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In vivohaploid induction based on maternal 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 maternal 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 maternal influence on HIR is controlled by a few moderate and many small effect QTL.

One of the critical limitations for the in vivo production of doubled haploid (DH) lines in maize (Zea maysL.) is the inability to effectively identify haploids in a significant proportion of induction crosses due to the possibility of complete or partial inhibition of the currently used R1‐nj(Navajo) color marker. In this study, we demonstrate that the R1‐njmarker could result in a high proportion of false positives among the haploids identified, besides being ineffective in germplasm with natural anthocyanin expression in pericarp tissue. To address these limitations, we developed haploid inducer lines with triple anthocyanin color markers, including the expression of anthocyanin coloration in the seedling roots and leaf sheaths, in addition to the Navajo marker on the seed. Although these inducers show acceptable haploid induction rates ranging from 8.6 to 10.2%, they exhibited relatively poor agronomic performance compared with tropicalized haploid inducers within tropical environments. The addition of the red root marker more accurately identified haploids among the germinating seedlings, including four tropical inbred lines and eight breeding populations that showed complete inhibition of R1‐nj. We also demonstrate that the red root marker can be used for haploid identification in germplasm with natural anthocyanin expression in the pericarp. A survey of 546 tropical inbreds and 244 landraces showed that anthocyanin accumulation in the roots of germinating seedlings is very rare compared with anthocyanin accumulation in the seed and leaf sheath tissues. As a result, the red root marker can serve as a highly complementary marker to R1‐njto enable effective identification of haploids within a wide range of tropical maize germplasm.