A Whole-Genome Association Scan Detects Several Genetic Regions Influencing Semen Quality Traits in the Boar’s Sperm

Boar’s semen quality is crucial for the efficiency of artificial insemination centers and the genetic progress in pig breeding. With the ultimate aim to develop a genetic test for the early prediction of semen quality traits in pigs, we carried out a genome-wide association scan (GWAS) for 53 sperm parameters including motility, abnormalities, viability and acrosome integrity, on 180 Pietrain boars. The boars were genotyped with the Axiom® Porcine Genotyping Array (Affymetrix) and 467,914 single nucleotide polymorphisms (SNPs) were used for the analysis. Single-SNP association analyses were performed under an additive genetic model with the Genome-wide Efficient Mixed-Model Association (GEMMA) software. We identified 44 genome-wide significant hits confirmed by at least 4 SNPs, for abnormalities of the head (17 regions), neck (3) and tail (3), acrosome integrity (5), viability (5) and motility (11). These hits mapped to 12 chromosomes and to unmapped scaffolds. The most significant hit affected acrosome integrity and mapped to chromosome 3:81.4-103.2 Mbp. (most significant SNP - rs322712738 - q-val = 7.06x10^-11). This hit harbors PSME4, a gene that is involved in nucleosome removal during spermatogenesis. In addition, we co-mapped the GWAS results with the list of transcripts detected in a RNA-seq experiment that we carried on boar sperm. In total, 652 genes present in the boar sperm transcriptome co-map with our sperm GWAS hits. These results suggest that the genetic architecture of boar sperm parameters might allow the development of a DNA test for the prediction of semen quality in piglets.