An association analysis between a polymorphism in the SEC24A gene and lipid traits recorded in Duroc pigs

By regulating the expression of low-density lipoprotein receptors (LDLR), the SEC24A protein modulates the clearance of plasma cholesterol in mice. The whole-genome sequencing of five Duroc boars that sired a Duroc purebred experimental population (LIPGEN population, 350 individuals) revealed the segregation of one putative nonsense mutation located at the SEC24A (rs336401826, c.44G>A) gene. Genotyping of this polymorphic site in the LIPGEN population highlighted the existence of a significant departure from the Hardy Weinberg equilibrium (χ2 = 5.05, p-value = 0.024527). Despite the fact that SEC24A inactivation should affect serum lipid concentrations, we did not observe an association between SEC24A genotype and such traits. A thorough revision of the annotation of the SEC24A rs336401826 SNP revealed that this polymorphism is probably located in the 5’UTR of the SEC24A gene, rather than at the beginning of the first exon, hence not introducing the predicted premature stop codon that could truncate the SEC24A protein. Given that the annotation of loss-of-function mutations in pigs is far from perfect, careful manual curation of such mutations is recommended before undertaking the analysis of their effects at the experimental level.This research was partially funded with grants AGL2013-48742-C2-1-R and AGL2013-48742-C2-2-R awarded by the Spanish Ministry of Economy and Competitiveness and grant 2014 SGR 1528 from the Agency for Management of University and Research Grants of the Generalitat de Catalunya. We also acknowledge the support of the Spanish Ministry of Economy and Competitivity for the Center of Excellence Severo Ochoa 2020-2023 [CEX2019-000902-S] grant awarded to the Centre for Research in Agricultural Genomics (CRAG, Bellaterra, Spain). Emilio Mármol-Sánchez was funded with a FPU Ph.D. grant from the Spanish Ministry of Education [FPU15/01733]. María Gracia Luigi-Sierra was funded with a FPI Ph.D. grant from the Spanish Ministry of Economy and Competitivity [BES-2017-079709].Peer reviewe