Identification of copy number variations and candidate genes for reproduction traits in Finnish pig populations

Animal breeding programs can be improved by genetic markers associated with production and reproduction traits. Reproduction traits are important for economic success of pig production and therefore development of genetic tools for selection is of high interest to pig breeding. In this study our objective was to identify genomic regions associated with fertility traits in two Finnish pig breeds using large scale SNP genotyping and genome wide association analysis and characterization of copy number variations (CNV). Since CNVs are structural variations of the genome they potentially have a large effect on gene expression and protein function. We analyzed 1265 genotyped boars for nine different reproduction traits and identified 46 CNV regions encompassing 13 genes. 11 of the CNV regions were shared between the breeds, 20 were unique to the Finnish Yorkshire and 15 to the Finnish Landrace. The genome wide association (GWAS) analysis identified zero to five reproduction associated genomic regions per trait. Furthermore, we identified 23 genomic regions with 20 candidate genes associated with fertility traits using GWAS analysis. The identified CNV regions were compared against GWAS regions to detect candidate regions with an effect on reproduction traits. This study reports candidate genes and genomic regions within two Finnish pig breeds for reproduction traits, which can be utilized in breeding programs.