PSIX-24 Genome-wide association mapping for additive and dominance effects in pig fertility

Abstract The aim of the work was to conduct GWAS for Total Number Born (TNB) based on the Gradient Boosting Machine (GBM) algorithm, taking into account additive and dominance effects. The study population consisted of 218 Landrace sows. DNA samples were genotyped using GGP HD Porcine. After filtering, 40358 SNPs are left for further analysis. The target variable is the Total Number Born estimated from the third farrow. To assess the additive (model A) and dominant (model D), the coding 0/1/2 and 0/1/0 were used, respectively. Based on the test results, the top 50 SNPs were selected for each of the models in accordance with the relative importance. Of the top 50 SNPs determined by model D, 36 SNPs were identified based on model A (of which 14 SNPs were included in the top of model A). However, the top 14 SNPs for Model D showed relative importance = 0 for Model A. The genes identified in Models A and D are responsible for Molecular functions: binding (GO: 0005488), catalytic activity (GO: 0003824), and transcriptional regulator activity (GO: 0140110); Biological process: cellular process (GO: 0009987), biological regulation (GO: 0065007), metabolic process (GO: 0008152); Cellular component: part of a cell (GO: 0044464) and a cell (GO: 0005623). Further research will allow a more detailed study of the genetic electrical energy of fertility traits in pigs. The results showed that the dominance effects has additional value for genomic effects that control pig fertility. This research was performed with financial support from the Russian Science Foundation (RSF) 19-76-10012.