNP showed a strong association with the percentage of palmitic and palmitoleic acids and elongation ratios in backfat. These results for ELOVL6 gene, support the hypothesis that it has a pleiotropic effect in backfat and muscle for the 119 Mb QTL, and reinforce this gene as a strong candidate for the SSC8 QTL for FA composition. Moreover, whole genome sequence (WGS) data from Iberian and Landrace pigs were used to identify 1,279 copy number variations (CNVs), merging into 540 swine CNV regions (CNVRs). The impact of four of them in growth and FA composition in intramuscular fat and backfat was studied. Association with carcass length and FA composition in backfat and intramuscular fat was showed for the CNVR112, containing the GPAT2 gene which catalyse the biosynthesis of triglycerides and glycerophospholipids. These results underline the importance of CNVRs affecting economically important traits in pigs. Finally, the adipose tissue mRNA expression of 44 candidate genes related with lipid metabolism was analyzed in 115 animals. The expression genome-wide association (eGWAS) identified 193 eSNPs located in 19 expression QTLs (eQTLs). Three out of 19 eQTLs corresponding to ACSM5, FABP4, and FADS2 were classified as cis-acting eQTLs, whereas the remaining 16 eQTLs had trans-regulatory effects. These findings and the polymorphisms evaluated for some of these genes provide new data to further understand the functional mechanisms implicated in the variation of meat quality traits in pigs.