Identification of Reproduction-Related Gene Polymorphisms Using Whole Transcriptome Sequencing in the Large White Pig Population

Recent developments in high-throughput sequencing techniques have enabled large-scale analysis of genetic variations and gene expression in different tissues and species, but gene expression patterns and genetic variations in livestock are not well-characterized. In this study, we have used high-throughput transcriptomic sequencing of the Finnish Large White to identify gene expression patterns and coding polymorphisms within the breed in the testis and oviduct. The main objective of this study was to identify polymorphisms within genes that are highly and specifically expressed in male and/or female reproductive organs. The differential expression (DE) analysis underlined 1234 genes highly expressed in the testis and 1501 in the oviduct. Furthermore, we used a novel in-house R-package hoardeR for the identification of novel genes and their orthologs, which underlined 55 additional DE genes based on orthologs in the human, cow, and sheep. Identification of polymorphisms in the dataset resulted in a total of 29,973 variants, of which 10,704 were known coding variants. Fifty-seven nonsynonymous SNPs were present among genes with high expression in the testis and 67 were present in the oviduct, underlining possible influential genes for reproduction traits. Seven genes (PGR, FRAS1, TCF4, ADAT1, SPAG6, PIWIL2, and DNAH8) with polymorphisms were highlighted as reproduction-related based on their biological function. The expression and SNPs of these genes were confirmed using RT-PCR and Sanger sequencing. The identified nonsynonymous mutations within genes highly expressed in the testis or oviduct provide a list of candidate genes for reproduction traits within the pig population and enable identification of biomarkers for sow and boar fertility.