High anther extrusion (AE) is of advantage to promote cross pollination and to ensure high level of pollen availability for hybrid wheat seed production and is therefore of major interest in hybrid breeding programs. Hence, the genetic architecture of anther extrusion was studied in the multi-parental population MAGIC-WHEAT WM-800 by genome wide association studies (GWAS) with a fivefold cross-validation to identify genes involved in a non-cleistogam flowering performance. Phenotypic data for 800 genotypes were collected in two years, showing strong variation for AE between the founder as well as within the WM-800 and high heritability of 75.66%, optimal requirements for a GWAS with 27.685 SNPs, a combination of 15k Illumina array and 135k Affymetrix array. GWAS revealed Rht-B1 and Rht-D1 as the major genetic players, whereas the short straw allele results in a lower AE. The insensitivity to gibberellin acid (GA) in the mutant allele lets speculate, that the reduced cell division and elongation leads to shorter anther filaments. Besides the old acquaintances for plant height, novel genetic regions determining anther extrusion were estimated. Chromosome 1B harboured a favourable allele from “Meister” which explained 5.25% of the phenotypic variation. According to the phenotypic data, Meister is the founder with strongest anther extrusion among all founder. Anther extrusion can as well be influenced by swelling of the lodicule, which forms at the base of the floret. Their expansion forces the lemma and palea apart, enabling the anthers to emerge. The significant SNP on chromosome 2A is localized in a genetic region with functional annotation in wheat; a plant invertase -pectin methylesterase inhibitor. These results were strengthened by the protein evidence of a pectin methyl esterase inhibitor of Aegilops tauschii at the same genetic region. Pectin methylesterase (PME) is the first enzyme acting on pectin, a major component of plant cell wall, and decisive in plant development. Therefore, the estimated genetic region at QTL on 2A could play an important role in plant development regarding anther extrusion. Additionally, the significant region could coincide with the genetic location of the homoeologous orthologs of the barley cleistogamy gene Cly1, designated as TaAP2-A on the long arm of chromosome 2. Further, a GWAS for Fusarium susceptibility and plant height estimated favorable and unfavorable overlapping regions for the examined traits. Therefore, we postulate that the results of GWAS for AE in combination with higher Fusarium tolerance would improve the modern gene pool by marker assisted selection.