In vivo haploid induction based on matal haploid inducers is the first step in deriving completely homozygous maize doubled haploid (DH) lines. Haploid induction rate (HIR) is influenced by both pollen parent inducing haploidy and the matal source germplasm used in induction crosses. This study was aimed at analyzing the influence of source germplasm on HIR using 671 tropical inbred lines organized in two association mapping panels. These two association mapping panels (AMP1 and AMP2) were crossed to two different Tropically Adapted Inducer Lines (TAILs). For HIR assessment, seeds from induction crosses were planted in the field and ploidy status of each surviving plant was assessed using a gold standard classification based on visual differences between the haploid and diploid plants. The analysis revealed significant variation for HIR and led to identification of several tropical inbred lines that respond very positively to haploid induction. Use of HIR data in a genome wide association study (GWAS) led to identification of twenty-seven and two SNPs that were significantly associated with HIR in AMP1 and AMP2, respectively. Meta-analysis of AMP1 and AMP2 GWAS led to identification of 52 SNPs with significant effect on HIR across both studies. Genome-wide prediction revealed moderate to high prediction accuracy within AMPs using random SNPs. Inclusion of the SNPs detected in GWAS into the prediction model led to improvement in prediction accuracy. Overall, the study revealed that the matal influence on HIR is controlled by a few moderate and many small effect QTL.