Morpho-physiological and transcriptome profiling reveal novel zinc deficiency-responsive genes in rice


Intensive farming has depleted the soil zinc (Zn) availability resulting in decreased crop productivity. Here, we attempt to understand the Zn deficiency response in rice through temporal transcriptome analysis. For this, rice seedlings were raised under Zn-deficient conditions up to 4 weeks followed by Zn re-supply for 3 days. Zn-deficient plants developed characteristic deficiency symptoms such as leaf bronzing, decrease in biomass, total chlorophyll, PSII efficiency, decreased carbonic anhydrase activity and increased ROS production. Interestingly, severe alterations in root system architecture were also observed. Comprehensive transcriptome analyses of rice seedlings were carried out after 2 (DEF2W) and 4 weeks (DEF4W) of Zn deficiency with respect to transcriptome profiles of corresponding Zn sufficient conditions (SUF2W, SUF4W). Additionally, to detect the potential Zn-responsive genes, transcriptome profile of Zn-recovered seedlings was compared with DEF4W. All differentially expressed Zn-responsive genes were categorized into early and late Zn deficiency response, and a set of 77 genes, induced and repressed on Zn deficiency and re-supply, respectively, was identified. These genes could be used as low Zn-responsive marker genes. Further, genes involved in membrane transport, phytosiderophore activity and organic acid biosynthesis showed high differential expression. Additionally, the present study unravelled several genes putatively associated with alterations in root system architecture under Zn deficiency and provides novel insights into the interpretation of morpho-physiological, biochemical and molecular regulation of zinc deficiency responses in rice.

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Our research is funded by core grant of NIPGR. H.S. acknowledges the ‘short-term research fellowship’ from NIPGR, DBT. B.T. acknowledges the DBT for financial support, M.P. thanks the Council for Scientific and Industrial Research for junior and senior research fellowships.

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Correspondence to Jitender Giri.

Electronic supplementary material

Table S1

List of primer sequences used for expression analysis using qRT-PCR (DOCX 13.3 kb)

Table S2

Morphological data for seedling growth after 2 weeks of Zn deficiency (XLSX 47.2 kb)

Table S3

Summary of total and aligned reads obtained under different Zn treatment conditions (DOCX 12.5 kb)

Table S4

DEGs showing significant differential expression in response to Zn deficiency and recovery conditions (q≤ 0.05) (XLSX 256 kb)

Table S5

List of different cis-elements recognized by bZIP transcription factors in the promoter of identified Zn-responsive marker genes (DOCX 15 kb)

Table S6

Linear fold changes and details of genes related to root system architecture (RSA) represented by DEGs in three Zn conditions (against their respective controls). Fold changes are significant with q value ≤0.05 (DOCX 22.3 kb)

Table S7

Detailed list of transcript abundances (up and down regulated) under DEF2W, DEF4W and REC3D and comparative list of gene expression between DEF2W vs DEF4W (XLSX 1649 kb)

Table S8

DEGs involved in different biotic /abiotic stresses and phytohormone metabolism under zinc deficiency (XLSX 184 kb)

Table S9

Comparative analysis of gene expression profiling studies carried out under Zn deficiency in rice (DOCX 13.9 kb)

Fig. S1

Zn concentration in shoot and root. Zn concentrations (μg/g dry weight) was measured in (A) shoot and (B) root of four-week-old seedlings raised under Zn sufficient (5 μM) and deficient (0.005 μM) Zn conditions. Data are means ±SD of three replicates containing 5 plants per experiments. Asterisk indicates significant difference from control at p ≤ 0.05 by Student’s t-test. (PDF 171 kb)

Fig. S2

Five ways Venn diagram showing the commonality and uniqueness of genes after two (DEF2W) and four weeks (DEF4W) of Zn deficiency and three days of recovery (REC3D). Venn 1, 2, 3 and 4 are comparison between SUF2W and SUF4W, SUF2W and DEF2W, SUF4W and DEF4W and DEF2W and DEF4W. The threshold for differential up or down regulation of gene expression was fixed at p value ≤ 0.05. (PDF 18.9 kb)

Fig. S3

Hierarchical clustering and heatmap representing the metabolic overview of Zn deficient and recovered plants based on the transcript abundances (Log base 2 fold changes) of respective genes. Representation is based on MapMan (V3.6.0). Heat maps were generated in MeV 4.6.0 (Multi Experiment Viewer) software on log2FCs corresponding to each gene. (PDF 624 kb)

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Bandyopadhyay, T., Mehra, P., Hairat, S. et al. Morpho-physiological and transcriptome profiling reveal novel zinc deficiency-responsive genes in rice. Funct Integr Genomics 17, 565–581 (2017).

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  • HMA
  • Reactive oxygen species
  • Root
  • Transcriptome
  • Zinc deficiency