Zea mays L. subsp. mays CML218 (16g-2004-23@ | Ames 27086) 5-DAP Seedling Shoot Apical Meristem (SAM) RNA-Seq
For the 369 genotypes from the SAM diversity panel (Leiboff et al., 2015), 15 seeds for each genotype were grown in paper rolls in Percival A100 growth chambers (Percival Scientific, Perry, IA) with 16h light (28C), 8h dark (21C) cycle. After five days of germination, SAM-enriched tissue and root tips of 1cm from three to ten seedlings were pooled for each genotype for RNA extraction. All RNA extractions were conducted using Qiagen RNeasy Plant Mini Kits (Qigen, Hilden, Germany) following the manufacturers protocol. RNA for all the samples were diluted with 30 l of RNase free water and was subjected to initial quality control using Qubit RNA Integrity and Quality Assay Kits (Thermo Fisher Scientific, Waltham, MA). RNA samples with concentrations greater than 100 ng/l were used to construct RNA-sequencing libraries. Indexed RNA-Seq libraries were prepared from the RNA samples from the SAM-enriched tissue using the TruSeq Stranded mRNA Kit (Illumina, San Diego, CA) and sequenced using NovaSeq6000 S4 (2 x150bp) instrument(s). Indexed RNA-Seq libraries were prepared RNA samples from root tips using QuantSeq 3 mRNA-Seq Library Prep FWD for Illumina (Lexogen, Vienna, Austria), and sequenced using NovaSeq6000 S2 (100-cycle single-end) instrument(s). RNA-Seq reads were processed and aligned to maize RefGen V5 (Hufford et al., 2021) as described in previous studies with the same diversity panel (Leiboff et al., 2015; Lin et al., 2017).