Integrated GWAS and linkage analysis to reveal genetic loci for maize ear traits

Maize ear architecture is a critical determinant of grain yield, yet its genetic basis remains incompletely understood. This study aims to explore novel genetic variations generated by radiation-induced mutagenesis, systematically dissect the genetic basis of key maize ear traits and develop molecular markers capable of effectively distinguishing germplasm with contrasting ear phenotypes. We conducted an integrated genomic analysis of four key ear traits (ear length (EL), diameter (ED), ear row number (ERN), and kernel number per row (KNR)) using two radiation-mutagenized populations: 1355 multi-background radiation-induced mutant lines (RMLs) derived from three elite inbred lines (ZH6218, T32, and ZNC442), and 626 radiation-induced mutant lines derived from the ZH6218 background (ZF6218), grown in two environments. Phenotypic evaluation revealed substantial variation, with ED and ERN showing high heritability, while KNR exhibited stronger genotype-environment interactions. Genome-wide association studies (GWAS) identified 53 suggestive QTNs, including three pleiotropic loci associated with both ED and KNR. Linkage mapping in ZF6218 uncovered 36 segregation distortion loci (SDLs), with eight novel loci contributing to ear morphology. Notably, a prominent KNR-associated SDL (SDL-KNR8.2) co-localized with a GWAS peak (S08_18815086), narrowing the candidate interval to 575 kb on chromosome 8 harboring 22 genes. Spatiotemporal expression profiling suggested three distinct gene clusters: early apical, intermediate elongation, and late differentiation, implicating hierarchical control of meristem development. In silico candidate gene analysis identified a C/T SNP in the second exon of Zm00001d008757 that is significantly associated with KNR variation, which may serve as a candidate marker for breeding selection. These findings provide a theoretical basis and candidate resources for understanding maize ear development, and warrant further validation before application in molecular breeding.