Maize (Zea mays L.) breeding contributed to significant yield gains in the past decades. However, it has been accompanied by narrowing its germplasm base. Breeding from exotic maize germplasm, such as BS39, provides a unique opportunity for broadening the genetic base of US Corn Belt germplasm. The in vivo doubled haploid (DH) technology is widely used into exotic germplasms because it has a great promise in purging mutational load of deleterious recessive alleles. Accounting for all the improvements of DH production over the years, genome duplication is still a major bottleneck. Its efficiency tends to be reduced when the technology is applied in exotic germplasm. The use of spontaneous haploid genome doubling (SHGD) can improve DH production, including in exotic germplasm. In this study, 663 maize inbred lines were derived from exotic germplasm, BS39, by DH and single-seed descent (SSD) breeding methods. Genotype-by-Sequencing (GBS) and Diversity Array Technology Sequencing (DArtSeq) was used for genotyping to understand the impact of SHGD on exploiting exotic germplasm. Also, in a testcross combination we measured traits as grain yield, moisture, plant and ear height, and stalk and root lodging. Inbred lines derived from BS39 represent a novel source of genetic diversity for US Corn Belt germplasm. Results indicate that the presence of alleles conferring SHGD in a breeding population will not affect the selection of higher performance lines and enable efficient evaluation of gametes from breeding populations. However, when using SHGD the chromosome 5 region close to the centromere was enriched by the SHGD donor genome, probably caused by an allele affecting SHGD.