GWAS analysis reveals candidate genes associated with dense tolerance (ear leaf structure) in maize (Zea mays L.)

Planting density is a major limiting factor for maize yield, and breeding for density tolerance breeding has become an urgent issue. The leaf structure of the maize ear leaf is the main factor that restricts planting density and yield composition. 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 compact and flat maize inbred lines. Enrichment analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) suggested that this gene is involved in the glycolysis process. The analysis of the basic properties of this gene revealed that it encodes a stable, basic protein consisting of 593 amino acids with some hydrophobic ability. The promoter region contains stress and hormone (ABA) related elements. The mutant of this gene increased the uppermost ear leaf angle (eLA) and the first leaf below the uppermost ear (bLA) by 4.96° and 0.97° compared with normal inbred lines. Overall, this research sheds light on the regulatory mechanism of ear and leaf structure that influence density tolerance and provides solid foundational work for the development of new varieties.