eQTL mapping in Brown Swiss bulls to identify variants associated with male fertility

Abstract

Fertility is an essential component of the livestock industry. In cattle, numerous QTL for male reproductive success fall within regulatory regions. However, the effects of these loci have not been investigated in detail or on a large scale. Here, we assemble a sizeable cohort of mature bulls to detect expression quantitative trait loci (eQTL) and assess their effects on fertility-related genes. To do this, we sequenced genomes and total RNA from the testes of 72 bulls. We recovered 13,185,795 DNA sequence variants with minor allele frequency >5%, an average of 283,587,831 clean RNA reads per sample and 18,528 testis-expressed genes (TPM>0.2 in 75% of samples). In total, 2,178 genes had significant cis-eQTL at a false discovery rate of 5% (11.76% of expressed genes). Several genes associated with fertility, including SPATA4 and SPATA22 (which are responsible for reproductive processes), had significant cis-eQTL and variation in transcript abundance across genotypes.