Time-series multi-omics analysis of micronutrient stress in sorghum bicolor reveals iron and zinc cross-talk and regulatory network conservation

Authors: MISHRA, ANKITA - Texas A&M University Institute For Advancing Health Through Agriculture; BHAT, ADITI - Brookhaven National Laboratory; KUMARI, SUNITA - Cold Spring Harbor Laboratory; SHARMA, REENA - Brookhaven National Laboratory; BRAYNEN, JANEEN - Cold Spring Harbor Laboratory; TEDESSE, DIMIRU - Brookhaven National Laboratory; ALAOUI, SARA EL - Argonne National Laboratory; SEAVER, SAM - Argonne National Laboratory; GROSJEANS, NICOLAS - Lawrence Berkeley National Laboratory; Ware, Doreen; XIE, MENG - Brookhaven National Laboratory; Paape, Timothy

Submitted to: Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/29/2025
Publication Date: N/A
Citation: N/A

Interpretive Summary: Sorghum (Sorghum bicolor) is grown as both grain and bioenergy crops and is an annual grass that is tolerant to drought and variable edaphic conditions. Grain sorghum has been the focus of ongoing biofortification efforts of micronutrients, including iron and zinc. In our manuscript we examined iron and zinc accumulation in Sorghum bicolor Btx623 at multiple time points over a 21-day time period. The sampling was done on leaf and root tissues collected at each time point under limiting and excess stress conditions, which included sampling these tissues for RNA. We generated 180 RNAseq libraries that provide a comprehensive examination of the root and shoot transcriptome. We used these data to identify differentially expressed genes at each time point, followed by a coexpression network analysis of root and leaf responses to construct gene regulatory networks (GRNs). The sorghum multi-omics dataset offers a valuable resource for functional genomics and gene regulatory network (GRN) analysis, facilitating studies on micronutrient uptake, transport, and chloroplast metabolic processes under Fe and Zn stress conditions. By linking gene expression data to phenotypic traits like micronutrient accumulation, yield, and stress tolerance, this dataset can complement genetic marker studies and improve trait breeding, particularly for bioenergy and agricultural applications. The data, including time-series RNA-seq from both root and leaf tissues, can also support in silico GRN analyses and help identify key genes and transcription factors involved in micronutrient regulation. This multi-omics approach provides insights into nutrient transport, metabolic pathways, and crop resilience, and will be instrumental for comparative studies across crop species, enhancing our understanding of micronutrient transport systems and aiding in the development of more resilient and nutrient-rich crops to address food security challenges.

Technical Abstract: 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 limit and Zn excess resulted in the largest phenotypic effects and transcriptional response in roots and leaves. Several of the reduction (Strategy I) and chelation strategy (Strategy II) genes that improve bioavailability of Fe and Zn in plant roots often used by non-grass and grass species respectively, were differentially expresssed. Gene regulatory network (GRN) analysis of roots revealed enrichment of genes from both strategies which stongly connect to SbFIT, SbPYE, and SbBTS as hub genes. The GRN for leaf responses showed SbPYE, and SbBTS hub genes connecting genes for chloroplast biosynthesis, Fe-S cluster assembly, photosynthesis genes, and ROS scavenging genes. The DEG and GRN analyses suggest sorghum uses a combined strategy for Fe and Zn uptake similar to rice. We also found strong overlap between Fe and Zn responsive GRNs, indicative of micronutrient cross-talk. We also found conservation of root and leaf GRNs, and known orthologous genes suggests strong constraint on homeostatsis networks in plants. These data will provide a resource for functional genetics to enhance micronutrient transport in sorghum, and opportunities to conduct further comparative GRN analysis across diverse crops species.