A combination of QTL mapping and genome‑wide association study revealed key genes for heat tolerance in maize

Integrated QTL GWAS identified three key genes, whose heat ind uction during maize germination was verified via RNA seq and qRT PCR analysis. Heat stress during germination critically impairs maize seedling establishment and yield stability, yet its genetic basis remains poorly understood. Here, 21 quantitative trait loci (QTLs) for heat tolerance were identified in a recombinant inbred line (RIL) population under heat stress (39 °C vs. 28 °C), including a major hypocotyl diameter QTL (qHDT2-1, LOD = 23.68). Concurrently, genome-wide association study (GWAS) in an association panel detected 213 significant SNPs associated with heat tolerance. Population-stable SNPs, pleiotropic SNPs and high-impact QTLs were integrated to identify candidate genes. Transcriptome analysis and GO enrichment prioritized 612 candidate genes, among which six heat-induced genes were selected. Subsequent validation confirmed Zm00001d005300, Zm00001d023524, and Zm00001d026563 as core regulators forming a coordinated heat-response network. We also found that heat stress had a relatively minor impact on germination rates, but significantly affects biomass accumulation and tissue morphology. This study identifies key genetic targets for breeding heat tolerant maize.