Maize (Zea mays L.), a globally significant cereal crop, is produced in vast quantities worldwide. However, its growth is severely constrained by low temperatures, particularly during seed germination, which significantly impairs seedling emergence. In this study, genetic diversity across six germination-associated phenotypic traits (RGR, RSL, RTL, RRSA, RRV, and RSVI) of 304 inbred lines was analyzed, to evaluate the capacity of these lines for low-temperature tolerance. Genome-wide association study (GWAS) was carried out by combining six germination-associated phenotypic traits and genotypic data from 30-fold resequencing. The gene ZmBARK1 was identified through integrated GWAS and RNA-seq analyses, and its association with low-temperature tolerance during maize germination was validated by quantitative real-time PCR (qRT-PCR). ZmBARK1, encoding BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1, was located on the bin 4.09 region of maize chromosome 4. Amino acid comparison and subcellular localization analyses revealed that ZmBARK1 is highly homologous to AtBAK1 and is localized to the plasma membrane of the cell, which may be involved in regulating brassinosteroid (BR) signaling. In addition, we revealed the role of ZmBARK1 in low-temperature tolerance during maize germination. Compared with wild-type (WT), the ethyl methanesulfonate (EMS) mutant zmbark1 was characterized by substantially enhanced low-temperature tolerance. Overall, these findings provide promising candidate genes, improve low-temperature tolerance in maize, and advance the understanding of regulatory mechanisms underlying maize’s response to low-temperature stress.

Planting density is a major limiting factor for maize yield, and breeding for density tolerance has become an urgent issue. The leaf structure of the maize ear leaf is the main factor that restricts planting density and yield components. In this study, a natural population of 201 maize inbred lines was used for genome-wide association analysis, which identified nine SNPs on chromosomes 2, 5, 8, 9, and 10 that were significantly associated with ear leaf type structure. Further verification through qRT-PCR confirmed the association of five candidate genes with these SNPs, with the Zm00001d008651 gene showing significant differential expression in the compact and flat maize inbred lines. Enrichment analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) databases suggested that this gene is involved in the glycolysis process. An analysis of the basic properties of this gene revealed that it encodes a stable, basic protein consisting of 593 amino acids with some hydrophobic properties. The promoter region contains stress and hormone (abscisic acid (ABA)) related elements. The mutant of this gene increased the first ear leaf angle (eLA) and leaf angle of the first leaf below the first ear (bLA) by 4.96 and 0.97°, respectively, compared with normal inbred lines. Overall, this research sheds light on the regulatory mechanism of ear and leaf structures that influence density tolerance and provides solid foundational work for the development of new varieties.