Genome-Wide Association Mapping of Ear Traits in Early-Maturing Maize Under Contrasting Planting Densities

Developing early-maturing maize varieties with improved tolerance to high-density planting is essential for enhancing yield in China. In this study, a unique panel of 498 cold-adapted early-maturing inbred lines were evaluated for ear length (EL) and ear diameter (ED) across two locations under contrasting planting densities in one growing season. Phenotypic analysis revealed abundant phenotypic variation in these ear traits among the tested lines, and there were significant correlations between environments. A total of 406,897 high-quality single nucleotide polymorphism markers (SNPs) were obtained from liquid chip analysis. Population structure analysis classified the early-maturing maize germplasm into 9 distinct genetic groups, with obvious genetic differentiation between groups. Linkage disequilibrium (LD) analysis demonstrated rapid LD decay and high genetic variation in the population. A genome-wide association study (GWAS) identified 380 quantitative trait loci (QTLs) for both ED and EL under two planting densities. In total, 138 and 89 annotated genes were identified within QTLs detected under normal and high-density planting conditions, respectively. Among them, Zm00001eb288330 (a TPX2 family protein) and Zm00001eb366770 (an OVATE family transcription factor), which were located close to the top SNPs for ED and EL under high planting density, were considered positional candidate genes based on their annotations. Furthermore, by integrating candidate gene analysis with selection signatures, we found that candidate genes detected under high-density planting conditions show signatures of ongoing selection during maize breeding. These findings identify candidate genes for future functional validation and breeding-oriented follow-up studies.