RNAseq analysis of Maize and Sorghum under nitrate limitation and recovery at different time points.

Nitrogen (N) is an essential macronutrient for plant growth and development. Maximizing Nitrogen Use Efficiency (NUE) in plants is vital to increasing crop production and reducing negative impacts on the environment. We aim to investigate transcriptional changes under sufficient and limiting nitrate conditions in maize and sorghum.Seeds of maize and sorghum were germinated on rag dolls and transferred to normal Hoagland nutrient solution after 3 DAG and 10 DAG, respectively in hydroponic tanks. After being in normal nitrate nutrient solution for 12 days, both maize and sorghum plants were transferred to a limiting nitrate solution (Ca(NO3)2 and Mg(NO3)2 in the nutrient solution were replaced with CaCl2 and MgSO4). Roots and leaves samples from the 5th leaf stage of the plant at 15 DAG and 21 DAG were harvested from maize and sorghum under limiting nitrate solution, respectively, at time 0, 30min, 3hours and 1 day. After 1 day of nitrate deprivation, nitrates were added to the nutrient solution to study nitrate recovery and roots and leaves samples for recovery were collected at 1day 30mins and 2days at normal nitrate nutrient solution.RNA-seq libraries were prepared following the NEBNext RNA-seq library prep Kit. Three biological replicates were taken per tissue and treatment, each of which consisted of 5 plants pooled together. Libraries were sequenced using the Illumina NextSeq2000. Reads were processed with trimmomatic for adapter removal and then mapped to the reference genome of maize (Zea mays B73v5) and sorghum (Sorghum bicolor BTx623 v3.1.1) using STAR and counts were obtained using Stringtie. For differential expression DESeq2 was used.