A genome-wide association study reveals additive and recessive alleles affecting male fertility in pigs

Understanding the genetic basis of male reproduction in mammals remains challenging. Commercial pig populations offer a unique model for studying fertility, as semen traits are routinely recorded using high-throughput systems.

In a large-scale GWAS of 15 semen traits based on 286,314 ejaculates collected from 2,954 boars of a purebred pig line, we identified 10 QTL, including four loci with recessive deleterious alleles. Several lead SNPs affected multiple semen traits. For example, a SNP on SSC6 was significantly associated with distal cytoplasmic droplets and with effects on tail abnormalities and sperm motility in a follow up analysis. The allele frequencies of some loci were different in older boar's, most likely due to culling based on poor semen quality. Using WGS, we identified six missense variants in high linkage disequilibrium (LD) with lead SNPs in genes related to sperm production (e.g., MEIOB, CFAP74 and UBE2B). Remarkably, the frequency of some alleles with predicted deleterious effects on semen traits increased between 2013 and 2019.

Our results highlight loci with major effects on semen quality, some of which are linked to functional variants in key genes involved in spermatogenesis. The information from this study can be used to select against deleterious alleles affecting semen characteristics in pigs and provides valuable insight into the genetics of mammalian male fertility.