Combining genome-wide association analyses and gene interaction networks to reveal new genes associated with carcass traits, meat quality and fatty acid profiles in pigs

Abstract

The various strains of Iberian pigs originate high quality processed products and represent a source of genetic variability that has not yet been deeply exploited, thus representing an opportunity to identify the genetic basis of traits with high economic relevance. The Alentejano breed is a strain of Iberian pigs that is characterized by excellent meat quality and slow growth rate, very well adapted to harsh climate conditions and usually raised outdoors in oak-tree forests. In this study, a sample of Iberian pigs from the Alentejano strain was genotyped with PorcineSNP60 v2 Beadchip to identify markers and candidate genes associated with a total of 153 different traits, including carcass, meat cuts, meat quality, fatty acid composition and derived metabolic indexes. To explore the biological role of the revealed associations, SNPs significant in GWAS which overlapped introns or gene regulatory regions were used to identify related genes, by generating gene interaction networks covering an enlarged and connected list of candidate genes. Using the genotypes of 31,434 SNPs that passed quality control steps, we performed single SNP association testing, using the GenABEL toolset and accounting for population stratification by principal component analysis. In these analyses, we identified novel associations for the index of desaturase and elongase activity of n − 3 c18:3 to c20:5 and for the content of cis-vaccenic acid in intramuscular fat, for the content of lauric acid in subcutaneous fat and for meat moisture and heart weight. The identified SNPs of interest were located within introns or within regulatory regions of 11 relevant genes, namely CRISPLD2, LDLRAD3, PPIL4, SOGA3, ME3, FLRT3, PPIL4, DOPEY2, CELC3A, and DSCAM. Based on these SNPs, we have further identified direct interactions with other genes and the biological processes involved in the regulation of these traits. Our results show that the study of a local pig breed allowed the identification of new genomic regions and candidate genes associated to several traits, and some of these are related with the levels of fatty acids that occur in high abundance in Iberian pigs and contribute positively to consumer health.