Fig. 1

Schematic pipeline of sp-GWAS coupled with BSA. Year1 (Generation-0): 5000 plants were planted in ~ 0.1 ha plots in four locations (20,000 plants total) and 96 individual plants were selected randomly in each location (384 in total) for genotyping and phenotyping. Based on the phenotypic distribution of 96 plants, the ~ 5% truncation threshold was identified for each location. All the ears from plants taller (Location 1 and 2) or shorter (Location 3 and 4) than the truncation threshold were harvested. Year2 (Generation-1): Harvested seeds (5000 kernels) from year1 (Generation-0) were grown again in same location and 96 plants per location (384 in total) were genotyped and phenotyped in the same manner as in year1. These populations are now named based on the selection regime; Generation1-Tall1, Generation1-Tall2, Generation1-Short1 and Generation1-Short2. Association analysis was done using all 768 (384 × 2) phenotyped and genotyped plants. Offspring of the selected individuals from year1 were used for the modified bulk segregant analysis using tall and short populations to define in silico bulks