Long-term selection pressure to develop highly homogenous stands has resulted in rare frequencies of outcrossing alleles in elite wheat varieties. In order to establish a robust hybrid wheat breeding system, varieties harboring alleles that promote outcrossing have to be developed. IPK Genebank maintains ~28,000 wheat genotypes collected from across the globe that hold rich allelic diversity. In this study, we developed two doubled haploid (DH) populations from Genebank hexaploid spring wheat accessions contrasting for anther extrusion (AE) which is a vital trait to promote outcrossing in wheat. The phenotypic data of AE based on three years field trials in both populations approximated a normal distribution with a wide variation. We also observed a positive and significant correlation among all the years with a broad-sense heritability of 0.89 and 0.79 for DH population-1 and 2, respectively. Both populations were genotyped with a 15k INFINIUM single nucleotide polymorphism (SNP) array resulting in 3,567 and 3,457 polymorphic SNP markers for DH population-1 and 2, respectively. Composite interval mapping was performed that identified quantitative trait loci (QTL) on chromosomes 1D, 2D, 4A, 4B, 5A, and 6B; with consistent QTLs (that are detected in all the years) on chromosome 4A in DH population-1, and on chromosomes 2D and 6B in DH population-2. The consistent QTL explained 17.18%, 32.88%, and 12.29% of phenotypic variance, respectively. The gene Cleistogamy1 cloned in barley promotes AE via swelling of the lodicules. A preliminary scan of the chromosome 2D QTL showed that the wheat homologue Ta-AP2-D lies within the QTL-region. A molecular marker for Ta-AP2-D was developed and is currently being tested in various association mapping panels. This study shows the use of Genebank diversity as a reservoir to find alleles which are otherwise difficult to detect in elite populations. The identification of large effect consistent QTL for AE is expected to help form the efficient male parental lines suitable for F1 hybrid seed production.