Genetic Dissection of Shelling Percentage in Maize via QTL Mapping Using a Maize-Teosinte Population

Background: Shelling percentage is an important trait affecting grain yield efficiency in maize, but its genetic basis remains insufficiently understood. Methods: In this study, a maize-teosinte BC2S2 population derived from Zheng58 and (Zea mays ssp. parviglumis, CIMMYTMA 8782) was used for phenotypic evaluation and QTL mapping of shelling percentage across two replicates and BLUP-based analysis. Candidate genes were further prioritized based on their positions within QTL support intervals, expression patterns, and functional annotation. Results: Two reproducible QTLs, qSP7 and qSP10, were identified on chromosomes 7 and 10, respectively. qSP7 explained 3.39–3.41% of the phenotypic variation, whereas qSP10 explained 2.96–6.45%. Within these intervals, Zm00001d021701, Zm00001d021708, and Zm00001d025739 were prioritized as candidate genes based on expression and annotation evidence. Conclusions: These results indicate that shelling percentage in maize is controlled by multiple loci with modest effects and provide a basis for future genetic analysis and marker development for this trait.