Autosomal recessive loci contribute significantly to quantitative variation of male fertility in a dairy cattle population

Cattle are ideally suited to investigate the genetics of male fertility. Semen from individual bulls is used for thousands of artificial inseminations for which the fertilization success is monitored. In a cohort of 3881 bulls that had genotypes at 589,791 SNPs, we reveal four novel recessive QTL for male fertility using haplotype-based association testing. We detect either missense or nonsense variants in SPATA16 , VWA3A, ENSBTAG00000006717 and ENSBTAG00000019919 that are in linkage disequilibrium with the QTL. A QTL for bull fertility on BTA1 is also associated with sperm head shape anomalies. Using whole-genome sequence and transcriptome data, we prioritise a missense variant (p.Ile193Met) in SPATA16 as candidate causal variant underlying this QTL. Our findings in a dairy cattle population provide evidence that recessive variants may contribute substantially to quantitative variation in male fertility in mammals.