Genome-wide association study and candidate gene identification for fall armyworm resistance in maize (Zea mays L.)

As a globally vital crop for human consumption, livestock feed, and industrial applications, maize (Zea mays L.) faces severe threats from the invasive pest fall armyworm (FAW), Spodoptera frugiperda. Exploring endogenous resistance genes represents a sustainable approach for FAW management. This study employed the Maize6H-60 K SNP array to characterize genetic diversity and population structure in 212 key inbred lines derived from southeastern Chinese breeding programs. Integrated with field-based resistance phenotyping data from 2023 and 2024, genome-wide association studies (GWAS) identified 21 SNP loci significantly associated with FAW resistance, distributed across chromosomes 1, 2, 3, 5, 6, and 7. Subsequent analyses pinpointed 25 candidate genes within these genomic regions. Gene Ontology (GO) annotation, promoter cis-acting element analysis, and transcriptomic profiling revealed that these genes are functionally enriched in signal transduction, cellular defense responses, and transcriptional regulation. Notably, their promoter regions harbored multiple hormone-responsive (e.g., jasmonic acid and salicylic acid) and stress-inducible cis-elements. Investigation of publicly available transcriptome datasets with qRT-PCR validation demonstrated that six candidate genes exhibited significant expression changes under FAW infestation, suggesting their pivotal roles in maize antiherbivore defense mechanisms. This study not only provides an important molecular basis for the genetic improvement of maize resistance to the fall armyworm but also offers new perspectives for further research on plant - insect interaction mechanisms. In addition, the study's outcomes offer a solid theoretical foundation for devising maize insect - resistance breeding strategies.