Maize Shoot Apical Meristem Characterization

Plants for all experiments were grown under standard conditions with 10-hr day cycles in Percival A100 growth chambers (Percival Scientific, Perry, IA) planted in 98-well trays with all edge positions filled with inbred B73. Soil media was a 1:1 mixture of Turface MVP (PROFILE Products LLC, Buffalo Grove, IL) and LM111 (Lambert Peat Moss, Qc, Canada). All plants were harvested 14 days after planting and quickly trimmed to small SAM-containing tissue cassettes and fixed in FAA (3.7% formalin, 5% acetic acid and 50% ethanol in water) on ice, overnight.
For initial modelling, 10 kernels from inbred B73 and 10 kernels from inbred W22 were planted as above. To map the maize SAM morphospace, kernels from 384 inbred varieties (Supplementary Data 1) were planted in randomized positions in 4 biological replicates. For RNA in situ hybridization, 10 kernels from select lines were grown as above in 2 biological replicates. To estimate SAM cell count and ASCS, 4 kernels from 14 inbred varieties were planted with 3 biological replicates: 3 ZmSDA1-ALT lines and 5 ZmBAK1-like1 ALT lines with remaining lines randomly chosen to equally represent the lower quartile (small), middle quartiles (intermediate) and upper quartile (large) of SAM volume with COM from ZmSDA1 and ZmBAK1-like1.