Transcriptome profiles of soybean leaves and roots in response to zinc deficiency.

Zinc (Zn) deficiency is a widespread agricultural problem in arable soils of the whole world. However, the molecular mechanisms underlying Zn deficiency response are largely unknown. Here, we analyzed the transcriptomic profilings of soybean leaves and roots in response to Zn deficiency through Illumina's high-throughput RNA sequencing in order to understand the molecular basis of Zn deficiency response in the plants. A total of 614 and 1011 gene loci were found to be differentially expressed in leaves and roots, respectively, and 88 loci were commonly found in both leaves and roots. Twelve differentially expressed genes (DEGs) were randomly selected for validation by qRT-PCR, and their fold changes were similar to that of RNA-seq. Gene ontology enrichment analysis showed that ion transport, nicotianamine biosynthetic process, and queuosine biosynthetic process were enriched in the up-regulated genes, while oxidation-reduction process and defense response were enriched in the down-regulated genes. Among the DEGs, 20 DEGs are potentially involved Zn homeostasis, including 7 ZIP (ZRT, IRT-related protein) transporter genes, 3 nicotianamine synthase genes, and 7 metallothionein genes; 40 DEGs are possibly involved in diverse hormonal signals, like auxin, cytokinin, ethylene, and gibberellin; 9 DEGs are putatively involved in calcium signaling; 85 DEGs are putative transcription factor genes. Nine DEGs were found to contain Zinc Deficiency Response Element (ZDRE) in their promoter regions. These results could provide comprehensive insights into the soybean response to Zn deficiency and will be helpful for further elucidation of the molecular mechanisms of Zn deficiency response and Zn deficiency tolerance in plants. This article is protected by copyright. All rights reserved.