Large deletions in the DNA primase large subunit PRIM2 are associated with NADP-malate dehydrogenase activity in a...

Large porcine F₂ crosses are a valuable resource for discovering QTL and genetic variants for relevant traits. Past studies have been largely limited to SNPs and short insertions and deletions. Structural variants (SVs) are becoming a major area of interest in this respect. Here we present results from a genome-wide association study with SVs imputed from medium-density SNP array to the whole genome sequence level that were used to investigate the genetic relationship between important production traits and metabolic enzyme activity in an F₂ cross based on the breeds Meishan, Piétrain, and European wild boar. Genetic and phenotypic correlations between the two trait classes were high. We were able to pinpoint common genetic loci to a QTL on SSC7, encompassing numerous large intron deletions in the PRIM2 gene as well as in HMGCLL1, BMP5, TRERF1, COL21A1, LRRC1, and UBR2. The most pronounced genetic associations were observed for the content of NADP-malate dehydrogenase in the tissue. Hence, we propose that the content and activity of malate dehydrogenase is directly connected to important pig production traits, and we present a comprehensive list of large intronic deletions as promising candidates for causality. The variants were validated in independent pig populations, where the majority of the discovered SVs were present, indicating that they are not only relevant to the breeds investigated here.