Genome doubling of haploids is one of the major constraints of large-scale doubled haploid (DH) technology. Improving spontaneous haploid genome doubling (SHGD) is an alternative to overcome this limitation. In this study, we aimed to construct a high-density linkage map based on genotyping by sequencing (GBS) of Single Nucleotide Polymorphism (SNPs), to detect QTL and QTL by environment (Q by E) interactions affecting SHGD, and to identify the best trait for mapping and selection of haploid male fertility (HMF). To this end, a bi-parental population of 220 F2:3 families was developed from a cross between A427 (high HMF) and CR1Ht (moderate HMF) to be used as donor. A high-density linkage map was constructed containing 4,171 SNP markers distributed over 10 chromosomes with an average distance between adjacent markers of 0.51 cM. QTL mapping for haploid fertile anther emergence (AE), pollen production (PP), tassel size (TS), and HMF, identified 27 QTL across three environments, and Q by E interactions were significant. A major QTL was identified on chromosome 5. This QTL explained over 45% of the observed variance for all traits across all environments. The introgression of this major QTL, using marker-assisted backcrossing, has great potential to overcome the need of using colchicine in DH line development.