Genome-wide association study identifies candidate genes and favorable haplotypes for maize lodging-related traits

Abstract Background Lodging is a major constraint limiting maize ( Zea mays L.) productivity and yield stability. Both stalk mechanical strength and root architecture contribute to lodging resistance. However, their combined genetic basis remains incompletely understood. This study jointly evaluated stalk mechanical and root architectural traits within a unified genome-wide association study framework to provide a more integrated understanding of the genetic architecture underlying maize lodging resistance. Results A panel of 300 maize inbred lines were evaluated for ten lodging-related traits across three environments. Genome-wide association studies based on 1,213,985 high-quality SNPs identified 1,175 significant trait-associated SNPs, of which 458 were consistently detected by at least two statistical models. Candidate gene analysis identified 26 genes potentially involved in lodging-related traits, including genes associated with cell wall organization, carbohydrate metabolism, polysaccharide biosynthesis, and glycosyltransferase activity. Haplotype analysis revealed significant phenotypic differences among haplotypes of 20 candidate genes and identified multiple favorable haplotypes associated with enhanced stalk mechanical strength and root architecture characteristics. Evaluation of 36 representative maize inbred lines revealed substantial variation in the accumulation of favorable alleles and suggested that tropical germplasm may provide useful allelic variation for lodging-resistance improvement. Among the candidate genes, ZmGUX1 ( Zm00001d038229 ) was associated with total nodal root number. A Ds element insertion mutant of ZmGUX1 exhibited a significant reduction in nodal root number and altered root tissue organization, supporting a role for ZmGUX1 in nodal root development. Conclusions These findings provide an integrated view of the genetic basis of lodging-related stalk and root traits in maize. The identified loci, candidate genes, and favorable haplotypes provide promising genetic resources for further functional validation and may facilitate marker-assisted selection and genomic breeding for improved lodging resistance.