Time series analysis of transcriptomic responses to iron and zinc stress in Sorghum

Micronutrient stress impacts growth, biomass production, and grain yield in crops. Multi-omics studies are valuable resources for identifying genes for functional studies for trait improvement such as accumulation of Fe or Zn under deficient or excess conditions for bioenergy or grain agriculture. We conducted transcriptomics and ionomics analyses on Sorghum bicolor BTx623, grown under Fe and Zn limiting and excess conditions over a 21-day time-period. To identify early and late transcriptional response in roots and leaves, 180 RNAseq libraries were sequenced for differential expression and coexpression network analyses. Fe and Zn accumulation was measured using ICP-MS at each time point and a fluorometer was used to estimate chlorophyll content in leaves. Among the four treatments, Fe limiting and Zn excess resulted in the largest phenotypic effects and transcriptional response in roots and leaves. Sorghum seedlings were grown in a hydroponic growth system for one week and then transplanted into modified Hoagland’s solution for acclimation. After three-week acclimation in hydroponics, seedlings were randomized and transplanted into modified Hoagland’s solutions with different zinc sulphate and ferric sodium EDTA concentrations for low, medium and high iron and zinc stress treatments. For RNA tissue sampling, leaf and root samples were collected from three individual plants to represent three biological replicates. Root tissues were sampled at 7 time points starting from untreated control and after individual stress treatments on 1hour, 2 days, 4 days, 7 days, 14 days, and 21 days for each low, medium and high iron and zinc stress treatments. Leaf discs were sampled from the young leaf from the same plant at 6 time points starting from untreated control and 2 days, 4 days, 7 days, 14 days, and 21 days after individual stress treatments of iron and zinc stress.