Ear traits are key contributors to grain yield in maize; therefore, exploring their genetic basis facilitates the improvement of grain yield. However, the underlying molecular mechanisms of ear traits remain obscure in both inbred lines and hybrids. Here, two association panels, respectively, comprising 203 inbred lines (IP) and 246 F₁ hybrids (HP) were employed to identify candidate genes for six ear traits. The IP showed higher phenotypic variation and lower phenotypic mean than the HP for all traits, except ear tip-barrenness length. By conducting a genome-wide association study (GWAS) across multiple environments, 101 and 228 significant single-nucleotide polymorphisms (SNPs) associated with six ear traits were identified in the IP and HP, respectively. Of these significant SNPs identified in the HP, most showed complete–incomplete dominance and over-dominance effects for each ear trait. Combining a gene co-expression network with GWAS results, 186 and 440 candidate genes were predicted in the IP and HP, respectively, including known ear development genes ids1 and sid1. Of these, nine candidate genes were detected in both populations and expressed in maize ear and spikelet tissues. Furthermore, two key shared genes (GRMZM2G143330 and GRMZM2G171139) in both populations were found to be significantly associated with ear traits in the maize Goodman diversity panel with high-density variations. These findings advance our knowledge of the genetic architecture of ear traits between inbred lines and hybrids and provide a valuable resource for the genetic improvement of ear traits in maize.

穗性状是玉米产量的关键因素；因此，探索其遗传基础有助于提高粮食产量。然而，自交系和杂种中穗性状的潜在分子机制仍然不清楚。在这里，两个关联小组分别包含 203 个自交系 (IP) 和 246 个 F ₁杂种 (HP)，用于鉴定六个穗性状的候选基因。除耳尖不育长度外，IP 的所有性状都比 HP 表现出更高的表型变异和更低的表型平均值。通过跨多个环境进行全基因组关联研究 (GWAS)，在 IP 和 HP 中分别鉴定出与 6 个耳朵性状相关的 101 个和 228 个显着单核苷酸多态性 (SNP)。在 HP 中鉴定的这些重要 SNP 中，大多数对每个耳朵性状都表现出完全-不完全显性和过度显性效应。结合基因共表达网络和GWAS结果，在IP和HP中分别预测了186个和440个候选基因，包括已知的耳发育基因ids1和sid1。其中，在两个群体中均检测到九个候选基因，并在玉米穗和小穗组织中表达。此外，发现两个群体中的两个关键共享基因（GRMZM2G143330和GRMZM2G171139）与具有高密度变异的玉米 Goodman 多样性面板中的穗性状显着相关。这些发现增进了我们对自交系和杂交种之间穗性状遗传结构的认识，并为玉米穗性状的遗传改良提供了宝贵的资源。