Beyond GWAS: A Gene-Transcription Factor Network for Number of Teats in Pigs

In recent years, Genome-Wide Association Studies (GWAS) have been performed for a large variety of traits in different species. In pigs, number of teats (NT) has been extensively investigated due to its importance to the mothering ability of sows. However, in general, our knowledge of the molecular basis of complex traits, such as NT, is still deficient. Therefore, for a better understanding of the genetic architecture of complex phenotypes we need to go beyond GWAS. Of the potential post GWAS analysis the construction of candidate gene-transcription factor (gene-TF) networks is one attractive possibility. In this study our aim was to construct a gene-TF network, from a Bayesian GWAS based on Illumina 60K Porcine Beadchip for 1,657 animals, in order to gain additional insights into the genetic mechanisms of NT in a commercial pig population and to build a resource of possible candidate genes. From the significant SNPs identified on chromosome 7, an important chromosome for NT, we identified 3 QTLs overlapping 11 genes. These genes were used to obtain a list of TFs from which we selected the most relevant TFs for our trait based on their GO terms and on literature. From the selected TFs we constructed a gene-TF network showing their interaction with the 11 QTL genes and pointing out the most likely candidate genes for NT (e.g. PROX2, YLPM1 and KLHL31).