A Genome-Wide Association Study Dissects the Genetic Architecture of Three Brace-Root Traits in Maize

Brace roots are important organs affecting maize resistance to lodging. Analyzing the genetic basis of the brace-root traits can help to improve maize lodging resistance. In this study, an association panel of 508 maize inbred lines was evaluated for three brace-root traits and subjected to genome-wide association analysis of tier number (TN), brace-root number (RN), and radius of brace-root circle (RBR), across two environments. Using the fixed and random model circulating probability unification (FarmCPU) combined with Bonferroni and Benjamini–Hochberg false discovery rate (FDR) correction, we identified suggestive candidate associations (p < 1 × 10−5) and four groups of environment-specific linkage disequilibrium single nucleotide polymorphisms (SNPs); no SNP reached genome-wide significance after multiple-testing correction. Within the linkage disequilibrium (LD) intervals of these SNPs, 14 candidate genes were identified and functionally annotated. The genetic loci and candidate genes associated with variation in maize brace-root traits mined in this study can help to further reveal their genetic basis and provide a theoretical basis for future functional studies of relevant regulatory genes.