Genome-Wide Association Study Dissects the Genetic Architecture of Pericarp Traits in Fresh-Eating Maize

Pericarp characteristics are key factors determining the eating quality of fresh-eating maize. This study aimed to elucidate the genetic basis of traits such as pericarp thickness, break force, and brittleness in fresh-eating maize, identify key genes regulating these traits, and provide a theoretical foundation for improving mouthfeel quality through molecular marker-assisted breeding. Using 196 fresh-eating maize inbred lines with diverse genetic backgrounds, pericarp-related traits were phenotypically measured using a texture analyzer. Genotyping was performed using the GenoBaits Maize 45K Panel chip (MolBreeding, Shijiazhuang City, China). Genome-wide association studies (GWAS) were conducted to identify significantly associated SNP loci, and candidate genes were screened for functional annotation. Phenotypic analysis revealed a significant positive correlation between pericarp thickness and break force, and a significant negative correlation between break force and brittleness. GWAS detected 21, 2, and 1 stable SNPs significantly associated with pericarp thickness, break force, and brittleness, respectively. A total of 47 candidate genes for pericarp thickness, 7 for break force, and 4 for brittleness were identified. Functional annotation indicated that the candidate gene Zm00001eb314860 (ZmbZIP130), annotated as a member of the bZIP transcription factor family, may function as a pleiotropic gene involved in regulating pericarp-related traits. These findings demonstrate that pericarp traits in fresh-eating maize are controlled by multiple genes. The significant loci and candidate genes identified in this study lay a foundation for further elucidating the molecular mechanisms underlying pericarp quality formation and for molecular breeding.