Genome-wide association study identifies key loci and candidate genes for maize grain yield-related traits

Grain traits, including kernel dimensions and weight, are key determinants of maize yield and quality. To dissect their genetic basis, we evaluated kernel length, width, thickness, 100‑kernel weight, and volume in 187 maize accessions across two years, revealing significant trait correlations consistent with shared genetic regulation. Genome‑wide association studies identified 284 stable loci associated with these traits over both years, with 199, 225, 7, 8, and 6 loci linked to kernel length, width, thickness, 100‑kernel weight, and volume, respectively. Phenotypic effect analysis highlighted 284 favorable alleles, enabling the prediction of promising hybrid combinations for multi‑locus pyramiding. From associated regions, 41 candidate genes were prioritized, and functional enrichment analyses indicated their involvement in transcriptional regulation, phosphorylation, and steroid biosynthesis. Key candidate genes linked to chromatin remodeling, ribosome assembly, translation, phosphorylation, and carbohydrate metabolism (e.g., 4‑coumarate‑CoA ligase) were highlighted as potential regulators of grain development. This study provides novel genetic resources and a theoretical foundation for marker‑assisted breeding aimed at optimizing whole‑grain phenotypes and enhancing maize productivity.