Significant associations ( P < 5.8 × 10−4) under water stress observed across agronomic traits and locations. All 64 strong associations for WS (P < 5.8 × 10−4 as the cut-off) that were observed on 10 maize chromosomes were pooled over a heat map. The strongly associated SNPs are appended by their positions on the chromosomes. Based on the P values, a heat map was generated for seven agronomic traits – anthesis-to-silking interval (ASI), ear girth (EG), ear length (EL), grain yield (GY), 100-kernel weight (HKW), kernels per row (KR), and the number of kernel rows (KRN) – recorded at three locations and mean of phenotypic data at all locations, and four models (see Methods for details) under waters-stressed conditions. Out of these 64 SNP associations, 31 were close to the drought-tolerant genes that regulate some molecular and physiological functions leading to drought tolerance (refer Figure 4).