A Candidate Gene-Transcription Factor Network for Number of Stillborn Piglets

Reproductive traits such as stillborn piglets (SB) are important for the pig industry since they are directly involved with higher and more sustainable production. However, as many of these traits show low heritability, it is genetically challenging to improve pigs for reproduction. Genomic studies are expected to be especially useful for traits with low heritability, thus SB could be a well suited candidate trait for genomic selection and genome wide association studies (GWAS). Besides, additional network analysis, like gene-transcription factor (gene-TF) networks derived from genes linked to significant SNPs/QTLs, will enable a genetic dissection of complex phenotypes found by GWAS. Toward this, we performed a GWAS for SB using the Illumina 60K Porcine Beadchip for 1200 animals. From the significant SNPs identified through GWAS we identified a QTL region on chromosome 1 and extracted 6 genes overlapping the QTL region which were used to obtain a list of TF used to construct a TF-network showing their interaction to the genes. The TF-network analysis pointed out genes, e.g. SOCS4 and LGALS3, as the most probable candidate genes for SB in this QTL. The present approach provides, a rich information resource toward new candidate genes for SB hereby increasing our understanding of the molecular mechanisms underlying this trait.