Genome-Wide Association Study and Genomic Prediction of Sperm Quality Traits in Pietrain Pigs

In the present study, a genome-wide association study (GWAS), estimation of genetic parameters, and prediction of breeding values for semen quality and quantity traits in Pietrain pigs were performed. The traits inferred were total number of sperm, motility, volume, and density. Traits were recorded from 2012 to 2021 using a CASA system (computer aided sperm analysis) and provided data from 96,815 ejaculates from 1647 Pietrain boars. The animals were kept in three Austrian artificial insemination (AI) stations. Genomic data were analysed using Illumina 60 and 80 k SNP arrays and yielded 43,430 markers from 909 individuals after quality control. Genome-wide association was based on a mixed linear association model with phenotypic pre-correction. GWAS revealed three possible associations for total number of sperm on chromosome 8, 16, and 17, including two genes from the cadherin family (PCDH15, CDH12). Genetic parameters and breeding values were estimated using a single-step GBLUP (ssGBLUP) procedure for total number of sperm and motility. Estimated heritabilities for total number of sperm and motility were 25.9% and 11.5%, respectively. Genetic correlation was -0.321 between motility and sperm density, and 0.419 between motility and ejaculate volume. Breeding value estimation provided proof of the advantage of ssGBLUP compared to pedigree-based BLUP in this study, as reliabilities (r²) were significantly higher for young boars without phenotypes (0.346 vs. 0.196 for total number of sperm and 0.276 vs. 0.190 for motility). This indicates positive response to selection if included in routine genetic evaluation.