Genome‐wide association study and pathway analysis to dissect the genetic control of stay‐green in a Brazilian panel of tropical maize inbred lines

Abstract The stay‐green trait enables plants to sustain photosynthesis under severe biotic and abiotic stresses and is positively correlated with grain yield in maize ( Zea mays L). Despite its importance, information on the inheritance and genetic basis of stay‐green in tropical maize remains limited. This study used genome‐wide association study (GWAS) to identify chromosomal regions and candidate genes associated with stay‐green. Using 350,643 high‐quality genome‐wide single nucleotide polymorphism (SNP) markers generated through genotyping‐by‐sequencing of 320 tropical maize inbred lines, we performed GWAS for stay‐green using phenotypic data collected in two environments during the 2017/2018 season in Brazil. The experimental design was an α‐lattice design with three replicates. GWAS identified 27 significant SNPs ( p < 0.05) associated with stay‐green, from which 27 candidate genes were inferred based on their proximity (±5 kb) to these SNPs and their functional annotation from the B73 maize reference genome (AGPv4). Pathway analysis revealed 71 unique (although frequently related) biological pathways ( p < 0.02), including processes related to sterol, mannitol, UDP‐beta‐L‐arabinose, hydroxycinnamic acid amides, and cuticular wax biosynthesis, spermidine regulation, and jasmonate signaling, all mechanisms known to influence drought stress responses. These results provide valuable genetic resources and candidate markers for breeding for improved stay‐green tropical maize, with potential for developing breeder‐friendly molecular markers to facilitate selection.